Starting phenix.real_space_refine
on Wed Feb 12 10:24:54 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/6xov_22281/02_2025/6xov_22281.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/6xov_22281/02_2025/6xov_22281.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=3.3
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/cci-nas-00/data/ceres_data/6xov_22281/02_2025/6xov_22281.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/6xov_22281/02_2025/6xov_22281.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/6xov_22281/02_2025/6xov_22281.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/6xov_22281/02_2025/6xov_22281.cif"
  }
  resolution = 3.3
  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      39      5.16       5
     C    4935      2.51       5
     N    1313      2.21       5
     O    1468      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 15 residue(s): 0.04s

  Monomer Library directory:
    "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5592/modules/chem_data/mon_lib"
  Total number of atoms: 7755
  Number of models: 1
  Model: ""
    Number of chains: 3
    Chain: "A"
      Number of atoms: 7713
      Number of conformers: 2
      Conformer: "A"
        Number of residues, atoms: 966, 7699
          Classifications: {'peptide': 966}
          Modifications used: {'COO': 1}
          Link IDs: {'CIS': 2, 'PTRANS': 60, 'TRANS': 903}
          Chain breaks: 1
      Conformer: "B"
        Number of residues, atoms: 966, 7699
          Classifications: {'peptide': 966}
          Modifications used: {'COO': 1}
          Link IDs: {'CIS': 2, 'PTRANS': 60, 'TRANS': 903}
          Chain breaks: 1
          bond proxies already assigned to first conformer: 7874
    Chain: "B"
      Number of atoms: 27
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 3, 27
          Classifications: {'peptide': 3}
          Link IDs: {'TRANS': 2}
    Chain: "C"
      Number of atoms: 15
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 3, 15
          Classifications: {'peptide': 3}
          Incomplete info: {'truncation_to_alanine': 3}
          Link IDs: {'TRANS': 2}
          Unresolved non-hydrogen bonds: 6
          Unresolved non-hydrogen angles: 9
          Unresolved non-hydrogen dihedrals: 3
          Planarities with less than four sites: {'UNK:plan-1': 3}
          Unresolved non-hydrogen planarities: 3
  Residues with excluded nonbonded symmetry interactions: 2
    residue:
      pdb=" N  ASER A 723 " occ=0.42
      ... (10 atoms not shown)
      pdb=" OG BSER A 723 " occ=0.58
    residue:
      pdb=" N  AASN A 915 " occ=0.59
      ... (14 atoms not shown)
      pdb=" ND2BASN A 915 " occ=0.41
  Time building chain proxies: 8.35, per 1000 atoms: 1.08
  Number of scatterers: 7755
  At special positions: 0
  Unit cell: (86.355, 88.065, 98.325, 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      39     16.00
     O    1468      8.00
     N    1313      7.00
     C    4935      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: 2.22
  Conformation dependent library (CDL) restraints added in 1.9 seconds
  

  1938 Ramachandran restraints generated.
    969 Oldfield, 0 Emsley, 969 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  1840

  Finding SS restraints...
    Secondary structure from input PDB file:
      45 helices and 8 sheets defined
      52.2% alpha, 16.9% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 1.16
  Creating SS restraints...
    Processing helix  chain 'A' and resid 32 through 38
    Processing helix  chain 'A' and resid 101 through 110
    Processing helix  chain 'A' and resid 122 through 127
    Processing helix  chain 'A' and resid 152 through 169
    Processing helix  chain 'A' and resid 173 through 181
    Processing helix  chain 'A' and resid 201 through 210
    Processing helix  chain 'A' and resid 212 through 226
    Processing helix  chain 'A' and resid 229 through 233
    Processing helix  chain 'A' and resid 241 through 245
      removed outlier: 3.617A  pdb=" N   GLU A 244 " --> pdb=" O   CYS A 241 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 246 through 258
    Processing helix  chain 'A' and resid 259 through 261
      No H-bonds generated for 'chain 'A' and resid 259 through 261'
    Processing helix  chain 'A' and resid 272 through 282
      removed outlier: 4.270A  pdb=" N   HIS A 276 " --> pdb=" O   PRO A 272 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 284 through 288
    Processing helix  chain 'A' and resid 339 through 355
    Processing helix  chain 'A' and resid 359 through 365
    Processing helix  chain 'A' and resid 366 through 369
      removed outlier: 3.748A  pdb=" N   GLY A 369 " --> pdb=" O   ILE A 366 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'A' and resid 366 through 369'
    Processing helix  chain 'A' and resid 397 through 399
      No H-bonds generated for 'chain 'A' and resid 397 through 399'
    Processing helix  chain 'A' and resid 400 through 419
    Processing helix  chain 'A' and resid 421 through 438
    Processing helix  chain 'A' and resid 442 through 456
      removed outlier: 5.376A  pdb=" N   SER A 453 " --> pdb=" O   SER A 449 " (cutoff:3.500A)
      removed outlier: 4.978A  pdb=" N   CYS A 454 " --> pdb=" O   TYR A 450 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 461 through 466
      removed outlier: 3.547A  pdb=" N   LYS A 466 " --> pdb=" O   VAL A 462 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 466 through 481
      removed outlier: 3.674A  pdb=" N   ASN A 481 " --> pdb=" O   CYS A 477 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 483 through 494
    Processing helix  chain 'A' and resid 509 through 527
    Processing helix  chain 'A' and resid 530 through 550
    Processing helix  chain 'A' and resid 608 through 612
      removed outlier: 3.574A  pdb=" N   LEU A 611 " --> pdb=" O   PRO A 608 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 614 through 623
      removed outlier: 4.553A  pdb=" N   THR A 623 " --> pdb=" O   CYS A 619 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 631 through 643
    Processing helix  chain 'A' and resid 676 through 690
    Processing helix  chain 'A' and resid 696 through 713
      removed outlier: 3.678A  pdb=" N   GLY A 713 " --> pdb=" O   GLU A 709 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 714 through 716
      No H-bonds generated for 'chain 'A' and resid 714 through 716'
    Processing helix  chain 'A' and resid 717 through 728
    Processing helix  chain 'A' and resid 731 through 742
    Processing helix  chain 'A' and resid 742 through 755
      removed outlier: 3.758A  pdb=" N   VAL A 746 " --> pdb=" O   GLY A 742 " (cutoff:3.500A)
      removed outlier: 3.882A  pdb=" N   MET A 755 " --> pdb=" O   ARG A 751 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 758 through 763
    Processing helix  chain 'A' and resid 764 through 773
      removed outlier: 4.120A  pdb=" N   HIS A 771 " --> pdb=" O   ARG A 767 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 788 through 802
    Processing helix  chain 'A' and resid 877 through 894
      removed outlier: 3.775A  pdb=" N   ALA A 881 " --> pdb=" O   ASP A 877 " (cutoff:3.500A)
      removed outlier: 3.938A  pdb=" N   SER A 882 " --> pdb=" O   PRO A 878 " (cutoff:3.500A)
      removed outlier: 3.892A  pdb=" N   ILE A 885 " --> pdb=" O   ALA A 881 " (cutoff:3.500A)
      removed outlier: 3.920A  pdb=" N   ARG A 888 " --> pdb=" O   LYS A 884 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 894 through 899
    Processing helix  chain 'A' and resid 928 through 944
      removed outlier: 3.516A  pdb=" N   VAL A 939 " --> pdb=" O   PHE A 935 " (cutoff:3.500A)
      removed outlier: 3.520A  pdb=" N   ASP A 940 " --> pdb=" O   GLY A 936 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 948 through 963
      removed outlier: 3.813A  pdb=" N   ILE A 952 " --> pdb=" O   THR A 948 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 973 through 979
      removed outlier: 3.763A  pdb=" N   PHE A 977 " --> pdb=" O   GLY A 973 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 982 through 995
      removed outlier: 3.526A  pdb=" N   PHE A 994 " --> pdb=" O   ARG A 990 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 997 through 1009
      removed outlier: 3.509A  pdb=" N   ASP A1006 " --> pdb=" O   LEU A1002 " (cutoff:3.500A)
      removed outlier: 3.915A  pdb=" N   ARG A1007 " --> pdb=" O   ALA A1003 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 1025 through 1031
      removed outlier: 3.671A  pdb=" N   ASP A1031 " --> pdb=" O   LYS A1027 " (cutoff:3.500A)
    Processing sheet with id=AA1, first strand: chain 'A' and resid 45 through 46
      removed outlier: 5.714A  pdb=" N   VAL A  51 " --> pdb=" O   THR A  68 " (cutoff:3.500A)
      removed outlier: 6.910A  pdb=" N   THR A  68 " --> pdb=" O   VAL A  51 " (cutoff:3.500A)
      removed outlier: 3.627A  pdb=" N   GLN A  53 " --> pdb=" O   LYS A  66 " (cutoff:3.500A)
      removed outlier: 6.205A  pdb=" N   ARG A  75 " --> pdb=" O   PHE A 265 " (cutoff:3.500A)
      removed outlier: 7.808A  pdb=" N   THR A 267 " --> pdb=" O   ARG A  75 " (cutoff:3.500A)
      removed outlier: 6.233A  pdb=" N   LEU A  77 " --> pdb=" O   THR A 267 " (cutoff:3.500A)
    Processing sheet with id=AA2, first strand: chain 'A' and resid 45 through 46
      removed outlier: 5.714A  pdb=" N   VAL A  51 " --> pdb=" O   THR A  68 " (cutoff:3.500A)
      removed outlier: 6.910A  pdb=" N   THR A  68 " --> pdb=" O   VAL A  51 " (cutoff:3.500A)
      removed outlier: 3.627A  pdb=" N   GLN A  53 " --> pdb=" O   LYS A  66 " (cutoff:3.500A)
      removed outlier: 6.205A  pdb=" N   ARG A  75 " --> pdb=" O   PHE A 265 " (cutoff:3.500A)
      removed outlier: 7.808A  pdb=" N   THR A 267 " --> pdb=" O   ARG A  75 " (cutoff:3.500A)
      removed outlier: 6.233A  pdb=" N   LEU A  77 " --> pdb=" O   THR A 267 " (cutoff:3.500A)
    Processing sheet with id=AA3, first strand: chain 'A' and resid 182 through 185
    Processing sheet with id=AA4, first strand: chain 'A' and resid 311 through 313
      removed outlier: 7.175A  pdb=" N   VAL A 328 " --> pdb=" O   GLN A 394 " (cutoff:3.500A)
      removed outlier: 5.492A  pdb=" N   GLN A 394 " --> pdb=" O   VAL A 328 " (cutoff:3.500A)
    Processing sheet with id=AA5, first strand: chain 'A' and resid 577 through 578
    Processing sheet with id=AA6, first strand: chain 'A' and resid 588 through 589
      removed outlier: 5.474A  pdb=" N   CYS A 588 " --> pdb=" O   ALA A 784 " (cutoff:3.500A)
      removed outlier: 3.752A  pdb=" N   SER A 649 " --> pdb=" O   LEU A 667 " (cutoff:3.500A)
    Processing sheet with id=AA7, first strand: chain 'A' and resid 588 through 589
      removed outlier: 5.474A  pdb=" N   CYS A 588 " --> pdb=" O   ALA A 784 " (cutoff:3.500A)
    Processing sheet with id=AA8, first strand: chain 'A' and resid 907 through 912
      removed outlier: 3.557A  pdb=" N   VAL A 866 " --> pdb=" O   SER A 922 " (cutoff:3.500A)
      removed outlier: 5.387A  pdb=" N   ASN A 864 " --> pdb=" O   ARG A 924 " (cutoff:3.500A)
      removed outlier: 3.650A  pdb=" N   GLY A1017 " --> pdb=" O   CYS A 869 " (cutoff:3.500A)
      removed outlier: 5.655A  pdb=" N   HIS A 856 " --> pdb=" O   ARG A1037 " (cutoff:3.500A)

