Starting phenix.real_space_refine
on Wed Mar 12 09:05:38 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/7pd8_13331/03_2025/7pd8_13331.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/7pd8_13331/03_2025/7pd8_13331.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=4.2
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/cci-nas-00/data/ceres_data/7pd8_13331/03_2025/7pd8_13331.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/7pd8_13331/03_2025/7pd8_13331.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/7pd8_13331/03_2025/7pd8_13331.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/7pd8_13331/03_2025/7pd8_13331.cif"
  }
  resolution = 4.2
  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=   0.002
Set stop_for_unknowns flag
  Set to: True
Assert model is a single copy model
Assert all atoms have isotropic ADPs
Construct map_model_manager
Extract box with map and model
Check model and map are aligned
Set scattering table
  Set to: electron
  Number of scattering types: 4
    Type Number    sf(0)   Gaussians
     S      56      5.16       5
     C    4936      2.51       5
     N    1269      2.21       5
     O    1381      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 52 residue(s): 0.05s

  Monomer Library directory:
    "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5624/modules/chem_data/mon_lib"
  Total number of atoms: 7642
  Number of models: 1
  Model: ""
    Number of chains: 2
    Chain: "A"
      Number of atoms: 6676
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 842, 6676
          Classifications: {'peptide': 842}
          Incomplete info: {'truncation_to_alanine': 4}
          Link IDs: {'PTRANS': 20, 'TRANS': 821}
          Chain breaks: 6
          Unresolved non-hydrogen bonds: 7
          Unresolved non-hydrogen angles: 9
          Unresolved non-hydrogen dihedrals: 5
          Unresolved non-hydrogen chiralities: 1
          Planarities with less than four sites: {'ASP:plan': 1}
          Unresolved non-hydrogen planarities: 3
    Chain: "B"
      Number of atoms: 966
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 128, 966
          Classifications: {'peptide': 128}
          Link IDs: {'PTRANS': 3, 'TRANS': 124}
  Time building chain proxies: 5.94, per 1000 atoms: 0.78
  Number of scatterers: 7642
  At special positions: 0
  Unit cell: (93.15, 78.57, 144.99, 90, 90, 90)
  Space group: P 1 (No. 1)
  Number of sites at special positions: 0
  Number of scattering types: 4
    Type Number    sf(0)
     S      56     16.00
     O    1381      8.00
     N    1269      7.00
     C    4936      6.00
    sf(0) = scattering factor at diffraction angle 0.

  Number of disulfides: simple=0, symmetry=0

  Automatic linking
    Parameters for automatic linking
      Linking & cutoffs
        Metal                : Auto  - 3.00
        Amino acid           : True  - 1.90
        Carbohydrate         : True  - 1.99
        Ligands              : True  - 1.99
        Small molecules      : False - 1.98
        Amino acid - RNA/DNA : False
      
  Number of custom bonds: simple=0, symmetry=0
  Time building additional restraints: 2.08
  Conformation dependent library (CDL) restraints added in 1.0 seconds
  

  1908 Ramachandran restraints generated.
    954 Oldfield, 0 Emsley, 954 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  1810

  Finding SS restraints...
    Secondary structure from input PDB file:
      37 helices and 6 sheets defined
      64.2% alpha, 6.3% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 0.73
  Creating SS restraints...
    Processing helix  chain 'A' and resid 99 through 108
      removed outlier: 3.585A  pdb=" N   ALA A 103 " --> pdb=" O   ASN A  99 " (cutoff:3.500A)
      removed outlier: 4.105A  pdb=" N   MET A 105 " --> pdb=" O   GLU A 101 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 108 through 136
      removed outlier: 3.599A  pdb=" N   THR A 112 " --> pdb=" O   CYS A 108 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 145 through 163
    Processing helix  chain 'A' and resid 171 through 193
      removed outlier: 4.020A  pdb=" N   GLN A 193 " --> pdb=" O   ALA A 189 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 219 through 236
    Processing helix  chain 'A' and resid 241 through 260
    Processing helix  chain 'A' and resid 279 through 336
      removed outlier: 3.918A  pdb=" N   PHE A 310 " --> pdb=" O   SER A 306 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 339 through 347
    Processing helix  chain 'A' and resid 402 through 407
    Processing helix  chain 'A' and resid 413 through 434
      removed outlier: 3.796A  pdb=" N   GLU A 432 " --> pdb=" O   ARG A 428 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 457 through 481
      removed outlier: 3.758A  pdb=" N   GLU A 479 " --> pdb=" O   GLN A 475 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 511 through 523
      removed outlier: 3.781A  pdb=" N   ASN A 515 " --> pdb=" O   SER A 511 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 533 through 537
    Processing helix  chain 'A' and resid 784 through 808
      removed outlier: 3.642A  pdb=" N   LEU A 788 " --> pdb=" O   THR A 784 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 817 through 844
      removed outlier: 3.781A  pdb=" N   LEU A 821 " --> pdb=" O   PRO A 817 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 850 through 857
      removed outlier: 3.543A  pdb=" N   ARG A 854 " --> pdb=" O   THR A 850 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 858 through 860
      No H-bonds generated for 'chain 'A' and resid 858 through 860'
    Processing helix  chain 'A' and resid 861 through 885
      removed outlier: 3.599A  pdb=" N   HIS A 866 " --> pdb=" O   TRP A 862 " (cutoff:3.500A)
      Proline residue:  A 876  - end of helix
      removed outlier: 4.058A  pdb=" N   HIS A 883 " --> pdb=" O   ALA A 879 " (cutoff:3.500A)
      removed outlier: 3.846A  pdb=" N   VAL A 884 " --> pdb=" O   VAL A 880 " (cutoff:3.500A)
      removed outlier: 3.620A  pdb=" N   THR A 885 " --> pdb=" O   TYR A 881 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 891 through 908
      removed outlier: 3.647A  pdb=" N   THR A 895 " --> pdb=" O   ASN A 891 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 909 through 911
      No H-bonds generated for 'chain 'A' and resid 909 through 911'
    Processing helix  chain 'A' and resid 917 through 936
      Proline residue:  A 931  - end of helix
    Processing helix  chain 'A' and resid 978 through 1037
      removed outlier: 4.222A  pdb=" N   ALA A1015 " --> pdb=" O   GLY A1011 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 1038 through 1048
      removed outlier: 4.949A  pdb=" N   GLN A1044 " --> pdb=" O   HIS A1040 " (cutoff:3.500A)
      removed outlier: 4.523A  pdb=" N   LEU A1045 " --> pdb=" O   VAL A1041 " (cutoff:3.500A)
      removed outlier: 3.743A  pdb=" N   LYS A1046 " --> pdb=" O   ALA A1042 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 1066 through 1072
      removed outlier: 4.071A  pdb=" N   GLU A1070 " --> pdb=" O   VAL A1066 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 1079 through 1098
    Processing helix  chain 'A' and resid 1099 through 1103
    Processing helix  chain 'A' and resid 1133 through 1157
      removed outlier: 4.398A  pdb=" N   GLN A1137 " --> pdb=" O   GLN A1133 " (cutoff:3.500A)
      removed outlier: 3.719A  pdb=" N   ASN A1156 " --> pdb=" O   ASP A1152 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 1189 through 1201
      removed outlier: 4.373A  pdb=" N   ASN A1193 " --> pdb=" O   GLY A1189 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 1210 through 1219
    Processing helix  chain 'B' and resid 13 through 25
    Processing helix  chain 'B' and resid 26 through 36
    Processing helix  chain 'B' and resid 49 through 58
      removed outlier: 3.549A  pdb=" N   PHE B  57 " --> pdb=" O   LEU B  53 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 59 through 70
    Processing helix  chain 'B' and resid 82 through 89
    Processing helix  chain 'B' and resid 92 through 102
      removed outlier: 3.884A  pdb=" N   VAL B  98 " --> pdb=" O   GLU B  94 " (cutoff:3.500A)
      removed outlier: 4.197A  pdb=" N   LEU B  99 " --> pdb=" O   ILE B  95 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 115 through 123
      removed outlier: 3.993A  pdb=" N   LEU B 119 " --> pdb=" O   THR B 115 " (cutoff:3.500A)
      removed outlier: 3.631A  pdb=" N   ALA B 120 " --> pdb=" O   PRO B 116 " (cutoff:3.500A)
      removed outlier: 3.748A  pdb=" N   ILE B 121 " --> pdb=" O   PHE B 117 " (cutoff:3.500A)
      removed outlier: 3.556A  pdb=" N   ASN B 123 " --> pdb=" O   LEU B 119 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 125 through 135
      removed outlier: 3.659A  pdb=" N   VAL B 131 " --> pdb=" O   ASP B 127 " (cutoff:3.500A)
      removed outlier: 3.985A  pdb=" N   ALA B 135 " --> pdb=" O   VAL B 131 " (cutoff:3.500A)
    Processing sheet with id=AA1, first strand: chain 'A' and resid 388 through 391
    Processing sheet with id=AA2, first strand: chain 'A' and resid 436 through 439
      removed outlier: 4.907A  pdb=" N   LYS A 437 " --> pdb=" O   VAL A 448 " (cutoff:3.500A)
      removed outlier: 5.549A  pdb=" N   VAL A 448 " --> pdb=" O   LYS A 437 " (cutoff:3.500A)
      removed outlier: 3.742A  pdb=" N   ASP A 399 " --> pdb=" O   ARG A 487 " (cutoff:3.500A)
      removed outlier: 3.521A  pdb=" N   ARG A 487 " --> pdb=" O   ASP A 399 " (cutoff:3.500A)
      removed outlier: 8.554A  pdb=" N   HIS A 530 " --> pdb=" O   MET A 486 " (cutoff:3.500A)
      removed outlier: 7.538A  pdb=" N   VAL A 488 " --> pdb=" O   HIS A 530 " (cutoff:3.500A)
      removed outlier: 8.451A  pdb=" N   SER A 532 " --> pdb=" O   VAL A 488 " (cutoff:3.500A)
    Processing sheet with id=AA3, first strand: chain 'A' and resid 1052 through 1055
    Processing sheet with id=AA4, first strand: chain 'A' and resid 1064 through 1065
      removed outlier: 3.749A  pdb=" N   ARG A1165 " --> pdb=" O   SER A1064 " (cutoff:3.500A)
    Processing sheet with id=AA5, first strand: chain 'A' and resid 1106 through 1109
      removed outlier: 6.949A  pdb=" N   MET A1116 " --> pdb=" O   ILE A1108 " (cutoff:3.500A)
    Processing sheet with id=AA6, first strand: chain 'A' and resid 1208 through 1209
      removed outlier: 3.585A  pdb=" N   TYR A1241 " --> pdb=" O   VAL A1209 " (cutoff:3.500A)
      removed outlier: 5.569A  pdb=" N   LEU A1242 " --> pdb=" O   TYR A1226 " (cutoff:3.500A)
      removed outlier: 5.373A  pdb=" N   TYR A1226 " --> pdb=" O   LEU A1242 " (cutoff:3.500A)

