Starting phenix.real_space_refine
on Fri Mar 14 05:16:14 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/8dcx_27330/03_2025/8dcx_27330.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/8dcx_27330/03_2025/8dcx_27330.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=2.8
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/cci-nas-00/data/ceres_data/8dcx_27330/03_2025/8dcx_27330.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/8dcx_27330/03_2025/8dcx_27330.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/8dcx_27330/03_2025/8dcx_27330.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/8dcx_27330/03_2025/8dcx_27330.cif"
  }
  resolution = 2.8
  write_initial_geo_file = False
  refinement {
    macro_cycles = 10
  }
  qi {
    qm_restraints {
      package {
        program = *test
      }
    }
  }


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

Validating inputs
Origin is already at (0, 0, 0), no shifts will be applied
-------------------------------------------------------------------------------
Processing inputs
*****************
Set random seed
  Set to: 0
Set model cs if undefined
Decide on map wrapping
  Map wrapping is set to: False
Normalize map: mean=0, sd=1
  Input map: mean=   0.000 sd=   1.000
Set stop_for_unknowns flag
  Set to: True
Assert model is a single copy model
Assert all atoms have isotropic ADPs
Construct map_model_manager
Extract box with map and model
Check model and map are aligned
Set scattering table
  Set to: electron
  Number of scattering types: 4
    Type Number    sf(0)   Gaussians
     S      70      5.16       5
     C    6141      2.51       5
     N    1655      2.21       5
     O    1761      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 7 residue(s): 0.03s

  Monomer Library directory:
    "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5624/modules/chem_data/mon_lib"
  Total number of atoms: 9627
  Number of models: 1
  Model: ""
    Number of chains: 2
    Chain: "A"
      Number of atoms: 7621
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 930, 7621
          Classifications: {'peptide': 930}
          Link IDs: {'PCIS': 1, 'PTRANS': 42, 'TRANS': 886}
          Chain breaks: 10
    Chain: "B"
      Number of atoms: 2006
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 236, 2006
          Classifications: {'peptide': 236}
          Link IDs: {'PCIS': 1, 'PTRANS': 3, 'TRANS': 231}
          Chain breaks: 1
  Time building chain proxies: 5.83, per 1000 atoms: 0.61
  Number of scatterers: 9627
  At special positions: 0
  Unit cell: (84.032, 132.288, 108.16, 90, 90, 90)
  Space group: P 1 (No. 1)
  Number of sites at special positions: 0
  Number of scattering types: 4
    Type Number    sf(0)
     S      70     16.00
     O    1761      8.00
     N    1655      7.00
     C    6141      6.00
    sf(0) = scattering factor at diffraction angle 0.

  Number of disulfides: simple=0, symmetry=0

  Automatic linking
    Parameters for automatic linking
      Linking & cutoffs
        Metal                : Auto  - 3.00
        Amino acid           : True  - 1.90
        Carbohydrate         : True  - 1.99
        Ligands              : True  - 1.99
        Small molecules      : False - 1.98
        Amino acid - RNA/DNA : False
      
  Number of custom bonds: simple=0, symmetry=0
  Time building additional restraints: 2.52
  Conformation dependent library (CDL) restraints added in 1.1 seconds
  

  2280 Ramachandran restraints generated.
    1140 Oldfield, 0 Emsley, 1140 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  2238

  Finding SS restraints...
    Secondary structure from input PDB file:
      42 helices and 11 sheets defined
      49.8% alpha, 11.1% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 1.04
  Creating SS restraints...
    Processing helix  chain 'A' and resid 41 through 56
      removed outlier: 3.999A  pdb=" N   ILE A  45 " --> pdb=" O   THR A  41 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 64 through 68
    Processing helix  chain 'A' and resid 88 through 92
    Processing helix  chain 'A' and resid 108 through 122
    Processing helix  chain 'A' and resid 125 through 131
      removed outlier: 3.672A  pdb=" N   MET A 130 " --> pdb=" O   GLU A 127 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 133 through 155
      removed outlier: 3.646A  pdb=" N   GLN A 137 " --> pdb=" O   ASP A 133 " (cutoff:3.500A)
      removed outlier: 3.876A  pdb=" N   LEU A 144 " --> pdb=" O   ARG A 140 " (cutoff:3.500A)
      removed outlier: 4.171A  pdb=" N   ASN A 145 " --> pdb=" O   ARG A 141 " (cutoff:3.500A)
      removed outlier: 3.736A  pdb=" N   VAL A 146 " --> pdb=" O   ASN A 142 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 159 through 167
      removed outlier: 3.662A  pdb=" N   ALA A 163 " --> pdb=" O   PRO A 159 " (cutoff:3.500A)
      removed outlier: 3.578A  pdb=" N   TYR A 167 " --> pdb=" O   ALA A 163 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 181 through 189
      removed outlier: 4.117A  pdb=" N   LYS A 184 " --> pdb=" O   ILE A 181 " (cutoff:3.500A)
      removed outlier: 5.044A  pdb=" N   ASP A 186 " --> pdb=" O   ASN A 183 " (cutoff:3.500A)
      removed outlier: 6.775A  pdb=" N   LYS A 187 " --> pdb=" O   LYS A 184 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 216 through 226
      removed outlier: 3.755A  pdb=" N   VAL A 220 " --> pdb=" O   VAL A 216 " (cutoff:3.500A)
      removed outlier: 3.754A  pdb=" N   ARG A 226 " --> pdb=" O   ALA A 222 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 272 through 280
    Processing helix  chain 'A' and resid 289 through 297
      removed outlier: 4.045A  pdb=" N   LEU A 293 " --> pdb=" O   ALA A 289 " (cutoff:3.500A)
      removed outlier: 3.743A  pdb=" N   LEU A 297 " --> pdb=" O   LEU A 293 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 326 through 330
      removed outlier: 3.909A  pdb=" N   VAL A 329 " --> pdb=" O   SER A 326 " (cutoff:3.500A)
      removed outlier: 3.869A  pdb=" N   ILE A 330 " --> pdb=" O   LEU A 327 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'A' and resid 326 through 330'
    Processing helix  chain 'A' and resid 488 through 494
      removed outlier: 4.095A  pdb=" N   ILE A 492 " --> pdb=" O   ASP A 488 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 528 through 537
    Processing helix  chain 'A' and resid 544 through 554
    Processing helix  chain 'A' and resid 555 through 563
      removed outlier: 3.930A  pdb=" N   VAL A 559 " --> pdb=" O   HIS A 556 " (cutoff:3.500A)
      removed outlier: 3.596A  pdb=" N   THR A 560 " --> pdb=" O   TYR A 557 " (cutoff:3.500A)
      Proline residue:  A 562  - end of helix
    Processing helix  chain 'A' and resid 564 through 570
      removed outlier: 3.795A  pdb=" N   LEU A 569 " --> pdb=" O   LEU A 565 " (cutoff:3.500A)
      removed outlier: 4.153A  pdb=" N   LEU A 570 " --> pdb=" O   PRO A 566 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 576 through 589
      removed outlier: 3.557A  pdb=" N   ASP A 589 " --> pdb=" O   CYS A 585 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 597 through 603
      removed outlier: 3.777A  pdb=" N   LEU A 602 " --> pdb=" O   MET A 599 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 608 through 623
    Processing helix  chain 'A' and resid 624 through 638
      removed outlier: 5.327A  pdb=" N   ILE A 633 " --> pdb=" O   SER A 629 " (cutoff:3.500A)
      removed outlier: 5.930A  pdb=" N   GLN A 634 " --> pdb=" O   GLN A 630 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 647 through 658
      removed outlier: 3.579A  pdb=" N   ARG A 651 " --> pdb=" O   ASN A 647 " (cutoff:3.500A)
      removed outlier: 3.799A  pdb=" N   LYS A 655 " --> pdb=" O   ARG A 651 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 660 through 673
    Processing helix  chain 'A' and resid 680 through 695
    Processing helix  chain 'A' and resid 697 through 718
      removed outlier: 4.111A  pdb=" N   HIS A 701 " --> pdb=" O   MET A 697 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 741 through 748
      removed outlier: 4.173A  pdb=" N   MET A 745 " --> pdb=" O   ARG A 741 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 807 through 828
    Processing helix  chain 'A' and resid 857 through 864
    Processing helix  chain 'A' and resid 875 through 885
      removed outlier: 4.216A  pdb=" N   ASN A 885 " --> pdb=" O   LEU A 881 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 886 through 889
      removed outlier: 4.086A  pdb=" N   ILE A 889 " --> pdb=" O   LYS A 886 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'A' and resid 886 through 889'
    Processing helix  chain 'A' and resid 890 through 911
    Processing helix  chain 'A' and resid 957 through 965
      removed outlier: 3.746A  pdb=" N   LEU A 961 " --> pdb=" O   THR A 957 " (cutoff:3.500A)
      removed outlier: 4.079A  pdb=" N   VAL A 963 " --> pdb=" O   ASP A 959 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 974 through 993
      removed outlier: 3.662A  pdb=" N   GLN A 993 " --> pdb=" O   LEU A 989 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 994 through 1005
      removed outlier: 4.135A  pdb=" N   PHE A 998 " --> pdb=" O   HIS A 994 " (cutoff:3.500A)
      removed outlier: 3.871A  pdb=" N   MET A1005 " --> pdb=" O   LEU A1001 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 1006 through 1009
      removed outlier: 4.323A  pdb=" N   GLY A1009 " --> pdb=" O   LEU A1006 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'A' and resid 1006 through 1009'
    Processing helix  chain 'A' and resid 1015 through 1018
    Processing helix  chain 'A' and resid 1019 through 1026
      removed outlier: 3.752A  pdb=" N   ARG A1023 " --> pdb=" O   ILE A1019 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 1031 through 1048
    Processing helix  chain 'B' and resid 339 through 347
    Processing helix  chain 'B' and resid 400 through 410
    Processing helix  chain 'B' and resid 454 through 516
      removed outlier: 3.590A  pdb=" N   GLN B 475 " --> pdb=" O   THR B 471 " (cutoff:3.500A)
      removed outlier: 5.532A  pdb=" N   GLU B 507 " --> pdb=" O   ARG B 503 " (cutoff:3.500A)
      removed outlier: 5.368A  pdb=" N   TYR B 508 " --> pdb=" O   TYR B 504 " (cutoff:3.500A)
      removed outlier: 3.607A  pdb=" N   GLY B 516 " --> pdb=" O   PHE B 512 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 518 through 582
      Proline residue:  B 568  - end of helix
    Processing sheet with id=AA1, first strand: chain 'A' and resid 79 through 81
    Processing sheet with id=AA2, first strand: chain 'A' and resid 205 through 211
      removed outlier: 8.647A  pdb=" N   LEU A 285 " --> pdb=" O   ILE A 191 " (cutoff:3.500A)
      removed outlier: 6.081A  pdb=" N   VAL A 193 " --> pdb=" O   LEU A 285 " (cutoff:3.500A)
      removed outlier: 7.560A  pdb=" N   LEU A 287 " --> pdb=" O   VAL A 193 " (cutoff:3.500A)
      removed outlier: 7.108A  pdb=" N   TRP A 195 " --> pdb=" O   LEU A 287 " (cutoff:3.500A)
    Processing sheet with id=AA3, first strand: chain 'A' and resid 382 through 392
      removed outlier: 6.278A  pdb=" N   LEU A 339 " --> pdb=" O   TRP A 383 " (cutoff:3.500A)
      removed outlier: 5.754A  pdb=" N   GLU A 385 " --> pdb=" O   LYS A 337 " (cutoff:3.500A)
      removed outlier: 4.217A  pdb=" N   LYS A 337 " --> pdb=" O   GLU A 385 " (cutoff:3.500A)
      removed outlier: 5.964A  pdb=" N   LEU A 387 " --> pdb=" O   ARG A 335 " (cutoff:3.500A)
      removed outlier: 4.290A  pdb=" N   ARG A 335 " --> pdb=" O   LEU A 387 " (cutoff:3.500A)
      removed outlier: 6.544A  pdb=" N   TYR A 389 " --> pdb=" O   ALA A 333 " (cutoff:3.500A)
      removed outlier: 6.944A  pdb=" N   ALA A 333 " --> pdb=" O   TYR A 389 " (cutoff:3.500A)
      removed outlier: 4.985A  pdb=" N   ILE A 338 " --> pdb=" O   GLU A 476 " (cutoff:3.500A)
      removed outlier: 6.537A  pdb=" N   GLU A 476 " --> pdb=" O   ILE A 338 " (cutoff:3.500A)
    Processing sheet with id=AA4, first strand: chain 'A' and resid 365 through 366
      removed outlier: 3.579A  pdb=" N   GLU A 365 " --> pdb=" O   HIS A 362 " (cutoff:3.500A)
    Processing sheet with id=AA5, first strand: chain 'A' and resid 371 through 372
      removed outlier: 3.557A  pdb=" N   THR A 358 " --> pdb=" O   VAL A 371 " (cutoff:3.500A)
    Processing sheet with id=AA6, first strand: chain 'A' and resid 751 through 753
      removed outlier: 4.236A  pdb=" N   PHE A 751 " --> pdb=" O   LEU A 761 " (cutoff:3.500A)
      removed outlier: 5.603A  pdb=" N   HIS A 759 " --> pdb=" O   SER A 753 " (cutoff:3.500A)
    Processing sheet with id=AA7, first strand: chain 'A' and resid 779 through 782
    Processing sheet with id=AA8, first strand: chain 'A' and resid 854 through 856
    Processing sheet with id=AA9, first strand: chain 'B' and resid 354 through 355
    Processing sheet with id=AB1, first strand: chain 'B' and resid 357 through 358
    Processing sheet with id=AB2, first strand: chain 'B' and resid 384 through 386

