Starting phenix.real_space_refine
on Fri Feb 14 04:08:43 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/7e2i_30958/02_2025/7e2i_30958.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/7e2i_30958/02_2025/7e2i_30958.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=4.07
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/cci-nas-00/data/ceres_data/7e2i_30958/02_2025/7e2i_30958.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/7e2i_30958/02_2025/7e2i_30958.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/7e2i_30958/02_2025/7e2i_30958.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/7e2i_30958/02_2025/7e2i_30958.cif"
  }
  resolution = 4.07
  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=   0.001 sd=   0.006
Set stop_for_unknowns flag
  Set to: True
Assert model is a single copy model
Assert all atoms have isotropic ADPs
  Anisotropic ADP refinement not supported. Converting 1208 atoms to isotropic.
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: 5
    Type Number    sf(0)   Gaussians
     Zn      1      6.06       5
     S      67      5.16       5
     C    5595      2.51       5
     N    1354      2.21       5
     O    1552      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 17 residue(s): 0.02s

  Monomer Library directory:
    "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5592/modules/chem_data/mon_lib"
  Total number of atoms: 8569
  Number of models: 1
  Model: ""
    Number of chains: 4
    Chain: "G"
      Number of atoms: 1209
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 151, 1209
          Classifications: {'peptide': 151}
          Incomplete info: {'truncation_to_alanine': 1}
          Link IDs: {'PTRANS': 5, 'TRANS': 145}
          Unresolved non-hydrogen bonds: 4
          Unresolved non-hydrogen angles: 4
          Unresolved non-hydrogen dihedrals: 4
    Chain: "D"
      Number of atoms: 7058
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 907, 7058
          Classifications: {'peptide': 907}
          Incomplete info: {'truncation_to_alanine': 36}
          Link IDs: {'PTRANS': 37, 'TRANS': 869}
          Chain breaks: 4
          Unresolved non-hydrogen bonds: 155
          Unresolved non-hydrogen angles: 191
          Unresolved non-hydrogen dihedrals: 132
          Unresolved non-hydrogen chiralities: 8
          Planarities with less than four sites: {'GLN:plan1': 3, 'HIS:plan': 1, 'TYR:plan': 3, 'ASP:plan': 5, 'PHE:plan': 1, 'GLU:plan': 2, 'ARG:plan': 5}
          Unresolved non-hydrogen planarities: 92
    Chain: "G"
      Number of atoms: 1
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 1, 1
          Unusual residues: {' ZN': 1}
          Classifications: {'undetermined': 1}
    Chain: "D"
      Number of atoms: 301
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 11, 301
          Unusual residues: {'NAG': 4, 'Y01': 7}
          Classifications: {'undetermined': 11}
          Link IDs: {None: 10}
          Unresolved non-hydrogen bonds: 4
          Unresolved non-hydrogen angles: 8
          Unresolved non-hydrogen dihedrals: 12
          Unresolved non-hydrogen chiralities: 4
  Time building chain proxies: 5.04, per 1000 atoms: 0.59
  Number of scatterers: 8569
  At special positions: 0
  Unit cell: (109.172, 115.856, 115.856, 90, 90, 90)
  Space group: P 1 (No. 1)
  Number of sites at special positions: 0
  Number of scattering types: 5
    Type Number    sf(0)
     Zn      1     29.99
     S      67     16.00
     O    1552      8.00
     N    1354      7.00
     C    5595      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
  Links applied
    NAG-ASN
      " NAG D1608 " - " ASN D 476 "
      " NAG D1610 " - " ASN D 917 "
      " NAG D1611 " - " ASN D 836 "
  Time building additional restraints: 2.67
  Conformation dependent library (CDL) restraints added in 926.6 milliseconds
  
  Dynamic metal coordination
    Zn2+ tetrahedral coordination
      pdb="  ZN G 501 "
        pdb="ZN    ZN G 501 " - pdb=" NE2 HIS G 140 "
        pdb="ZN    ZN G 501 " - pdb=" ND1 HIS G 182 "


  2092 Ramachandran restraints generated.
    1046 Oldfield, 0 Emsley, 1046 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  2012

  Finding SS restraints...
    Secondary structure from input PDB file:
      33 helices and 5 sheets defined
      55.0% alpha, 4.1% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 0.74
  Creating SS restraints...
    Processing helix  chain 'G' and resid 71 through 74
    Processing helix  chain 'G' and resid 100 through 117
      removed outlier: 3.604A  pdb=" N   LYS G 105 " --> pdb=" O   ARG G 101 " (cutoff:3.500A)
    Processing helix  chain 'G' and resid 138 through 143
      removed outlier: 3.754A  pdb=" N   GLU G 142 " --> pdb=" O   SER G 138 " (cutoff:3.500A)
    Processing helix  chain 'G' and resid 155 through 168
      removed outlier: 3.592A  pdb=" N   GLY G 159 " --> pdb=" O   ARG G 155 " (cutoff:3.500A)
      removed outlier: 3.855A  pdb=" N   ARG G 163 " --> pdb=" O   GLY G 159 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 182 through 186
      removed outlier: 4.083A  pdb=" N   ALA D 186 " --> pdb=" O   ALA D 182 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'D' and resid 182 through 186'
    Processing helix  chain 'D' and resid 189 through 210
    Processing helix  chain 'D' and resid 230 through 243
    Processing helix  chain 'D' and resid 315 through 330
    Processing helix  chain 'D' and resid 353 through 363
    Processing helix  chain 'D' and resid 372 through 388
      removed outlier: 3.505A  pdb=" N   SER D 376 " --> pdb=" O   GLU D 372 " (cutoff:3.500A)
      removed outlier: 3.567A  pdb=" N   HIS D 388 " --> pdb=" O   THR D 384 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 423 through 430
    Processing helix  chain 'D' and resid 463 through 472
      removed outlier: 4.479A  pdb=" N   ILE D 467 " --> pdb=" O   SER D 463 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 492 through 503
      removed outlier: 4.366A  pdb=" N   GLN D 497 " --> pdb=" O   HIS D 493 " (cutoff:3.500A)
      removed outlier: 4.692A  pdb=" N   ASP D 498 " --> pdb=" O   SER D 494 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 504 through 522
      removed outlier: 3.518A  pdb=" N   ALA D 508 " --> pdb=" O   THR D 504 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 524 through 548
    Processing helix  chain 'D' and resid 558 through 587
      removed outlier: 3.834A  pdb=" N   LEU D 563 " --> pdb=" O   ASN D 559 " (cutoff:3.500A)
      removed outlier: 6.288A  pdb=" N   ILE D 564 " --> pdb=" O   LEU D 560 " (cutoff:3.500A)
      removed outlier: 4.390A  pdb=" N   ILE D 565 " --> pdb=" O   THR D 561 " (cutoff:3.500A)
      removed outlier: 3.697A  pdb=" N   VAL D 576 " --> pdb=" O   ASN D 572 " (cutoff:3.500A)
      removed outlier: 3.977A  pdb=" N   LEU D 577 " --> pdb=" O   ASN D 573 " (cutoff:3.500A)
      removed outlier: 3.576A  pdb=" N   ASP D 587 " --> pdb=" O   TYR D 583 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 592 through 623
      removed outlier: 5.132A  pdb=" N   LEU D 606 " --> pdb=" O   GLN D 602 " (cutoff:3.500A)
      removed outlier: 5.185A  pdb=" N   SER D 607 " --> pdb=" O   HIS D 603 " (cutoff:3.500A)
      removed outlier: 4.960A  pdb=" N   THR D 615 " --> pdb=" O   THR D 611 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 627 through 659
      removed outlier: 4.537A  pdb=" N   PHE D 633 " --> pdb=" O   ALA D 629 " (cutoff:3.500A)
      Proline residue:  D 653  - end of helix
    Processing helix  chain 'D' and resid 688 through 718
      removed outlier: 5.084A  pdb=" N   LEU D 710 " --> pdb=" O   PHE D 706 " (cutoff:3.500A)
      Proline residue:  D 711  - end of helix
    Processing helix  chain 'D' and resid 719 through 738
    Processing helix  chain 'D' and resid 748 through 752
      removed outlier: 3.676A  pdb=" N   PHE D 752 " --> pdb=" O   LEU D 749 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 759 through 765
      removed outlier: 4.261A  pdb=" N   ASP D 765 " --> pdb=" O   PHE D 761 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 768 through 771
    Processing helix  chain 'D' and resid 772 through 779
    Processing helix  chain 'D' and resid 820 through 835
    Processing helix  chain 'D' and resid 851 through 860
      removed outlier: 4.006A  pdb=" N   THR D 855 " --> pdb=" O   CYS D 851 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 883 through 902
      removed outlier: 4.347A  pdb=" N   LYS D 891 " --> pdb=" O   GLU D 887 " (cutoff:3.500A)
      removed outlier: 3.757A  pdb=" N   ARG D 892 " --> pdb=" O   LEU D 888 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 936 through 953
      removed outlier: 3.965A  pdb=" N   MET D 940 " --> pdb=" O   ALA D 936 " (cutoff:3.500A)
      removed outlier: 4.005A  pdb=" N   SER D 953 " --> pdb=" O   SER D 949 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 971 through 1004
    Processing helix  chain 'D' and resid 1005 through 1030
    Processing helix  chain 'D' and resid 1036 through 1059
      removed outlier: 4.479A  pdb=" N   VAL D1040 " --> pdb=" O   VAL D1036 " (cutoff:3.500A)
      removed outlier: 3.740A  pdb=" N   THR D1041 " --> pdb=" O   LEU D1037 " (cutoff:3.500A)
      removed outlier: 4.230A  pdb=" N   ILE D1042 " --> pdb=" O   GLU D1038 " (cutoff:3.500A)
      removed outlier: 3.802A  pdb=" N   SER D1043 " --> pdb=" O   SER D1039 " (cutoff:3.500A)
      removed outlier: 3.803A  pdb=" N   VAL D1046 " --> pdb=" O   ILE D1042 " (cutoff:3.500A)
      removed outlier: 3.700A  pdb=" N   GLY D1047 " --> pdb=" O   SER D1043 " (cutoff:3.500A)
      removed outlier: 3.626A  pdb=" N   ASN D1051 " --> pdb=" O   GLY D1047 " (cutoff:3.500A)
      removed outlier: 4.733A  pdb=" N   PHE D1052 " --> pdb=" O   LEU D1048 " (cutoff:3.500A)
      removed outlier: 4.022A  pdb=" N   ALA D1053 " --> pdb=" O   SER D1049 " (cutoff:3.500A)
      removed outlier: 4.320A  pdb=" N   HIS D1055 " --> pdb=" O   ASN D1051 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 1068 through 1098
      removed outlier: 3.520A  pdb=" N   VAL D1072 " --> pdb=" O   ARG D1068 " (cutoff:3.500A)
      removed outlier: 3.554A  pdb=" N   ILE D1073 " --> pdb=" O   GLU D1069 " (cutoff:3.500A)
      removed outlier: 5.569A  pdb=" N   SER D1081 " --> pdb=" O   SER D1077 " (cutoff:3.500A)
      removed outlier: 5.564A  pdb=" N   ALA D1082 " --> pdb=" O   ARG D1078 " (cutoff:3.500A)
      removed outlier: 4.441A  pdb=" N   THR D1090 " --> pdb=" O   ALA D1086 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 1102 through 1133
      removed outlier: 3.792A  pdb=" N   THR D1106 " --> pdb=" O   VAL D1102 " (cutoff:3.500A)
      removed outlier: 4.148A  pdb=" N   CYS D1131 " --> pdb=" O   PHE D1127 " (cutoff:3.500A)
    Processing sheet with id=AA1, first strand: chain 'G' and resid 76 through 78
    Processing sheet with id=AA2, first strand: chain 'G' and resid 85 through 86
      removed outlier: 7.775A  pdb=" N   ILE G  85 " --> pdb=" O   VAL G 124 " (cutoff:3.500A)
      removed outlier: 8.935A  pdb=" N   GLU G 126 " --> pdb=" O   ILE G  85 " (cutoff:3.500A)
      removed outlier: 6.911A  pdb=" N   ASP G 147 " --> pdb=" O   THR G 125 " (cutoff:3.500A)
    Processing sheet with id=AA3, first strand: chain 'D' and resid 451 through 459
      removed outlier: 4.668A  pdb=" N   SER D 301 " --> pdb=" O   SER D 456 " (cutoff:3.500A)
      removed outlier: 7.631A  pdb=" N   ARG D 302 " --> pdb=" O   ILE D 487 " (cutoff:3.500A)
      removed outlier: 5.473A  pdb=" N   ILE D 487 " --> pdb=" O   ARG D 302 " (cutoff:3.500A)
      removed outlier: 6.818A  pdb=" N   VAL D 304 " --> pdb=" O   THR D 485 " (cutoff:3.500A)
    Processing sheet with id=AA4, first strand: chain 'D' and resid 788 through 789
    Processing sheet with id=AA5, first strand: chain 'D' and resid 913 through 914
      removed outlier: 6.290A  pdb=" N   ARG D 913 " --> pdb=" O   ARG D 921 " (cutoff:3.500A)