    424 hydrogen bonds defined for protein.
    1210 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: 3.27

  Time building geometry restraints manager: 2.51 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: 1906
        1.33 -     1.45: 1564
        1.45 -     1.57: 4416
        1.57 -     1.69: 0
        1.69 -     1.81: 62
  Bond restraints: 7948
  Sorted by residual:
  bond pdb=" N   PHE A 318 "
       pdb=" CA  PHE A 318 "
    ideal  model  delta    sigma   weight residual
    1.457  1.484 -0.026 1.29e-02 6.01e+03 4.12e+00
  bond pdb=" C   ILE A 242 "
       pdb=" N   PRO A 243 "
    ideal  model  delta    sigma   weight residual
    1.336  1.356 -0.020 1.08e-02 8.57e+03 3.49e+00
  bond pdb=" CA  PHE A 318 "
       pdb=" C   PHE A 318 "
    ideal  model  delta    sigma   weight residual
    1.523  1.542 -0.019 1.34e-02 5.57e+03 2.04e+00
  bond pdb=" N   GLY A 626 "
       pdb=" CA  GLY A 626 "
    ideal  model  delta    sigma   weight residual
    1.449  1.470 -0.020 1.45e-02 4.76e+03 1.98e+00
  bond pdb=" CB  ASN A 136 "
       pdb=" CG  ASN A 136 "
    ideal  model  delta    sigma   weight residual
    1.516  1.483  0.033 2.50e-02 1.60e+03 1.73e+00
  ... (remaining 7943 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     2.48: 10604
        2.48 -     4.96: 149
        4.96 -     7.45: 20
        7.45 -     9.93: 3
        9.93 -    12.41: 1
  Bond angle restraints: 10777
  Sorted by residual:
  angle pdb=" N   PHE A 318 "
        pdb=" CA  PHE A 318 "
        pdb=" C   PHE A 318 "
      ideal   model   delta    sigma   weight residual
     110.80  123.21  -12.41 2.13e+00 2.20e-01 3.39e+01
  angle pdb=" C   SER A 317 "
        pdb=" CA  SER A 317 "
        pdb=" CB  SER A 317 "
      ideal   model   delta    sigma   weight residual
     109.90  118.86   -8.96 1.56e+00 4.11e-01 3.30e+01
  angle pdb=" N   LYS A 324 "
        pdb=" CA  LYS A 324 "
        pdb=" C   LYS A 324 "
      ideal   model   delta    sigma   weight residual
     108.56  117.67   -9.11 1.74e+00 3.30e-01 2.74e+01
  angle pdb=" C   ASP A 321 "
        pdb=" N   PRO A 322 "
        pdb=" CA  PRO A 322 "
      ideal   model   delta    sigma   weight residual
     119.28  124.67   -5.39 1.10e+00 8.26e-01 2.41e+01
  angle pdb=" N   ILE A 758 "
        pdb=" CA  ILE A 758 "
        pdb=" C   ILE A 758 "
      ideal   model   delta    sigma   weight residual
     112.17  108.46    3.71 9.50e-01 1.11e+00 1.52e+01
  ... (remaining 10772 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    17.82: 4339
       17.82 -    35.64: 381
       35.64 -    53.46: 62
       53.46 -    71.27: 12
       71.27 -    89.09: 8
  Dihedral angle restraints: 4802
    sinusoidal: 1960
      harmonic: 2842
  Sorted by residual:
  dihedral pdb=" C   PHE A 318 "
           pdb=" N   PHE A 318 "
           pdb=" CA  PHE A 318 "
           pdb=" CB  PHE A 318 "
      ideal   model   delta  harmonic     sigma   weight residual
    -122.60 -135.25   12.65     0      2.50e+00 1.60e-01 2.56e+01
  dihedral pdb=" CA  PHE A 210 "
           pdb=" C   PHE A 210 "
           pdb=" N   THR A 211 "
           pdb=" CA  THR A 211 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  155.34   24.66     0      5.00e+00 4.00e-02 2.43e+01
  dihedral pdb=" N   PHE A 318 "
           pdb=" C   PHE A 318 "
           pdb=" CA  PHE A 318 "
           pdb=" CB  PHE A 318 "
      ideal   model   delta  harmonic     sigma   weight residual
     122.80  134.48  -11.68     0      2.50e+00 1.60e-01 2.18e+01
  ... (remaining 4799 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.110: 1156
       0.110 -    0.220: 23
       0.220 -    0.330: 1
       0.330 -    0.440: 0
       0.440 -    0.550: 1
  Chirality restraints: 1181
  Sorted by residual:
  chirality pdb=" CA  PHE A 318 "
            pdb=" N   PHE A 318 "
            pdb=" C   PHE A 318 "
            pdb=" CB  PHE A 318 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    1.96    0.55 2.00e-01 2.50e+01 7.57e+00
  chirality pdb=" CA  THR A 876 "
            pdb=" N   THR A 876 "
            pdb=" C   THR A 876 "
            pdb=" CB  THR A 876 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.53    2.21    0.32 2.00e-01 2.50e+01 2.58e+00
  chirality pdb=" CA  LYS A 324 "
            pdb=" N   LYS A 324 "
            pdb=" C   LYS A 324 "
            pdb=" CB  LYS A 324 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.33    0.18 2.00e-01 2.50e+01 8.44e-01
  ... (remaining 1178 not shown)