    449 hydrogen bonds defined for protein.
    1260 hydrogen bond angles defined for protein.
    Restraints generated for nucleic acids:
      0 hydrogen bonds
      0 hydrogen bond angles
      0 basepair planarities
      0 basepair parallelities
      0 stacking parallelities
  Total time for adding SS restraints: 3.29

  Time building geometry restraints manager: 3.00 seconds

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

  Histogram of bond lengths:
        1.22 -     1.34: 3137
        1.34 -     1.46: 1907
        1.46 -     1.58: 4673
        1.58 -     1.69: 1
        1.69 -     1.81: 110
  Bond restraints: 9828
  Sorted by residual:
  bond pdb=" CB  PRO B 427 "
       pdb=" CG  PRO B 427 "
    ideal  model  delta    sigma   weight residual
    1.492  1.589 -0.097 5.00e-02 4.00e+02 3.77e+00
  bond pdb=" N   ASP B 387 "
       pdb=" CA  ASP B 387 "
    ideal  model  delta    sigma   weight residual
    1.457  1.476 -0.019 1.29e-02 6.01e+03 2.11e+00
  bond pdb=" CG  PRO B 395 "
       pdb=" CD  PRO B 395 "
    ideal  model  delta    sigma   weight residual
    1.512  1.487  0.025 2.70e-02 1.37e+03 8.64e-01
  bond pdb=" CG1 ILE A 894 "
       pdb=" CD1 ILE A 894 "
    ideal  model  delta    sigma   weight residual
    1.513  1.477  0.036 3.90e-02 6.57e+02 8.61e-01
  bond pdb=" CG  MET A1004 "
       pdb=" SD  MET A1004 "
    ideal  model  delta    sigma   weight residual
    1.803  1.780  0.023 2.50e-02 1.60e+03 8.46e-01
  ... (remaining 9823 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     1.62: 12896
        1.62 -     3.24: 303
        3.24 -     4.86: 39
        4.86 -     6.48: 6
        6.48 -     8.10: 3
  Bond angle restraints: 13247
  Sorted by residual:
  angle pdb=" N   GLY A 439 "
        pdb=" CA  GLY A 439 "
        pdb=" C   GLY A 439 "
      ideal   model   delta    sigma   weight residual
     110.43  114.62   -4.19 1.35e+00 5.49e-01 9.62e+00
  angle pdb=" C   LEU B 420 "
        pdb=" N   ASP B 421 "
        pdb=" CA  ASP B 421 "
      ideal   model   delta    sigma   weight residual
     121.54  127.37   -5.83 1.91e+00 2.74e-01 9.32e+00
  angle pdb=" N   GLU B 462 "
        pdb=" CA  GLU B 462 "
        pdb=" CB  GLU B 462 "
      ideal   model   delta    sigma   weight residual
     110.28  114.90   -4.62 1.55e+00 4.16e-01 8.89e+00
  angle pdb=" N   GLU A1037 "
        pdb=" CA  GLU A1037 "
        pdb=" CB  GLU A1037 "
      ideal   model   delta    sigma   weight residual
     110.28  114.75   -4.47 1.55e+00 4.16e-01 8.32e+00
  angle pdb=" CA  PRO B 427 "
        pdb=" N   PRO B 427 "
        pdb=" CD  PRO B 427 "
      ideal   model   delta    sigma   weight residual
     112.00  108.15    3.85 1.40e+00 5.10e-01 7.55e+00
  ... (remaining 13242 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    18.00: 5299
       18.00 -    36.00: 594
       36.00 -    53.99: 85
       53.99 -    71.99: 15
       71.99 -    89.99: 8
  Dihedral angle restraints: 6001
    sinusoidal: 2559
      harmonic: 3442
  Sorted by residual:
  dihedral pdb=" CA  LYS A 440 "
           pdb=" C   LYS A 440 "
           pdb=" N   MET A 441 "
           pdb=" CA  MET A 441 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00 -162.39  -17.61     0      5.00e+00 4.00e-02 1.24e+01
  dihedral pdb=" CA  TYR A 165 "
           pdb=" C   TYR A 165 "
           pdb=" N   VAL A 166 "
           pdb=" CA  VAL A 166 "
      ideal   model   delta  harmonic     sigma   weight residual
    -180.00 -162.71  -17.29     0      5.00e+00 4.00e-02 1.20e+01
  dihedral pdb=" CB  GLU A 474 "
           pdb=" CG  GLU A 474 "
           pdb=" CD  GLU A 474 "
           pdb=" OE1 GLU A 474 "
      ideal   model   delta sinusoidal    sigma   weight residual
       0.00   89.28  -89.28     1      3.00e+01 1.11e-03 1.05e+01
  ... (remaining 5998 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.056: 1208
       0.056 -    0.111: 207
       0.111 -    0.167: 18
       0.167 -    0.223: 2
       0.223 -    0.278: 1
  Chirality restraints: 1436
  Sorted by residual:
  chirality pdb=" CB  ILE A 561 "
            pdb=" CA  ILE A 561 "
            pdb=" CG1 ILE A 561 "
            pdb=" CG2 ILE A 561 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.64    2.37    0.28 2.00e-01 2.50e+01 1.94e+00
  chirality pdb=" CG  LEU A 793 "
            pdb=" CB  LEU A 793 "
            pdb=" CD1 LEU A 793 "
            pdb=" CD2 LEU A 793 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.59   -2.77    0.18 2.00e-01 2.50e+01 7.70e-01
  chirality pdb=" CA  ILE B 381 "
            pdb=" N   ILE B 381 "
            pdb=" C   ILE B 381 "
            pdb=" CB  ILE B 381 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.43    2.61   -0.17 2.00e-01 2.50e+01 7.49e-01
  ... (remaining 1433 not shown)

  Planarity restraints: 1693
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CB  PHE A 744 "   -0.017 2.00e-02 2.50e+03   1.81e-02 5.75e+00
        pdb=" CG  PHE A 744 "    0.042 2.00e-02 2.50e+03
        pdb=" CD1 PHE A 744 "   -0.005 2.00e-02 2.50e+03
        pdb=" CD2 PHE A 744 "   -0.013 2.00e-02 2.50e+03
        pdb=" CE1 PHE A 744 "   -0.008 2.00e-02 2.50e+03
        pdb=" CE2 PHE A 744 "    0.001 2.00e-02 2.50e+03
        pdb=" CZ  PHE A 744 "    0.001 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   LEU A 297 "    0.035 5.00e-02 4.00e+02   5.29e-02 4.48e+00
        pdb=" N   PRO A 298 "   -0.092 5.00e-02 4.00e+02
        pdb=" CA  PRO A 298 "    0.028 5.00e-02 4.00e+02
        pdb=" CD  PRO A 298 "    0.029 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  GLU A 710 "   -0.008 2.00e-02 2.50e+03   1.70e-02 2.88e+00
        pdb=" C   GLU A 710 "    0.029 2.00e-02 2.50e+03
        pdb=" O   GLU A 710 "   -0.011 2.00e-02 2.50e+03
        pdb=" N   LYS A 711 "   -0.010 2.00e-02 2.50e+03
  ... (remaining 1690 not shown)

  Histogram of nonbonded interaction distances:
        2.20 -     2.74: 660
        2.74 -     3.28: 9908
        3.28 -     3.82: 15885
        3.82 -     4.36: 18308
        4.36 -     4.90: 31056
  Nonbonded interactions: 75817
  Sorted by model distance:
  nonbonded pdb=" O   MET A1005 "
            pdb=" OG  SER A1008 "
     model   vdw
     2.195 3.040
  nonbonded pdb=" O   CYS A 971 "
            pdb=" OG1 THR A 974 "
     model   vdw
     2.255 3.040
  nonbonded pdb=" O   LEU A 568 "
            pdb=" OG  SER A 571 "
     model   vdw
     2.256 3.040
  nonbonded pdb=" O   HIS A 450 "
            pdb=" NE2 GLN A1014 "
     model   vdw
     2.259 3.120
  nonbonded pdb=" O   LEU A 367 "
            pdb=" ND2 ASN A 575 "
     model   vdw
     2.259 3.120
  ... (remaining 75812 not shown)

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

  No NCS relation were found !!!