    425 hydrogen bonds defined for protein.
    1254 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: 2.39

  Time building geometry restraints manager: 2.91 seconds

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

  Histogram of bond lengths:
        1.20 -     1.32: 1356
        1.32 -     1.44: 2434
        1.44 -     1.57: 4908
        1.57 -     1.69: 0
        1.69 -     1.81: 103
  Bond restraints: 8801
  Sorted by residual:
  bond pdb=" CB  TRP D 966 "
       pdb=" CG  TRP D 966 "
    ideal  model  delta    sigma   weight residual
    1.498  1.414  0.084 3.10e-02 1.04e+03 7.31e+00
  bond pdb=" C   MET D 785 "
       pdb=" N   PRO D 786 "
    ideal  model  delta    sigma   weight residual
    1.333  1.307  0.026 1.20e-02 6.94e+03 4.85e+00
  bond pdb=" C   SER D 758 "
       pdb=" N   HIS D 759 "
    ideal  model  delta    sigma   weight residual
    1.331  1.287  0.044 2.07e-02 2.33e+03 4.57e+00
  bond pdb=" CG  ASN D 476 "
       pdb=" ND2 ASN D 476 "
    ideal  model  delta    sigma   weight residual
    1.328  1.369 -0.041 2.10e-02 2.27e+03 3.90e+00
  bond pdb=" C   LEU D 749 "
       pdb=" N   SER D 750 "
    ideal  model  delta    sigma   weight residual
    1.331  1.301  0.031 1.62e-02 3.81e+03 3.57e+00
  ... (remaining 8796 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     1.63: 11391
        1.63 -     3.26: 511
        3.26 -     4.88: 75
        4.88 -     6.51: 19
        6.51 -     8.14: 9
  Bond angle restraints: 12005
  Sorted by residual:
  angle pdb=" N   PHE D 255 "
        pdb=" CA  PHE D 255 "
        pdb=" C   PHE D 255 "
      ideal   model   delta    sigma   weight residual
     108.19  116.33   -8.14 1.29e+00 6.01e-01 3.98e+01
  angle pdb=" N   PRO D 254 "
        pdb=" CA  PRO D 254 "
        pdb=" C   PRO D 254 "
      ideal   model   delta    sigma   weight residual
     112.47  120.58   -8.11 2.06e+00 2.36e-01 1.55e+01
  angle pdb=" C   PRO D 254 "
        pdb=" N   PHE D 255 "
        pdb=" CA  PHE D 255 "
      ideal   model   delta    sigma   weight residual
     122.08  115.53    6.55 1.84e+00 2.95e-01 1.27e+01
  angle pdb=" C   LEU D 749 "
        pdb=" N   SER D 750 "
        pdb=" CA  SER D 750 "
      ideal   model   delta    sigma   weight residual
     122.31  115.38    6.93 2.00e+00 2.50e-01 1.20e+01
  angle pdb=" C   PHE D 554 "
        pdb=" N   PHE D 555 "
        pdb=" CA  PHE D 555 "
      ideal   model   delta    sigma   weight residual
     121.80  113.75    8.05 2.44e+00 1.68e-01 1.09e+01
  ... (remaining 12000 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    16.97: 4962
       16.97 -    33.95: 491
       33.95 -    50.92: 77
       50.92 -    67.90: 23
       67.90 -    84.87: 5
  Dihedral angle restraints: 5558
    sinusoidal: 2452
      harmonic: 3106
  Sorted by residual:
  dihedral pdb=" CA  SER D 290 "
           pdb=" C   SER D 290 "
           pdb=" N   PHE D 291 "
           pdb=" CA  PHE D 291 "
      ideal   model   delta  harmonic     sigma   weight residual
    -180.00 -155.86  -24.14     0      5.00e+00 4.00e-02 2.33e+01
  dihedral pdb=" CA  TYR D 253 "
           pdb=" C   TYR D 253 "
           pdb=" N   PRO D 254 "
           pdb=" CA  PRO D 254 "
      ideal   model   delta  harmonic     sigma   weight residual
    -180.00 -156.84  -23.16     0      5.00e+00 4.00e-02 2.15e+01
  dihedral pdb=" CA  PHE D1127 "
           pdb=" C   PHE D1127 "
           pdb=" N   GLN D1128 "
           pdb=" CA  GLN D1128 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  157.63   22.37     0      5.00e+00 4.00e-02 2.00e+01
  ... (remaining 5555 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.132: 1367
       0.132 -    0.264: 14
       0.264 -    0.396: 0
       0.396 -    0.529: 1
       0.529 -    0.661: 1
  Chirality restraints: 1383
  Sorted by residual:
  chirality pdb=" C1  NAG D1610 "
            pdb=" ND2 ASN D 917 "
            pdb=" C2  NAG D1610 "
            pdb=" O5  NAG D1610 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.40   -1.74   -0.66 2.00e-01 2.50e+01 1.09e+01
  chirality pdb=" C1  NAG D1611 "
            pdb=" ND2 ASN D 836 "
            pdb=" C2  NAG D1611 "
            pdb=" O5  NAG D1611 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.40   -1.93   -0.47 2.00e-01 2.50e+01 5.45e+00
  chirality pdb=" CA  PRO D 254 "
            pdb=" N   PRO D 254 "
            pdb=" C   PRO D 254 "
            pdb=" CB  PRO D 254 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.72    2.49    0.23 2.00e-01 2.50e+01 1.31e+00
  ... (remaining 1380 not shown)