  Planarity restraints: 1407
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CB  TYR A 163 "   -0.027 2.00e-02 2.50e+03   1.76e-02 6.17e+00
        pdb=" CG  TYR A 163 "    0.041 2.00e-02 2.50e+03
        pdb=" CD1 TYR A 163 "   -0.004 2.00e-02 2.50e+03
        pdb=" CD2 TYR A 163 "   -0.001 2.00e-02 2.50e+03
        pdb=" CE1 TYR A 163 "    0.001 2.00e-02 2.50e+03
        pdb=" CE2 TYR A 163 "   -0.002 2.00e-02 2.50e+03
        pdb=" CZ  TYR A 163 "   -0.002 2.00e-02 2.50e+03
        pdb=" OH  TYR A 163 "   -0.007 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  TYR A 146 "   -0.009 2.00e-02 2.50e+03   1.82e-02 3.32e+00
        pdb=" C   TYR A 146 "    0.032 2.00e-02 2.50e+03
        pdb=" O   TYR A 146 "   -0.012 2.00e-02 2.50e+03
        pdb=" N   PRO A 147 "   -0.011 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   VAL A 102 "    0.030 5.00e-02 4.00e+02   4.54e-02 3.29e+00
        pdb=" N   PRO A 103 "   -0.078 5.00e-02 4.00e+02
        pdb=" CA  PRO A 103 "    0.022 5.00e-02 4.00e+02
        pdb=" CD  PRO A 103 "    0.026 5.00e-02 4.00e+02
  ... (remaining 1404 not shown)

  Histogram of nonbonded interaction distances:
        2.10 -     2.66: 160
        2.66 -     3.22: 7612
        3.22 -     3.78: 12070
        3.78 -     4.34: 16710
        4.34 -     4.90: 27480
  Nonbonded interactions: 64032
  Sorted by model distance:
  nonbonded pdb=" OD1 ASP A 373 "
            pdb=" N   PHE A 374 "
     model   vdw
     2.100 3.120
  nonbonded pdb=" O   LEU A 365 "
            pdb=" OG  SER A 368 "
     model   vdw
     2.199 3.040
  nonbonded pdb=" OG  SER A 997 "
            pdb=" OD1 ASP A 999 "
     model   vdw
     2.220 3.040
  nonbonded pdb=" OG1 THR A  50 "
            pdb=" OD1 ASP A  70 "
     model   vdw
     2.234 3.040
  nonbonded pdb=" O   SER A 190 "
            pdb=" OH  TYR A 538 "
     model   vdw
     2.235 3.040
  ... (remaining 64027 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=0.41 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:             0.870
  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:          0.320
  Check model and map are aligned:         0.070
  Set scattering table:                    0.070
  Process input model:                     26.730
  Find NCS groups from input model:        0.090
  Set up NCS constraints:                  0.040
  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:2.710
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   30.920
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8013
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      :  0.005   0.044   7948  Z= 0.296
  Angle     :  0.758  12.411  10777  Z= 0.433
  Chirality :  0.048   0.550   1181
  Planarity :  0.006   0.045   1407
  Dihedral  : 14.282  89.092   2962
  Min Nonbonded Distance : 2.100

Molprobity Statistics.
  All-atom Clashscore : 13.73
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.98 %
    Favored  : 95.02 %
  Rotamer:
    Outliers :  0.35 %
    Allowed  :  0.58 %
    Favored  : 99.07 %
  Cbeta Deviations :  0.11 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.22 %
    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: -1.92 (0.27), residues: 969
  helix: -0.29 (0.25), residues: 444
  sheet: -2.18 (0.37), residues: 174
  loop : -1.91 (0.34), residues: 351

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.031   0.002   TRP A 455 
 HIS   0.010   0.001   HIS A 108 
 PHE   0.022   0.002   PHE B  20 
 TYR   0.041   0.002   TYR A 163 
 ARG   0.004   0.000   ARG A 725 

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

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

  1938 Ramachandran restraints generated.
    969 Oldfield, 0 Emsley, 969 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1938 Ramachandran restraints generated.
    969 Oldfield, 0 Emsley, 969 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  96 residues out of total 858 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 3
    poor density    : 93
  time to evaluate  : 1.089 
Fit side-chains
   revert: symmetry clash
REVERT: A   76 TYR cc_start: 0.8126 (t80) cc_final: 0.7824 (t80)
REVERT: A  106 LEU cc_start: 0.8882 (tp) cc_final: 0.8531 (tp)
REVERT: A  517 VAL cc_start: 0.8318 (p) cc_final: 0.8008 (p)
REVERT: A  520 THR cc_start: 0.8784 (m) cc_final: 0.8509 (p)
REVERT: A  884 LYS cc_start: 0.8779 (ttmt) cc_final: 0.8566 (tppt)
REVERT: A  925 ASP cc_start: 0.7173 (t0) cc_final: 0.6894 (t0)
REVERT: A  953 ASP cc_start: 0.7911 (t70) cc_final: 0.7687 (t0)
  outliers start: 3
  outliers final: 0
  residues processed: 94
  average time/residue: 0.2026
  time to fit residues: 27.0622
Evaluate side-chains
  66 residues out of total 858 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 66
  time to evaluate  : 0.947 
-------------------------------------------------------------------------------
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:    0.7980
   chunk 72 optimal weight:    0.1980
   chunk 40 optimal weight:    3.9990
   chunk 24 optimal weight:    5.9990
   chunk 49 optimal weight:    4.9990
   chunk 38 optimal weight:    1.9990
   chunk 75 optimal weight:    4.9990
   chunk 29 optimal weight:    5.9990
   chunk 45 optimal weight:    0.9980
   chunk 56 optimal weight:    1.9990
   chunk 87 optimal weight:    6.9990
   overall best weight:    1.1984