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

Found NCS groups:
  found none.
Set up NCS constraints
  No NCS constraints will be used in refinement.
Set refine NCS operators
Adjust number of macro_cycles
  Number of macro_cycles: 10
Reset NCS operators
Extract rigid body selections
Check and reset occupancies
  Occupancies: min=1.00 max=1.00 mean=1.00
Load rotamer database and sin/cos tables
Set ADP refinement strategy
  ADPs will be refined as individual isotropic
Make a string to write initial .geo file
Internal consistency checks
Time:
  Set random seed:                         0.000
  Set model cs if undefined:               0.000
  Decide on map wrapping:                  0.000
  Normalize map: mean=0, sd=1:             1.060
  Set stop_for_unknowns flag:              0.000
  Assert model is a single copy model:     0.000
  Assert all atoms have isotropic ADPs:    0.000
  Construct map_model_manager:             0.010
  Extract box with map and model:          0.420
  Check model and map are aligned:         0.070
  Set scattering table:                    0.100
  Process input model:                     25.410
  Find NCS groups from input model:        0.120
  Set up NCS constraints:                  0.040
  Set refine NCS operators:                0.000
  Adjust number of macro_cycles:           0.000
  Reset NCS operators:                     0.000
  Extract rigid body selections:           0.000
  Check and reset occupancies:             0.000
  Load rotamer database and sin/cos tables:13.050
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   40.280
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.5862
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      :  0.003   0.097   9828  Z= 0.211
  Angle     :  0.584   8.095  13247  Z= 0.309
  Chirality :  0.042   0.278   1436
  Planarity :  0.004   0.062   1693
  Dihedral  : 14.710  89.989   3763
  Min Nonbonded Distance : 2.195

Molprobity Statistics.
  All-atom Clashscore : 13.47
  Ramachandran Plot:
    Outliers :  0.09 %
    Allowed  :  5.35 %
    Favored  : 94.56 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  0.37 %
    Favored  : 99.63 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 4.26 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -0.04 (0.26), residues: 1140
  helix:  0.73 (0.24), residues: 513
  sheet: -0.33 (0.50), residues: 123
  loop : -0.66 (0.29), residues: 504

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.009   0.001   TRP A 669 
 HIS   0.005   0.001   HIS A 931 
 PHE   0.042   0.002   PHE A 744 
 TYR   0.013   0.001   TYR B 556 
 ARG   0.006   0.000   ARG A 832 

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

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

  2280 Ramachandran restraints generated.
    1140 Oldfield, 0 Emsley, 1140 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2280 Ramachandran restraints generated.
    1140 Oldfield, 0 Emsley, 1140 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  169 residues out of total 1073 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 169
  time to evaluate  : 1.063 
Fit side-chains
   revert: symmetry clash
REVERT: A  355 TYR cc_start: 0.7073 (p90) cc_final: 0.6803 (p90)
REVERT: A  405 SER cc_start: 0.8209 (p) cc_final: 0.7997 (p)
REVERT: A  545 GLU cc_start: 0.7084 (pm20) cc_final: 0.6808 (pm20)
REVERT: A  546 GLN cc_start: 0.7425 (mp10) cc_final: 0.6894 (tm130)
REVERT: A  549 ASP cc_start: 0.8054 (m-30) cc_final: 0.7700 (m-30)
REVERT: A  849 GLU cc_start: 0.6795 (mt-10) cc_final: 0.6487 (mm-30)
REVERT: B  359 ASP cc_start: 0.7680 (m-30) cc_final: 0.7379 (m-30)
  outliers start: 0
  outliers final: 0
  residues processed: 169
  average time/residue: 1.1814
  time to fit residues: 216.6169
Evaluate side-chains
  149 residues out of total 1073 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 149
  time to evaluate  : 1.092 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 116
   random chunks:
   chunk 97 optimal weight:    6.9990
   chunk 87 optimal weight:    0.4980
   chunk 48 optimal weight:    2.9990
   chunk 30 optimal weight:    0.9980
   chunk 59 optimal weight:    0.5980
   chunk 46 optimal weight:    0.5980
   chunk 90 optimal weight:    3.9990
   chunk 35 optimal weight:    4.9990
   chunk 55 optimal weight:    0.0980
   chunk 67 optimal weight:    5.9990
   chunk 105 optimal weight:    9.9990
   overall best weight:    0.5580

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

Flipped N/Q/H residues before XYZ refinement:
** A 546 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 661 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 928 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 931 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
A1000 ASN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.5024 r_free = 0.5024 target = 0.264347 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 53)----------------|
| r_work = 0.4563 r_free = 0.4563 target = 0.202926 restraints weight = 11470.731|
|-----------------------------------------------------------------------------|
r_work (start): 0.4523 rms_B_bonded: 4.13
r_work: 0.4337 rms_B_bonded: 4.87 restraints_weight: 0.5000
r_work (final): 0.4337
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.5809
moved from start:          0.0994

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.054   9828  Z= 0.183
  Angle     :  0.569   7.703  13247  Z= 0.293
  Chirality :  0.041   0.148   1436
  Planarity :  0.004   0.064   1693
  Dihedral  :  4.030  17.301   1275
  Min Nonbonded Distance : 2.494

Molprobity Statistics.
  All-atom Clashscore : 10.71
  Ramachandran Plot:
    Outliers :  0.09 %
    Allowed  :  4.56 %
    Favored  : 95.35 %
  Rotamer:
    Outliers :  1.12 %
    Allowed  :  9.97 %
    Favored  : 88.91 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 4.26 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.25 (0.26), residues: 1140
  helix:  1.05 (0.23), residues: 522
  sheet: -0.28 (0.52), residues: 112
  loop : -0.60 (0.28), residues: 506

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.020   0.001   TRP A 479 
 HIS   0.004   0.001   HIS B 365 
 PHE   0.032   0.002   PHE A 744 
 TYR   0.016   0.001   TYR B 556 
 ARG   0.004   0.000   ARG A 765 

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

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

  2280 Ramachandran restraints generated.
    1140 Oldfield, 0 Emsley, 1140 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2280 Ramachandran restraints generated.
    1140 Oldfield, 0 Emsley, 1140 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  175 residues out of total 1073 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 163
  time to evaluate  : 0.985 
Fit side-chains
REVERT: A   30 MET cc_start: 0.4577 (mmp) cc_final: 0.4055 (mmm)
REVERT: A  123 MET cc_start: 0.6378 (ppp) cc_final: 0.6081 (ppp)
REVERT: A  286 MET cc_start: 0.5593 (tmt) cc_final: 0.4588 (ptm)
REVERT: A  355 TYR cc_start: 0.7051 (p90) cc_final: 0.6463 (p90)
REVERT: A  405 SER cc_start: 0.8549 (p) cc_final: 0.8346 (p)
REVERT: A  443 LEU cc_start: 0.6984 (OUTLIER) cc_final: 0.6706 (mt)
REVERT: A  479 TRP cc_start: 0.6906 (t-100) cc_final: 0.6659 (t-100)
REVERT: A  546 GLN cc_start: 0.7802 (mp10) cc_final: 0.7156 (tm130)
REVERT: A  549 ASP cc_start: 0.8538 (m-30) cc_final: 0.8227 (m-30)
REVERT: A  579 GLU cc_start: 0.4989 (tt0) cc_final: 0.4602 (tt0)
REVERT: A  608 ASP cc_start: 0.8281 (t70) cc_final: 0.8015 (t70)
REVERT: A  745 MET cc_start: 0.7112 (mpp) cc_final: 0.6813 (mmt)
REVERT: A  811 MET cc_start: 0.7256 (OUTLIER) cc_final: 0.6587 (mpp)
REVERT: A  825 GLN cc_start: 0.6594 (tm-30) cc_final: 0.6198 (tp-100)
REVERT: A  849 GLU cc_start: 0.7302 (mt-10) cc_final: 0.6744 (mm-30)
REVERT: A  899 ARG cc_start: 0.7990 (mmt90) cc_final: 0.7544 (mmm-85)
REVERT: A 1055 MET cc_start: 0.2404 (mpp) cc_final: 0.2105 (mpp)
REVERT: B  355 PHE cc_start: 0.6543 (p90) cc_final: 0.6201 (p90)
REVERT: B  359 ASP cc_start: 0.8043 (m-30) cc_final: 0.7584 (m-30)
  outliers start: 12
  outliers final: 2
  residues processed: 168
  average time/residue: 1.1331
  time to fit residues: 207.0197
Evaluate side-chains
  152 residues out of total 1073 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 4
    poor density    : 148
  time to evaluate  : 1.223 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  443 LEU
Chi-restraints excluded: chain A residue  636 VAL
Chi-restraints excluded: chain A residue  811 MET
Chi-restraints excluded: chain A residue  845 VAL
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 116
   random chunks:
   chunk 91 optimal weight:    5.9990
   chunk 105 optimal weight:   10.0000
   chunk 98 optimal weight:    7.9990
   chunk 31 optimal weight:    6.9990
   chunk 69 optimal weight:    1.9990
   chunk 104 optimal weight:    8.9990
   chunk 103 optimal weight:    3.9990
   chunk 99 optimal weight:    1.9990
   chunk 102 optimal weight:   10.0000
   chunk 84 optimal weight:    3.9990
   chunk 108 optimal weight:    5.9990
   overall best weight:    3.5990