  Planarity restraints: 1468
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  GLN D 883 "    0.012 2.00e-02 2.50e+03   2.37e-02 5.61e+00
        pdb=" C   GLN D 883 "   -0.041 2.00e-02 2.50e+03
        pdb=" O   GLN D 883 "    0.015 2.00e-02 2.50e+03
        pdb=" N   GLU D 884 "    0.014 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   SER D 456 "   -0.031 5.00e-02 4.00e+02   4.65e-02 3.46e+00
        pdb=" N   PRO D 457 "    0.080 5.00e-02 4.00e+02
        pdb=" CA  PRO D 457 "   -0.024 5.00e-02 4.00e+02
        pdb=" CD  PRO D 457 "   -0.026 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CB  PHE D 291 "    0.004 2.00e-02 2.50e+03   1.26e-02 2.79e+00
        pdb=" CG  PHE D 291 "   -0.022 2.00e-02 2.50e+03
        pdb=" CD1 PHE D 291 "    0.021 2.00e-02 2.50e+03
        pdb=" CD2 PHE D 291 "    0.001 2.00e-02 2.50e+03
        pdb=" CE1 PHE D 291 "   -0.011 2.00e-02 2.50e+03
        pdb=" CE2 PHE D 291 "    0.009 2.00e-02 2.50e+03
        pdb=" CZ  PHE D 291 "   -0.002 2.00e-02 2.50e+03
  ... (remaining 1465 not shown)

  Histogram of nonbonded interaction distances:
        2.06 -     2.63: 166
        2.63 -     3.19: 9307
        3.19 -     3.76: 13529
        3.76 -     4.33: 17745
        4.33 -     4.90: 26852
  Nonbonded interactions: 67599
  Sorted by model distance:
  nonbonded pdb=" O   PRO D 350 "
            pdb=" ND2 ASN D 356 "
     model   vdw
     2.056 3.120
  nonbonded pdb=" OD1 ASP G 147 "
            pdb="ZN    ZN G 501 "
     model   vdw
     2.074 2.230
  nonbonded pdb=" OE1 GLU G 176 "
            pdb="ZN    ZN G 501 "
     model   vdw
     2.094 2.230
  nonbonded pdb=" O   ALA D1059 "
            pdb=" OG  SER D1075 "
     model   vdw
     2.105 3.040
  nonbonded pdb=" O   GLU G  53 "
            pdb=" OG  SER G  59 "
     model   vdw
     2.106 3.040
  ... (remaining 67594 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=0.00 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:             0.370
  Set stop_for_unknowns flag:              0.000
  Assert model is a single copy model:     0.000
  Assert all atoms have isotropic ADPs:    0.060
  Construct map_model_manager:             0.000
  Extract box with map and model:          0.320
  Check model and map are aligned:         0.060
  Set scattering table:                    0.090
  Process input model:                     23.500
  Find NCS groups from input model:        0.100
  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:             0.000
  Load rotamer database and sin/cos tables:2.740
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   27.270
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7933
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      :  0.006   0.084   8801  Z= 0.401
  Angle     :  0.820   8.141  12005  Z= 0.439
  Chirality :  0.051   0.661   1383
  Planarity :  0.005   0.047   1465
  Dihedral  : 13.723  84.873   3546
  Min Nonbonded Distance : 2.056

Molprobity Statistics.
  All-atom Clashscore : 20.89
  Ramachandran Plot:
    Outliers :  0.10 %
    Allowed  : 11.66 %
    Favored  : 88.24 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  5.74 %
    Favored  : 94.26 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -4.32 (0.21), residues: 1046
  helix: -2.23 (0.18), residues: 534
  sheet: -3.19 (0.67), residues: 52
  loop : -3.60 (0.26), residues: 460

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.022   0.002   TRP D1120 
 HIS   0.005   0.001   HIS D 778 
 PHE   0.024   0.002   PHE D 967 
 TYR   0.017   0.002   TYR D1060 
 ARG   0.012   0.001   ARG D 329 

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

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

  2092 Ramachandran restraints generated.
    1046 Oldfield, 0 Emsley, 1046 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2092 Ramachandran restraints generated.
    1046 Oldfield, 0 Emsley, 1046 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  261 residues out of total 926 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 261
  time to evaluate  : 0.870 
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: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: G   81 ASN cc_start: 0.8670 (t0) cc_final: 0.8455 (t0)
REVERT: G   98 MET cc_start: 0.8708 (ptm) cc_final: 0.8233 (ptp)
REVERT: G  102 CYS cc_start: 0.9143 (t) cc_final: 0.8353 (t)
REVERT: G  141 TYR cc_start: 0.8299 (m-10) cc_final: 0.7834 (m-10)
REVERT: G  154 ASP cc_start: 0.8478 (m-30) cc_final: 0.8256 (m-30)
REVERT: G  175 TYR cc_start: 0.7553 (t80) cc_final: 0.6516 (t80)
REVERT: G  186 LYS cc_start: 0.8525 (ttmt) cc_final: 0.8247 (ttmt)
REVERT: G  188 GLU cc_start: 0.8442 (mm-30) cc_final: 0.8219 (mm-30)
REVERT: D  343 THR cc_start: 0.7712 (t) cc_final: 0.7454 (m)
REVERT: D  460 LYS cc_start: 0.9241 (pttm) cc_final: 0.8865 (pttm)
REVERT: D  502 MET cc_start: 0.8768 (tmm) cc_final: 0.8526 (tmm)
REVERT: D  530 MET cc_start: 0.8998 (tpp) cc_final: 0.8459 (tpp)
REVERT: D  595 GLU cc_start: 0.8961 (mp0) cc_final: 0.8512 (mp0)
REVERT: D  641 ILE cc_start: 0.9617 (tp) cc_final: 0.9379 (tp)
REVERT: D  753 GLN cc_start: 0.8912 (pt0) cc_final: 0.8634 (pt0)
REVERT: D  796 GLU cc_start: 0.9079 (mt-10) cc_final: 0.8031 (tm-30)
REVERT: D  896 GLU cc_start: 0.8496 (mt-10) cc_final: 0.8030 (mt-10)
REVERT: D  926 GLU cc_start: 0.8271 (pm20) cc_final: 0.8006 (pm20)
REVERT: D 1011 TYR cc_start: 0.9243 (m-80) cc_final: 0.8795 (m-80)
REVERT: D 1097 MET cc_start: 0.9178 (ttm) cc_final: 0.8868 (tmm)
REVERT: D 1126 PHE cc_start: 0.8840 (t80) cc_final: 0.8417 (t80)
REVERT: D 1128 GLN cc_start: 0.9315 (mp10) cc_final: 0.9031 (mp10)
REVERT: D 1129 CYS cc_start: 0.9471 (t) cc_final: 0.8999 (t)
  outliers start: 0
  outliers final: 0
  residues processed: 261
  average time/residue: 0.2031
  time to fit residues: 73.0072
Evaluate side-chains
  202 residues out of total 926 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 202
  time to evaluate  : 0.941 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 105
   random chunks:
   chunk 88 optimal weight:    0.9990
   chunk 79 optimal weight:   10.0000
   chunk 44 optimal weight:    0.8980
   chunk 27 optimal weight:    3.9990
   chunk 53 optimal weight:    4.9990
   chunk 42 optimal weight:    0.3980
   chunk 82 optimal weight:    8.9990
   chunk 31 optimal weight:    6.9990
   chunk 50 optimal weight:    2.9990
   chunk 61 optimal weight:    3.9990
   chunk 95 optimal weight:    5.9990
   overall best weight:    1.8586

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

Flipped N/Q/H residues before XYZ refinement:
D 252 ASN
** D 315 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
D 327 ASN
D 356 ASN
D 362 ASN
D 363 ASN
** D 572 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
D 622 ASN
D 659 HIS
** D 824 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
D 842 GLN
D 964 ASN
D 977 GLN

Total number of N/Q/H flips: 10

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3708 r_free = 0.3708 target = 0.113573 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 29)----------------|
| r_work = 0.3300 r_free = 0.3300 target = 0.087965 restraints weight = 22742.811|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 27)----------------|
| r_work = 0.3306 r_free = 0.3306 target = 0.089133 restraints weight = 12562.442|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 24)----------------|
| r_work = 0.3323 r_free = 0.3323 target = 0.090189 restraints weight = 8751.032|
|-----------------------------------------------------------------------------|
r_work (final): 0.3310
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7816
moved from start:          0.1803

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.049   8801  Z= 0.225
  Angle     :  0.702   9.351  12005  Z= 0.362
  Chirality :  0.043   0.254   1383
  Planarity :  0.005   0.042   1465
  Dihedral  :  7.354  54.891   1710
  Min Nonbonded Distance : 2.056

Molprobity Statistics.
  All-atom Clashscore : 12.95
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  8.99 %
    Favored  : 91.01 %
  Rotamer:
    Outliers :  0.22 %
    Allowed  :  6.64 %
    Favored  : 93.14 %
  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: -2.52 (0.25), residues: 1046
  helix: -0.49 (0.21), residues: 538
  sheet: -3.26 (0.63), residues: 58
  loop : -2.96 (0.28), residues: 450

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.018   0.001   TRP D 651 
 HIS   0.003   0.001   HIS G 182 
 PHE   0.025   0.002   PHE D 291 
 TYR   0.013   0.001   TYR G  80 
 ARG   0.011   0.001   ARG G  61 

