Starting phenix.real_space_refine
on Tue Mar 11 17:51:07 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/8h3u_32828/03_2025/8h3u_32828.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/8h3u_32828/03_2025/8h3u_32828.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=4.7
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/cci-nas-00/data/ceres_data/8h3u_32828/03_2025/8h3u_32828.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/8h3u_32828/03_2025/8h3u_32828.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/8h3u_32828/03_2025/8h3u_32828.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/8h3u_32828/03_2025/8h3u_32828.cif"
  }
  resolution = 4.7
  write_initial_geo_file = False
  refinement {
    macro_cycles = 10
  }
  qi {
    qm_restraints {
      package {
        program = *test
      }
    }
  }


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

Validating inputs
Origin is already at (0, 0, 0), no shifts will be applied
-------------------------------------------------------------------------------
Processing inputs
*****************
Set random seed
  Set to: 0
Set model cs if undefined
Decide on map wrapping
  Map wrapping is set to: False
Normalize map: mean=0, sd=1
  Input map: mean=   0.001 sd=   0.020
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      44      5.16       5
     C    4023      2.51       5
     N    1076      2.21       5
     O    1240      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 1 residue(s): 0.02s

  Monomer Library directory:
    "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5624/modules/chem_data/mon_lib"
  Total number of atoms: 6383
  Number of models: 1
  Model: ""
    Number of chains: 2
    Chain: "A"
      Number of atoms: 4539
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 583, 4539
          Classifications: {'peptide': 583}
          Link IDs: {'PTRANS': 28, 'TRANS': 554}
          Chain breaks: 1
    Chain: "B"
      Number of atoms: 1844
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 235, 1844
          Classifications: {'peptide': 235}
          Modifications used: {'COO': 1}
          Link IDs: {'PTRANS': 14, 'TRANS': 220}
  Time building chain proxies: 4.60, per 1000 atoms: 0.72
  Number of scatterers: 6383
  At special positions: 0
  Unit cell: (94.14, 94.14, 154.808, 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      44     16.00
     O    1240      8.00
     N    1076      7.00
     C    4023      6.00
    sf(0) = scattering factor at diffraction angle 0.

  Number of disulfides: simple=14, symmetry=0
    Simple disulfide: pdb=" SG  CYS A 184 " - pdb=" SG  CYS A 197 " distance=2.03
    Simple disulfide: pdb=" SG  CYS A 191 " - pdb=" SG  CYS A 210 " distance=2.03
    Simple disulfide: pdb=" SG  CYS A 204 " - pdb=" SG  CYS A 221 " distance=2.03
    Simple disulfide: pdb=" SG  CYS A 225 " - pdb=" SG  CYS A 253 " distance=2.03
    Simple disulfide: pdb=" SG  CYS A 347 " - pdb=" SG  CYS A 354 " distance=2.03
    Simple disulfide: pdb=" SG  CYS A 422 " - pdb=" SG  CYS A 502 " distance=2.03
    Simple disulfide: pdb=" SG  CYS A 650 " - pdb=" SG  CYS A 668 " distance=2.03
    Simple disulfide: pdb=" SG  CYS A 662 " - pdb=" SG  CYS A 677 " distance=2.03
    Simple disulfide: pdb=" SG  CYS A 716 " - pdb=" SG  CYS A 767 " distance=2.03
    Simple disulfide: pdb=" SG  CYS A 772 " - pdb=" SG  CYS B 896 " distance=2.03
    Simple disulfide: pdb=" SG  CYS B 810 " - pdb=" SG  CYS B 826 " distance=2.03
    Simple disulfide: pdb=" SG  CYS B 910 " - pdb=" SG  CYS B 977 " distance=2.03
    Simple disulfide: pdb=" SG  CYS B 941 " - pdb=" SG  CYS B 956 " distance=2.03
    Simple disulfide: pdb=" SG  CYS B 967 " - pdb=" SG  CYS B 995 " distance=2.03

  Automatic linking
    Parameters for automatic linking
      Linking & cutoffs
        Metal                : Auto  - 3.00
        Amino acid           : True  - 1.90
        Carbohydrate         : True  - 1.99
        Ligands              : True  - 1.99
        Small molecules      : False - 1.98
        Amino acid - RNA/DNA : False
      
  Number of custom bonds: simple=0, symmetry=0
  Time building additional restraints: 1.54
  Conformation dependent library (CDL) restraints added in 962.2 milliseconds
  

  1624 Ramachandran restraints generated.
    812 Oldfield, 0 Emsley, 812 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  1496