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

Flipped N/Q/H residues before XYZ refinement:
A 362 HIS
** A 370 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 630 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 661 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 749 GLN
** A 928 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 931 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
B 527 ASN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4910 r_free = 0.4910 target = 0.251919 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 55)----------------|
| r_work = 0.4411 r_free = 0.4411 target = 0.188180 restraints weight = 11672.576|
|-----------------------------------------------------------------------------|
r_work (start): 0.4340 rms_B_bonded: 4.07
r_work: 0.4146 rms_B_bonded: 4.78 restraints_weight: 0.5000
r_work (final): 0.4146
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6049
moved from start:          0.1793

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.008   0.070   9828  Z= 0.497
  Angle     :  0.774   8.437  13247  Z= 0.395
  Chirality :  0.048   0.166   1436
  Planarity :  0.005   0.072   1693
  Dihedral  :  4.793  17.875   1275
  Min Nonbonded Distance : 2.444

Molprobity Statistics.
  All-atom Clashscore : 17.94
  Ramachandran Plot:
    Outliers :  0.09 %
    Allowed  :  6.05 %
    Favored  : 93.86 %
  Rotamer:
    Outliers :  3.26 %
    Allowed  : 14.17 %
    Favored  : 82.57 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 4.26 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -0.45 (0.25), residues: 1140
  helix:  0.56 (0.23), residues: 520
  sheet: -0.92 (0.46), residues: 122
  loop : -0.98 (0.28), residues: 498

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.015   0.003   TRP A 424 
 HIS   0.010   0.001   HIS A 362 
 PHE   0.032   0.003   PHE A 744 
 TYR   0.023   0.002   TYR B 556 
 ARG   0.008   0.001   ARG A 916 

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

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

  2280 Ramachandran restraints generated.
    1140 Oldfield, 0 Emsley, 1140 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2280 Ramachandran restraints generated.
    1140 Oldfield, 0 Emsley, 1140 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  204 residues out of total 1073 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 35
    poor density    : 169
  time to evaluate  : 1.126 
Fit side-chains
   revert: symmetry clash
REVERT: A  123 MET cc_start: 0.6319 (ppp) cc_final: 0.6090 (ppp)
REVERT: A  267 LEU cc_start: 0.7301 (OUTLIER) cc_final: 0.7098 (tp)
REVERT: A  270 TYR cc_start: 0.8556 (m-80) cc_final: 0.8340 (m-80)
REVERT: A  355 TYR cc_start: 0.7151 (p90) cc_final: 0.6734 (p90)
REVERT: A  428 ASN cc_start: 0.7856 (m-40) cc_final: 0.7332 (m-40)
REVERT: A  479 TRP cc_start: 0.6999 (t-100) cc_final: 0.6677 (t-100)
REVERT: A  545 GLU cc_start: 0.8396 (pm20) cc_final: 0.8149 (pm20)
REVERT: A  546 GLN cc_start: 0.7777 (mp10) cc_final: 0.7369 (tm130)
REVERT: A  549 ASP cc_start: 0.8681 (m-30) cc_final: 0.8381 (m-30)
REVERT: A  579 GLU cc_start: 0.5378 (tt0) cc_final: 0.4725 (tt0)
REVERT: A  596 GLU cc_start: 0.7152 (tp30) cc_final: 0.6314 (tp30)
REVERT: A  745 MET cc_start: 0.6942 (mpp) cc_final: 0.6635 (mmt)
REVERT: A  760 GLN cc_start: 0.6946 (mp10) cc_final: 0.6597 (mm-40)
REVERT: A  811 MET cc_start: 0.7338 (OUTLIER) cc_final: 0.6841 (mpp)
REVERT: A  825 GLN cc_start: 0.6599 (tm-30) cc_final: 0.6112 (tp-100)
REVERT: A  849 GLU cc_start: 0.7505 (mt-10) cc_final: 0.7016 (mt-10)
REVERT: A  886 LYS cc_start: 0.7674 (OUTLIER) cc_final: 0.7427 (mmpt)
REVERT: A  899 ARG cc_start: 0.8117 (mmt90) cc_final: 0.7790 (mmm-85)
REVERT: A  925 ASP cc_start: 0.7762 (t70) cc_final: 0.6990 (p0)
REVERT: A 1055 MET cc_start: 0.2043 (mpp) cc_final: 0.1578 (mpp)
REVERT: B  359 ASP cc_start: 0.8146 (m-30) cc_final: 0.7788 (m-30)
REVERT: B  398 PHE cc_start: 0.6997 (m-80) cc_final: 0.6434 (t80)
  outliers start: 35
  outliers final: 10
  residues processed: 188
  average time/residue: 1.1088
  time to fit residues: 225.3897
Evaluate side-chains
  178 residues out of total 1073 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 165
  time to evaluate  : 1.145 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  149 GLU
Chi-restraints excluded: chain A residue  253 LYS
Chi-restraints excluded: chain A residue  267 LEU
Chi-restraints excluded: chain A residue  358 THR
Chi-restraints excluded: chain A residue  368 CYS
Chi-restraints excluded: chain A residue  620 GLU
Chi-restraints excluded: chain A residue  636 VAL
Chi-restraints excluded: chain A residue  700 LYS
Chi-restraints excluded: chain A residue  811 MET
Chi-restraints excluded: chain A residue  886 LYS
Chi-restraints excluded: chain B residue  369 THR
Chi-restraints excluded: chain B residue  381 ILE
Chi-restraints excluded: chain B residue  460 SER
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 116
   random chunks:
   chunk 53 optimal weight:    0.9980
   chunk 0 optimal weight:   20.0000
   chunk 89 optimal weight:    0.8980
   chunk 63 optimal weight:    0.7980
   chunk 68 optimal weight:    2.9990
   chunk 75 optimal weight:    3.9990
   chunk 14 optimal weight:    8.9990
   chunk 19 optimal weight:    7.9990
   chunk 24 optimal weight:    0.7980
   chunk 10 optimal weight:    1.9990
   chunk 83 optimal weight:    2.9990
   overall best weight:    1.0982

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

Flipped N/Q/H residues before XYZ refinement:
** A 114 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 380 ASN
A 419 HIS
** A 630 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 703 ASN
A 749 GLN
** A 928 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 931 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** A1047 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4996 r_free = 0.4996 target = 0.260131 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 47)----------------|
| r_work = 0.4528 r_free = 0.4528 target = 0.198354 restraints weight = 11526.383|
|-----------------------------------------------------------------------------|
r_work (start): 0.4471 rms_B_bonded: 4.10
r_work: 0.4287 rms_B_bonded: 4.77 restraints_weight: 0.5000
r_work (final): 0.4287
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.5925
moved from start:          0.1807

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.062   9828  Z= 0.231
  Angle     :  0.608   7.346  13247  Z= 0.312
  Chirality :  0.042   0.167   1436
  Planarity :  0.004   0.071   1693
  Dihedral  :  4.406  17.296   1275
  Min Nonbonded Distance : 2.398

Molprobity Statistics.
  All-atom Clashscore : 12.33
  Ramachandran Plot:
    Outliers :  0.09 %
    Allowed  :  4.47 %
    Favored  : 95.44 %
  Rotamer:
    Outliers :  2.98 %
    Allowed  : 17.52 %
    Favored  : 79.50 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 4.26 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -0.19 (0.25), residues: 1140
  helix:  0.76 (0.23), residues: 526
  sheet: -0.88 (0.47), residues: 122
  loop : -0.83 (0.29), residues: 492

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.010   0.002   TRP A 669 
 HIS   0.006   0.001   HIS A 676 
 PHE   0.032   0.002   PHE A 744 
 TYR   0.015   0.001   TYR B 556 
 ARG   0.005   0.000   ARG A 765 

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

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

  2280 Ramachandran restraints generated.
    1140 Oldfield, 0 Emsley, 1140 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2280 Ramachandran restraints generated.
    1140 Oldfield, 0 Emsley, 1140 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  194 residues out of total 1073 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 32
    poor density    : 162
  time to evaluate  : 0.992 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  123 MET cc_start: 0.6278 (ppp) cc_final: 0.5983 (ppp)
REVERT: A  355 TYR cc_start: 0.7043 (p90) cc_final: 0.6523 (p90)
REVERT: A  443 LEU cc_start: 0.7095 (OUTLIER) cc_final: 0.6892 (mt)
REVERT: A  479 TRP cc_start: 0.7045 (t-100) cc_final: 0.6732 (t-100)
REVERT: A  545 GLU cc_start: 0.8167 (pm20) cc_final: 0.7937 (pm20)
REVERT: A  546 GLN cc_start: 0.7826 (mp10) cc_final: 0.7336 (tm130)
REVERT: A  549 ASP cc_start: 0.8638 (m-30) cc_final: 0.8325 (m-30)
REVERT: A  579 GLU cc_start: 0.5332 (tt0) cc_final: 0.4614 (tt0)
REVERT: A  587 VAL cc_start: 0.4414 (OUTLIER) cc_final: 0.3045 (m)
REVERT: A  596 GLU cc_start: 0.7122 (tp30) cc_final: 0.6423 (tp30)
REVERT: A  599 MET cc_start: 0.7781 (OUTLIER) cc_final: 0.7553 (ttp)
REVERT: A  608 ASP cc_start: 0.8383 (t70) cc_final: 0.7993 (t70)
REVERT: A  638 VAL cc_start: 0.6767 (m) cc_final: 0.6533 (m)
REVERT: A  745 MET cc_start: 0.7105 (mpp) cc_final: 0.6764 (mmt)
REVERT: A  783 TRP cc_start: 0.6638 (m-90) cc_final: 0.6391 (m-90)
REVERT: A  811 MET cc_start: 0.7316 (OUTLIER) cc_final: 0.6713 (mpp)
REVERT: A  825 GLN cc_start: 0.6566 (tm-30) cc_final: 0.6064 (tp-100)
REVERT: A  886 LYS cc_start: 0.7710 (OUTLIER) cc_final: 0.7429 (mmpt)
REVERT: A  899 ARG cc_start: 0.7968 (mmt90) cc_final: 0.7741 (mmm-85)
REVERT: A 1037 GLU cc_start: 0.6900 (OUTLIER) cc_final: 0.6504 (mm-30)
REVERT: A 1055 MET cc_start: 0.2154 (mpp) cc_final: 0.1285 (mpp)
REVERT: B  359 ASP cc_start: 0.8148 (m-30) cc_final: 0.7801 (m-30)
  outliers start: 32
  outliers final: 11
  residues processed: 176
  average time/residue: 1.0393
  time to fit residues: 198.3332
Evaluate side-chains
  170 residues out of total 1073 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 17
    poor density    : 153
  time to evaluate  : 1.050 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  130 MET
Chi-restraints excluded: chain A residue  149 GLU
Chi-restraints excluded: chain A residue  443 LEU
Chi-restraints excluded: chain A residue  475 LEU
Chi-restraints excluded: chain A residue  587 VAL
Chi-restraints excluded: chain A residue  599 MET
Chi-restraints excluded: chain A residue  603 ASP
Chi-restraints excluded: chain A residue  620 GLU
Chi-restraints excluded: chain A residue  636 VAL
Chi-restraints excluded: chain A residue  811 MET
Chi-restraints excluded: chain A residue  816 ILE
Chi-restraints excluded: chain A residue  848 ILE
Chi-restraints excluded: chain A residue  886 LYS
Chi-restraints excluded: chain A residue 1037 GLU
Chi-restraints excluded: chain B residue  401 VAL
Chi-restraints excluded: chain B residue  420 LEU
Chi-restraints excluded: chain B residue  460 SER
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 116
   random chunks:
   chunk 46 optimal weight:    2.9990
   chunk 80 optimal weight:    6.9990
   chunk 39 optimal weight:    7.9990
   chunk 16 optimal weight:    5.9990
   chunk 62 optimal weight:    0.0370
   chunk 47 optimal weight:    2.9990
   chunk 97 optimal weight:    7.9990
   chunk 21 optimal weight:    0.0670
   chunk 107 optimal weight:   10.0000
   chunk 6 optimal weight:    0.0980
   chunk 74 optimal weight:    4.9990
   overall best weight:    1.2400