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

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

  2092 Ramachandran restraints generated.
    1046 Oldfield, 0 Emsley, 1046 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2092 Ramachandran restraints generated.
    1046 Oldfield, 0 Emsley, 1046 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  249 residues out of total 926 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 2
    poor density    : 247
  time to evaluate  : 1.038 
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: G   98 MET cc_start: 0.8464 (ptm) cc_final: 0.8219 (ptp)
REVERT: G  106 LEU cc_start: 0.9450 (tt) cc_final: 0.9178 (pp)
REVERT: G  141 TYR cc_start: 0.8261 (m-10) cc_final: 0.7868 (m-10)
REVERT: G  154 ASP cc_start: 0.8382 (m-30) cc_final: 0.8162 (m-30)
REVERT: G  175 TYR cc_start: 0.7352 (t80) cc_final: 0.7148 (t80)
REVERT: G  184 SER cc_start: 0.8619 (p) cc_final: 0.8370 (p)
REVERT: G  186 LYS cc_start: 0.8447 (ttmt) cc_final: 0.8208 (ttmt)
REVERT: D  373 ARG cc_start: 0.9358 (mmt-90) cc_final: 0.8804 (mmp80)
REVERT: D  454 LEU cc_start: 0.8479 (tp) cc_final: 0.8165 (tp)
REVERT: D  460 LYS cc_start: 0.9203 (pttp) cc_final: 0.8960 (pttm)
REVERT: D  502 MET cc_start: 0.8546 (tmm) cc_final: 0.8127 (tpp)
REVERT: D  518 MET cc_start: 0.8808 (mtm) cc_final: 0.8566 (mtm)
REVERT: D  530 MET cc_start: 0.9132 (tpp) cc_final: 0.8427 (tpp)
REVERT: D  575 PHE cc_start: 0.8871 (m-10) cc_final: 0.8090 (m-80)
REVERT: D  579 ASP cc_start: 0.8893 (m-30) cc_final: 0.8657 (m-30)
REVERT: D  753 GLN cc_start: 0.8734 (pt0) cc_final: 0.8467 (pt0)
REVERT: D  796 GLU cc_start: 0.8979 (mt-10) cc_final: 0.7974 (tm-30)
REVERT: D  926 GLU cc_start: 0.8043 (pm20) cc_final: 0.7696 (pm20)
REVERT: D  996 PHE cc_start: 0.8718 (t80) cc_final: 0.8509 (t80)
REVERT: D 1011 TYR cc_start: 0.8984 (m-80) cc_final: 0.8621 (m-80)
REVERT: D 1085 MET cc_start: 0.8862 (tpp) cc_final: 0.8445 (tpp)
REVERT: D 1126 PHE cc_start: 0.8719 (t80) cc_final: 0.8303 (t80)
  outliers start: 2
  outliers final: 1
  residues processed: 249
  average time/residue: 0.1840
  time to fit residues: 64.7635
Evaluate side-chains
  206 residues out of total 926 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 205
  time to evaluate  : 0.982 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 105
   random chunks:
   chunk 58 optimal weight:    0.8980
   chunk 42 optimal weight:   10.0000
   chunk 101 optimal weight:    0.9980
   chunk 13 optimal weight:   20.0000
   chunk 54 optimal weight:    6.9990
   chunk 84 optimal weight:    7.9990
   chunk 30 optimal weight:    1.9990
   chunk 93 optimal weight:    1.9990
   chunk 86 optimal weight:    8.9990
   chunk 44 optimal weight:    5.9990
   chunk 79 optimal weight:    2.9990
   overall best weight:    1.7786

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

Flipped N/Q/H residues before XYZ refinement:
** D 333 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
D 362 ASN
** D 572 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
D 842 GLN
D1107 GLN
D1128 GLN

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3735 r_free = 0.3735 target = 0.115216 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 33)----------------|
| r_work = 0.3313 r_free = 0.3313 target = 0.088875 restraints weight = 22854.411|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 29)----------------|
| r_work = 0.3341 r_free = 0.3341 target = 0.091385 restraints weight = 12737.192|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 26)----------------|
| r_work = 0.3355 r_free = 0.3355 target = 0.092207 restraints weight = 8417.205|
|-----------------------------------------------------------------------------|
r_work (final): 0.3342
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7795
moved from start:          0.2450

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.045   8801  Z= 0.208
  Angle     :  0.679   9.389  12005  Z= 0.347
  Chirality :  0.042   0.235   1383
  Planarity :  0.004   0.043   1465
  Dihedral  :  7.074  53.332   1710
  Min Nonbonded Distance : 2.109

Molprobity Statistics.
  All-atom Clashscore : 12.65
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  8.03 %
    Favored  : 91.97 %
  Rotamer:
    Outliers :  0.11 %
    Allowed  :  5.17 %
    Favored  : 94.71 %
  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: -1.81 (0.26), residues: 1046
  helix:  0.18 (0.22), residues: 534
  sheet: -3.29 (0.62), residues: 57
  loop : -2.67 (0.29), residues: 455

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.012   0.001   TRP D 651 
 HIS   0.002   0.001   HIS G 182 
 PHE   0.029   0.002   PHE D 292 
 TYR   0.014   0.001   TYR D 468 
 ARG   0.010   0.001   ARG G  61 

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

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

  2092 Ramachandran restraints generated.
    1046 Oldfield, 0 Emsley, 1046 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2092 Ramachandran restraints generated.
    1046 Oldfield, 0 Emsley, 1046 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  251 residues out of total 926 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 250
  time to evaluate  : 1.002 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: G   80 TYR cc_start: 0.9246 (m-10) cc_final: 0.8800 (m-80)
REVERT: G  141 TYR cc_start: 0.8236 (m-10) cc_final: 0.7826 (m-10)
REVERT: G  150 THR cc_start: 0.7746 (t) cc_final: 0.7497 (t)
REVERT: G  157 LYS cc_start: 0.8180 (mmmt) cc_final: 0.7919 (tptt)
REVERT: G  175 TYR cc_start: 0.7542 (t80) cc_final: 0.7200 (t80)
REVERT: G  184 SER cc_start: 0.8960 (p) cc_final: 0.8358 (p)
REVERT: G  186 LYS cc_start: 0.8439 (ttmt) cc_final: 0.8164 (tmtt)
REVERT: D  401 MET cc_start: 0.7594 (ptp) cc_final: 0.7374 (ptp)
REVERT: D  460 LYS cc_start: 0.9140 (pttp) cc_final: 0.8855 (pttm)
REVERT: D  467 ILE cc_start: 0.9269 (mp) cc_final: 0.8927 (mp)
REVERT: D  502 MET cc_start: 0.8333 (tmm) cc_final: 0.8000 (tpp)
REVERT: D  518 MET cc_start: 0.8848 (mtm) cc_final: 0.8555 (mtm)
REVERT: D  530 MET cc_start: 0.9124 (tpp) cc_final: 0.8346 (tpp)
REVERT: D  575 PHE cc_start: 0.8876 (m-10) cc_final: 0.8124 (m-80)
REVERT: D  579 ASP cc_start: 0.8787 (m-30) cc_final: 0.8559 (m-30)
REVERT: D  595 GLU cc_start: 0.9051 (pt0) cc_final: 0.8846 (mp0)
REVERT: D  722 LEU cc_start: 0.9174 (tt) cc_final: 0.8937 (tt)
REVERT: D  753 GLN cc_start: 0.8640 (pt0) cc_final: 0.8318 (pt0)
REVERT: D  796 GLU cc_start: 0.8892 (mt-10) cc_final: 0.7887 (tm-30)
REVERT: D  805 LYS cc_start: 0.9093 (pttm) cc_final: 0.8758 (pttm)
REVERT: D  926 GLU cc_start: 0.7968 (pm20) cc_final: 0.7626 (pm20)
REVERT: D  966 TRP cc_start: 0.7815 (m100) cc_final: 0.7024 (m100)
REVERT: D 1006 ILE cc_start: 0.9020 (mp) cc_final: 0.8570 (mt)
REVERT: D 1011 TYR cc_start: 0.8852 (m-10) cc_final: 0.8619 (m-80)
REVERT: D 1051 ASN cc_start: 0.9351 (t0) cc_final: 0.9100 (t0)
REVERT: D 1126 PHE cc_start: 0.8805 (t80) cc_final: 0.8397 (t80)
REVERT: D 1129 CYS cc_start: 0.9151 (t) cc_final: 0.8934 (t)
  outliers start: 1
  outliers final: 0
  residues processed: 251
  average time/residue: 0.1983
  time to fit residues: 70.0286
Evaluate side-chains
  216 residues out of total 926 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 216
  time to evaluate  : 0.916 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 105
   random chunks:
   chunk 26 optimal weight:    4.9990
   chunk 57 optimal weight:    3.9990
   chunk 101 optimal weight:    0.4980
   chunk 11 optimal weight:    3.9990
   chunk 65 optimal weight:    6.9990
   chunk 27 optimal weight:    0.9990
   chunk 37 optimal weight:    8.9990
   chunk 52 optimal weight:    6.9990
   chunk 39 optimal weight:    5.9990
   chunk 67 optimal weight:    5.9990
   chunk 31 optimal weight:   10.0000
   overall best weight:    2.8988

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

Flipped N/Q/H residues before XYZ refinement:
D 362 ASN
D 572 ASN
D 842 GLN
D1128 GLN

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3730 r_free = 0.3730 target = 0.114841 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 34)----------------|
| r_work = 0.3300 r_free = 0.3300 target = 0.088545 restraints weight = 22646.834|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 26)----------------|
| r_work = 0.3338 r_free = 0.3338 target = 0.091012 restraints weight = 11687.481|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 30)----------------|
| r_work = 0.3368 r_free = 0.3368 target = 0.092982 restraints weight = 7611.798|
|-----------------------------------------------------------------------------|
r_work (final): 0.3353
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7769
moved from start:          0.2651