  Finding SS restraints...
    Secondary structure from input PDB file:
      11 helices and 13 sheets defined
      8.1% alpha, 24.1% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 0.80
  Creating SS restraints...
    Processing helix  chain 'A' and resid 201 through 203
      No H-bonds generated for 'chain 'A' and resid 201 through 203'
    Processing helix  chain 'A' and resid 213 through 217
    Processing helix  chain 'A' and resid 286 through 290
      removed outlier: 3.762A  pdb=" N   SER A 289 " --> pdb=" O   VAL A 286 " (cutoff:3.500A)
      removed outlier: 3.505A  pdb=" N   LYS A 290 " --> pdb=" O   GLY A 287 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'A' and resid 286 through 290'
    Processing helix  chain 'A' and resid 340 through 346
    Processing helix  chain 'A' and resid 531 through 534
    Processing helix  chain 'A' and resid 671 through 675
    Processing helix  chain 'A' and resid 708 through 719
    Processing helix  chain 'B' and resid 833 through 835
      No H-bonds generated for 'chain 'B' and resid 833 through 835'
    Processing helix  chain 'B' and resid 937 through 945
    Processing helix  chain 'B' and resid 1007 through 1009
      No H-bonds generated for 'chain 'B' and resid 1007 through 1009'
    Processing helix  chain 'B' and resid 1010 through 1019
      removed outlier: 3.965A  pdb=" N   PHE B1017 " --> pdb=" O   TRP B1013 " (cutoff:3.500A)
      removed outlier: 4.065A  pdb=" N   HIS B1019 " --> pdb=" O   GLN B1015 " (cutoff:3.500A)
    Processing sheet with id=AA1, first strand: chain 'A' and resid 188 through 190
      removed outlier: 3.732A  pdb=" N   ILE A 198 " --> pdb=" O   SER A 189 " (cutoff:3.500A)
    Processing sheet with id=AA2, first strand: chain 'A' and resid 230 through 231
      removed outlier: 6.433A  pdb=" N   LEU A 280 " --> pdb=" O   SER A 295 " (cutoff:3.500A)
      removed outlier: 4.568A  pdb=" N   SER A 295 " --> pdb=" O   LEU A 280 " (cutoff:3.500A)
      removed outlier: 7.337A  pdb=" N   ILE A 282 " --> pdb=" O   ARG A 293 " (cutoff:3.500A)
    Processing sheet with id=AA3, first strand: chain 'A' and resid 235 through 239
      removed outlier: 3.537A  pdb=" N   GLY A 236 " --> pdb=" O   TYR A 331 " (cutoff:3.500A)
      removed outlier: 7.218A  pdb=" N   GLY A 326 " --> pdb=" O   PHE A 272 " (cutoff:3.500A)
      removed outlier: 4.331A  pdb=" N   PHE A 272 " --> pdb=" O   GLY A 326 " (cutoff:3.500A)
      removed outlier: 6.977A  pdb=" N   ASN A 328 " --> pdb=" O   ASP A 270 " (cutoff:3.500A)
    Processing sheet with id=AA4, first strand: chain 'A' and resid 357 through 358
    Processing sheet with id=AA5, first strand: chain 'A' and resid 367 through 370
      removed outlier: 3.704A  pdb=" N   ILE A 369 " --> pdb=" O   TYR A 393 " (cutoff:3.500A)
      removed outlier: 4.011A  pdb=" N   TYR A 393 " --> pdb=" O   ILE A 369 " (cutoff:3.500A)
      removed outlier: 12.752A  pdb=" N   PHE A 392 " --> pdb=" O   ASP A 494 " (cutoff:3.500A)
      removed outlier: 6.957A  pdb=" N   ASP A 494 " --> pdb=" O   PHE A 392 " (cutoff:3.500A)
      removed outlier: 3.583A  pdb=" N   ILE A 394 " --> pdb=" O   LEU A 492 " (cutoff:3.500A)
      removed outlier: 5.677A  pdb=" N   LEU A 492 " --> pdb=" O   HIS A 428 " (cutoff:3.500A)
      removed outlier: 7.016A  pdb=" N   HIS A 428 " --> pdb=" O   LEU A 492 " (cutoff:3.500A)
      removed outlier: 5.202A  pdb=" N   ASP A 494 " --> pdb=" O   TRP A 426 " (cutoff:3.500A)
      removed outlier: 3.721A  pdb=" N   TRP A 426 " --> pdb=" O   ASP A 494 " (cutoff:3.500A)