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

Flipped N/Q/H residues before XYZ refinement:
A 114 ASN
** A 370 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 630 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 703 ASN
A 749 GLN
A 917 HIS
** A 928 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 931 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
A1014 GLN
A1047 HIS

Total number of N/Q/H flips: 6

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4990 r_free = 0.4990 target = 0.259721 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 46)----------------|
| r_work = 0.4532 r_free = 0.4532 target = 0.199006 restraints weight = 11378.357|
|-----------------------------------------------------------------------------|
r_work (start): 0.4453 rms_B_bonded: 4.02
r_work: 0.4263 rms_B_bonded: 4.78 restraints_weight: 0.5000
r_work (final): 0.4263
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.5915
moved from start:          0.1969

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.046   9828  Z= 0.233
  Angle     :  0.607   7.804  13247  Z= 0.310
  Chirality :  0.042   0.160   1436
  Planarity :  0.004   0.070   1693
  Dihedral  :  4.307  16.454   1275
  Min Nonbonded Distance : 2.292

Molprobity Statistics.
  All-atom Clashscore : 11.81
  Ramachandran Plot:
    Outliers :  0.09 %
    Allowed  :  4.74 %
    Favored  : 95.18 %
  Rotamer:
    Outliers :  3.17 %
    Allowed  : 18.92 %
    Favored  : 77.91 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 4.26 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -0.13 (0.26), residues: 1140
  helix:  0.88 (0.23), residues: 526
  sheet: -1.02 (0.46), residues: 123
  loop : -0.83 (0.29), residues: 491

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.013   0.002   TRP A 195 
 HIS   0.022   0.002   HIS A1047 
 PHE   0.036   0.002   PHE A 744 
 TYR   0.015   0.001   TYR B 556 
 ARG   0.008   0.000   ARG A 832 

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

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

  2280 Ramachandran restraints generated.
    1140 Oldfield, 0 Emsley, 1140 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2280 Ramachandran restraints generated.
    1140 Oldfield, 0 Emsley, 1140 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  196 residues out of total 1073 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 34
    poor density    : 162
  time to evaluate  : 0.946 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  123 MET cc_start: 0.6295 (ppp) cc_final: 0.5903 (ppp)
REVERT: A  355 TYR cc_start: 0.7027 (p90) cc_final: 0.6540 (p90)
REVERT: A  479 TRP cc_start: 0.7095 (t-100) cc_final: 0.6771 (t-100)
REVERT: A  545 GLU cc_start: 0.8129 (pm20) cc_final: 0.7850 (pm20)
REVERT: A  546 GLN cc_start: 0.7833 (mp10) cc_final: 0.7361 (tm130)
REVERT: A  549 ASP cc_start: 0.8643 (m-30) cc_final: 0.8331 (m-30)
REVERT: A  579 GLU cc_start: 0.5198 (tt0) cc_final: 0.4550 (tt0)
REVERT: A  587 VAL cc_start: 0.4383 (OUTLIER) cc_final: 0.3892 (t)
REVERT: A  596 GLU cc_start: 0.7144 (tp30) cc_final: 0.6452 (tp30)
REVERT: A  608 ASP cc_start: 0.8376 (t70) cc_final: 0.7995 (t70)
REVERT: A  610 MET cc_start: 0.6962 (mpp) cc_final: 0.6731 (mpp)
REVERT: A  683 ARG cc_start: 0.5955 (ttm110) cc_final: 0.5713 (ttm-80)
REVERT: A  745 MET cc_start: 0.7034 (mpp) cc_final: 0.6713 (mmt)
REVERT: A  811 MET cc_start: 0.7262 (OUTLIER) cc_final: 0.6782 (mpp)
REVERT: A  825 GLN cc_start: 0.6540 (tm-30) cc_final: 0.6001 (tp-100)
REVERT: A  849 GLU cc_start: 0.7411 (mt-10) cc_final: 0.6592 (mm-30)
REVERT: A  886 LYS cc_start: 0.7750 (OUTLIER) cc_final: 0.7447 (mmpt)
REVERT: A  925 ASP cc_start: 0.7731 (OUTLIER) cc_final: 0.6681 (p0)
REVERT: A  982 GLU cc_start: 0.6369 (pt0) cc_final: 0.5832 (pm20)
REVERT: A 1037 GLU cc_start: 0.6880 (OUTLIER) cc_final: 0.6484 (mm-30)
REVERT: A 1055 MET cc_start: 0.2040 (mpp) cc_final: 0.1143 (mpp)
REVERT: B  355 PHE cc_start: 0.6274 (p90) cc_final: 0.6004 (p90)
REVERT: B  359 ASP cc_start: 0.8216 (m-30) cc_final: 0.7887 (m-30)
  outliers start: 34
  outliers final: 12
  residues processed: 180
  average time/residue: 1.0431
  time to fit residues: 203.3762
Evaluate side-chains
  169 residues out of total 1073 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 17
    poor density    : 152
  time to evaluate  : 1.079 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  149 GLU
Chi-restraints excluded: chain A residue  587 VAL
Chi-restraints excluded: chain A residue  603 ASP
Chi-restraints excluded: chain A residue  620 GLU
Chi-restraints excluded: chain A residue  636 VAL
Chi-restraints excluded: chain A residue  811 MET
Chi-restraints excluded: chain A residue  816 ILE
Chi-restraints excluded: chain A residue  848 ILE
Chi-restraints excluded: chain A residue  886 LYS
Chi-restraints excluded: chain A residue  917 HIS
Chi-restraints excluded: chain A residue  925 ASP
Chi-restraints excluded: chain A residue  983 MET
Chi-restraints excluded: chain A residue 1037 GLU
Chi-restraints excluded: chain B residue  369 THR
Chi-restraints excluded: chain B residue  401 VAL
Chi-restraints excluded: chain B residue  420 LEU
Chi-restraints excluded: chain B residue  460 SER
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 116
   random chunks:
   chunk 60 optimal weight:    1.9990
   chunk 8 optimal weight:    0.8980
   chunk 115 optimal weight:   10.0000
   chunk 17 optimal weight:    6.9990
   chunk 44 optimal weight:    0.9980
   chunk 13 optimal weight:    0.6980
   chunk 97 optimal weight:    1.9990
   chunk 27 optimal weight:    1.9990
   chunk 2 optimal weight:    2.9990
   chunk 34 optimal weight:    0.9980
   chunk 41 optimal weight:   10.0000
   overall best weight:    1.1182

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

Flipped N/Q/H residues before XYZ refinement:
** A 370 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 630 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 749 GLN
A 917 HIS
** A 928 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 931 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
A1014 GLN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.5002 r_free = 0.5002 target = 0.260917 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 44)----------------|
| r_work = 0.4549 r_free = 0.4549 target = 0.200356 restraints weight = 11456.059|
|-----------------------------------------------------------------------------|
r_work (start): 0.4418 rms_B_bonded: 4.03
r_work: 0.4224 rms_B_bonded: 4.81 restraints_weight: 0.5000
r_work (final): 0.4224
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.5896
moved from start:          0.2038

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.047   9828  Z= 0.217
  Angle     :  0.607   7.702  13247  Z= 0.306
  Chirality :  0.041   0.160   1436
  Planarity :  0.004   0.069   1693
  Dihedral  :  4.292  17.972   1275
  Min Nonbonded Distance : 2.493

Molprobity Statistics.
  All-atom Clashscore : 11.13
  Ramachandran Plot:
    Outliers :  0.09 %
    Allowed  :  4.21 %
    Favored  : 95.70 %
  Rotamer:
    Outliers :  2.52 %
    Allowed  : 20.78 %
    Favored  : 76.70 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 4.26 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -0.08 (0.26), residues: 1140
  helix:  0.93 (0.23), residues: 527
  sheet: -1.07 (0.46), residues: 123
  loop : -0.79 (0.29), residues: 490

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.018   0.001   TRP A 783 
 HIS   0.010   0.001   HIS A 917 
 PHE   0.039   0.002   PHE A 744 
 TYR   0.015   0.001   TYR B 556 
 ARG   0.006   0.000   ARG A 916 