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

Flipped N/Q/H residues before XYZ refinement:
** A 128 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 394 GLN
A 552 GLN
** A 590 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 987 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3365 r_free = 0.3365 target = 0.072846 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 34)----------------|
| r_work = 0.3044 r_free = 0.3044 target = 0.058115 restraints weight = 58638.971|
|-----------------------------------------------------------------------------|
r_work (start): 0.3028 rms_B_bonded: 6.16
r_work: 0.2839 rms_B_bonded: 6.03 restraints_weight: 2.0000
r_work (final): 0.2839
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.2849
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.2849 r_free = 0.2849    target_work(ls_wunit_k1) = 0.051         |
| occupancies: max = 1.00  min = 0.41   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.2849 r_free = 0.2849    target_work(ls_wunit_k1) = 0.051         |
| occupancies: max = 1.00  min = 0.28   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.2849
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8080
moved from start:          0.1427

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.033   7948  Z= 0.209
  Angle     :  0.665   9.042  10777  Z= 0.341
  Chirality :  0.044   0.204   1181
  Planarity :  0.006   0.048   1407
  Dihedral  :  5.065  45.023   1043
  Min Nonbonded Distance : 2.449

Molprobity Statistics.
  All-atom Clashscore : 9.18
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.01 %
    Favored  : 96.99 %
  Rotamer:
    Outliers :  0.81 %
    Allowed  :  6.96 %
    Favored  : 92.23 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.22 %
    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: -0.84 (0.28), residues: 969
  helix:  0.58 (0.25), residues: 462
  sheet: -1.55 (0.39), residues: 166
  loop : -1.49 (0.35), residues: 341

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.023   0.002   TRP A 851 
 HIS   0.005   0.001   HIS A 108 
 PHE   0.011   0.001   PHE A 344 
 TYR   0.018   0.002   TYR A 163 
 ARG   0.011   0.001   ARG A 751 

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

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

  1938 Ramachandran restraints generated.
    969 Oldfield, 0 Emsley, 969 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1938 Ramachandran restraints generated.
    969 Oldfield, 0 Emsley, 969 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  89 residues out of total 858 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 7
    poor density    : 82
  time to evaluate  : 0.976 
Fit side-chains
   revert: symmetry clash
REVERT: A  604 LEU cc_start: 0.8810 (mt) cc_final: 0.8579 (mt)
REVERT: A  640 GLU cc_start: 0.8717 (mt-10) cc_final: 0.8277 (mp0)
REVERT: A  755 MET cc_start: 0.8071 (mtm) cc_final: 0.7307 (ptp)
REVERT: A  792 THR cc_start: 0.9365 (m) cc_final: 0.9165 (p)
REVERT: A  884 LYS cc_start: 0.8654 (ttmt) cc_final: 0.8360 (tppt)
REVERT: A  917 ILE cc_start: 0.8847 (mm) cc_final: 0.8638 (mm)
REVERT: A  925 ASP cc_start: 0.8473 (t0) cc_final: 0.7724 (t0)
REVERT: A  953 ASP cc_start: 0.8346 (t70) cc_final: 0.8048 (t0)
  outliers start: 7
  outliers final: 4
  residues processed: 83
  average time/residue: 0.1726
  time to fit residues: 21.2932
Evaluate side-chains
  76 residues out of total 858 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 4
    poor density    : 72
  time to evaluate  : 0.893 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  105 ILE
Chi-restraints excluded: chain A residue  434 ILE
Chi-restraints excluded: chain A residue  931 THR
Chi-restraints excluded: chain A residue  985 MET
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 96
   random chunks:
   chunk 38 optimal weight:    2.9990
   chunk 21 optimal weight:    3.9990
   chunk 31 optimal weight:    2.9990
   chunk 77 optimal weight:    3.9990
   chunk 82 optimal weight:    4.9990
   chunk 17 optimal weight:    0.9990
   chunk 83 optimal weight:    7.9990
   chunk 25 optimal weight:    2.9990
   chunk 72 optimal weight:    2.9990
   chunk 75 optimal weight:    3.9990
   chunk 74 optimal weight:    6.9990
   overall best weight:    2.5990

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

Flipped N/Q/H residues before XYZ refinement:
A 128 ASN
** A 590 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 987 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3323 r_free = 0.3323 target = 0.070746 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 37)----------------|
| r_work = 0.2999 r_free = 0.2999 target = 0.056178 restraints weight = 63025.951|
|-----------------------------------------------------------------------------|
r_work (start): 0.2990 rms_B_bonded: 6.19
r_work: 0.2798 rms_B_bonded: 5.99 restraints_weight: 2.0000
r_work (final): 0.2798
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.2808
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.2808 r_free = 0.2808    target_work(ls_wunit_k1) = 0.050         |
| occupancies: max = 1.00  min = 0.28   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.2808 r_free = 0.2808    target_work(ls_wunit_k1) = 0.050         |
| occupancies: max = 1.00  min = 0.30   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.2808
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8163
moved from start:          0.1774

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.036   7948  Z= 0.300
  Angle     :  0.650   8.614  10777  Z= 0.334
  Chirality :  0.044   0.185   1181
  Planarity :  0.005   0.047   1407
  Dihedral  :  5.022  43.304   1043
  Min Nonbonded Distance : 2.497

Molprobity Statistics.
  All-atom Clashscore : 10.09
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.15 %
    Favored  : 95.85 %
  Rotamer:
    Outliers :  0.93 %
    Allowed  :  8.47 %
    Favored  : 90.60 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.22 %
    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: -0.50 (0.28), residues: 969
  helix:  0.76 (0.24), residues: 466
  sheet: -1.17 (0.39), residues: 167
  loop : -1.32 (0.37), residues: 336

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.026   0.002   TRP A 455 
 HIS   0.004   0.001   HIS A 856 
 PHE   0.028   0.002   PHE A 389 
 TYR   0.017   0.002   TYR A 163 
 ARG   0.005   0.001   ARG A 751 

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

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

  1938 Ramachandran restraints generated.
    969 Oldfield, 0 Emsley, 969 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1938 Ramachandran restraints generated.
    969 Oldfield, 0 Emsley, 969 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  83 residues out of total 858 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 8
    poor density    : 75
  time to evaluate  : 0.896 
Fit side-chains
   revert: symmetry clash
REVERT: A   97 MET cc_start: 0.8536 (mmm) cc_final: 0.8313 (mmm)
REVERT: A  168 PHE cc_start: 0.8319 (m-10) cc_final: 0.8112 (m-10)
REVERT: A  436 MET cc_start: 0.9090 (ttm) cc_final: 0.8727 (tmm)
REVERT: A  640 GLU cc_start: 0.8691 (mt-10) cc_final: 0.8277 (mp0)
REVERT: A  659 MET cc_start: 0.8067 (tpp) cc_final: 0.7580 (tpt)
REVERT: A  755 MET cc_start: 0.8125 (mtm) cc_final: 0.7489 (ptp)
REVERT: A  859 MET cc_start: 0.9034 (mmt) cc_final: 0.8763 (mmm)
REVERT: A  884 LYS cc_start: 0.8790 (ttmt) cc_final: 0.8412 (tppt)
REVERT: A  925 ASP cc_start: 0.8656 (t0) cc_final: 0.8062 (t0)
REVERT: A  953 ASP cc_start: 0.8300 (t70) cc_final: 0.8092 (t0)
  outliers start: 8
  outliers final: 6
  residues processed: 76
  average time/residue: 0.1538
  time to fit residues: 17.6260
Evaluate side-chains
  71 residues out of total 858 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 6
    poor density    : 65
  time to evaluate  : 0.844 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  233 VAL
Chi-restraints excluded: chain A residue  280 ILE
Chi-restraints excluded: chain A residue  434 ILE
Chi-restraints excluded: chain A residue  657 SER
Chi-restraints excluded: chain A residue  928 THR
Chi-restraints excluded: chain A residue  931 THR
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 96
   random chunks:
   chunk 83 optimal weight:    9.9990
   chunk 58 optimal weight:    3.9990
   chunk 84 optimal weight:    0.8980
   chunk 32 optimal weight:    0.4980
   chunk 81 optimal weight:    0.7980
   chunk 94 optimal weight:   10.0000
   chunk 44 optimal weight:    0.9980
   chunk 60 optimal weight:    4.9990
   chunk 40 optimal weight:    0.9980
   chunk 67 optimal weight:    6.9990
   chunk 18 optimal weight:    0.7980
   overall best weight:    0.7980