    Processing sheet with id=AA6, first strand: chain 'A' and resid 405 through 407
      removed outlier: 3.521A  pdb=" N   SER A 438 " --> pdb=" O   ASN A 480 " (cutoff:3.500A)
      removed outlier: 3.599A  pdb=" N   PHE A 482 " --> pdb=" O   LYS A 436 " (cutoff:3.500A)
      removed outlier: 4.382A  pdb=" N   LYS A 436 " --> pdb=" O   PHE A 482 " (cutoff:3.500A)
      removed outlier: 3.921A  pdb=" N   PHE A 452 " --> pdb=" O   ILE A 439 " (cutoff:3.500A)
      removed outlier: 6.977A  pdb=" N   ILE A 441 " --> pdb=" O   THR A 450 " (cutoff:3.500A)
      removed outlier: 5.876A  pdb=" N   THR A 450 " --> pdb=" O   ILE A 441 " (cutoff:3.500A)
    Processing sheet with id=AA7, first strand: chain 'A' and resid 536 through 537
      removed outlier: 3.696A  pdb=" N   PHE A 537 " --> pdb=" O   ALA A 629 " (cutoff:3.500A)
      removed outlier: 4.075A  pdb=" N   ALA A 629 " --> pdb=" O   PHE A 537 " (cutoff:3.500A)
      removed outlier: 6.662A  pdb=" N   ASN A 630 " --> pdb=" O   PHE A 568 " (cutoff:3.500A)
      removed outlier: 5.238A  pdb=" N   PHE A 568 " --> pdb=" O   ASN A 630 " (cutoff:3.500A)
      removed outlier: 7.409A  pdb=" N   THR A 632 " --> pdb=" O   LEU A 566 " (cutoff:3.500A)
      removed outlier: 5.863A  pdb=" N   LEU A 566 " --> pdb=" O   THR A 632 " (cutoff:3.500A)
    Processing sheet with id=AA8, first strand: chain 'A' and resid 594 through 596
      removed outlier: 3.695A  pdb=" N   ALA A 594 " --> pdb=" O   ILE A 582 " (cutoff:3.500A)
    Processing sheet with id=AA9, first strand: chain 'A' and resid 693 through 694
    Processing sheet with id=AB1, first strand: chain 'A' and resid 724 through 729
      removed outlier: 3.631A  pdb=" N   GLN A 766 " --> pdb=" O   SER A 726 " (cutoff:3.500A)
      removed outlier: 3.692A  pdb=" N   LYS A 728 " --> pdb=" O   ARG A 764 " (cutoff:3.500A)
    Processing sheet with id=AB2, first strand: chain 'A' and resid 740 through 743
      removed outlier: 3.570A  pdb=" N   THR A 752 " --> pdb=" O   LYS A 740 " (cutoff:3.500A)
    Processing sheet with id=AB3, first strand: chain 'B' and resid 789 through 790
      removed outlier: 3.687A  pdb=" N   SER B 789 " --> pdb=" O   GLU B 930 " (cutoff:3.500A)
      removed outlier: 3.872A  pdb=" N   GLN B 929 " --> pdb=" O   GLY B 914 " (cutoff:3.500A)
      removed outlier: 3.594A  pdb=" N   GLY B 914 " --> pdb=" O   GLN B 929 " (cutoff:3.500A)
      removed outlier: 4.214A  pdb=" N   ALA B 913 " --> pdb=" O   PRO B 974 " (cutoff:3.500A)
      removed outlier: 3.713A  pdb=" N   GLY B 987 " --> pdb=" O   LEU B 975 " (cutoff:3.500A)
      removed outlier: 7.300A  pdb=" N   CYS B 977 " --> pdb=" O   LEU B 985 " (cutoff:3.500A)
      removed outlier: 5.952A  pdb=" N   LEU B 985 " --> pdb=" O   CYS B 977 " (cutoff:3.500A)
      removed outlier: 7.193A  pdb=" N   VAL B1003 " --> pdb=" O   SER B 990 " (cutoff:3.500A)
    Processing sheet with id=AB4, first strand: chain 'B' and resid 808 through 812
      removed outlier: 6.242A  pdb=" N   LEU B 808 " --> pdb=" O   TYR B 804 " (cutoff:3.500A)
      removed outlier: 6.441A  pdb=" N   TYR B 804 " --> pdb=" O   LEU B 808 " (cutoff:3.500A)
      removed outlier: 4.305A  pdb=" N   CYS B 810 " --> pdb=" O   LEU B 802 " (cutoff:3.500A)
      removed outlier: 3.814A  pdb=" N   LEU B 802 " --> pdb=" O   CYS B 810 " (cutoff:3.500A)
      removed outlier: 3.566A  pdb=" N   VAL B 800 " --> pdb=" O   ALA B 812 " (cutoff:3.500A)
      removed outlier: 5.603A  pdb=" N   TRP B 837 " --> pdb=" O   ILE B 859 " (cutoff:3.500A)
      removed outlier: 4.107A  pdb=" N   GLU B 861 " --> pdb=" O   HIS B 881 " (cutoff:3.500A)