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

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

  2280 Ramachandran restraints generated.
    1140 Oldfield, 0 Emsley, 1140 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2280 Ramachandran restraints generated.
    1140 Oldfield, 0 Emsley, 1140 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  188 residues out of total 1073 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 27
    poor density    : 161
  time to evaluate  : 1.035 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  123 MET cc_start: 0.6426 (ppp) cc_final: 0.6015 (ppp)
REVERT: A  355 TYR cc_start: 0.6972 (p90) cc_final: 0.6498 (p90)
REVERT: A  479 TRP cc_start: 0.7110 (t-100) cc_final: 0.6801 (t-100)
REVERT: A  545 GLU cc_start: 0.8139 (pm20) cc_final: 0.7918 (pm20)
REVERT: A  546 GLN cc_start: 0.7829 (mp10) cc_final: 0.7446 (tm130)
REVERT: A  549 ASP cc_start: 0.8658 (m-30) cc_final: 0.8346 (m-30)
REVERT: A  579 GLU cc_start: 0.5146 (tt0) cc_final: 0.4530 (tt0)
REVERT: A  587 VAL cc_start: 0.4442 (OUTLIER) cc_final: 0.3971 (t)
REVERT: A  596 GLU cc_start: 0.7179 (tp30) cc_final: 0.6478 (tp30)
REVERT: A  608 ASP cc_start: 0.8322 (t70) cc_final: 0.7934 (t70)
REVERT: A  610 MET cc_start: 0.7015 (mpp) cc_final: 0.6664 (mpp)
REVERT: A  630 GLN cc_start: 0.8092 (tp-100) cc_final: 0.7702 (tp-100)
REVERT: A  683 ARG cc_start: 0.5968 (ttm110) cc_final: 0.5751 (ttm-80)
REVERT: A  745 MET cc_start: 0.7031 (mpp) cc_final: 0.6827 (mmt)
REVERT: A  811 MET cc_start: 0.7338 (OUTLIER) cc_final: 0.6834 (mpp)
REVERT: A  825 GLN cc_start: 0.6547 (tm-30) cc_final: 0.6001 (tp-100)
REVERT: A  849 GLU cc_start: 0.7472 (mt-10) cc_final: 0.6615 (mm-30)
REVERT: A  886 LYS cc_start: 0.7776 (mmtt) cc_final: 0.7458 (mmpt)
REVERT: A  899 ARG cc_start: 0.7971 (mmt90) cc_final: 0.7662 (mmm-85)
REVERT: A  925 ASP cc_start: 0.7714 (OUTLIER) cc_final: 0.6655 (p0)
REVERT: A 1037 GLU cc_start: 0.6866 (OUTLIER) cc_final: 0.6488 (mm-30)
REVERT: A 1055 MET cc_start: 0.2053 (mpp) cc_final: 0.1074 (mpp)
REVERT: B  355 PHE cc_start: 0.6211 (p90) cc_final: 0.5979 (p90)
REVERT: B  359 ASP cc_start: 0.8197 (m-30) cc_final: 0.7875 (m-30)
  outliers start: 27
  outliers final: 12
  residues processed: 176
  average time/residue: 1.1043
  time to fit residues: 210.7670
Evaluate side-chains
  171 residues out of total 1073 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 155
  time to evaluate  : 1.012 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  149 GLU
Chi-restraints excluded: chain A residue  484 VAL
Chi-restraints excluded: chain A residue  587 VAL
Chi-restraints excluded: chain A residue  603 ASP
Chi-restraints excluded: chain A residue  620 GLU
Chi-restraints excluded: chain A residue  636 VAL
Chi-restraints excluded: chain A residue  811 MET
Chi-restraints excluded: chain A residue  816 ILE
Chi-restraints excluded: chain A residue  848 ILE
Chi-restraints excluded: chain A residue  925 ASP
Chi-restraints excluded: chain A residue  983 MET
Chi-restraints excluded: chain A residue 1037 GLU
Chi-restraints excluded: chain B residue  369 THR
Chi-restraints excluded: chain B residue  401 VAL
Chi-restraints excluded: chain B residue  420 LEU
Chi-restraints excluded: chain B residue  460 SER
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 116
   random chunks:
   chunk 81 optimal weight:    0.9980
   chunk 23 optimal weight:    1.9990
   chunk 89 optimal weight:    2.9990
   chunk 108 optimal weight:    5.9990
   chunk 21 optimal weight:    0.1980
   chunk 71 optimal weight:    3.9990
   chunk 77 optimal weight:    0.9990
   chunk 106 optimal weight:    7.9990
   chunk 43 optimal weight:    0.9980
   chunk 34 optimal weight:    0.8980
   chunk 70 optimal weight:    1.9990
   overall best weight:    0.8182

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

Flipped N/Q/H residues before XYZ refinement:
A 380 ASN
** A 630 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 749 GLN
A 917 HIS
** A 928 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 931 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
A1014 GLN

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.5008 r_free = 0.5008 target = 0.262535 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 53)----------------|
| r_work = 0.4566 r_free = 0.4566 target = 0.202653 restraints weight = 11474.276|
|-----------------------------------------------------------------------------|
r_work (start): 0.4501 rms_B_bonded: 4.01
r_work: 0.4318 rms_B_bonded: 4.73 restraints_weight: 0.5000
r_work (final): 0.4318
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.5866
moved from start:          0.2131

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.041   9828  Z= 0.196
  Angle     :  0.612   9.720  13247  Z= 0.307
  Chirality :  0.041   0.183   1436
  Planarity :  0.004   0.067   1693
  Dihedral  :  4.159  19.513   1275
  Min Nonbonded Distance : 2.302

Molprobity Statistics.
  All-atom Clashscore : 10.61
  Ramachandran Plot:
    Outliers :  0.09 %
    Allowed  :  4.30 %
    Favored  : 95.61 %
  Rotamer:
    Outliers :  2.61 %
    Allowed  : 21.53 %
    Favored  : 75.86 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 4.26 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.06 (0.26), residues: 1140
  helix:  1.06 (0.23), residues: 527
  sheet: -1.01 (0.47), residues: 123
  loop : -0.73 (0.29), residues: 490

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.025   0.002   TRP A 783 
 HIS   0.006   0.001   HIS A 917 
 PHE   0.036   0.002   PHE A 744 
 TYR   0.014   0.001   TYR B 556 
 ARG   0.005   0.000   ARG A 832 

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

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

  2280 Ramachandran restraints generated.
    1140 Oldfield, 0 Emsley, 1140 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2280 Ramachandran restraints generated.
    1140 Oldfield, 0 Emsley, 1140 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  187 residues out of total 1073 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 28
    poor density    : 159
  time to evaluate  : 0.985 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  123 MET cc_start: 0.6438 (ppp) cc_final: 0.5975 (ppp)
REVERT: A  355 TYR cc_start: 0.6967 (p90) cc_final: 0.6413 (p90)
REVERT: A  479 TRP cc_start: 0.7144 (t-100) cc_final: 0.6840 (t-100)
REVERT: A  489 MET cc_start: 0.8545 (mmp) cc_final: 0.7762 (mpp)
REVERT: A  545 GLU cc_start: 0.8168 (pm20) cc_final: 0.7888 (pm20)
REVERT: A  546 GLN cc_start: 0.7838 (mp10) cc_final: 0.7437 (tm130)
REVERT: A  549 ASP cc_start: 0.8601 (m-30) cc_final: 0.8290 (m-30)
REVERT: A  579 GLU cc_start: 0.5012 (tt0) cc_final: 0.4421 (tt0)
REVERT: A  587 VAL cc_start: 0.4507 (OUTLIER) cc_final: 0.3131 (m)
REVERT: A  605 ASN cc_start: 0.7473 (m-40) cc_final: 0.6880 (m-40)
REVERT: A  608 ASP cc_start: 0.8273 (t70) cc_final: 0.7921 (t70)
REVERT: A  610 MET cc_start: 0.7017 (mpp) cc_final: 0.6658 (mpp)
REVERT: A  630 GLN cc_start: 0.8064 (tp-100) cc_final: 0.7738 (tp-100)
REVERT: A  745 MET cc_start: 0.7023 (mpp) cc_final: 0.6819 (mmt)
REVERT: A  811 MET cc_start: 0.7316 (OUTLIER) cc_final: 0.6678 (mpp)
REVERT: A  825 GLN cc_start: 0.6573 (tm-30) cc_final: 0.6026 (tp-100)
REVERT: A  886 LYS cc_start: 0.7776 (mmtt) cc_final: 0.7451 (mmpt)
REVERT: A  899 ARG cc_start: 0.7961 (mmt90) cc_final: 0.7715 (mmm-85)
REVERT: A  925 ASP cc_start: 0.7716 (t70) cc_final: 0.6645 (p0)
REVERT: A 1037 GLU cc_start: 0.6845 (OUTLIER) cc_final: 0.6565 (mm-30)
REVERT: A 1055 MET cc_start: 0.2125 (mpp) cc_final: 0.1239 (mpp)
REVERT: B  359 ASP cc_start: 0.8176 (m-30) cc_final: 0.7857 (m-30)
  outliers start: 28
  outliers final: 15
  residues processed: 177
  average time/residue: 1.0639
  time to fit residues: 204.1377
Evaluate side-chains
  169 residues out of total 1073 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 18
    poor density    : 151
  time to evaluate  : 1.405 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  149 GLU
Chi-restraints excluded: chain A residue  437 VAL
Chi-restraints excluded: chain A residue  484 VAL
Chi-restraints excluded: chain A residue  587 VAL
Chi-restraints excluded: chain A residue  603 ASP
Chi-restraints excluded: chain A residue  620 GLU
Chi-restraints excluded: chain A residue  636 VAL
Chi-restraints excluded: chain A residue  700 LYS
Chi-restraints excluded: chain A residue  811 MET
Chi-restraints excluded: chain A residue  816 ILE
Chi-restraints excluded: chain A residue  848 ILE
Chi-restraints excluded: chain A residue  917 HIS
Chi-restraints excluded: chain A residue  983 MET
Chi-restraints excluded: chain A residue 1037 GLU
Chi-restraints excluded: chain B residue  369 THR
Chi-restraints excluded: chain B residue  401 VAL
Chi-restraints excluded: chain B residue  420 LEU
Chi-restraints excluded: chain B residue  460 SER
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 116
   random chunks:
   chunk 92 optimal weight:    4.9990
   chunk 0 optimal weight:   20.0000
   chunk 45 optimal weight:    0.5980
   chunk 25 optimal weight:    4.9990
   chunk 11 optimal weight:    0.9990
   chunk 42 optimal weight:    8.9990
   chunk 53 optimal weight:    0.7980
   chunk 48 optimal weight:    0.9990
   chunk 67 optimal weight:    0.9980
   chunk 115 optimal weight:    6.9990
   chunk 94 optimal weight:    9.9990
   overall best weight:    0.8784