    476 hydrogen bonds defined for protein.
    1401 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: 2.54

  Time building geometry restraints manager: 2.47 seconds

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

  Histogram of bond lengths:
        1.22 -     1.34: 2433
        1.34 -     1.46: 1600
        1.46 -     1.58: 3684
        1.58 -     1.69: 1
        1.69 -     1.81: 88
  Bond restraints: 7806
  Sorted by residual:
  bond pdb=" CB  TRP A 862 "
       pdb=" CG  TRP A 862 "
    ideal  model  delta    sigma   weight residual
    1.498  1.620 -0.122 3.10e-02 1.04e+03 1.56e+01
  bond pdb=" CB  PHE A 232 "
       pdb=" CG  PHE A 232 "
    ideal  model  delta    sigma   weight residual
    1.502  1.437  0.065 2.30e-02 1.89e+03 7.87e+00
  bond pdb=" CB  VAL A 907 "
       pdb=" CG2 VAL A 907 "
    ideal  model  delta    sigma   weight residual
    1.521  1.437  0.084 3.30e-02 9.18e+02 6.45e+00
  bond pdb=" CB  VAL A 986 "
       pdb=" CG1 VAL A 986 "
    ideal  model  delta    sigma   weight residual
    1.521  1.439  0.082 3.30e-02 9.18e+02 6.18e+00
  bond pdb=" CG1 ILE A 291 "
       pdb=" CD1 ILE A 291 "
    ideal  model  delta    sigma   weight residual
    1.513  1.422  0.091 3.90e-02 6.57e+02 5.50e+00
  ... (remaining 7801 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     2.72: 10284
        2.72 -     5.45: 238
        5.45 -     8.17: 27
        8.17 -    10.90: 9
       10.90 -    13.62: 5
  Bond angle restraints: 10563
  Sorted by residual:
  angle pdb=" CA  TYR A1072 "
        pdb=" C   TYR A1072 "
        pdb=" O   TYR A1072 "
      ideal   model   delta    sigma   weight residual
     119.49  113.57    5.92 1.21e+00 6.83e-01 2.39e+01
  angle pdb=" N   ASN A 356 "
        pdb=" CA  ASN A 356 "
        pdb=" C   ASN A 356 "
      ideal   model   delta    sigma   weight residual
     114.31  108.05    6.26 1.29e+00 6.01e-01 2.35e+01
  angle pdb=" C   ASP A 344 "
        pdb=" N   ASP A 345 "
        pdb=" CA  ASP A 345 "
      ideal   model   delta    sigma   weight residual
     120.38  126.61   -6.23 1.37e+00 5.33e-01 2.07e+01
  angle pdb=" C   SER A 813 "
        pdb=" N   THR A 814 "
        pdb=" CA  THR A 814 "
      ideal   model   delta    sigma   weight residual
     120.69  107.60   13.09 2.95e+00 1.15e-01 1.97e+01
  angle pdb=" CA  LEU A 231 "
        pdb=" CB  LEU A 231 "
        pdb=" CG  LEU A 231 "
      ideal   model   delta    sigma   weight residual
     116.30  102.68   13.62 3.50e+00 8.16e-02 1.51e+01
  ... (remaining 10558 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    17.11: 3969
       17.11 -    34.23: 513
       34.23 -    51.34: 89
       51.34 -    68.46: 18
       68.46 -    85.57: 6
  Dihedral angle restraints: 4595
    sinusoidal: 1788
      harmonic: 2807
  Sorted by residual:
  dihedral pdb=" CA  PRO A 816 "
           pdb=" C   PRO A 816 "
           pdb=" N   PRO A 817 "
           pdb=" CA  PRO A 817 "
      ideal   model   delta  harmonic     sigma   weight residual
    -180.00 -152.46  -27.54     0      5.00e+00 4.00e-02 3.03e+01
  dihedral pdb=" CA  LEU A 978 "
           pdb=" C   LEU A 978 "
           pdb=" N   ILE A 979 "
           pdb=" CA  ILE A 979 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  152.68   27.32     0      5.00e+00 4.00e-02 2.99e+01
  dihedral pdb=" CA  GLU A1043 "
           pdb=" C   GLU A1043 "
           pdb=" N   GLN A1044 "
           pdb=" CA  GLN A1044 "
      ideal   model   delta  harmonic     sigma   weight residual
    -180.00 -154.54  -25.46     0      5.00e+00 4.00e-02 2.59e+01
  ... (remaining 4592 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.036: 672
       0.036 -    0.072: 351
       0.072 -    0.108: 144
       0.108 -    0.144: 29
       0.144 -    0.180: 13
  Chirality restraints: 1209
  Sorted by residual:
  chirality pdb=" CB  ILE A1022 "
            pdb=" CA  ILE A1022 "
            pdb=" CG1 ILE A1022 "
            pdb=" CG2 ILE A1022 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.64    2.82   -0.18 2.00e-01 2.50e+01 8.10e-01
  chirality pdb=" CA  LEU A 875 "
            pdb=" N   LEU A 875 "
            pdb=" C   LEU A 875 "
            pdb=" CB  LEU A 875 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.34    0.18 2.00e-01 2.50e+01 7.66e-01
  chirality pdb=" CA  PHE A 987 "
            pdb=" N   PHE A 987 "
            pdb=" C   PHE A 987 "
            pdb=" CB  PHE A 987 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.34    0.17 2.00e-01 2.50e+01 7.53e-01
  ... (remaining 1206 not shown)