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

Flipped N/Q/H residues before XYZ refinement:
** A 590 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 664 GLN
** A 987 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3386 r_free = 0.3386 target = 0.073642 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 25)----------------|
| r_work = 0.3059 r_free = 0.3059 target = 0.058659 restraints weight = 67054.350|
|-----------------------------------------------------------------------------|
r_work (start): 0.3044 rms_B_bonded: 6.57
r_work: 0.2845 rms_B_bonded: 6.34 restraints_weight: 2.0000
r_work (final): 0.2845
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.2852
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.2852 r_free = 0.2852    target_work(ls_wunit_k1) = 0.051         |
| occupancies: max = 1.00  min = 0.30   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.2852 r_free = 0.2852    target_work(ls_wunit_k1) = 0.051         |
| occupancies: max = 1.00  min = 0.30   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.2852
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8098
moved from start:          0.2194

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.033   7948  Z= 0.165
  Angle     :  0.594  11.519  10777  Z= 0.297
  Chirality :  0.042   0.199   1181
  Planarity :  0.005   0.048   1407
  Dihedral  :  4.583  38.428   1043
  Min Nonbonded Distance : 2.539

Molprobity Statistics.
  All-atom Clashscore : 8.40
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.60 %
    Favored  : 97.40 %
  Rotamer:
    Outliers :  0.70 %
    Allowed  :  9.05 %
    Favored  : 90.26 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.22 %
    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:  0.19 (0.28), residues: 969
  helix:  1.32 (0.24), residues: 458
  sheet: -0.78 (0.41), residues: 164
  loop : -0.95 (0.37), residues: 347

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.022   0.001   TRP A 851 
 HIS   0.003   0.001   HIS A 186 
 PHE   0.029   0.001   PHE A 389 
 TYR   0.008   0.001   TYR A 380 
 ARG   0.004   0.000   ARG A 747 

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

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

  1938 Ramachandran restraints generated.
    969 Oldfield, 0 Emsley, 969 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1938 Ramachandran restraints generated.
    969 Oldfield, 0 Emsley, 969 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  80 residues out of total 858 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 6
    poor density    : 74
  time to evaluate  : 0.918 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   97 MET cc_start: 0.8610 (mmm) cc_final: 0.8390 (mmm)
REVERT: A  187 GLU cc_start: 0.8066 (mm-30) cc_final: 0.7849 (mm-30)
REVERT: A  436 MET cc_start: 0.9147 (ttm) cc_final: 0.8759 (tmm)
REVERT: A  573 GLU cc_start: 0.8044 (pm20) cc_final: 0.7494 (pm20)
REVERT: A  640 GLU cc_start: 0.8704 (mt-10) cc_final: 0.8284 (mp0)
REVERT: A  659 MET cc_start: 0.8072 (tpp) cc_final: 0.7715 (tpp)
REVERT: A  755 MET cc_start: 0.7996 (mtm) cc_final: 0.7782 (ptm)
REVERT: A  859 MET cc_start: 0.8976 (mmt) cc_final: 0.8767 (mmm)
REVERT: A  884 LYS cc_start: 0.8703 (ttmt) cc_final: 0.8393 (tppt)
REVERT: A  925 ASP cc_start: 0.8641 (t0) cc_final: 0.8141 (t0)
REVERT: A  953 ASP cc_start: 0.8322 (t70) cc_final: 0.8116 (t0)
REVERT: B   20 PHE cc_start: 0.6214 (p90) cc_final: 0.5868 (p90)
  outliers start: 6
  outliers final: 3
  residues processed: 76
  average time/residue: 0.1806
  time to fit residues: 20.1304
Evaluate side-chains
  68 residues out of total 858 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 3
    poor density    : 65
  time to evaluate  : 0.833 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  233 VAL
Chi-restraints excluded: chain A residue  434 ILE
Chi-restraints excluded: chain A residue  931 THR
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 96
   random chunks:
   chunk 25 optimal weight:    8.9990
   chunk 95 optimal weight:    5.9990
   chunk 14 optimal weight:    6.9990
   chunk 37 optimal weight:    2.9990
   chunk 63 optimal weight:    7.9990
   chunk 70 optimal weight:    5.9990
   chunk 73 optimal weight:    0.7980
   chunk 44 optimal weight:    0.9990
   chunk 19 optimal weight:    1.9990
   chunk 71 optimal weight:    7.9990
   chunk 10 optimal weight:    5.9990
   overall best weight:    2.5588

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

Flipped N/Q/H residues before XYZ refinement:
** A 590 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 635 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 987 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3325 r_free = 0.3325 target = 0.070641 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 35)----------------|
| r_work = 0.3019 r_free = 0.3019 target = 0.056732 restraints weight = 61491.891|
|-----------------------------------------------------------------------------|
r_work (start): 0.3004 rms_B_bonded: 5.97
r_work: 0.2817 rms_B_bonded: 5.82 restraints_weight: 2.0000
r_work (final): 0.2817
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.2826
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.2826 r_free = 0.2826    target_work(ls_wunit_k1) = 0.050         |
| occupancies: max = 1.00  min = 0.30   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.2826 r_free = 0.2826    target_work(ls_wunit_k1) = 0.050         |
| occupancies: max = 1.00  min = 0.31   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.2826
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8190
moved from start:          0.2255

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.036   7948  Z= 0.289
  Angle     :  0.626  10.203  10777  Z= 0.316
  Chirality :  0.043   0.184   1181
  Planarity :  0.005   0.046   1407
  Dihedral  :  4.738  39.625   1043
  Min Nonbonded Distance : 2.551

Molprobity Statistics.
  All-atom Clashscore : 9.83
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.53 %
    Favored  : 96.47 %
  Rotamer:
    Outliers :  0.81 %
    Allowed  :  9.98 %
    Favored  : 89.21 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.22 %
    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:  0.07 (0.29), residues: 969
  helix:  1.21 (0.24), residues: 465
  sheet: -0.87 (0.40), residues: 173
  loop : -1.00 (0.38), residues: 331

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.019   0.002   TRP A 851 
 HIS   0.004   0.001   HIS A 856 
 PHE   0.024   0.002   PHE A 389 
 TYR   0.018   0.002   TYR A 450 
 ARG   0.004   0.000   ARG A 751 