    132 hydrogen bonds defined for protein.
    336 hydrogen bond angles defined for protein.
    Restraints generated for nucleic acids:
      0 hydrogen bonds
      0 hydrogen bond angles
      0 basepair planarities
      0 basepair parallelities
      0 stacking parallelities
  Total time for adding SS restraints: 2.09

  Time building geometry restraints manager: 1.88 seconds

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

  Histogram of bond lengths:
        1.23 -     1.34: 2125
        1.34 -     1.46: 1508
        1.46 -     1.58: 2856
        1.58 -     1.69: 0
        1.69 -     1.81: 54
  Bond restraints: 6543
  Sorted by residual:
  bond pdb=" C   PHE A 542 "
       pdb=" N   PRO A 543 "
    ideal  model  delta    sigma   weight residual
    1.337  1.356 -0.019 1.06e-02 8.90e+03 3.24e+00
  bond pdb=" N   PHE A 542 "
       pdb=" CA  PHE A 542 "
    ideal  model  delta    sigma   weight residual
    1.457  1.481 -0.024 1.41e-02 5.03e+03 2.95e+00
  bond pdb=" N   ASN A 541 "
       pdb=" CA  ASN A 541 "
    ideal  model  delta    sigma   weight residual
    1.466  1.487 -0.021 1.51e-02 4.39e+03 1.93e+00
  bond pdb=" N   ILE B 840 "
       pdb=" CA  ILE B 840 "
    ideal  model  delta    sigma   weight residual
    1.459  1.474 -0.015 1.19e-02 7.06e+03 1.62e+00
  bond pdb=" N   ILE A 750 "
       pdb=" CA  ILE A 750 "
    ideal  model  delta    sigma   weight residual
    1.459  1.474 -0.015 1.19e-02 7.06e+03 1.52e+00
  ... (remaining 6538 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     1.61: 8710
        1.61 -     3.21: 177
        3.21 -     4.82: 12
        4.82 -     6.42: 3
        6.42 -     8.03: 2
  Bond angle restraints: 8904
  Sorted by residual:
  angle pdb=" CA  PHE A 542 "
        pdb=" C   PHE A 542 "
        pdb=" N   PRO A 543 "
      ideal   model   delta    sigma   weight residual
     118.44  126.47   -8.03 1.59e+00 3.96e-01 2.55e+01
  angle pdb=" CA  PHE A 542 "
        pdb=" C   PHE A 542 "
        pdb=" O   PHE A 542 "
      ideal   model   delta    sigma   weight residual
     120.16  114.14    6.02 1.37e+00 5.33e-01 1.93e+01
  angle pdb=" N   PRO A 543 "
        pdb=" CA  PRO A 543 "
        pdb=" C   PRO A 543 "
      ideal   model   delta    sigma   weight residual
     114.27  109.53    4.74 1.35e+00 5.49e-01 1.23e+01
  angle pdb=" C   PHE A 542 "
        pdb=" N   PRO A 543 "
        pdb=" CA  PRO A 543 "
      ideal   model   delta    sigma   weight residual
     120.04  116.43    3.61 1.08e+00 8.57e-01 1.12e+01
  angle pdb=" N   VAL B 827 "
        pdb=" CA  VAL B 827 "
        pdb=" C   VAL B 827 "
      ideal   model   delta    sigma   weight residual
     112.29  109.19    3.10 9.40e-01 1.13e+00 1.08e+01
  ... (remaining 8899 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    16.40: 3743
       16.40 -    32.79: 111
       32.79 -    49.19: 20
       49.19 -    65.58: 1
       65.58 -    81.98: 3
  Dihedral angle restraints: 3878
    sinusoidal: 1540
      harmonic: 2338
  Sorted by residual:
  dihedral pdb=" CA  SER A 539 "
           pdb=" C   SER A 539 "
           pdb=" N   THR A 540 "
           pdb=" CA  THR A 540 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  161.25   18.75     0      5.00e+00 4.00e-02 1.41e+01
  dihedral pdb=" CB  GLU B 952 "
           pdb=" CG  GLU B 952 "
           pdb=" CD  GLU B 952 "
           pdb=" OE1 GLU B 952 "
      ideal   model   delta sinusoidal    sigma   weight residual
       0.00  -81.98   81.98     1      3.00e+01 1.11e-03 9.18e+00
  dihedral pdb=" N   TYR A 635 "
           pdb=" CA  TYR A 635 "
           pdb=" CB  TYR A 635 "
           pdb=" CG  TYR A 635 "
      ideal   model   delta sinusoidal    sigma   weight residual
     -60.00 -110.96   50.96     3      1.50e+01 4.44e-03 8.96e+00
  ... (remaining 3875 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.027: 561
       0.027 -    0.053: 264
       0.053 -    0.080: 49
       0.080 -    0.107: 63
       0.107 -    0.133: 24
  Chirality restraints: 961
  Sorted by residual:
  chirality pdb=" CA  ASN A 541 "
            pdb=" N   ASN A 541 "
            pdb=" C   ASN A 541 "
            pdb=" CB  ASN A 541 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.64   -0.13 2.00e-01 2.50e+01 4.45e-01
  chirality pdb=" CA  ILE A 490 "
            pdb=" N   ILE A 490 "
            pdb=" C   ILE A 490 "
            pdb=" CB  ILE A 490 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.43    2.56   -0.12 2.00e-01 2.50e+01 3.86e-01
  chirality pdb=" CB  VAL A 691 "
            pdb=" CA  VAL A 691 "
            pdb=" CG1 VAL A 691 "
            pdb=" CG2 VAL A 691 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.63   -2.51   -0.12 2.00e-01 2.50e+01 3.57e-01
  ... (remaining 958 not shown)