  Planarity restraints: 1323
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CB  TRP A 918 "    0.020 2.00e-02 2.50e+03   1.51e-02 5.67e+00
        pdb=" CG  TRP A 918 "   -0.041 2.00e-02 2.50e+03
        pdb=" CD1 TRP A 918 "    0.014 2.00e-02 2.50e+03
        pdb=" CD2 TRP A 918 "   -0.001 2.00e-02 2.50e+03
        pdb=" NE1 TRP A 918 "    0.001 2.00e-02 2.50e+03
        pdb=" CE2 TRP A 918 "    0.002 2.00e-02 2.50e+03
        pdb=" CE3 TRP A 918 "    0.000 2.00e-02 2.50e+03
        pdb=" CZ2 TRP A 918 "    0.002 2.00e-02 2.50e+03
        pdb=" CZ3 TRP A 918 "    0.003 2.00e-02 2.50e+03
        pdb=" CH2 TRP A 918 "    0.001 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  VAL A 994 "   -0.010 2.00e-02 2.50e+03   1.98e-02 3.91e+00
        pdb=" C   VAL A 994 "    0.034 2.00e-02 2.50e+03
        pdb=" O   VAL A 994 "   -0.013 2.00e-02 2.50e+03
        pdb=" N   TRP A 995 "   -0.012 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CB  PHE A 987 "   -0.014 2.00e-02 2.50e+03   1.33e-02 3.09e+00
        pdb=" CG  PHE A 987 "    0.030 2.00e-02 2.50e+03
        pdb=" CD1 PHE A 987 "   -0.009 2.00e-02 2.50e+03
        pdb=" CD2 PHE A 987 "   -0.003 2.00e-02 2.50e+03
        pdb=" CE1 PHE A 987 "    0.003 2.00e-02 2.50e+03
        pdb=" CE2 PHE A 987 "   -0.003 2.00e-02 2.50e+03
        pdb=" CZ  PHE A 987 "   -0.004 2.00e-02 2.50e+03
  ... (remaining 1320 not shown)

  Histogram of nonbonded interaction distances:
        2.00 -     2.58: 139
        2.58 -     3.16: 7866
        3.16 -     3.74: 13057
        3.74 -     4.32: 17552
        4.32 -     4.90: 26012
  Nonbonded interactions: 64626
  Sorted by model distance:
  nonbonded pdb=" O   PHE A 912 "
            pdb=" NH1 ARG A 920 "
     model   vdw
     2.003 3.120
  nonbonded pdb=" OH  TYR A1226 "
            pdb=" OG1 THR A1229 "
     model   vdw
     2.098 3.040
  nonbonded pdb=" O   SER A 532 "
            pdb=" OG1 THR A 535 "
     model   vdw
     2.123 3.040
  nonbonded pdb=" O   PRO A1100 "
            pdb=" OG  SER A1103 "
     model   vdw
     2.134 3.040
  nonbonded pdb=" NE2 GLN A 389 "
            pdb=" OG1 THR A 494 "
     model   vdw
     2.154 3.120
  ... (remaining 64621 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:             2.350
  Set stop_for_unknowns flag:              0.000
  Assert model is a single copy model:     0.000
  Assert all atoms have isotropic ADPs:    0.000
  Construct map_model_manager:             0.020
  Extract box with map and model:          0.350
  Check model and map are aligned:         0.060
  Set scattering table:                    0.070
  Process input model:                     22.850
  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:3.050
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   28.870
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7858
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      :  0.009   0.122   7806  Z= 0.586
  Angle     :  1.080  13.622  10563  Z= 0.612
  Chirality :  0.051   0.180   1209
  Planarity :  0.005   0.042   1323
  Dihedral  : 15.646  85.573   2785
  Min Nonbonded Distance : 2.003

Molprobity Statistics.
  All-atom Clashscore : 34.24
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  : 11.22 %
    Favored  : 88.78 %
  Rotamer:
    Outliers :  1.09 %
    Allowed  : 13.82 %
    Favored  : 85.09 %
  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: -4.82 (0.20), residues: 954
  helix: -2.69 (0.16), residues: 569
  sheet: -4.06 (0.40), residues: 84
  loop : -3.52 (0.29), residues: 301

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.041   0.003   TRP A 918 
 HIS   0.009   0.002   HIS A 866 
 PHE   0.030   0.003   PHE A 987 
 TYR   0.018   0.003   TYR A1185 
 ARG   0.016   0.001   ARG A 920 

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

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

  1908 Ramachandran restraints generated.
    954 Oldfield, 0 Emsley, 954 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1908 Ramachandran restraints generated.
    954 Oldfield, 0 Emsley, 954 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  202 residues out of total 829 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 9
    poor density    : 193
  time to evaluate  : 0.805 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  145 MET cc_start: 0.8257 (mmt) cc_final: 0.7691 (mmt)
REVERT: A  167 LEU cc_start: 0.8320 (tp) cc_final: 0.7928 (tt)
REVERT: A  288 HIS cc_start: 0.7954 (m90) cc_final: 0.7671 (m90)
REVERT: A  446 TYR cc_start: 0.7975 (p90) cc_final: 0.7669 (p90)
REVERT: A  465 MET cc_start: 0.8638 (ttt) cc_final: 0.8263 (ttt)
REVERT: A  793 LEU cc_start: 0.9331 (tp) cc_final: 0.9010 (tp)
REVERT: A  798 PHE cc_start: 0.8332 (OUTLIER) cc_final: 0.8090 (t80)
REVERT: A 1095 GLU cc_start: 0.8386 (mt-10) cc_final: 0.8050 (mt-10)
REVERT: A 1107 LYS cc_start: 0.8546 (ttpt) cc_final: 0.8069 (ttmt)
REVERT: A 1115 TYR cc_start: 0.7761 (t80) cc_final: 0.6679 (t80)
REVERT: A 1147 MET cc_start: 0.9248 (ttm) cc_final: 0.8775 (tmm)
  outliers start: 9
  outliers final: 5
  residues processed: 201
  average time/residue: 0.2044
  time to fit residues: 55.0190
Evaluate side-chains
  161 residues out of total 829 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 6
    poor density    : 155
  time to evaluate  : 0.831 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 96
   random chunks:
   chunk 81 optimal weight:    6.9990
   chunk 72 optimal weight:    4.9990
   chunk 40 optimal weight:    9.9990
   chunk 24 optimal weight:    0.9990
   chunk 49 optimal weight:    0.7980
   chunk 38 optimal weight:    1.9990
   chunk 75 optimal weight:    7.9990
   chunk 29 optimal weight:    0.9990
   chunk 45 optimal weight:    4.9990
   chunk 56 optimal weight:    4.9990
   chunk 87 optimal weight:    6.9990
   overall best weight:    1.9588

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

Flipped N/Q/H residues before XYZ refinement:
** A 220 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 262 HIS
A 319 HIS
A 389 GLN
A 883 HIS
** A 998 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
A1028 GLN
A1075 ASN
A1135 HIS
** A1154 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
A1155 ASN
B  48 HIS
B 107 ASN

Total number of N/Q/H flips: 10

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4190 r_free = 0.4190 target = 0.127012 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 32)----------------|
| r_work = 0.3697 r_free = 0.3697 target = 0.091407 restraints weight = 20256.987|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 26)----------------|
| r_work = 0.3674 r_free = 0.3674 target = 0.092438 restraints weight = 14106.420|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 25)----------------|
| r_work = 0.3682 r_free = 0.3682 target = 0.093050 restraints weight = 9064.816|
|-----------------------------------------------------------------------------|
r_work (final): 0.3677
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7581
moved from start:          0.2541