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

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

  1938 Ramachandran restraints generated.
    969 Oldfield, 0 Emsley, 969 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1938 Ramachandran restraints generated.
    969 Oldfield, 0 Emsley, 969 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  71 residues out of total 858 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 7
    poor density    : 64
  time to evaluate  : 0.935 
Fit side-chains
   revert: symmetry clash
REVERT: A  168 PHE cc_start: 0.8278 (m-10) cc_final: 0.8053 (m-10)
REVERT: A  187 GLU cc_start: 0.8145 (mm-30) cc_final: 0.7922 (mm-30)
REVERT: A  436 MET cc_start: 0.9163 (ttm) cc_final: 0.8726 (tmm)
REVERT: A  640 GLU cc_start: 0.8681 (mt-10) cc_final: 0.8316 (mp0)
REVERT: A  659 MET cc_start: 0.8153 (tpp) cc_final: 0.7761 (tpp)
REVERT: A  859 MET cc_start: 0.9032 (mmt) cc_final: 0.8822 (mmm)
REVERT: A  884 LYS cc_start: 0.8800 (ttmt) cc_final: 0.8458 (tppt)
REVERT: A  925 ASP cc_start: 0.8647 (t0) cc_final: 0.8129 (t0)
REVERT: B   20 PHE cc_start: 0.6215 (p90) cc_final: 0.5988 (p90)
  outliers start: 7
  outliers final: 5
  residues processed: 66
  average time/residue: 0.1875
  time to fit residues: 18.0823
Evaluate side-chains
  67 residues out of total 858 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 5
    poor density    : 62
  time to evaluate  : 1.044 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  233 VAL
Chi-restraints excluded: chain A residue  280 ILE
Chi-restraints excluded: chain A residue  434 ILE
Chi-restraints excluded: chain A residue  669 SER
Chi-restraints excluded: chain A residue  931 THR
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 96
   random chunks:
   chunk 16 optimal weight:    0.9990
   chunk 85 optimal weight:    1.9990
   chunk 38 optimal weight:    3.9990
   chunk 86 optimal weight:    0.9980
   chunk 53 optimal weight:    5.9990
   chunk 47 optimal weight:    9.9990
   chunk 57 optimal weight:    0.8980
   chunk 34 optimal weight:    2.9990
   chunk 41 optimal weight:    4.9990
   chunk 55 optimal weight:    1.9990
   chunk 43 optimal weight:    4.9990
   overall best weight:    1.3786

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

Flipped N/Q/H residues before XYZ refinement:
A 552 GLN
** A 590 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 635 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 987 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3362 r_free = 0.3362 target = 0.072388 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 37)----------------|
| r_work = 0.3052 r_free = 0.3052 target = 0.058119 restraints weight = 51881.935|
|-----------------------------------------------------------------------------|
r_work (start): 0.3033 rms_B_bonded: 5.73
r_work: 0.2847 rms_B_bonded: 5.71 restraints_weight: 2.0000
r_work (final): 0.2847
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.2857
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.2857 r_free = 0.2857    target_work(ls_wunit_k1) = 0.051         |
| occupancies: max = 1.00  min = 0.31   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.2857 r_free = 0.2857    target_work(ls_wunit_k1) = 0.051         |
| occupancies: max = 1.00  min = 0.33   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.2857
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8116
moved from start:          0.2463

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.036   7948  Z= 0.195
  Angle     :  0.586  10.193  10777  Z= 0.295
  Chirality :  0.041   0.140   1181
  Planarity :  0.005   0.045   1407
  Dihedral  :  4.598  42.483   1043
  Min Nonbonded Distance : 2.508

Molprobity Statistics.
  All-atom Clashscore : 8.72
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.12 %
    Favored  : 96.88 %
  Rotamer:
    Outliers :  0.70 %
    Allowed  : 10.67 %
    Favored  : 88.63 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.22 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.35 (0.29), residues: 969
  helix:  1.50 (0.25), residues: 460
  sheet: -0.86 (0.40), residues: 177
  loop : -0.84 (0.38), residues: 332

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.023   0.001   TRP A 851 
 HIS   0.003   0.001   HIS A 186 
 PHE   0.026   0.001   PHE A 389 
 TYR   0.014   0.001   TYR A 450 
 ARG   0.004   0.000   ARG A 747 

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

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

  1938 Ramachandran restraints generated.
    969 Oldfield, 0 Emsley, 969 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1938 Ramachandran restraints generated.
    969 Oldfield, 0 Emsley, 969 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  71 residues out of total 858 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 6
    poor density    : 65
  time to evaluate  : 0.903 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  187 GLU cc_start: 0.8172 (mm-30) cc_final: 0.7935 (mm-30)
REVERT: A  436 MET cc_start: 0.9159 (ttm) cc_final: 0.8740 (tmm)
REVERT: A  659 MET cc_start: 0.8120 (tpp) cc_final: 0.7750 (tpp)
REVERT: A  853 MET cc_start: 0.8230 (mmt) cc_final: 0.7984 (mmt)
REVERT: A  859 MET cc_start: 0.8993 (mmt) cc_final: 0.8781 (mmm)
REVERT: A  884 LYS cc_start: 0.8727 (ttmt) cc_final: 0.8395 (tppt)
REVERT: A  925 ASP cc_start: 0.8668 (t0) cc_final: 0.8155 (t0)
REVERT: B   20 PHE cc_start: 0.6147 (p90) cc_final: 0.5813 (p90)
  outliers start: 6
  outliers final: 5
  residues processed: 67
  average time/residue: 0.1852
  time to fit residues: 18.2419
Evaluate side-chains
  65 residues out of total 858 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 5
    poor density    : 60
  time to evaluate  : 0.900 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  233 VAL
Chi-restraints excluded: chain A residue  280 ILE
Chi-restraints excluded: chain A residue  434 ILE
Chi-restraints excluded: chain A residue  669 SER
Chi-restraints excluded: chain A residue  931 THR
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 96
   random chunks:
   chunk 35 optimal weight:    6.9990
   chunk 1 optimal weight:    0.9990
   chunk 46 optimal weight:    3.9990
   chunk 55 optimal weight:    5.9990
   chunk 94 optimal weight:    8.9990
   chunk 53 optimal weight:    4.9990
   chunk 62 optimal weight:    0.0040
   chunk 49 optimal weight:    9.9990
   chunk 67 optimal weight:    0.0970
   chunk 72 optimal weight:    5.9990
   chunk 31 optimal weight:    6.9990
   overall best weight:    2.0196

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

Flipped N/Q/H residues before XYZ refinement:
** A 590 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 635 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 987 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3344 r_free = 0.3344 target = 0.071406 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 37)----------------|
| r_work = 0.3025 r_free = 0.3025 target = 0.056906 restraints weight = 62576.917|
|-----------------------------------------------------------------------------|
r_work (start): 0.3009 rms_B_bonded: 6.24
r_work: 0.2814 rms_B_bonded: 6.03 restraints_weight: 2.0000
r_work (final): 0.2814
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.2824
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.2824 r_free = 0.2824    target_work(ls_wunit_k1) = 0.050         |
| occupancies: max = 1.00  min = 0.33   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.2824 r_free = 0.2824    target_work(ls_wunit_k1) = 0.050         |
| occupancies: max = 1.00  min = 0.34   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.2824
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8153
moved from start:          0.2549

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.035   7948  Z= 0.243
  Angle     :  0.602   8.425  10777  Z= 0.304
  Chirality :  0.042   0.144   1181
  Planarity :  0.005   0.045   1407
  Dihedral  :  4.664  42.962   1043
  Min Nonbonded Distance : 2.523

Molprobity Statistics.
  All-atom Clashscore : 9.63
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.43 %
    Favored  : 96.57 %
  Rotamer:
    Outliers :  0.93 %
    Allowed  : 11.14 %
    Favored  : 87.94 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.22 %
    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:  0.39 (0.29), residues: 969
  helix:  1.51 (0.25), residues: 461
  sheet: -0.80 (0.40), residues: 178
  loop : -0.83 (0.38), residues: 330

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.021   0.001   TRP A 851 
 HIS   0.003   0.001   HIS A 856 
 PHE   0.025   0.002   PHE A 389 
 TYR   0.013   0.002   TYR A 632 
 ARG   0.003   0.000   ARG A 747 