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.046   8801  Z= 0.251
  Angle     :  0.686   9.222  12005  Z= 0.351
  Chirality :  0.042   0.224   1383
  Planarity :  0.004   0.045   1465
  Dihedral  :  7.113  52.895   1710
  Min Nonbonded Distance : 2.062

Molprobity Statistics.
  All-atom Clashscore : 13.59
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  8.80 %
    Favored  : 91.20 %
  Rotamer:
    Outliers :  0.11 %
    Allowed  :  4.72 %
    Favored  : 95.16 %
  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: -1.58 (0.26), residues: 1046
  helix:  0.40 (0.23), residues: 527
  sheet: -3.07 (0.65), residues: 51
  loop : -2.58 (0.29), residues: 468

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.014   0.001   TRP D 651 
 HIS   0.003   0.001   HIS D 941 
 PHE   0.018   0.002   PHE D 455 
 TYR   0.018   0.001   TYR D 499 
 ARG   0.010   0.000   ARG G  61 

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

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

  2092 Ramachandran restraints generated.
    1046 Oldfield, 0 Emsley, 1046 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2092 Ramachandran restraints generated.
    1046 Oldfield, 0 Emsley, 1046 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  250 residues out of total 926 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 249
  time to evaluate  : 0.903 
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: G   80 TYR cc_start: 0.9297 (m-10) cc_final: 0.9008 (m-10)
REVERT: G  141 TYR cc_start: 0.8192 (m-10) cc_final: 0.7749 (m-10)
REVERT: G  150 THR cc_start: 0.7860 (t) cc_final: 0.7572 (t)
REVERT: G  175 TYR cc_start: 0.7659 (t80) cc_final: 0.7409 (t80)
REVERT: G  186 LYS cc_start: 0.8393 (ttmt) cc_final: 0.8019 (tmtt)
REVERT: D  195 MET cc_start: 0.8398 (mmt) cc_final: 0.8184 (mmp)
REVERT: D  460 LYS cc_start: 0.9128 (pttp) cc_final: 0.8794 (pttm)
REVERT: D  502 MET cc_start: 0.8396 (tmm) cc_final: 0.8003 (tmm)
REVERT: D  518 MET cc_start: 0.8832 (mtm) cc_final: 0.8510 (mtt)
REVERT: D  530 MET cc_start: 0.9065 (tpp) cc_final: 0.8256 (tpp)
REVERT: D  575 PHE cc_start: 0.8879 (m-10) cc_final: 0.8144 (m-80)
REVERT: D  579 ASP cc_start: 0.8701 (m-30) cc_final: 0.8450 (m-30)
REVERT: D  722 LEU cc_start: 0.9184 (tt) cc_final: 0.8963 (tt)
REVERT: D  753 GLN cc_start: 0.8685 (pt0) cc_final: 0.8351 (pt0)
REVERT: D  796 GLU cc_start: 0.9027 (mt-10) cc_final: 0.8710 (mp0)
REVERT: D  805 LYS cc_start: 0.9198 (pttm) cc_final: 0.8986 (pttm)
REVERT: D  812 LEU cc_start: 0.9308 (pp) cc_final: 0.8617 (pp)
REVERT: D  926 GLU cc_start: 0.7988 (pm20) cc_final: 0.7613 (pm20)
REVERT: D 1006 ILE cc_start: 0.9068 (mp) cc_final: 0.8672 (mt)
REVERT: D 1011 TYR cc_start: 0.8934 (m-10) cc_final: 0.8540 (m-80)
REVERT: D 1126 PHE cc_start: 0.8839 (t80) cc_final: 0.8426 (t80)
  outliers start: 1
  outliers final: 0
  residues processed: 249
  average time/residue: 0.2076
  time to fit residues: 72.1854
Evaluate side-chains
  208 residues out of total 926 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 208
  time to evaluate  : 0.913 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 105
   random chunks:
   chunk 99 optimal weight:   10.0000
   chunk 101 optimal weight:    6.9990
   chunk 12 optimal weight:    7.9990
   chunk 63 optimal weight:   10.0000
   chunk 22 optimal weight:    0.9980
   chunk 102 optimal weight:    0.0270
   chunk 85 optimal weight:    1.9990
   chunk 103 optimal weight:    4.9990
   chunk 45 optimal weight:    0.9980
   chunk 87 optimal weight:    1.9990
   chunk 28 optimal weight:    4.9990
   overall best weight:    1.2042

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

Flipped N/Q/H residues before XYZ refinement:
D 362 ASN
D 572 ASN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3769 r_free = 0.3769 target = 0.117585 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 32)----------------|
| r_work = 0.3364 r_free = 0.3364 target = 0.092184 restraints weight = 22396.879|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 26)----------------|
| r_work = 0.3394 r_free = 0.3394 target = 0.094503 restraints weight = 10787.082|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 24)----------------|
| r_work = 0.3403 r_free = 0.3403 target = 0.095223 restraints weight = 7401.770|
|-----------------------------------------------------------------------------|
r_work (final): 0.3391
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7746
moved from start:          0.3133

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.045   8801  Z= 0.184
  Angle     :  0.665  11.371  12005  Z= 0.338
  Chirality :  0.041   0.232   1383
  Planarity :  0.004   0.048   1465
  Dihedral  :  6.817  53.780   1710
  Min Nonbonded Distance : 2.071

Molprobity Statistics.
  All-atom Clashscore : 11.18
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  7.93 %
    Favored  : 92.07 %
  Rotamer:
    Outliers :  0.11 %
    Allowed  :  3.94 %
    Favored  : 95.95 %
  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: -1.32 (0.26), residues: 1046
  helix:  0.67 (0.23), residues: 519
  sheet: -3.05 (0.63), residues: 51
  loop : -2.47 (0.28), residues: 476

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.013   0.001   TRP D 651 
 HIS   0.002   0.000   HIS G 180 
 PHE   0.031   0.001   PHE D 996 
 TYR   0.012   0.001   TYR D 734 
 ARG   0.002   0.000   ARG D 331 

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

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

  2092 Ramachandran restraints generated.
    1046 Oldfield, 0 Emsley, 1046 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2092 Ramachandran restraints generated.
    1046 Oldfield, 0 Emsley, 1046 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  250 residues out of total 926 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 249
  time to evaluate  : 0.932 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: G   63 GLU cc_start: 0.8653 (tp30) cc_final: 0.8173 (tp30)
REVERT: G   80 TYR cc_start: 0.9238 (m-10) cc_final: 0.8926 (m-10)
REVERT: G   98 MET cc_start: 0.8984 (ptt) cc_final: 0.8594 (ptt)
REVERT: G  102 CYS cc_start: 0.8891 (t) cc_final: 0.7735 (t)
REVERT: G  141 TYR cc_start: 0.8092 (m-10) cc_final: 0.7825 (m-10)
REVERT: G  150 THR cc_start: 0.7959 (t) cc_final: 0.7597 (t)
REVERT: D  460 LYS cc_start: 0.9096 (pttp) cc_final: 0.8764 (pttm)
REVERT: D  502 MET cc_start: 0.8290 (tmm) cc_final: 0.7926 (tmm)
REVERT: D  518 MET cc_start: 0.8800 (mtm) cc_final: 0.8472 (mtt)
REVERT: D  530 MET cc_start: 0.9113 (tpp) cc_final: 0.8282 (tpp)
REVERT: D  575 PHE cc_start: 0.8859 (m-10) cc_final: 0.8142 (m-80)
REVERT: D  579 ASP cc_start: 0.8647 (m-30) cc_final: 0.8415 (m-30)
REVERT: D  595 GLU cc_start: 0.9016 (mp0) cc_final: 0.8516 (mp0)
REVERT: D  747 LEU cc_start: 0.9082 (mm) cc_final: 0.8855 (mm)
REVERT: D  796 GLU cc_start: 0.8934 (mt-10) cc_final: 0.7922 (tm-30)
REVERT: D  805 LYS cc_start: 0.9156 (pttm) cc_final: 0.8804 (pttm)
REVERT: D  926 GLU cc_start: 0.7920 (pm20) cc_final: 0.7585 (pm20)
REVERT: D  966 TRP cc_start: 0.7717 (m100) cc_final: 0.6963 (m100)
REVERT: D  986 ILE cc_start: 0.9252 (tp) cc_final: 0.9038 (tp)
REVERT: D 1011 TYR cc_start: 0.8957 (m-10) cc_final: 0.8554 (m-80)
REVERT: D 1051 ASN cc_start: 0.9317 (t0) cc_final: 0.9062 (t0)
REVERT: D 1126 PHE cc_start: 0.8826 (t80) cc_final: 0.8399 (t80)
  outliers start: 1
  outliers final: 0
  residues processed: 249
  average time/residue: 0.1866
  time to fit residues: 65.2032
Evaluate side-chains
  216 residues out of total 926 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 216
  time to evaluate  : 0.923 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 105
   random chunks:
   chunk 11 optimal weight:   20.0000
   chunk 3 optimal weight:    9.9990
   chunk 72 optimal weight:    0.7980
   chunk 58 optimal weight:    0.0670
   chunk 16 optimal weight:    6.9990
   chunk 60 optimal weight:   20.0000
   chunk 101 optimal weight:    0.7980
   chunk 53 optimal weight:    9.9990
   chunk 82 optimal weight:    9.9990
   chunk 79 optimal weight:    5.9990
   chunk 45 optimal weight:    5.9990
   overall best weight:    2.7322