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.049   7806  Z= 0.271
  Angle     :  0.728   9.698  10563  Z= 0.376
  Chirality :  0.043   0.181   1209
  Planarity :  0.005   0.051   1323
  Dihedral  :  5.562  29.363   1036
  Min Nonbonded Distance : 2.558

Molprobity Statistics.
  All-atom Clashscore : 17.48
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.18 %
    Favored  : 93.82 %
  Rotamer:
    Outliers :  0.24 %
    Allowed  :  5.33 %
    Favored  : 94.42 %
  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: -2.49 (0.25), residues: 954
  helix: -0.81 (0.19), residues: 585
  sheet: -3.53 (0.43), residues: 88
  loop : -2.51 (0.35), residues: 281

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.013   0.001   TRP A 918 
 HIS   0.006   0.001   HIS A 530 
 PHE   0.022   0.002   PHE A 912 
 TYR   0.017   0.002   TYR A 261 
 ARG   0.006   0.001   ARG A 920 

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

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

  1908 Ramachandran restraints generated.
    954 Oldfield, 0 Emsley, 954 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1908 Ramachandran restraints generated.
    954 Oldfield, 0 Emsley, 954 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  217 residues out of total 829 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 2
    poor density    : 215
  time to evaluate  : 1.027 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  167 LEU cc_start: 0.8341 (tp) cc_final: 0.7868 (tt)
REVERT: A  233 LEU cc_start: 0.9334 (mm) cc_final: 0.8956 (mm)
REVERT: A  288 HIS cc_start: 0.7687 (m90) cc_final: 0.7358 (m90)
REVERT: A  419 LEU cc_start: 0.9615 (tp) cc_final: 0.9098 (tp)
REVERT: A  423 PHE cc_start: 0.8970 (m-10) cc_final: 0.8732 (m-80)
REVERT: A  465 MET cc_start: 0.8963 (ttt) cc_final: 0.8391 (ttp)
REVERT: A 1095 GLU cc_start: 0.8352 (mt-10) cc_final: 0.8030 (mt-10)
REVERT: A 1107 LYS cc_start: 0.8372 (ttpt) cc_final: 0.8088 (ttmt)
REVERT: A 1147 MET cc_start: 0.8954 (ttm) cc_final: 0.8377 (tmm)
REVERT: A 1149 VAL cc_start: 0.9233 (t) cc_final: 0.8930 (t)
REVERT: A 1198 MET cc_start: 0.8138 (tpp) cc_final: 0.7649 (tpp)
REVERT: B   78 TRP cc_start: 0.7448 (t-100) cc_final: 0.6895 (t-100)
  outliers start: 2
  outliers final: 0
  residues processed: 217
  average time/residue: 0.1810
  time to fit residues: 53.5365
Evaluate side-chains
  167 residues out of total 829 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 167
  time to evaluate  : 0.849 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 96
   random chunks:
   chunk 3 optimal weight:    4.9990
   chunk 26 optimal weight:    9.9990
   chunk 41 optimal weight:    1.9990
   chunk 53 optimal weight:    1.9990
   chunk 56 optimal weight:    8.9990
   chunk 27 optimal weight:    5.9990
   chunk 40 optimal weight:    9.9990
   chunk 18 optimal weight:    0.8980
   chunk 66 optimal weight:    8.9990
   chunk 23 optimal weight:    8.9990
   chunk 62 optimal weight:    0.5980
   overall best weight:    2.0986

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

Flipped N/Q/H residues before XYZ refinement:
** A 998 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
A1154 ASN
A1237 GLN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4211 r_free = 0.4211 target = 0.128384 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.3577 r_free = 0.3577 target = 0.087048 restraints weight = 20782.796|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 34)----------------|
| r_work = 0.3632 r_free = 0.3632 target = 0.090356 restraints weight = 12881.780|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 29)----------------|
| r_work = 0.3649 r_free = 0.3649 target = 0.091315 restraints weight = 7211.421|
|-----------------------------------------------------------------------------|
r_work (final): 0.3639
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7684
moved from start:          0.3356

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.048   7806  Z= 0.256
  Angle     :  0.701   9.696  10563  Z= 0.362
  Chirality :  0.044   0.233   1209
  Planarity :  0.004   0.044   1323
  Dihedral  :  5.252  27.458   1036
  Min Nonbonded Distance : 2.438

Molprobity Statistics.
  All-atom Clashscore : 16.69
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.18 %
    Favored  : 93.82 %
  Rotamer:
    Outliers :  0.24 %
    Allowed  :  6.55 %
    Favored  : 93.21 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -1.62 (0.26), residues: 954
  helix: -0.10 (0.20), residues: 586
  sheet: -3.32 (0.44), residues: 84
  loop : -2.21 (0.36), residues: 284

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.008   0.001   TRP A 918 
 HIS   0.005   0.001   HIS A 866 
 PHE   0.046   0.002   PHE A 184 
 TYR   0.027   0.002   TYR A1083 
 ARG   0.004   0.001   ARG B  23 

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

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

  1908 Ramachandran restraints generated.
    954 Oldfield, 0 Emsley, 954 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1908 Ramachandran restraints generated.
    954 Oldfield, 0 Emsley, 954 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  212 residues out of total 829 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 2
    poor density    : 210
  time to evaluate  : 0.793 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  167 LEU cc_start: 0.8496 (tp) cc_final: 0.8017 (tt)
REVERT: A  419 LEU cc_start: 0.9637 (tp) cc_final: 0.9428 (tp)
REVERT: A  445 TYR cc_start: 0.7682 (t80) cc_final: 0.7439 (t80)
REVERT: A  446 TYR cc_start: 0.7805 (p90) cc_final: 0.7493 (p90)
REVERT: A  465 MET cc_start: 0.9200 (ttt) cc_final: 0.8534 (ttp)
REVERT: A  545 MET cc_start: 0.7795 (mpp) cc_final: 0.7483 (mmt)
REVERT: A  854 ARG cc_start: 0.8100 (tpm170) cc_final: 0.7797 (tpm170)
REVERT: A 1107 LYS cc_start: 0.8325 (ttpt) cc_final: 0.8004 (ttmt)
REVERT: A 1147 MET cc_start: 0.9111 (ttm) cc_final: 0.8537 (tmm)
REVERT: A 1198 MET cc_start: 0.8424 (tpp) cc_final: 0.8009 (tpp)
REVERT: B   29 GLU cc_start: 0.9384 (tm-30) cc_final: 0.9087 (pp20)
REVERT: B   78 TRP cc_start: 0.7712 (t-100) cc_final: 0.7030 (t-100)
  outliers start: 2
  outliers final: 1
  residues processed: 211
  average time/residue: 0.1788
  time to fit residues: 52.3946
Evaluate side-chains
  167 residues out of total 829 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 166
  time to evaluate  : 0.748 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 96
   random chunks:
   chunk 15 optimal weight:    1.9990
   chunk 37 optimal weight:   20.0000
   chunk 49 optimal weight:    0.7980
   chunk 16 optimal weight:    0.8980
   chunk 67 optimal weight:    7.9990
   chunk 53 optimal weight:    0.8980
   chunk 44 optimal weight:   20.0000
   chunk 7 optimal weight:   10.0000
   chunk 46 optimal weight:    8.9990
   chunk 84 optimal weight:    3.9990
   chunk 0 optimal weight:    9.9990
   overall best weight:    1.7184

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

Flipped N/Q/H residues before XYZ refinement:
** A 998 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A1170 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4224 r_free = 0.4224 target = 0.129416 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 47)----------------|
| r_work = 0.3590 r_free = 0.3590 target = 0.087086 restraints weight = 20424.915|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 42)----------------|
| r_work = 0.3641 r_free = 0.3641 target = 0.089911 restraints weight = 11479.222|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 41)----------------|
| r_work = 0.3674 r_free = 0.3674 target = 0.091834 restraints weight = 7610.901|
|-----------------------------------------------------------------------------|
r_work (final): 0.3664
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7661
moved from start:          0.3911