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

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

  1938 Ramachandran restraints generated.
    969 Oldfield, 0 Emsley, 969 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1938 Ramachandran restraints generated.
    969 Oldfield, 0 Emsley, 969 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  70 residues out of total 858 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 8
    poor density    : 62
  time to evaluate  : 0.987 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  187 GLU cc_start: 0.8174 (mm-30) cc_final: 0.7937 (mm-30)
REVERT: A  659 MET cc_start: 0.8114 (tpp) cc_final: 0.7735 (tpp)
REVERT: A  884 LYS cc_start: 0.8765 (ttmt) cc_final: 0.8428 (tppt)
REVERT: A  925 ASP cc_start: 0.8701 (t0) cc_final: 0.8183 (t0)
REVERT: B   20 PHE cc_start: 0.6191 (p90) cc_final: 0.5881 (p90)
  outliers start: 8
  outliers final: 7
  residues processed: 65
  average time/residue: 0.1903
  time to fit residues: 18.1616
Evaluate side-chains
  67 residues out of total 858 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 7
    poor density    : 60
  time to evaluate  : 0.885 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  145 LEU
Chi-restraints excluded: chain A residue  233 VAL
Chi-restraints excluded: chain A residue  280 ILE
Chi-restraints excluded: chain A residue  434 ILE
Chi-restraints excluded: chain A residue  625 LEU
Chi-restraints excluded: chain A residue  669 SER
Chi-restraints excluded: chain A residue  931 THR
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 96
   random chunks:
   chunk 80 optimal weight:    4.9990
   chunk 59 optimal weight:    6.9990
   chunk 84 optimal weight:    5.9990
   chunk 7 optimal weight:    3.9990
   chunk 52 optimal weight:    0.0050
   chunk 35 optimal weight:    0.8980
   chunk 65 optimal weight:    0.4980
   chunk 86 optimal weight:    4.9990
   chunk 87 optimal weight:    0.8980
   chunk 78 optimal weight:    0.7980
   chunk 55 optimal weight:    2.9990
   overall best weight:    0.6194

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

Flipped N/Q/H residues before XYZ refinement:
A 590 GLN
A 635 GLN
** A 987 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3391 r_free = 0.3391 target = 0.073956 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 38)----------------|
| r_work = 0.3078 r_free = 0.3078 target = 0.059346 restraints weight = 63104.109|
|-----------------------------------------------------------------------------|
r_work (start): 0.3063 rms_B_bonded: 6.31
r_work: 0.2867 rms_B_bonded: 6.11 restraints_weight: 2.0000
r_work (final): 0.2867
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.2875
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.2875 r_free = 0.2875    target_work(ls_wunit_k1) = 0.052         |
| occupancies: max = 1.00  min = 0.34   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.2875 r_free = 0.2875    target_work(ls_wunit_k1) = 0.052         |
| occupancies: max = 1.00  min = 0.36   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.2875
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8086
moved from start:          0.2802

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.040   7948  Z= 0.153
  Angle     :  0.574   9.031  10777  Z= 0.286
  Chirality :  0.041   0.132   1181
  Planarity :  0.004   0.045   1407
  Dihedral  :  4.427  40.992   1043
  Min Nonbonded Distance : 2.500

Molprobity Statistics.
  All-atom Clashscore : 7.88
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.91 %
    Favored  : 97.09 %
  Rotamer:
    Outliers :  0.93 %
    Allowed  : 11.48 %
    Favored  : 87.59 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.22 %
    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:  0.71 (0.29), residues: 969
  helix:  1.71 (0.25), residues: 467
  sheet: -0.67 (0.40), residues: 176
  loop : -0.58 (0.38), residues: 326

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.023   0.001   TRP A 851 
 HIS   0.003   0.001   HIS A 186 
 PHE   0.029   0.001   PHE A 389 
 TYR   0.008   0.001   TYR A 721 
 ARG   0.003   0.000   ARG A 747 

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

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

  1938 Ramachandran restraints generated.
    969 Oldfield, 0 Emsley, 969 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1938 Ramachandran restraints generated.
    969 Oldfield, 0 Emsley, 969 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  72 residues out of total 858 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 8
    poor density    : 64
  time to evaluate  : 0.901 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  187 GLU cc_start: 0.8179 (mm-30) cc_final: 0.7940 (mm-30)
REVERT: A  436 MET cc_start: 0.9187 (ttm) cc_final: 0.8753 (tmm)
REVERT: A  659 MET cc_start: 0.8135 (tpp) cc_final: 0.7800 (tpp)
REVERT: A  853 MET cc_start: 0.8291 (mmt) cc_final: 0.7997 (mmm)
REVERT: A  884 LYS cc_start: 0.8702 (ttmt) cc_final: 0.8402 (tppt)
REVERT: A  925 ASP cc_start: 0.8669 (t0) cc_final: 0.8182 (t0)
REVERT: B   20 PHE cc_start: 0.6225 (p90) cc_final: 0.5888 (p90)
  outliers start: 8
  outliers final: 7
  residues processed: 68
  average time/residue: 0.1932
  time to fit residues: 19.0124
Evaluate side-chains
  65 residues out of total 858 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 7
    poor density    : 58
  time to evaluate  : 0.873 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  145 LEU
Chi-restraints excluded: chain A residue  233 VAL
Chi-restraints excluded: chain A residue  434 ILE
Chi-restraints excluded: chain A residue  625 LEU
Chi-restraints excluded: chain A residue  669 SER
Chi-restraints excluded: chain A residue  928 THR
Chi-restraints excluded: chain A residue  931 THR
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 96
   random chunks:
   chunk 72 optimal weight:    3.9990
   chunk 53 optimal weight:    0.8980
   chunk 67 optimal weight:    1.9990
   chunk 16 optimal weight:    5.9990
   chunk 75 optimal weight:    4.9990
   chunk 89 optimal weight:    0.1980
   chunk 41 optimal weight:    2.9990
   chunk 65 optimal weight:    6.9990
   chunk 78 optimal weight:    4.9990
   chunk 52 optimal weight:   10.0000
   chunk 28 optimal weight:    6.9990
   overall best weight:    2.0186

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

Flipped N/Q/H residues before XYZ refinement:
** A 987 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3344 r_free = 0.3344 target = 0.072121 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 30)----------------|
| r_work = 0.3059 r_free = 0.3059 target = 0.059160 restraints weight = 40616.890|
|-----------------------------------------------------------------------------|
r_work (start): 0.3048 rms_B_bonded: 4.94
r_work (final): 0.3048
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3047
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3047 r_free = 0.3047    target_work(ls_wunit_k1) = 0.058         |
| occupancies: max = 1.00  min = 0.36   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3047 r_free = 0.3047    target_work(ls_wunit_k1) = 0.058         |
| occupancies: max = 1.00  min = 0.39   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.3047
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8042
moved from start:          0.2777

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.038   7948  Z= 0.243
  Angle     :  0.613   8.542  10777  Z= 0.307
  Chirality :  0.042   0.142   1181
  Planarity :  0.005   0.042   1407
  Dihedral  :  4.568  40.377   1043
  Min Nonbonded Distance : 2.501

Molprobity Statistics.
  All-atom Clashscore : 9.70
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.32 %
    Favored  : 96.68 %
  Rotamer:
    Outliers :  1.04 %
    Allowed  : 11.72 %
    Favored  : 87.24 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.22 %
    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 (0.29), residues: 969
  helix:  1.60 (0.25), residues: 473
  sheet: -0.61 (0.40), residues: 177
  loop : -0.65 (0.39), residues: 319

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.025   0.002   TRP A 851 
 HIS   0.004   0.001   HIS A 856 
 PHE   0.025   0.002   PHE A 389 
 TYR   0.013   0.002   TYR A 632 
 ARG   0.005   0.000   ARG A1037 