  Planarity restraints: 1179
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  THR A 540 "   -0.015 2.00e-02 2.50e+03   3.01e-02 9.07e+00
        pdb=" C   THR A 540 "    0.052 2.00e-02 2.50e+03
        pdb=" O   THR A 540 "   -0.020 2.00e-02 2.50e+03
        pdb=" N   ASN A 541 "   -0.018 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   GLU A 532 "    0.023 5.00e-02 4.00e+02   3.44e-02 1.89e+00
        pdb=" N   PRO A 533 "   -0.059 5.00e-02 4.00e+02
        pdb=" CA  PRO A 533 "    0.017 5.00e-02 4.00e+02
        pdb=" CD  PRO A 533 "    0.019 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   LYS A 245 "   -0.017 5.00e-02 4.00e+02   2.60e-02 1.08e+00
        pdb=" N   PRO A 246 "    0.045 5.00e-02 4.00e+02
        pdb=" CA  PRO A 246 "   -0.013 5.00e-02 4.00e+02
        pdb=" CD  PRO A 246 "   -0.015 5.00e-02 4.00e+02
  ... (remaining 1176 not shown)

  Histogram of nonbonded interaction distances:
        2.28 -     2.80: 1763
        2.80 -     3.33: 5581
        3.33 -     3.85: 10111
        3.85 -     4.38: 11704
        4.38 -     4.90: 20083
  Nonbonded interactions: 49242
  Sorted by model distance:
  nonbonded pdb=" ND2 ASN B 848 "
            pdb=" OG  SER B 851 "
     model   vdw
     2.279 3.120
  nonbonded pdb=" OD2 ASP B 874 "
            pdb=" ND2 ASN B 875 "
     model   vdw
     2.297 3.120
  nonbonded pdb=" OD1 ASP A 584 "
            pdb=" OG1 THR A 609 "
     model   vdw
     2.299 3.040
  nonbonded pdb=" O   PRO A 397 "
            pdb=" NZ  LYS A 483 "
     model   vdw
     2.321 3.120
  nonbonded pdb=" O   ASP A 578 "
            pdb=" OG1 THR A 597 "
     model   vdw
     2.355 3.040
  ... (remaining 49237 not shown)

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

  No NCS relation were found !!!