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.041   7806  Z= 0.228
  Angle     :  0.686  11.587  10563  Z= 0.351
  Chirality :  0.043   0.152   1209
  Planarity :  0.004   0.040   1323
  Dihedral  :  5.028  26.063   1036
  Min Nonbonded Distance : 2.463

Molprobity Statistics.
  All-atom Clashscore : 16.04
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.14 %
    Favored  : 94.86 %
  Rotamer:
    Outliers :  0.12 %
    Allowed  :  3.52 %
    Favored  : 96.36 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -1.16 (0.27), residues: 954
  helix:  0.24 (0.20), residues: 594
  sheet: -2.81 (0.46), residues: 94
  loop : -2.11 (0.39), residues: 266

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.022   0.002   TRP A1159 
 HIS   0.006   0.001   HIS A 319 
 PHE   0.044   0.002   PHE A 184 
 TYR   0.025   0.002   TYR A1083 
 ARG   0.005   0.001   ARG B  23 

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

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

  1908 Ramachandran restraints generated.
    954 Oldfield, 0 Emsley, 954 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1908 Ramachandran restraints generated.
    954 Oldfield, 0 Emsley, 954 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  204 residues out of total 829 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 203
  time to evaluate  : 0.863 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  167 LEU cc_start: 0.8528 (tp) cc_final: 0.8114 (tt)
REVERT: A  423 PHE cc_start: 0.8992 (m-80) cc_final: 0.8783 (m-80)
REVERT: A  445 TYR cc_start: 0.7677 (t80) cc_final: 0.7263 (t80)
REVERT: A  446 TYR cc_start: 0.7877 (p90) cc_final: 0.7347 (p90)
REVERT: A  465 MET cc_start: 0.9102 (ttt) cc_final: 0.8493 (ttp)
REVERT: A  545 MET cc_start: 0.7854 (mpp) cc_final: 0.7456 (mmt)
REVERT: A  854 ARG cc_start: 0.8033 (tpm170) cc_final: 0.7697 (tpm170)
REVERT: A  922 SER cc_start: 0.9369 (m) cc_final: 0.9143 (m)
REVERT: A 1107 LYS cc_start: 0.8315 (ttpt) cc_final: 0.7977 (ttmt)
REVERT: A 1147 MET cc_start: 0.9127 (ttm) cc_final: 0.8587 (tmm)
REVERT: B   23 ARG cc_start: 0.9540 (ptt-90) cc_final: 0.9213 (ptt90)
REVERT: B   78 TRP cc_start: 0.7676 (t-100) cc_final: 0.6961 (t-100)
  outliers start: 1
  outliers final: 0
  residues processed: 204
  average time/residue: 0.1700
  time to fit residues: 48.5630
Evaluate side-chains
  166 residues out of total 829 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 166
  time to evaluate  : 0.843 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 96
   random chunks:
   chunk 10 optimal weight:    0.9980
   chunk 26 optimal weight:    0.9990
   chunk 76 optimal weight:    8.9990
   chunk 72 optimal weight:    0.8980
   chunk 51 optimal weight:    5.9990
   chunk 16 optimal weight:    0.9990
   chunk 1 optimal weight:    3.9990
   chunk 41 optimal weight:    0.9980
   chunk 66 optimal weight:    4.9990
   chunk 70 optimal weight:    0.9990
   chunk 2 optimal weight:    1.9990
   overall best weight:    0.9784

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

Flipped N/Q/H residues before XYZ refinement:
** A 998 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
A1131 HIS
B  92 HIS

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4257 r_free = 0.4257 target = 0.131284 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 42)----------------|
| r_work = 0.3774 r_free = 0.3774 target = 0.095709 restraints weight = 19358.802|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 27)----------------|
| r_work = 0.3727 r_free = 0.3727 target = 0.095304 restraints weight = 13615.475|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 27)----------------|
| r_work = 0.3743 r_free = 0.3743 target = 0.096104 restraints weight = 9647.388|
|-----------------------------------------------------------------------------|
r_work (final): 0.3745
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7518
moved from start:          0.4491

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.055   7806  Z= 0.188
  Angle     :  0.658   9.687  10563  Z= 0.333
  Chirality :  0.042   0.156   1209
  Planarity :  0.004   0.036   1323
  Dihedral  :  4.797  25.403   1036
  Min Nonbonded Distance : 2.480

Molprobity Statistics.
  All-atom Clashscore : 13.42
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.03 %
    Favored  : 94.97 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  3.76 %
    Favored  : 96.24 %
  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: -0.74 (0.27), residues: 954
  helix:  0.60 (0.20), residues: 595
  sheet: -2.62 (0.49), residues: 92
  loop : -2.05 (0.38), residues: 267

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.020   0.001   TRP A 995 
 HIS   0.005   0.001   HIS B  92 
 PHE   0.047   0.002   PHE A 184 
 TYR   0.016   0.001   TYR A1083 
 ARG   0.004   0.000   ARG B  23 

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

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

  1908 Ramachandran restraints generated.
    954 Oldfield, 0 Emsley, 954 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1908 Ramachandran restraints generated.
    954 Oldfield, 0 Emsley, 954 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  217 residues out of total 829 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 217
  time to evaluate  : 0.827 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  167 LEU cc_start: 0.8516 (tp) cc_final: 0.8110 (tt)
REVERT: A  335 HIS cc_start: 0.7838 (m-70) cc_final: 0.7407 (m170)
REVERT: A  446 TYR cc_start: 0.7678 (p90) cc_final: 0.7290 (p90)
REVERT: A  465 MET cc_start: 0.9064 (ttt) cc_final: 0.8641 (ttp)
REVERT: A  483 MET cc_start: 0.7952 (tpt) cc_final: 0.6837 (mmt)
REVERT: A  516 LEU cc_start: 0.9419 (mt) cc_final: 0.9206 (mt)
REVERT: A  520 MET cc_start: 0.7941 (ttm) cc_final: 0.7714 (ttp)
REVERT: A  545 MET cc_start: 0.7829 (mpp) cc_final: 0.7538 (mpp)
REVERT: A  854 ARG cc_start: 0.7940 (tpm170) cc_final: 0.7586 (tpm170)
REVERT: A  875 LEU cc_start: 0.8494 (pp) cc_final: 0.8128 (pp)
REVERT: A  996 PHE cc_start: 0.7768 (m-80) cc_final: 0.7532 (m-10)
REVERT: A 1025 MET cc_start: 0.7877 (tpp) cc_final: 0.7218 (tpp)
REVERT: A 1107 LYS cc_start: 0.8174 (ttpt) cc_final: 0.7848 (ttmt)
REVERT: A 1142 PHE cc_start: 0.9208 (t80) cc_final: 0.9006 (t80)
REVERT: A 1147 MET cc_start: 0.9013 (ttm) cc_final: 0.8514 (tmm)
REVERT: A 1148 ARG cc_start: 0.9159 (ptp-170) cc_final: 0.8805 (ptp90)
REVERT: B   29 GLU cc_start: 0.9158 (tm-30) cc_final: 0.8897 (tm-30)
  outliers start: 0
  outliers final: 0
  residues processed: 217
  average time/residue: 0.1686
  time to fit residues: 50.7036
Evaluate side-chains
  162 residues out of total 829 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 162
  time to evaluate  : 0.775 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 96
   random chunks:
   chunk 88 optimal weight:    2.9990
   chunk 15 optimal weight:    6.9990
   chunk 19 optimal weight:    2.9990
   chunk 95 optimal weight:    5.9990
   chunk 18 optimal weight:    2.9990
   chunk 33 optimal weight:    8.9990
   chunk 42 optimal weight:    0.6980
   chunk 57 optimal weight:    3.9990
   chunk 43 optimal weight:    0.7980
   chunk 13 optimal weight:    1.9990
   chunk 5 optimal weight:    0.9980
   overall best weight:    1.4984