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

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

  1938 Ramachandran restraints generated.
    969 Oldfield, 0 Emsley, 969 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1938 Ramachandran restraints generated.
    969 Oldfield, 0 Emsley, 969 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  69 residues out of total 858 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 9
    poor density    : 60
  time to evaluate  : 0.928 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  187 GLU cc_start: 0.8234 (mm-30) cc_final: 0.8004 (mm-30)
REVERT: A  436 MET cc_start: 0.8634 (ttm) cc_final: 0.8309 (tmm)
REVERT: A  659 MET cc_start: 0.7987 (tpp) cc_final: 0.7679 (tpp)
REVERT: A  853 MET cc_start: 0.7641 (mmt) cc_final: 0.7420 (mmm)
REVERT: A  884 LYS cc_start: 0.8603 (ttmt) cc_final: 0.8300 (tppt)
REVERT: A  925 ASP cc_start: 0.8469 (t0) cc_final: 0.7960 (t0)
REVERT: B   20 PHE cc_start: 0.6278 (p90) cc_final: 0.5850 (p90)
  outliers start: 9
  outliers final: 7
  residues processed: 63
  average time/residue: 0.1942
  time to fit residues: 18.3033
Evaluate side-chains
  66 residues out of total 858 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 7
    poor density    : 59
  time to evaluate  : 0.935 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  145 LEU
Chi-restraints excluded: chain A residue  233 VAL
Chi-restraints excluded: chain A residue  434 ILE
Chi-restraints excluded: chain A residue  625 LEU
Chi-restraints excluded: chain A residue  669 SER
Chi-restraints excluded: chain A residue  928 THR
Chi-restraints excluded: chain A residue  931 THR
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 96
   random chunks:
   chunk 42 optimal weight:    6.9990
   chunk 86 optimal weight:    0.9990
   chunk 39 optimal weight:    2.9990
   chunk 1 optimal weight:    2.9990
   chunk 78 optimal weight:    0.9990
   chunk 44 optimal weight:    0.0040
   chunk 40 optimal weight:    3.9990
   chunk 17 optimal weight:    1.9990
   chunk 13 optimal weight:    5.9990
   chunk 37 optimal weight:    6.9990
   chunk 30 optimal weight:    8.9990
   overall best weight:    1.4000

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

Flipped N/Q/H residues before XYZ refinement:
** A 987 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3361 r_free = 0.3361 target = 0.072324 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 34)----------------|
| r_work = 0.3058 r_free = 0.3058 target = 0.058425 restraints weight = 48015.430|
|-----------------------------------------------------------------------------|
r_work (start): 0.3043 rms_B_bonded: 5.47
r_work (final): 0.3043
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3044
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3044 r_free = 0.3044    target_work(ls_wunit_k1) = 0.058         |
| occupancies: max = 1.00  min = 0.39   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3044 r_free = 0.3044    target_work(ls_wunit_k1) = 0.058         |
| occupancies: max = 1.00  min = 0.41   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.3044
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8023
moved from start:          0.2838

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.042   7948  Z= 0.196
  Angle     :  0.594   8.853  10777  Z= 0.295
  Chirality :  0.041   0.139   1181
  Planarity :  0.004   0.043   1407
  Dihedral  :  4.493  42.689   1043
  Min Nonbonded Distance : 2.485

Molprobity Statistics.
  All-atom Clashscore : 9.11
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.22 %
    Favored  : 96.78 %
  Rotamer:
    Outliers :  0.93 %
    Allowed  : 12.06 %
    Favored  : 87.01 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.22 %
    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:  0.71 (0.29), residues: 969
  helix:  1.66 (0.25), residues: 472
  sheet: -0.58 (0.40), residues: 178
  loop : -0.62 (0.38), residues: 319

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.025   0.002   TRP A 851 
 HIS   0.003   0.001   HIS A 186 
 PHE   0.027   0.001   PHE A 389 
 TYR   0.010   0.001   TYR A 721 
 ARG   0.003   0.000   ARG A1037 

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

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

  1938 Ramachandran restraints generated.
    969 Oldfield, 0 Emsley, 969 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1938 Ramachandran restraints generated.
    969 Oldfield, 0 Emsley, 969 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  65 residues out of total 858 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 8
    poor density    : 57
  time to evaluate  : 0.969 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  187 GLU cc_start: 0.8210 (mm-30) cc_final: 0.7974 (mm-30)
REVERT: A  436 MET cc_start: 0.8623 (ttm) cc_final: 0.8312 (tmm)
REVERT: A  595 MET cc_start: 0.8457 (OUTLIER) cc_final: 0.8185 (mtp)
REVERT: A  659 MET cc_start: 0.8009 (tpp) cc_final: 0.7684 (tpp)
REVERT: A  853 MET cc_start: 0.7629 (mmt) cc_final: 0.7417 (mmm)
REVERT: A  884 LYS cc_start: 0.8577 (ttmt) cc_final: 0.8285 (tppt)
REVERT: A  925 ASP cc_start: 0.8486 (t0) cc_final: 0.8006 (t0)
REVERT: A 1037 ARG cc_start: 0.7306 (mpt-90) cc_final: 0.7056 (mmt90)
REVERT: B   20 PHE cc_start: 0.6287 (p90) cc_final: 0.5831 (p90)
  outliers start: 8
  outliers final: 7
  residues processed: 60
  average time/residue: 0.1961
  time to fit residues: 17.3822
Evaluate side-chains
  64 residues out of total 858 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 8
    poor density    : 56
  time to evaluate  : 0.899 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  145 LEU
Chi-restraints excluded: chain A residue  233 VAL
Chi-restraints excluded: chain A residue  434 ILE
Chi-restraints excluded: chain A residue  595 MET
Chi-restraints excluded: chain A residue  625 LEU
Chi-restraints excluded: chain A residue  669 SER
Chi-restraints excluded: chain A residue  928 THR
Chi-restraints excluded: chain A residue  931 THR
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 96
   random chunks:
   chunk 7 optimal weight:    0.6980
   chunk 86 optimal weight:    0.9990
   chunk 88 optimal weight:    4.9990
   chunk 30 optimal weight:   10.0000
   chunk 42 optimal weight:    3.9990
   chunk 35 optimal weight:    1.9990
   chunk 49 optimal weight:    5.9990
   chunk 52 optimal weight:    6.9990
   chunk 14 optimal weight:    3.9990
   chunk 37 optimal weight:    3.9990
   chunk 62 optimal weight:    0.0040
   overall best weight:    1.5398

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

Flipped N/Q/H residues before XYZ refinement:
** A 987 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3360 r_free = 0.3360 target = 0.071938 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 36)----------------|
| r_work = 0.3052 r_free = 0.3052 target = 0.057794 restraints weight = 52431.908|
|-----------------------------------------------------------------------------|
r_work (start): 0.3035 rms_B_bonded: 5.72
r_work (final): 0.3035
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3034
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3034 r_free = 0.3034    target_work(ls_wunit_k1) = 0.057         |
| occupancies: max = 1.00  min = 0.41   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3034 r_free = 0.3034    target_work(ls_wunit_k1) = 0.057         |
| occupancies: max = 1.00  min = 0.41   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.3034
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8034
moved from start:          0.2918

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.039   7948  Z= 0.207
  Angle     :  0.595   8.776  10777  Z= 0.294
  Chirality :  0.041   0.138   1181
  Planarity :  0.004   0.043   1407
  Dihedral  :  4.463  40.701   1043
  Min Nonbonded Distance : 2.492

Molprobity Statistics.
  All-atom Clashscore : 9.11
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.12 %
    Favored  : 96.88 %
  Rotamer:
    Outliers :  0.81 %
    Allowed  : 12.30 %
    Favored  : 86.89 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.22 %
    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:  0.77 (0.29), residues: 969
  helix:  1.75 (0.25), residues: 466
  sheet: -0.56 (0.40), residues: 178
  loop : -0.60 (0.38), residues: 325

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.025   0.002   TRP A 851 
 HIS   0.003   0.001   HIS A 856 
 PHE   0.026   0.001   PHE A 389 
 TYR   0.011   0.001   TYR A 721 
 ARG   0.004   0.000   ARG A 747 
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 4123.18 seconds
wall clock time: 74 minutes 6.85 seconds (4446.85 seconds total)