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

Flipped N/Q/H residues before XYZ refinement:
D 362 ASN
D 363 ASN
D 572 ASN
** D 644 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3732 r_free = 0.3732 target = 0.114972 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 34)----------------|
| r_work = 0.3315 r_free = 0.3315 target = 0.089145 restraints weight = 22269.815|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 32)----------------|
| r_work = 0.3344 r_free = 0.3344 target = 0.091212 restraints weight = 11094.595|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 36)----------------|
| r_work = 0.3372 r_free = 0.3372 target = 0.092888 restraints weight = 7767.980|
|-----------------------------------------------------------------------------|
r_work (final): 0.3358
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7764
moved from start:          0.3236

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.044   8801  Z= 0.240
  Angle     :  0.695  10.648  12005  Z= 0.355
  Chirality :  0.042   0.242   1383
  Planarity :  0.004   0.044   1465
  Dihedral  :  6.941  54.629   1710
  Min Nonbonded Distance : 2.057

Molprobity Statistics.
  All-atom Clashscore : 12.54
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  9.27 %
    Favored  : 90.73 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  3.04 %
    Favored  : 96.96 %
  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: -1.31 (0.26), residues: 1046
  helix:  0.51 (0.23), residues: 527
  sheet: -2.82 (0.65), residues: 49
  loop : -2.33 (0.29), residues: 470

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.013   0.001   TRP D 651 
 HIS   0.008   0.001   HIS D1055 
 PHE   0.028   0.002   PHE D 996 
 TYR   0.021   0.001   TYR D 499 
 ARG   0.005   0.000   ARG D 329 

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

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

  2092 Ramachandran restraints generated.
    1046 Oldfield, 0 Emsley, 1046 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2092 Ramachandran restraints generated.
    1046 Oldfield, 0 Emsley, 1046 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  246 residues out of total 926 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 246
  time to evaluate  : 0.945 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: G   63 GLU cc_start: 0.8758 (tp30) cc_final: 0.8217 (tp30)
REVERT: G   80 TYR cc_start: 0.9263 (m-10) cc_final: 0.8934 (m-10)
REVERT: G   98 MET cc_start: 0.8993 (ptt) cc_final: 0.8609 (ptt)
REVERT: G  102 CYS cc_start: 0.8956 (t) cc_final: 0.7952 (t)
REVERT: G  141 TYR cc_start: 0.8151 (m-10) cc_final: 0.7802 (m-10)
REVERT: G  150 THR cc_start: 0.7897 (t) cc_final: 0.7505 (t)
REVERT: G  175 TYR cc_start: 0.7613 (t80) cc_final: 0.7158 (t80)
REVERT: D  218 ASP cc_start: 0.8580 (m-30) cc_final: 0.8351 (m-30)
REVERT: D  460 LYS cc_start: 0.9161 (pttp) cc_final: 0.8838 (pttm)
REVERT: D  502 MET cc_start: 0.8254 (tmm) cc_final: 0.7873 (tmm)
REVERT: D  518 MET cc_start: 0.8841 (mtm) cc_final: 0.8511 (mtt)
REVERT: D  530 MET cc_start: 0.9097 (tpp) cc_final: 0.8378 (tpp)
REVERT: D  575 PHE cc_start: 0.8868 (m-10) cc_final: 0.8160 (m-80)
REVERT: D  579 ASP cc_start: 0.8680 (m-30) cc_final: 0.8422 (m-30)
REVERT: D  595 GLU cc_start: 0.9014 (mp0) cc_final: 0.8463 (mp0)
REVERT: D  753 GLN cc_start: 0.8653 (pm20) cc_final: 0.8449 (pt0)
REVERT: D  778 HIS cc_start: 0.8646 (t70) cc_final: 0.8426 (t-90)
REVERT: D  796 GLU cc_start: 0.8992 (mt-10) cc_final: 0.8007 (tm-30)
REVERT: D  926 GLU cc_start: 0.8001 (pm20) cc_final: 0.7633 (pm20)
REVERT: D  966 TRP cc_start: 0.7931 (m100) cc_final: 0.7182 (m100)
REVERT: D 1011 TYR cc_start: 0.9085 (m-10) cc_final: 0.8645 (m-80)
REVERT: D 1126 PHE cc_start: 0.8811 (t80) cc_final: 0.8501 (t80)
  outliers start: 0
  outliers final: 0
  residues processed: 246
  average time/residue: 0.1858
  time to fit residues: 65.2033
Evaluate side-chains
  204 residues out of total 926 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 204
  time to evaluate  : 0.915 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 105
   random chunks:
   chunk 82 optimal weight:    7.9990
   chunk 79 optimal weight:    2.9990
   chunk 87 optimal weight:    4.9990
   chunk 80 optimal weight:    7.9990
   chunk 74 optimal weight:    9.9990
   chunk 99 optimal weight:    5.9990
   chunk 23 optimal weight:    7.9990
   chunk 72 optimal weight:   10.0000
   chunk 78 optimal weight:    8.9990
   chunk 59 optimal weight:    3.9990
   chunk 11 optimal weight:    9.9990
   overall best weight:    5.1990

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

Flipped N/Q/H residues before XYZ refinement:
D 362 ASN
D 363 ASN
D 572 ASN
D 778 HIS

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3669 r_free = 0.3669 target = 0.110999 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 31)----------------|
| r_work = 0.3252 r_free = 0.3252 target = 0.085394 restraints weight = 23195.570|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 25)----------------|
| r_work = 0.3265 r_free = 0.3265 target = 0.086812 restraints weight = 12293.010|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 27)----------------|
| r_work = 0.3281 r_free = 0.3281 target = 0.087779 restraints weight = 8664.410|
|-----------------------------------------------------------------------------|
r_work (final): 0.3269
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7862
moved from start:          0.3083

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.006   0.076   8801  Z= 0.372
  Angle     :  0.779  10.090  12005  Z= 0.403
  Chirality :  0.045   0.246   1383
  Planarity :  0.005   0.045   1465
  Dihedral  :  7.521  57.170   1710
  Min Nonbonded Distance : 2.042

Molprobity Statistics.
  All-atom Clashscore : 15.07
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  : 10.13 %
    Favored  : 89.87 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  3.60 %
    Favored  : 96.40 %
  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: -1.54 (0.26), residues: 1046
  helix:  0.28 (0.22), residues: 532
  sheet: -3.14 (0.64), residues: 51
  loop : -2.37 (0.29), residues: 463

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.017   0.002   TRP D 651 
 HIS   0.006   0.001   HIS D1055 
 PHE   0.021   0.002   PHE D1122 
 TYR   0.015   0.002   TYR D 499 
 ARG   0.006   0.000   ARG D 329 

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

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

  2092 Ramachandran restraints generated.
    1046 Oldfield, 0 Emsley, 1046 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2092 Ramachandran restraints generated.
    1046 Oldfield, 0 Emsley, 1046 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  240 residues out of total 926 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 240
  time to evaluate  : 0.948 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: G   80 TYR cc_start: 0.9279 (m-10) cc_final: 0.9048 (m-10)
REVERT: G   98 MET cc_start: 0.9050 (ptt) cc_final: 0.8650 (ptt)
REVERT: G  102 CYS cc_start: 0.8969 (t) cc_final: 0.8029 (t)
REVERT: G  139 LEU cc_start: 0.8377 (mm) cc_final: 0.8055 (mm)
REVERT: G  141 TYR cc_start: 0.8251 (m-10) cc_final: 0.7884 (m-10)
REVERT: G  144 ARG cc_start: 0.9088 (mmm-85) cc_final: 0.8839 (mmm-85)
REVERT: G  150 THR cc_start: 0.7842 (t) cc_final: 0.7495 (t)
REVERT: G  175 TYR cc_start: 0.7593 (t80) cc_final: 0.7138 (t80)
REVERT: D  218 ASP cc_start: 0.8613 (m-30) cc_final: 0.8342 (m-30)
REVERT: D  287 HIS cc_start: 0.7884 (t-90) cc_final: 0.7666 (t-90)
REVERT: D  460 LYS cc_start: 0.9180 (pttp) cc_final: 0.8950 (pttm)
REVERT: D  502 MET cc_start: 0.8292 (tmm) cc_final: 0.7795 (tpp)
REVERT: D  530 MET cc_start: 0.9082 (tpp) cc_final: 0.8308 (tpp)
REVERT: D  575 PHE cc_start: 0.8876 (m-10) cc_final: 0.8672 (m-10)
REVERT: D  595 GLU cc_start: 0.9055 (mp0) cc_final: 0.8467 (mp0)
REVERT: D  648 MET cc_start: 0.9266 (tpt) cc_final: 0.8963 (tpp)
REVERT: D  722 LEU cc_start: 0.9176 (tt) cc_final: 0.8908 (tp)
REVERT: D  796 GLU cc_start: 0.9019 (mt-10) cc_final: 0.7957 (tm-30)
REVERT: D  926 GLU cc_start: 0.8123 (pm20) cc_final: 0.7727 (pm20)
REVERT: D 1011 TYR cc_start: 0.9120 (m-10) cc_final: 0.8717 (m-80)
REVERT: D 1052 PHE cc_start: 0.9150 (m-10) cc_final: 0.8918 (m-10)
REVERT: D 1126 PHE cc_start: 0.8858 (t80) cc_final: 0.8332 (t80)
  outliers start: 0
  outliers final: 0
  residues processed: 240
  average time/residue: 0.1819
  time to fit residues: 61.9907
Evaluate side-chains
  205 residues out of total 926 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 205
  time to evaluate  : 1.020 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 105
   random chunks:
   chunk 102 optimal weight:    0.8980
   chunk 7 optimal weight:    4.9990
   chunk 74 optimal weight:    2.9990
   chunk 91 optimal weight:    4.9990
   chunk 48 optimal weight:    5.9990
   chunk 46 optimal weight:    7.9990
   chunk 18 optimal weight:    0.0970
   chunk 47 optimal weight:    3.9990
   chunk 9 optimal weight:   40.0000
   chunk 43 optimal weight:    0.7980
   chunk 23 optimal weight:    0.4980
   overall best weight:    1.0580