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

Flipped N/Q/H residues before XYZ refinement:
A 335 HIS
** A 998 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4247 r_free = 0.4247 target = 0.131419 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 44)----------------|
| r_work = 0.3771 r_free = 0.3771 target = 0.096122 restraints weight = 19803.533|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 30)----------------|
| r_work = 0.3723 r_free = 0.3723 target = 0.095304 restraints weight = 13248.840|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 27)----------------|
| r_work = 0.3737 r_free = 0.3737 target = 0.096353 restraints weight = 9111.525|
|-----------------------------------------------------------------------------|
r_work (final): 0.3741
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7520
moved from start:          0.4776

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.034   7806  Z= 0.211
  Angle     :  0.682   9.668  10563  Z= 0.348
  Chirality :  0.043   0.179   1209
  Planarity :  0.004   0.039   1323
  Dihedral  :  4.670  25.091   1036
  Min Nonbonded Distance : 2.429

Molprobity Statistics.
  All-atom Clashscore : 14.86
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.24 %
    Favored  : 94.76 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  2.30 %
    Favored  : 97.70 %
  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: -0.74 (0.27), residues: 954
  helix:  0.54 (0.20), residues: 593
  sheet: -2.36 (0.52), residues: 86
  loop : -2.02 (0.37), residues: 275

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.028   0.002   TRP A1159 
 HIS   0.009   0.001   HIS B  85 
 PHE   0.038   0.002   PHE A 184 
 TYR   0.021   0.002   TYR A1102 
 ARG   0.006   0.001   ARG B  23 

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

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

  1908 Ramachandran restraints generated.
    954 Oldfield, 0 Emsley, 954 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1908 Ramachandran restraints generated.
    954 Oldfield, 0 Emsley, 954 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  201 residues out of total 829 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 201
  time to evaluate  : 0.795 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  167 LEU cc_start: 0.8415 (tp) cc_final: 0.8017 (tt)
REVERT: A  446 TYR cc_start: 0.7706 (p90) cc_final: 0.7415 (p90)
REVERT: A  465 MET cc_start: 0.9044 (ttt) cc_final: 0.8605 (ttp)
REVERT: A  545 MET cc_start: 0.7762 (mpp) cc_final: 0.7369 (mmt)
REVERT: A  854 ARG cc_start: 0.7969 (tpm170) cc_final: 0.7619 (tpm170)
REVERT: A 1001 PHE cc_start: 0.7980 (m-10) cc_final: 0.7741 (m-10)
REVERT: A 1025 MET cc_start: 0.7907 (tpp) cc_final: 0.7323 (tpp)
REVERT: A 1088 GLU cc_start: 0.9009 (mt-10) cc_final: 0.8282 (mt-10)
REVERT: A 1107 LYS cc_start: 0.8166 (ttpt) cc_final: 0.7785 (ttmt)
REVERT: A 1147 MET cc_start: 0.8932 (ttm) cc_final: 0.8416 (tmm)
REVERT: A 1148 ARG cc_start: 0.9152 (ptp-170) cc_final: 0.8890 (ptp-110)
REVERT: B   29 GLU cc_start: 0.9068 (tm-30) cc_final: 0.8743 (tm-30)
REVERT: B   32 ILE cc_start: 0.9404 (mt) cc_final: 0.9088 (mt)
REVERT: B   36 ASN cc_start: 0.7494 (m110) cc_final: 0.7243 (t0)
REVERT: B   56 TRP cc_start: 0.6165 (t-100) cc_final: 0.4928 (t-100)
REVERT: B   78 TRP cc_start: 0.7276 (t-100) cc_final: 0.6779 (t-100)
  outliers start: 0
  outliers final: 0
  residues processed: 201
  average time/residue: 0.1662
  time to fit residues: 46.9291
Evaluate side-chains
  163 residues out of total 829 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 163
  time to evaluate  : 1.137 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 96
   random chunks:
   chunk 9 optimal weight:    0.7980
   chunk 64 optimal weight:    7.9990
   chunk 69 optimal weight:    8.9990
   chunk 78 optimal weight:    1.9990
   chunk 49 optimal weight:    0.8980
   chunk 59 optimal weight:    2.9990
   chunk 42 optimal weight:    0.9980
   chunk 10 optimal weight:    0.9980
   chunk 58 optimal weight:    0.6980
   chunk 34 optimal weight:   10.0000
   chunk 36 optimal weight:    5.9990
   overall best weight:    0.8780

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

Flipped N/Q/H residues before XYZ refinement:
A 335 HIS
** A 998 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4253 r_free = 0.4253 target = 0.131661 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 65)----------------|
| r_work = 0.3672 r_free = 0.3672 target = 0.091363 restraints weight = 19775.365|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 42)----------------|
| r_work = 0.3714 r_free = 0.3714 target = 0.093898 restraints weight = 11729.855|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 41)----------------|
| r_work = 0.3744 r_free = 0.3744 target = 0.095635 restraints weight = 8079.705|
|-----------------------------------------------------------------------------|
r_work (final): 0.3734
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7569
moved from start:          0.5066

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.033   7806  Z= 0.175
  Angle     :  0.664   9.669  10563  Z= 0.333
  Chirality :  0.042   0.170   1209
  Planarity :  0.004   0.039   1323
  Dihedral  :  4.610  22.494   1036
  Min Nonbonded Distance : 2.459

Molprobity Statistics.
  All-atom Clashscore : 13.09
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.61 %
    Favored  : 95.39 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  2.67 %
    Favored  : 97.33 %
  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 (0.27), residues: 954
  helix:  0.64 (0.20), residues: 597
  sheet: -2.24 (0.50), residues: 97
  loop : -2.01 (0.38), residues: 260

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.023   0.001   TRP A 995 
 HIS   0.009   0.001   HIS B  85 
 PHE   0.049   0.002   PHE A 184 
 TYR   0.020   0.002   TYR A 261 
 ARG   0.007   0.000   ARG B  23 

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

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

  1908 Ramachandran restraints generated.
    954 Oldfield, 0 Emsley, 954 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1908 Ramachandran restraints generated.
    954 Oldfield, 0 Emsley, 954 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  200 residues out of total 829 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 200
  time to evaluate  : 0.802 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  167 LEU cc_start: 0.8418 (tp) cc_final: 0.7995 (tt)
REVERT: A  335 HIS cc_start: 0.7801 (m-70) cc_final: 0.7335 (m170)
REVERT: A  446 TYR cc_start: 0.7629 (p90) cc_final: 0.7388 (p90)
REVERT: A  465 MET cc_start: 0.9103 (ttt) cc_final: 0.8687 (ttp)
REVERT: A  516 LEU cc_start: 0.9407 (mt) cc_final: 0.9194 (mt)
REVERT: A  519 LEU cc_start: 0.9428 (mt) cc_final: 0.9228 (pp)
REVERT: A  545 MET cc_start: 0.7801 (mpp) cc_final: 0.7377 (mmt)
REVERT: A  854 ARG cc_start: 0.7886 (tpm170) cc_final: 0.7570 (tpm170)
REVERT: A 1083 TYR cc_start: 0.8773 (m-80) cc_final: 0.8569 (m-80)
REVERT: A 1088 GLU cc_start: 0.9255 (mt-10) cc_final: 0.8474 (mt-10)
REVERT: A 1107 LYS cc_start: 0.8579 (ttpt) cc_final: 0.8377 (ttmt)
REVERT: A 1115 TYR cc_start: 0.7654 (t80) cc_final: 0.6870 (t80)
REVERT: A 1140 PHE cc_start: 0.8989 (t80) cc_final: 0.8730 (t80)
REVERT: A 1147 MET cc_start: 0.9098 (ttm) cc_final: 0.8532 (tmm)
REVERT: A 1148 ARG cc_start: 0.9266 (ptp-170) cc_final: 0.9002 (ptp-110)
REVERT: A 1153 PHE cc_start: 0.8854 (t80) cc_final: 0.8580 (t80)
REVERT: B   20 GLU cc_start: 0.9176 (tm-30) cc_final: 0.8828 (tm-30)
REVERT: B   29 GLU cc_start: 0.9173 (tm-30) cc_final: 0.8716 (tm-30)
REVERT: B   32 ILE cc_start: 0.9490 (mt) cc_final: 0.9209 (mt)
REVERT: B   56 TRP cc_start: 0.6238 (t-100) cc_final: 0.5227 (t-100)
REVERT: B   78 TRP cc_start: 0.7389 (t-100) cc_final: 0.6954 (t-100)
  outliers start: 0
  outliers final: 0
  residues processed: 200
  average time/residue: 0.1691
  time to fit residues: 47.6829
Evaluate side-chains
  163 residues out of total 829 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 163
  time to evaluate  : 0.810 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 96
   random chunks:
   chunk 46 optimal weight:    1.9990
   chunk 45 optimal weight:    2.9990
   chunk 69 optimal weight:    5.9990
   chunk 29 optimal weight:    7.9990
   chunk 77 optimal weight:    0.8980
   chunk 54 optimal weight:    4.9990
   chunk 60 optimal weight:    0.6980
   chunk 3 optimal weight:    4.9990
   chunk 93 optimal weight:   30.0000
   chunk 36 optimal weight:    3.9990
   chunk 74 optimal weight:    0.9990
   overall best weight:    1.5186