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

Flipped N/Q/H residues before XYZ refinement:
A 380 ASN
** A 630 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 749 GLN
A 917 HIS
** A 931 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
A1014 GLN
A1047 HIS

Total number of N/Q/H flips: 5

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.5008 r_free = 0.5008 target = 0.261883 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 47)----------------|
| r_work = 0.4555 r_free = 0.4555 target = 0.201303 restraints weight = 11578.652|
|-----------------------------------------------------------------------------|
r_work (start): 0.4497 rms_B_bonded: 4.08
r_work: 0.4314 rms_B_bonded: 4.79 restraints_weight: 0.5000
r_work (final): 0.4314
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.5865
moved from start:          0.2191

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.061   9828  Z= 0.216
  Angle     :  0.645   9.643  13247  Z= 0.322
  Chirality :  0.042   0.161   1436
  Planarity :  0.004   0.068   1693
  Dihedral  :  4.162  19.681   1275
  Min Nonbonded Distance : 2.284

Molprobity Statistics.
  All-atom Clashscore : 11.23
  Ramachandran Plot:
    Outliers :  0.09 %
    Allowed  :  4.39 %
    Favored  : 95.53 %
  Rotamer:
    Outliers :  2.33 %
    Allowed  : 22.37 %
    Favored  : 75.30 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 4.26 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.05 (0.26), residues: 1140
  helix:  1.02 (0.23), residues: 527
  sheet: -0.83 (0.49), residues: 116
  loop : -0.76 (0.29), residues: 497

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.020   0.001   TRP A 783 
 HIS   0.015   0.001   HIS A 917 
 PHE   0.042   0.002   PHE A 744 
 TYR   0.018   0.001   TYR A 343 
 ARG   0.005   0.000   ARG A 832 

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

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

  2280 Ramachandran restraints generated.
    1140 Oldfield, 0 Emsley, 1140 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2280 Ramachandran restraints generated.
    1140 Oldfield, 0 Emsley, 1140 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  178 residues out of total 1073 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 25
    poor density    : 153
  time to evaluate  : 1.138 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  123 MET cc_start: 0.6426 (ppp) cc_final: 0.5939 (ppp)
REVERT: A  355 TYR cc_start: 0.6961 (p90) cc_final: 0.6412 (p90)
REVERT: A  479 TRP cc_start: 0.7131 (t-100) cc_final: 0.6816 (t-100)
REVERT: A  545 GLU cc_start: 0.8222 (pm20) cc_final: 0.7905 (pm20)
REVERT: A  546 GLN cc_start: 0.7818 (mp10) cc_final: 0.7354 (tm130)
REVERT: A  549 ASP cc_start: 0.8625 (m-30) cc_final: 0.8321 (m-30)
REVERT: A  579 GLU cc_start: 0.5088 (tt0) cc_final: 0.4495 (tt0)
REVERT: A  587 VAL cc_start: 0.4492 (OUTLIER) cc_final: 0.3111 (m)
REVERT: A  605 ASN cc_start: 0.7468 (m-40) cc_final: 0.6872 (m-40)
REVERT: A  608 ASP cc_start: 0.8311 (t70) cc_final: 0.7982 (t70)
REVERT: A  610 MET cc_start: 0.7075 (mpp) cc_final: 0.6792 (mpp)
REVERT: A  630 GLN cc_start: 0.8078 (tp-100) cc_final: 0.7754 (tp-100)
REVERT: A  811 MET cc_start: 0.7303 (OUTLIER) cc_final: 0.6673 (mpp)
REVERT: A  825 GLN cc_start: 0.6584 (tm-30) cc_final: 0.6028 (tp-100)
REVERT: A  849 GLU cc_start: 0.7513 (mt-10) cc_final: 0.6707 (mm-30)
REVERT: A  886 LYS cc_start: 0.7745 (mmtt) cc_final: 0.7405 (mmpt)
REVERT: A  899 ARG cc_start: 0.7945 (mmt90) cc_final: 0.7718 (mmm-85)
REVERT: A  925 ASP cc_start: 0.7732 (OUTLIER) cc_final: 0.6645 (p0)
REVERT: A 1037 GLU cc_start: 0.6846 (OUTLIER) cc_final: 0.6586 (mm-30)
REVERT: A 1055 MET cc_start: 0.2116 (mpp) cc_final: 0.1186 (mpp)
REVERT: B  359 ASP cc_start: 0.8226 (m-30) cc_final: 0.7912 (m-30)
REVERT: B  478 GLN cc_start: 0.4117 (OUTLIER) cc_final: 0.3907 (tt0)
  outliers start: 25
  outliers final: 14
  residues processed: 168
  average time/residue: 1.0340
  time to fit residues: 188.5575
Evaluate side-chains
  169 residues out of total 1073 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 19
    poor density    : 150
  time to evaluate  : 0.987 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  149 GLU
Chi-restraints excluded: chain A residue  437 VAL
Chi-restraints excluded: chain A residue  484 VAL
Chi-restraints excluded: chain A residue  587 VAL
Chi-restraints excluded: chain A residue  603 ASP
Chi-restraints excluded: chain A residue  620 GLU
Chi-restraints excluded: chain A residue  636 VAL
Chi-restraints excluded: chain A residue  700 LYS
Chi-restraints excluded: chain A residue  811 MET
Chi-restraints excluded: chain A residue  816 ILE
Chi-restraints excluded: chain A residue  848 ILE
Chi-restraints excluded: chain A residue  925 ASP
Chi-restraints excluded: chain A residue  983 MET
Chi-restraints excluded: chain A residue 1037 GLU
Chi-restraints excluded: chain B residue  369 THR
Chi-restraints excluded: chain B residue  401 VAL
Chi-restraints excluded: chain B residue  420 LEU
Chi-restraints excluded: chain B residue  460 SER
Chi-restraints excluded: chain B residue  478 GLN
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 116
   random chunks:
   chunk 72 optimal weight:    0.2980
   chunk 56 optimal weight:    0.9980
   chunk 32 optimal weight:    0.3980
   chunk 1 optimal weight:    8.9990
   chunk 89 optimal weight:    3.9990
   chunk 4 optimal weight:   30.0000
   chunk 62 optimal weight:    1.9990
   chunk 82 optimal weight:    4.9990
   chunk 88 optimal weight:    0.3980
   chunk 60 optimal weight:    2.9990
   chunk 11 optimal weight:    4.9990
   overall best weight:    0.8182

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

Flipped N/Q/H residues before XYZ refinement:
A 380 ASN
** A 630 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 749 GLN
A 917 HIS
** A 931 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
A1014 GLN

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.5006 r_free = 0.5006 target = 0.262122 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.4563 r_free = 0.4563 target = 0.202386 restraints weight = 11378.397|
|-----------------------------------------------------------------------------|
r_work (start): 0.4506 rms_B_bonded: 4.04
r_work: 0.4321 rms_B_bonded: 4.78 restraints_weight: 0.5000
r_work (final): 0.4321
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.5859
moved from start:          0.2270

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.048   9828  Z= 0.206
  Angle     :  0.650  10.269  13247  Z= 0.325
  Chirality :  0.043   0.222   1436
  Planarity :  0.004   0.067   1693
  Dihedral  :  4.160  20.068   1275
  Min Nonbonded Distance : 2.284

Molprobity Statistics.
  All-atom Clashscore : 11.08
  Ramachandran Plot:
    Outliers :  0.09 %
    Allowed  :  4.56 %
    Favored  : 95.35 %
  Rotamer:
    Outliers :  1.96 %
    Allowed  : 22.83 %
    Favored  : 75.21 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 4.26 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -0.02 (0.26), residues: 1140
  helix:  1.00 (0.23), residues: 526
  sheet: -0.85 (0.49), residues: 116
  loop : -0.84 (0.29), residues: 498

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.010   0.001   TRP A 783 
 HIS   0.006   0.001   HIS A 917 
 PHE   0.034   0.002   PHE A 744 
 TYR   0.018   0.001   TYR A 343 
 ARG   0.006   0.000   ARG A 832 

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

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

  2280 Ramachandran restraints generated.
    1140 Oldfield, 0 Emsley, 1140 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2280 Ramachandran restraints generated.
    1140 Oldfield, 0 Emsley, 1140 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  167 residues out of total 1073 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 21
    poor density    : 146
  time to evaluate  : 1.006 
Fit side-chains
   revert: symmetry clash
REVERT: A   30 MET cc_start: 0.4361 (mmp) cc_final: 0.3504 (mmm)
REVERT: A  123 MET cc_start: 0.6433 (ppp) cc_final: 0.5916 (ppp)
REVERT: A  355 TYR cc_start: 0.6961 (p90) cc_final: 0.6437 (p90)
REVERT: A  479 TRP cc_start: 0.7121 (t-100) cc_final: 0.6828 (t-100)
REVERT: A  545 GLU cc_start: 0.8181 (pm20) cc_final: 0.7828 (pm20)
REVERT: A  546 GLN cc_start: 0.7811 (mp10) cc_final: 0.7350 (tm130)
REVERT: A  549 ASP cc_start: 0.8618 (m-30) cc_final: 0.8311 (m-30)
REVERT: A  579 GLU cc_start: 0.4991 (tt0) cc_final: 0.4411 (tt0)
REVERT: A  587 VAL cc_start: 0.4469 (OUTLIER) cc_final: 0.3086 (m)
REVERT: A  608 ASP cc_start: 0.8265 (t70) cc_final: 0.7927 (t70)
REVERT: A  610 MET cc_start: 0.7084 (mpp) cc_final: 0.6754 (mpp)
REVERT: A  630 GLN cc_start: 0.8081 (tp-100) cc_final: 0.7766 (tp-100)
REVERT: A  772 MET cc_start: -0.0402 (pmt) cc_final: -0.1005 (ptp)
REVERT: A  806 ASP cc_start: 0.7042 (t70) cc_final: 0.6825 (OUTLIER)
REVERT: A  809 GLN cc_start: 0.6985 (pm20) cc_final: 0.6388 (pp30)
REVERT: A  811 MET cc_start: 0.7306 (OUTLIER) cc_final: 0.6820 (mpp)
REVERT: A  825 GLN cc_start: 0.6581 (tm-30) cc_final: 0.6021 (tp-100)
REVERT: A  849 GLU cc_start: 0.7463 (mt-10) cc_final: 0.6656 (mm-30)
REVERT: A  886 LYS cc_start: 0.7792 (mmtt) cc_final: 0.7447 (mmpt)
REVERT: A  899 ARG cc_start: 0.7948 (mmt90) cc_final: 0.7726 (mmm-85)
REVERT: A 1037 GLU cc_start: 0.6828 (OUTLIER) cc_final: 0.6573 (mm-30)
REVERT: A 1055 MET cc_start: 0.2272 (mpp) cc_final: 0.1383 (mpp)
REVERT: B  359 ASP cc_start: 0.8224 (m-30) cc_final: 0.7938 (m-30)
  outliers start: 21
  outliers final: 15
  residues processed: 160
  average time/residue: 1.0019
  time to fit residues: 174.4886
Evaluate side-chains
  164 residues out of total 1073 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 17
    poor density    : 147
  time to evaluate  : 0.964 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  380 ASN
Chi-restraints excluded: chain A residue  437 VAL
Chi-restraints excluded: chain A residue  484 VAL
Chi-restraints excluded: chain A residue  587 VAL
Chi-restraints excluded: chain A residue  620 GLU
Chi-restraints excluded: chain A residue  636 VAL
Chi-restraints excluded: chain A residue  700 LYS
Chi-restraints excluded: chain A residue  811 MET
Chi-restraints excluded: chain A residue  816 ILE
Chi-restraints excluded: chain A residue  848 ILE
Chi-restraints excluded: chain A residue  917 HIS
Chi-restraints excluded: chain A residue  983 MET
Chi-restraints excluded: chain A residue 1037 GLU
Chi-restraints excluded: chain B residue  369 THR
Chi-restraints excluded: chain B residue  401 VAL
Chi-restraints excluded: chain B residue  420 LEU
Chi-restraints excluded: chain B residue  460 SER
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 116
   random chunks:
   chunk 111 optimal weight:    5.9990
   chunk 4 optimal weight:   10.0000
   chunk 109 optimal weight:    8.9990
   chunk 33 optimal weight:    0.0370
   chunk 62 optimal weight:    8.9990
   chunk 28 optimal weight:    5.9990
   chunk 59 optimal weight:    0.5980
   chunk 91 optimal weight:    6.9990
   chunk 29 optimal weight:    0.9980
   chunk 32 optimal weight:    0.9980
   chunk 68 optimal weight:    0.9980
   overall best weight:    0.7258