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

Flipped N/Q/H residues before XYZ refinement:
D 362 ASN
D 363 ASN
D 572 ASN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3774 r_free = 0.3774 target = 0.117936 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 34)----------------|
| r_work = 0.3361 r_free = 0.3361 target = 0.091968 restraints weight = 22925.509|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 24)----------------|
| r_work = 0.3398 r_free = 0.3398 target = 0.094480 restraints weight = 10981.552|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 34)----------------|
| r_work = 0.3428 r_free = 0.3428 target = 0.096384 restraints weight = 7591.532|
|-----------------------------------------------------------------------------|
r_work (final): 0.3417
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7732
moved from start:          0.3546

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.038   8801  Z= 0.195
  Angle     :  0.715  10.475  12005  Z= 0.361
  Chirality :  0.042   0.237   1383
  Planarity :  0.004   0.044   1465
  Dihedral  :  7.015  56.622   1710
  Min Nonbonded Distance : 2.071

Molprobity Statistics.
  All-atom Clashscore : 10.71
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  7.65 %
    Favored  : 92.35 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  1.35 %
    Favored  : 98.65 %
  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: -1.26 (0.26), residues: 1046
  helix:  0.54 (0.23), residues: 529
  sheet: -2.98 (0.64), residues: 49
  loop : -2.29 (0.29), residues: 468

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.016   0.001   TRP D 651 
 HIS   0.008   0.001   HIS D 692 
 PHE   0.033   0.002   PHE D 996 
 TYR   0.024   0.001   TYR D 499 
 ARG   0.003   0.000   ARG D 329 

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

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

  2092 Ramachandran restraints generated.
    1046 Oldfield, 0 Emsley, 1046 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2092 Ramachandran restraints generated.
    1046 Oldfield, 0 Emsley, 1046 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  248 residues out of total 926 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 248
  time to evaluate  : 0.882 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: G   61 ARG cc_start: 0.8902 (pmt-80) cc_final: 0.8004 (pmt-80)
REVERT: G   80 TYR cc_start: 0.9197 (m-10) cc_final: 0.8867 (m-10)
REVERT: G   98 MET cc_start: 0.9052 (ptt) cc_final: 0.8646 (ptt)
REVERT: G  100 GLN cc_start: 0.6994 (tm-30) cc_final: 0.6784 (tm-30)
REVERT: G  102 CYS cc_start: 0.8906 (t) cc_final: 0.7799 (t)
REVERT: G  139 LEU cc_start: 0.8272 (mm) cc_final: 0.7934 (mm)
REVERT: G  141 TYR cc_start: 0.8150 (m-10) cc_final: 0.7818 (m-10)
REVERT: G  144 ARG cc_start: 0.8827 (mmm-85) cc_final: 0.8624 (mmm-85)
REVERT: G  150 THR cc_start: 0.7849 (t) cc_final: 0.7514 (t)
REVERT: G  175 TYR cc_start: 0.7580 (t80) cc_final: 0.7115 (t80)
REVERT: D  218 ASP cc_start: 0.8547 (m-30) cc_final: 0.8346 (m-30)
REVERT: D  401 MET cc_start: 0.7396 (ptp) cc_final: 0.7165 (ptp)
REVERT: D  460 LYS cc_start: 0.9155 (pttp) cc_final: 0.8890 (pttm)
REVERT: D  502 MET cc_start: 0.8207 (tmm) cc_final: 0.7802 (tpp)
REVERT: D  518 MET cc_start: 0.8858 (mtm) cc_final: 0.8420 (mtm)
REVERT: D  575 PHE cc_start: 0.8826 (m-10) cc_final: 0.8123 (m-80)
REVERT: D  579 ASP cc_start: 0.8673 (m-30) cc_final: 0.8457 (m-30)
REVERT: D  595 GLU cc_start: 0.9058 (mp0) cc_final: 0.8470 (mp0)
REVERT: D  648 MET cc_start: 0.9255 (tpt) cc_final: 0.9051 (tpp)
REVERT: D  796 GLU cc_start: 0.8877 (mt-10) cc_final: 0.7928 (tm-30)
REVERT: D  805 LYS cc_start: 0.9062 (pttm) cc_final: 0.8734 (pttm)
REVERT: D  926 GLU cc_start: 0.7886 (pm20) cc_final: 0.7548 (pm20)
REVERT: D  966 TRP cc_start: 0.7804 (m100) cc_final: 0.7170 (m100)
REVERT: D 1011 TYR cc_start: 0.9032 (m-10) cc_final: 0.8752 (m-80)
REVERT: D 1126 PHE cc_start: 0.9001 (t80) cc_final: 0.8450 (t80)
  outliers start: 0
  outliers final: 0
  residues processed: 248
  average time/residue: 0.1765
  time to fit residues: 62.6417
Evaluate side-chains
  212 residues out of total 926 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 212
  time to evaluate  : 1.271 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 105
   random chunks:
   chunk 64 optimal weight:    5.9990
   chunk 3 optimal weight:    8.9990
   chunk 24 optimal weight:    0.7980
   chunk 13 optimal weight:   30.0000
   chunk 36 optimal weight:    4.9990
   chunk 100 optimal weight:    1.9990
   chunk 80 optimal weight:    4.9990
   chunk 0 optimal weight:   30.0000
   chunk 18 optimal weight:    0.4980
   chunk 76 optimal weight:    0.2980
   chunk 30 optimal weight:    0.9990
   overall best weight:    0.9184

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

Flipped N/Q/H residues before XYZ refinement:
D 362 ASN
D 572 ASN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3778 r_free = 0.3778 target = 0.118534 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 49)----------------|
| r_work = 0.3345 r_free = 0.3345 target = 0.090693 restraints weight = 22532.315|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 32)----------------|
| r_work = 0.3391 r_free = 0.3391 target = 0.093565 restraints weight = 12291.811|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 45)----------------|
| r_work = 0.3422 r_free = 0.3422 target = 0.095472 restraints weight = 8255.334|
|-----------------------------------------------------------------------------|
r_work (final): 0.3409
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7723
moved from start:          0.3828

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.039   8801  Z= 0.188
  Angle     :  0.737  12.713  12005  Z= 0.367
  Chirality :  0.042   0.254   1383
  Planarity :  0.004   0.045   1465
  Dihedral  :  6.926  57.402   1710
  Min Nonbonded Distance : 2.080

Molprobity Statistics.
  All-atom Clashscore : 10.24
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  7.84 %
    Favored  : 92.16 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  0.90 %
    Favored  : 99.10 %
  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: -1.19 (0.27), residues: 1046
  helix:  0.65 (0.23), residues: 526
  sheet: -2.95 (0.65), residues: 49
  loop : -2.29 (0.29), residues: 471

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.015   0.001   TRP D 651 
 HIS   0.006   0.001   HIS D 692 
 PHE   0.019   0.002   PHE G  73 
 TYR   0.014   0.001   TYR D 974 
 ARG   0.003   0.000   ARG G  72 