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

Flipped N/Q/H residues before XYZ refinement:
A 262 HIS
** A 998 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4252 r_free = 0.4252 target = 0.130568 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 34)----------------|
| r_work = 0.3723 r_free = 0.3723 target = 0.093980 restraints weight = 19892.759|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 28)----------------|
| r_work = 0.3717 r_free = 0.3717 target = 0.094118 restraints weight = 12089.302|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 32)----------------|
| r_work = 0.3742 r_free = 0.3742 target = 0.095783 restraints weight = 8023.913|
|-----------------------------------------------------------------------------|
r_work (final): 0.3729
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7553
moved from start:          0.5248

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.048   7806  Z= 0.220
  Angle     :  0.714   9.871  10563  Z= 0.361
  Chirality :  0.044   0.214   1209
  Planarity :  0.004   0.043   1323
  Dihedral  :  4.663  22.061   1036
  Min Nonbonded Distance : 2.367

Molprobity Statistics.
  All-atom Clashscore : 13.62
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.03 %
    Favored  : 94.97 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  1.45 %
    Favored  : 98.55 %
  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: -0.66 (0.27), residues: 954
  helix:  0.59 (0.21), residues: 594
  sheet: -2.20 (0.50), residues: 97
  loop : -1.96 (0.38), residues: 263

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.023   0.001   TRP A 995 
 HIS   0.010   0.001   HIS B  85 
 PHE   0.036   0.002   PHE A 184 
 TYR   0.021   0.002   TYR A 909 
 ARG   0.004   0.000   ARG A 340 

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

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

  1908 Ramachandran restraints generated.
    954 Oldfield, 0 Emsley, 954 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1908 Ramachandran restraints generated.
    954 Oldfield, 0 Emsley, 954 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  201 residues out of total 829 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 201
  time to evaluate  : 0.782 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  167 LEU cc_start: 0.8448 (tp) cc_final: 0.7989 (tt)
REVERT: A  335 HIS cc_start: 0.7788 (m-70) cc_final: 0.7266 (m170)
REVERT: A  446 TYR cc_start: 0.7610 (p90) cc_final: 0.7320 (p90)
REVERT: A  465 MET cc_start: 0.9219 (ttt) cc_final: 0.8807 (ttp)
REVERT: A  516 LEU cc_start: 0.9402 (mt) cc_final: 0.9181 (mt)
REVERT: A  519 LEU cc_start: 0.9453 (mt) cc_final: 0.9239 (pp)
REVERT: A  854 ARG cc_start: 0.8044 (tpm170) cc_final: 0.7684 (tpm170)
REVERT: A  922 SER cc_start: 0.9308 (m) cc_final: 0.9094 (m)
REVERT: A 1088 GLU cc_start: 0.9194 (mt-10) cc_final: 0.8377 (mt-10)
REVERT: A 1115 TYR cc_start: 0.7621 (t80) cc_final: 0.6929 (t80)
REVERT: A 1142 PHE cc_start: 0.9215 (t80) cc_final: 0.8819 (t80)
REVERT: A 1147 MET cc_start: 0.8985 (ttm) cc_final: 0.8311 (tmm)
REVERT: B   29 GLU cc_start: 0.9157 (tm-30) cc_final: 0.8788 (tm-30)
REVERT: B   56 TRP cc_start: 0.6407 (t-100) cc_final: 0.5405 (t-100)
REVERT: B   78 TRP cc_start: 0.7284 (t-100) cc_final: 0.6811 (t-100)
REVERT: B   82 THR cc_start: 0.8217 (p) cc_final: 0.7995 (t)
  outliers start: 0
  outliers final: 0
  residues processed: 201
  average time/residue: 0.1784
  time to fit residues: 50.2664
Evaluate side-chains
  159 residues out of total 829 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 159
  time to evaluate  : 0.695 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 96
   random chunks:
   chunk 86 optimal weight:    4.9990
   chunk 32 optimal weight:    1.9990
   chunk 80 optimal weight:    9.9990
   chunk 17 optimal weight:    2.9990
   chunk 18 optimal weight:    1.9990
   chunk 89 optimal weight:    9.9990
   chunk 12 optimal weight:    0.7980
   chunk 84 optimal weight:    0.6980
   chunk 73 optimal weight:    0.5980
   chunk 24 optimal weight:    0.9990
   chunk 90 optimal weight:   30.0000
   overall best weight:    1.0184

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

Flipped N/Q/H residues before XYZ refinement:
** A 998 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4260 r_free = 0.4260 target = 0.132326 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 36)----------------|
| r_work = 0.3703 r_free = 0.3703 target = 0.094095 restraints weight = 20182.099|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 25)----------------|
| r_work = 0.3738 r_free = 0.3738 target = 0.095878 restraints weight = 14449.008|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 34)----------------|
| r_work = 0.3745 r_free = 0.3745 target = 0.096520 restraints weight = 9347.839|
|-----------------------------------------------------------------------------|
r_work (final): 0.3734
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7537
moved from start:          0.5512

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.047   7806  Z= 0.192
  Angle     :  0.696   9.730  10563  Z= 0.349
  Chirality :  0.043   0.188   1209
  Planarity :  0.004   0.039   1323
  Dihedral  :  4.657  21.890   1036
  Min Nonbonded Distance : 2.408

Molprobity Statistics.
  All-atom Clashscore : 12.77
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.51 %
    Favored  : 95.49 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  0.61 %
    Favored  : 99.39 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -0.53 (0.27), residues: 954
  helix:  0.65 (0.21), residues: 594
  sheet: -2.12 (0.50), residues: 97
  loop : -1.79 (0.38), residues: 263

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.015   0.001   TRP A1159 
 HIS   0.011   0.001   HIS A 335 
 PHE   0.050   0.002   PHE A 184 
 TYR   0.018   0.002   TYR A 261 
 ARG   0.006   0.000   ARG B  23 