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

Flipped N/Q/H residues before XYZ refinement:
** A 370 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 380 ASN
** A 630 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 749 GLN
A 917 HIS
** A 931 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
A1014 GLN

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.5018 r_free = 0.5018 target = 0.263066 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 43)----------------|
| r_work = 0.4573 r_free = 0.4573 target = 0.203224 restraints weight = 11512.240|
|-----------------------------------------------------------------------------|
r_work (start): 0.4482 rms_B_bonded: 4.07
r_work: 0.4291 rms_B_bonded: 4.84 restraints_weight: 0.5000
r_work (final): 0.4291
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.5854
moved from start:          0.2349

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.047   9828  Z= 0.208
  Angle     :  0.665  11.007  13247  Z= 0.330
  Chirality :  0.043   0.284   1436
  Planarity :  0.004   0.067   1693
  Dihedral  :  4.163  19.797   1275
  Min Nonbonded Distance : 2.276

Molprobity Statistics.
  All-atom Clashscore : 11.13
  Ramachandran Plot:
    Outliers :  0.09 %
    Allowed  :  4.56 %
    Favored  : 95.35 %
  Rotamer:
    Outliers :  1.86 %
    Allowed  : 23.39 %
    Favored  : 74.74 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 4.26 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -0.03 (0.26), residues: 1140
  helix:  0.98 (0.23), residues: 526
  sheet: -0.80 (0.49), residues: 116
  loop : -0.86 (0.28), residues: 498

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.011   0.001   TRP A 574 
 HIS   0.018   0.001   HIS A 917 
 PHE   0.039   0.002   PHE A 744 
 TYR   0.017   0.001   TYR A 343 
 ARG   0.006   0.000   ARG A 832 

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

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

  2280 Ramachandran restraints generated.
    1140 Oldfield, 0 Emsley, 1140 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2280 Ramachandran restraints generated.
    1140 Oldfield, 0 Emsley, 1140 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  167 residues out of total 1073 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 20
    poor density    : 147
  time to evaluate  : 1.074 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  123 MET cc_start: 0.6432 (ppp) cc_final: 0.5955 (ppp)
REVERT: A  355 TYR cc_start: 0.7003 (p90) cc_final: 0.6485 (p90)
REVERT: A  479 TRP cc_start: 0.7128 (t-100) cc_final: 0.6836 (t-100)
REVERT: A  489 MET cc_start: 0.8580 (mmp) cc_final: 0.7850 (mpp)
REVERT: A  545 GLU cc_start: 0.8119 (pm20) cc_final: 0.7803 (pm20)
REVERT: A  546 GLN cc_start: 0.7822 (mp10) cc_final: 0.7213 (tm130)
REVERT: A  549 ASP cc_start: 0.8615 (m-30) cc_final: 0.8303 (m-30)
REVERT: A  579 GLU cc_start: 0.4930 (tt0) cc_final: 0.4353 (tt0)
REVERT: A  587 VAL cc_start: 0.4455 (OUTLIER) cc_final: 0.3067 (m)
REVERT: A  608 ASP cc_start: 0.8186 (t70) cc_final: 0.7867 (t70)
REVERT: A  610 MET cc_start: 0.7104 (mpp) cc_final: 0.6774 (mpp)
REVERT: A  630 GLN cc_start: 0.8065 (tp-100) cc_final: 0.7769 (tp-100)
REVERT: A  772 MET cc_start: -0.0404 (pmt) cc_final: -0.1002 (ptp)
REVERT: A  809 GLN cc_start: 0.6950 (pm20) cc_final: 0.6398 (pp30)
REVERT: A  811 MET cc_start: 0.7323 (OUTLIER) cc_final: 0.6854 (mpp)
REVERT: A  825 GLN cc_start: 0.6523 (tm-30) cc_final: 0.6052 (tp-100)
REVERT: A  849 GLU cc_start: 0.7454 (mt-10) cc_final: 0.6645 (mm-30)
REVERT: A  886 LYS cc_start: 0.7813 (mmtt) cc_final: 0.7473 (mmpt)
REVERT: A  899 ARG cc_start: 0.7953 (mmt90) cc_final: 0.7739 (mmm-85)
REVERT: A  925 ASP cc_start: 0.7750 (t70) cc_final: 0.6601 (p0)
REVERT: A 1037 GLU cc_start: 0.6744 (OUTLIER) cc_final: 0.6500 (mm-30)
REVERT: A 1055 MET cc_start: 0.2261 (mpp) cc_final: 0.1425 (mpp)
REVERT: B  359 ASP cc_start: 0.8261 (m-30) cc_final: 0.7947 (m-30)
  outliers start: 20
  outliers final: 15
  residues processed: 160
  average time/residue: 1.0775
  time to fit residues: 187.3701
Evaluate side-chains
  162 residues out of total 1073 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 18
    poor density    : 144
  time to evaluate  : 1.070 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  437 VAL
Chi-restraints excluded: chain A residue  484 VAL
Chi-restraints excluded: chain A residue  587 VAL
Chi-restraints excluded: chain A residue  603 ASP
Chi-restraints excluded: chain A residue  620 GLU
Chi-restraints excluded: chain A residue  636 VAL
Chi-restraints excluded: chain A residue  700 LYS
Chi-restraints excluded: chain A residue  806 ASP
Chi-restraints excluded: chain A residue  811 MET
Chi-restraints excluded: chain A residue  816 ILE
Chi-restraints excluded: chain A residue  848 ILE
Chi-restraints excluded: chain A residue  917 HIS
Chi-restraints excluded: chain A residue  983 MET
Chi-restraints excluded: chain A residue 1037 GLU
Chi-restraints excluded: chain B residue  369 THR
Chi-restraints excluded: chain B residue  401 VAL
Chi-restraints excluded: chain B residue  420 LEU
Chi-restraints excluded: chain B residue  460 SER
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 116
   random chunks:
   chunk 16 optimal weight:    0.0570
   chunk 109 optimal weight:    9.9990
   chunk 5 optimal weight:    0.0270
   chunk 65 optimal weight:    0.0670
   chunk 99 optimal weight:    0.9980
   chunk 55 optimal weight:    0.7980
   chunk 61 optimal weight:    0.0980
   chunk 83 optimal weight:    0.7980
   chunk 69 optimal weight:    4.9990
   chunk 31 optimal weight:    0.3980
   chunk 32 optimal weight:    2.9990
   overall best weight:    0.1294

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

Flipped N/Q/H residues before XYZ refinement:
A 380 ASN
** A 630 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 749 GLN
A 782 ASN
A 809 GLN
A 917 HIS
** A 931 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
A1014 GLN
** B 365 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 6

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.5044 r_free = 0.5044 target = 0.266747 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 43)----------------|
| r_work = 0.4616 r_free = 0.4616 target = 0.208012 restraints weight = 11536.698|
|-----------------------------------------------------------------------------|
r_work (start): 0.4561 rms_B_bonded: 4.10
r_work: 0.4376 rms_B_bonded: 4.87 restraints_weight: 0.5000
r_work (final): 0.4376
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.5774
moved from start:          0.2489

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.044   9828  Z= 0.184
  Angle     :  0.661  10.768  13247  Z= 0.331
  Chirality :  0.043   0.207   1436
  Planarity :  0.004   0.068   1693
  Dihedral  :  4.117  21.459   1275
  Min Nonbonded Distance : 2.278

Molprobity Statistics.
  All-atom Clashscore : 10.66
  Ramachandran Plot:
    Outliers :  0.09 %
    Allowed  :  4.21 %
    Favored  : 95.70 %
  Rotamer:
    Outliers :  1.49 %
    Allowed  : 23.86 %
    Favored  : 74.65 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 4.26 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.07 (0.26), residues: 1140
  helix:  1.08 (0.23), residues: 526
  sheet: -0.62 (0.49), residues: 115
  loop : -0.88 (0.28), residues: 499

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.015   0.001   TRP A 574 
 HIS   0.008   0.001   HIS A 917 
 PHE   0.039   0.001   PHE A 744 
 TYR   0.017   0.001   TYR A 343 
 ARG   0.005   0.000   ARG A 832 
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 8992.73 seconds
wall clock time: 156 minutes 19.10 seconds (9379.10 seconds total)