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

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

  2092 Ramachandran restraints generated.
    1046 Oldfield, 0 Emsley, 1046 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2092 Ramachandran restraints generated.
    1046 Oldfield, 0 Emsley, 1046 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  244 residues out of total 926 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 244
  time to evaluate  : 0.962 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: G   61 ARG cc_start: 0.9052 (pmt-80) cc_final: 0.8620 (pmt-80)
REVERT: G   80 TYR cc_start: 0.9201 (m-10) cc_final: 0.8878 (m-10)
REVERT: G   98 MET cc_start: 0.9038 (ptt) cc_final: 0.8723 (ptt)
REVERT: G  102 CYS cc_start: 0.8967 (t) cc_final: 0.8090 (t)
REVERT: G  139 LEU cc_start: 0.8218 (mm) cc_final: 0.7994 (mm)
REVERT: G  141 TYR cc_start: 0.8088 (m-10) cc_final: 0.7758 (m-10)
REVERT: G  144 ARG cc_start: 0.8665 (mmm-85) cc_final: 0.8408 (mmm-85)
REVERT: G  150 THR cc_start: 0.7753 (t) cc_final: 0.7340 (t)
REVERT: D  218 ASP cc_start: 0.8600 (m-30) cc_final: 0.8316 (m-30)
REVERT: D  453 MET cc_start: 0.9184 (tmm) cc_final: 0.8378 (tmm)
REVERT: D  460 LYS cc_start: 0.9147 (pttp) cc_final: 0.8859 (pttm)
REVERT: D  502 MET cc_start: 0.8199 (tmm) cc_final: 0.7860 (tpp)
REVERT: D  575 PHE cc_start: 0.8810 (m-10) cc_final: 0.8455 (m-10)
REVERT: D  579 ASP cc_start: 0.8706 (m-30) cc_final: 0.8443 (m-30)
REVERT: D  595 GLU cc_start: 0.9059 (mp0) cc_final: 0.8498 (mp0)
REVERT: D  648 MET cc_start: 0.9266 (tpt) cc_final: 0.9042 (tpp)
REVERT: D  722 LEU cc_start: 0.9108 (tt) cc_final: 0.8698 (mm)
REVERT: D  747 LEU cc_start: 0.9082 (mm) cc_final: 0.8867 (mm)
REVERT: D  778 HIS cc_start: 0.8466 (t-90) cc_final: 0.8257 (t-90)
REVERT: D  796 GLU cc_start: 0.8889 (mt-10) cc_final: 0.7951 (tm-30)
REVERT: D  805 LYS cc_start: 0.9090 (pttm) cc_final: 0.8774 (pttm)
REVERT: D  895 MET cc_start: 0.8842 (tpp) cc_final: 0.8454 (mmm)
REVERT: D  926 GLU cc_start: 0.7938 (pm20) cc_final: 0.7517 (pm20)
REVERT: D  966 TRP cc_start: 0.7806 (m100) cc_final: 0.7127 (m100)
REVERT: D  986 ILE cc_start: 0.9056 (tp) cc_final: 0.8823 (tp)
REVERT: D 1011 TYR cc_start: 0.9155 (m-10) cc_final: 0.8728 (m-80)
REVERT: D 1085 MET cc_start: 0.8773 (tpp) cc_final: 0.7966 (tpp)
REVERT: D 1126 PHE cc_start: 0.8794 (t80) cc_final: 0.8274 (t80)
REVERT: D 1130 MET cc_start: 0.8880 (tmm) cc_final: 0.8519 (tmm)
  outliers start: 0
  outliers final: 0
  residues processed: 244
  average time/residue: 0.1658
  time to fit residues: 57.9759
Evaluate side-chains
  206 residues out of total 926 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 206
  time to evaluate  : 0.764 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 105
   random chunks:
   chunk 82 optimal weight:    9.9990
   chunk 45 optimal weight:    4.9990
   chunk 42 optimal weight:    7.9990
   chunk 84 optimal weight:    6.9990
   chunk 79 optimal weight:    5.9990
   chunk 36 optimal weight:    5.9990
   chunk 19 optimal weight:    6.9990
   chunk 46 optimal weight:    9.9990
   chunk 23 optimal weight:   20.0000
   chunk 69 optimal weight:   10.0000
   chunk 68 optimal weight:    0.6980
   overall best weight:    4.9388

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

Flipped N/Q/H residues before XYZ refinement:
G  50 ASN
D 362 ASN
D 363 ASN
D 388 HIS
D 572 ASN
D 779 HIS

Total number of N/Q/H flips: 6

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3686 r_free = 0.3686 target = 0.112299 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 37)----------------|
| r_work = 0.3275 r_free = 0.3275 target = 0.086628 restraints weight = 22966.775|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 25)----------------|
| r_work = 0.3292 r_free = 0.3292 target = 0.088283 restraints weight = 12198.156|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 27)----------------|
| r_work = 0.3308 r_free = 0.3308 target = 0.089272 restraints weight = 8481.649|
|-----------------------------------------------------------------------------|
r_work (final): 0.3293
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7905
moved from start:          0.3492

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.006   0.071   8801  Z= 0.363
  Angle     :  0.804  11.844  12005  Z= 0.409
  Chirality :  0.045   0.257   1383
  Planarity :  0.005   0.044   1465
  Dihedral  :  7.551  58.583   1710
  Min Nonbonded Distance : 2.039

Molprobity Statistics.
  All-atom Clashscore : 14.95
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  9.37 %
    Favored  : 90.63 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  1.24 %
    Favored  : 98.76 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 2.38 %
    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: -1.45 (0.26), residues: 1046
  helix:  0.33 (0.22), residues: 533
  sheet: -3.11 (0.65), residues: 49
  loop : -2.32 (0.29), residues: 464

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.028   0.002   TRP D 475 
 HIS   0.007   0.001   HIS D1055 
 PHE   0.042   0.003   PHE D 996 
 TYR   0.027   0.002   TYR D 499 
 ARG   0.004   0.000   ARG D 661 

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

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

  2092 Ramachandran restraints generated.
    1046 Oldfield, 0 Emsley, 1046 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2092 Ramachandran restraints generated.
    1046 Oldfield, 0 Emsley, 1046 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  236 residues out of total 926 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 236
  time to evaluate  : 0.946 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: G   61 ARG cc_start: 0.9107 (pmt-80) cc_final: 0.8343 (pmt-80)
REVERT: G   73 PHE cc_start: 0.9368 (t80) cc_final: 0.9134 (t80)
REVERT: G   80 TYR cc_start: 0.9216 (m-10) cc_final: 0.8948 (m-10)
REVERT: G   98 MET cc_start: 0.9088 (ptt) cc_final: 0.8744 (ptt)
REVERT: G  102 CYS cc_start: 0.8950 (t) cc_final: 0.7934 (t)
REVERT: G  141 TYR cc_start: 0.8286 (m-10) cc_final: 0.7918 (m-10)
REVERT: G  150 THR cc_start: 0.7833 (t) cc_final: 0.7445 (t)
REVERT: G  175 TYR cc_start: 0.7463 (t80) cc_final: 0.7138 (t80)
REVERT: D  218 ASP cc_start: 0.8536 (m-30) cc_final: 0.8325 (m-30)
REVERT: D  460 LYS cc_start: 0.9158 (pttp) cc_final: 0.8864 (pttm)
REVERT: D  502 MET cc_start: 0.8285 (tmm) cc_final: 0.7855 (tpp)
REVERT: D  575 PHE cc_start: 0.8845 (m-10) cc_final: 0.8539 (m-10)
REVERT: D  579 ASP cc_start: 0.8710 (m-30) cc_final: 0.8489 (m-30)
REVERT: D  595 GLU cc_start: 0.9018 (mp0) cc_final: 0.8452 (mp0)
REVERT: D  796 GLU cc_start: 0.8922 (mt-10) cc_final: 0.8034 (tm-30)
REVERT: D  926 GLU cc_start: 0.8009 (pm20) cc_final: 0.7730 (pm20)
REVERT: D 1011 TYR cc_start: 0.9075 (m-10) cc_final: 0.8716 (m-80)
REVERT: D 1085 MET cc_start: 0.8906 (tpp) cc_final: 0.8127 (tpp)
REVERT: D 1098 MET cc_start: 0.8720 (tpp) cc_final: 0.8418 (tpp)
REVERT: D 1126 PHE cc_start: 0.8879 (t80) cc_final: 0.8543 (t80)
REVERT: D 1128 GLN cc_start: 0.9035 (mp10) cc_final: 0.8664 (mp10)
  outliers start: 0
  outliers final: 0
  residues processed: 236
  average time/residue: 0.1753
  time to fit residues: 59.1248
Evaluate side-chains
  202 residues out of total 926 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 202
  time to evaluate  : 0.851 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 105
   random chunks:
   chunk 14 optimal weight:    8.9990
   chunk 50 optimal weight:    0.5980
   chunk 91 optimal weight:    9.9990
   chunk 40 optimal weight:    7.9990
   chunk 26 optimal weight:    0.8980
   chunk 99 optimal weight:    0.9990
   chunk 41 optimal weight:    6.9990
   chunk 52 optimal weight:    5.9990
   chunk 22 optimal weight:    0.0170
   chunk 48 optimal weight:    0.7980
   chunk 72 optimal weight:    0.0040
   overall best weight:    0.4630

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

Flipped N/Q/H residues before XYZ refinement:
G  50 ASN
D 362 ASN
D 572 ASN
D 803 ASN

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3786 r_free = 0.3786 target = 0.119246 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 34)----------------|
| r_work = 0.3386 r_free = 0.3386 target = 0.093751 restraints weight = 22630.413|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 26)----------------|
| r_work = 0.3411 r_free = 0.3411 target = 0.095526 restraints weight = 12075.854|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 30)----------------|
| r_work = 0.3443 r_free = 0.3443 target = 0.097617 restraints weight = 7866.116|
|-----------------------------------------------------------------------------|
r_work (final): 0.3433
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7728
moved from start:          0.4019

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.040   8801  Z= 0.188
  Angle     :  0.751  11.944  12005  Z= 0.372
  Chirality :  0.042   0.242   1383
  Planarity :  0.005   0.071   1465
  Dihedral  :  7.079  57.796   1710
  Min Nonbonded Distance : 2.073

Molprobity Statistics.
  All-atom Clashscore : 11.53
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  7.17 %
    Favored  : 92.83 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  1.01 %
    Favored  : 98.99 %
  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: -1.24 (0.26), residues: 1046
  helix:  0.59 (0.23), residues: 525
  sheet: -3.25 (0.62), residues: 51
  loop : -2.24 (0.29), residues: 470

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.015   0.001   TRP D1120 
 HIS   0.005   0.001   HIS D 692 
 PHE   0.022   0.002   PHE D 555 
 TYR   0.016   0.001   TYR D 499 
 ARG   0.007   0.000   ARG G  61 
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 2680.77 seconds
wall clock time: 48 minutes 59.33 seconds (2939.33 seconds total)