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

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

  1908 Ramachandran restraints generated.
    954 Oldfield, 0 Emsley, 954 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1908 Ramachandran restraints generated.
    954 Oldfield, 0 Emsley, 954 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  199 residues out of total 829 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 199
  time to evaluate  : 0.778 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  167 LEU cc_start: 0.8329 (tp) cc_final: 0.7847 (tt)
REVERT: A  335 HIS cc_start: 0.7809 (m-70) cc_final: 0.7587 (m170)
REVERT: A  446 TYR cc_start: 0.7588 (p90) cc_final: 0.7292 (p90)
REVERT: A  465 MET cc_start: 0.9184 (ttt) cc_final: 0.8791 (ttp)
REVERT: A  505 PHE cc_start: 0.9143 (p90) cc_final: 0.8756 (p90)
REVERT: A  516 LEU cc_start: 0.9386 (mt) cc_final: 0.9168 (mt)
REVERT: A  519 LEU cc_start: 0.9437 (mt) cc_final: 0.9224 (pp)
REVERT: A  854 ARG cc_start: 0.7862 (tpm170) cc_final: 0.7521 (tpm170)
REVERT: A 1088 GLU cc_start: 0.9196 (mt-10) cc_final: 0.8435 (mt-10)
REVERT: A 1111 ILE cc_start: 0.8710 (pt) cc_final: 0.8507 (pt)
REVERT: A 1142 PHE cc_start: 0.9287 (t80) cc_final: 0.8880 (t80)
REVERT: A 1147 MET cc_start: 0.8910 (ttm) cc_final: 0.8351 (tmm)
REVERT: B   29 GLU cc_start: 0.9239 (tm-30) cc_final: 0.8858 (tm-30)
REVERT: B   56 TRP cc_start: 0.6659 (t-100) cc_final: 0.5970 (t-100)
REVERT: B   78 TRP cc_start: 0.7164 (t-100) cc_final: 0.6809 (t-100)
  outliers start: 0
  outliers final: 0
  residues processed: 199
  average time/residue: 0.1703
  time to fit residues: 47.0509
Evaluate side-chains
  165 residues out of total 829 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 165
  time to evaluate  : 0.843 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 96
   random chunks:
   chunk 65 optimal weight:    1.9990
   chunk 24 optimal weight:    0.5980
   chunk 79 optimal weight:    0.0770
   chunk 85 optimal weight:    8.9990
   chunk 27 optimal weight:    0.9980
   chunk 4 optimal weight:    0.1980
   chunk 76 optimal weight:    4.9990
   chunk 87 optimal weight:    9.9990
   chunk 60 optimal weight:    4.9990
   chunk 49 optimal weight:    0.9980
   chunk 42 optimal weight:    0.8980
   overall best weight:    0.5538

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

Flipped N/Q/H residues before XYZ refinement:
** A 111 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 914 GLN
** A 998 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4285 r_free = 0.4285 target = 0.134605 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 59)----------------|
| r_work = 0.3727 r_free = 0.3727 target = 0.094865 restraints weight = 19943.000|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 44)----------------|
| r_work = 0.3773 r_free = 0.3773 target = 0.097465 restraints weight = 11987.848|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 33)----------------|
| r_work = 0.3797 r_free = 0.3797 target = 0.099020 restraints weight = 8232.048|
|-----------------------------------------------------------------------------|
r_work (final): 0.3782
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7491
moved from start:          0.5873

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.042   7806  Z= 0.180
  Angle     :  0.696   9.682  10563  Z= 0.345
  Chirality :  0.042   0.184   1209
  Planarity :  0.004   0.038   1323
  Dihedral  :  4.572  21.990   1036
  Min Nonbonded Distance : 2.432

Molprobity Statistics.
  All-atom Clashscore : 12.63
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.77 %
    Favored  : 96.23 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  0.36 %
    Favored  : 99.64 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -0.33 (0.27), residues: 954
  helix:  0.79 (0.21), residues: 594
  sheet: -1.93 (0.50), residues: 96
  loop : -1.74 (0.39), residues: 264

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.015   0.001   TRP A1159 
 HIS   0.009   0.001   HIS B  85 
 PHE   0.034   0.002   PHE A 184 
 TYR   0.019   0.001   TYR A 909 
 ARG   0.011   0.001   ARG B  23 

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

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

  1908 Ramachandran restraints generated.
    954 Oldfield, 0 Emsley, 954 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1908 Ramachandran restraints generated.
    954 Oldfield, 0 Emsley, 954 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  205 residues out of total 829 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 205
  time to evaluate  : 0.789 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  167 LEU cc_start: 0.8391 (tp) cc_final: 0.7912 (tt)
REVERT: A  446 TYR cc_start: 0.7586 (p90) cc_final: 0.7263 (p90)
REVERT: A  465 MET cc_start: 0.9114 (ttt) cc_final: 0.8763 (ttp)
REVERT: A  486 MET cc_start: 0.8517 (tpp) cc_final: 0.7747 (tpp)
REVERT: A  505 PHE cc_start: 0.9115 (p90) cc_final: 0.8825 (p90)
REVERT: A  516 LEU cc_start: 0.9384 (mt) cc_final: 0.9173 (mt)
REVERT: A  519 LEU cc_start: 0.9411 (mt) cc_final: 0.9188 (pp)
REVERT: A  854 ARG cc_start: 0.7827 (tpm170) cc_final: 0.7522 (tpm170)
REVERT: A  875 LEU cc_start: 0.8445 (pp) cc_final: 0.8218 (pp)
REVERT: A 1083 TYR cc_start: 0.8771 (m-80) cc_final: 0.8531 (m-80)
REVERT: A 1088 GLU cc_start: 0.9254 (mt-10) cc_final: 0.8747 (mt-10)
REVERT: A 1111 ILE cc_start: 0.8702 (pt) cc_final: 0.8395 (pt)
REVERT: A 1147 MET cc_start: 0.8944 (ttm) cc_final: 0.8433 (tmm)
REVERT: B   29 GLU cc_start: 0.9268 (tm-30) cc_final: 0.8939 (tm-30)
REVERT: B   56 TRP cc_start: 0.6694 (t-100) cc_final: 0.5975 (t-100)
REVERT: B   78 TRP cc_start: 0.7267 (t-100) cc_final: 0.6883 (t-100)
  outliers start: 0
  outliers final: 0
  residues processed: 205
  average time/residue: 0.1643
  time to fit residues: 47.4559
Evaluate side-chains
  164 residues out of total 829 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 164
  time to evaluate  : 0.798 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 96
   random chunks:
   chunk 92 optimal weight:    5.9990
   chunk 32 optimal weight:    2.9990
   chunk 63 optimal weight:    0.6980
   chunk 57 optimal weight:    1.9990
   chunk 19 optimal weight:    0.8980
   chunk 89 optimal weight:    5.9990
   chunk 8 optimal weight:    1.9990
   chunk 59 optimal weight:    0.7980
   chunk 33 optimal weight:    8.9990
   chunk 16 optimal weight:    2.9990
   chunk 76 optimal weight:    2.9990
   overall best weight:    1.2784

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

Flipped N/Q/H residues before XYZ refinement:
A 914 GLN
** A 998 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
A1008 HIS

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4267 r_free = 0.4267 target = 0.133196 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 48)----------------|
| r_work = 0.3764 r_free = 0.3764 target = 0.097341 restraints weight = 19843.628|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 28)----------------|
| r_work = 0.3761 r_free = 0.3761 target = 0.097525 restraints weight = 13419.043|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 23)----------------|
| r_work = 0.3755 r_free = 0.3755 target = 0.097077 restraints weight = 10076.726|
|-----------------------------------------------------------------------------|
r_work (final): 0.3743
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7506
moved from start:          0.5893

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.049   7806  Z= 0.204
  Angle     :  0.718  10.753  10563  Z= 0.358
  Chirality :  0.043   0.191   1209
  Planarity :  0.005   0.054   1323
  Dihedral  :  4.601  21.952   1036
  Min Nonbonded Distance : 2.413

Molprobity Statistics.
  All-atom Clashscore : 13.88
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.30 %
    Favored  : 95.70 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  0.36 %
    Favored  : 99.64 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -0.40 (0.27), residues: 954
  helix:  0.75 (0.21), residues: 596
  sheet: -1.88 (0.50), residues: 100
  loop : -1.85 (0.38), residues: 258

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.015   0.001   TRP A1159 
 HIS   0.008   0.001   HIS B  85 
 PHE   0.061   0.002   PHE A 184 
 TYR   0.016   0.002   TYR A 261 
 ARG   0.010   0.000   ARG B  23 
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 2825.51 seconds
wall clock time: 49 minutes 51.24 seconds (2991.24 seconds total)