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

Found NCS groups:
  found none.
Set up NCS constraints
  No NCS constraints will be used in refinement.
Set refine NCS operators
Adjust number of macro_cycles
  Number of macro_cycles: 10
Reset NCS operators
Extract rigid body selections
Check and reset occupancies
  Occupancies: min=1.00 max=1.00 mean=1.00
Load rotamer database and sin/cos tables
Set ADP refinement strategy
  ADPs will be refined as group one per residue
Make a string to write initial .geo file
Internal consistency checks
Time:
  Set random seed:                         0.000
  Set model cs if undefined:               0.000
  Decide on map wrapping:                  0.000
  Normalize map: mean=0, sd=1:             1.970
  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:          0.250
  Check model and map are aligned:         0.050
  Set scattering table:                    0.050
  Process input model:                     19.670
  Find NCS groups from input model:        0.070
  Set up NCS constraints:                  0.020
  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:3.130
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   25.220
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.4185
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      :  0.002   0.025   6543  Z= 0.126
  Angle     :  0.560   8.027   8904  Z= 0.352
  Chirality :  0.040   0.133    961
  Planarity :  0.003   0.034   1179
  Dihedral  :  7.770  81.978   2340
  Min Nonbonded Distance : 2.279

Molprobity Statistics.
  All-atom Clashscore : 8.94
  Ramachandran Plot:
    Outliers :  0.12 %
    Allowed  :  5.79 %
    Favored  : 94.09 %
  Rotamer:
    Outliers :  1.98 %
    Allowed  :  3.67 %
    Favored  : 94.35 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -3.28 (0.25), residues: 812
  helix: -2.88 (0.47), residues: 50
  sheet: -1.02 (0.34), residues: 196
  loop : -2.74 (0.22), residues: 566

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.003   0.000   TRP A 255 
 HIS   0.002   0.000   HIS B 881 
 PHE   0.005   0.001   PHE A 693 
 TYR   0.008   0.001   TYR A 276 
 ARG   0.001   0.000   ARG B 807 

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

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

  1624 Ramachandran restraints generated.
    812 Oldfield, 0 Emsley, 812 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1624 Ramachandran restraints generated.
    812 Oldfield, 0 Emsley, 812 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  142 residues out of total 708 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 128
  time to evaluate  : 0.672 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  529 GLU cc_start: 0.7177 (mp0) cc_final: 0.6080 (tm-30)
REVERT: A  555 ILE cc_start: 0.6198 (mt) cc_final: 0.5992 (tp)
REVERT: A  620 ASP cc_start: 0.8656 (m-30) cc_final: 0.8429 (m-30)
REVERT: B  809 LEU cc_start: 0.7996 (mt) cc_final: 0.7145 (mt)
REVERT: B  927 ILE cc_start: 0.7961 (mm) cc_final: 0.6967 (mt)
REVERT: B 1004 TYR cc_start: 0.6665 (m-80) cc_final: 0.6350 (m-80)
  outliers start: 14
  outliers final: 5
  residues processed: 135
  average time/residue: 0.2385
  time to fit residues: 40.3860
Evaluate side-chains
  110 residues out of total 708 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 5
    poor density    : 105
  time to evaluate  : 0.649 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 81
   random chunks:
   chunk 68 optimal weight:    0.0050
   chunk 61 optimal weight:    2.9990
   chunk 34 optimal weight:    4.9990
   chunk 20 optimal weight:    9.9990
   chunk 41 optimal weight:    0.5980
   chunk 32 optimal weight:    2.9990
   chunk 63 optimal weight:    7.9990
   chunk 24 optimal weight:    0.9990
   chunk 38 optimal weight:    0.5980
   chunk 47 optimal weight:    3.9990
   chunk 73 optimal weight:    0.0030
   overall best weight:    0.4406

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

Flipped N/Q/H residues before XYZ refinement:
A 484 ASN
** A 660 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 710 GLN
** A 713 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 717 GLN
A 766 GLN
B 921 GLN
** B 929 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
B 943 GLN
B 980 ASN

Total number of N/Q/H flips: 7

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.5389 r_free = 0.5389 target = 0.322957 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 68)----------------|
| r_work = 0.5310 r_free = 0.5310 target = 0.309272 restraints weight = 33914.684|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 47)----------------|
| r_work = 0.5332 r_free = 0.5332 target = 0.310571 restraints weight = 27366.585|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 43)----------------|
| r_work = 0.5339 r_free = 0.5339 target = 0.311426 restraints weight = 21823.066|
|-----------------------------------------------------------------------------|
r_work (final): 0.5048
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.3720
moved from start:          0.2153

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.055   6543  Z= 0.174
  Angle     :  0.538  10.175   8904  Z= 0.279
  Chirality :  0.044   0.166    961
  Planarity :  0.004   0.043   1179
  Dihedral  :  3.325  29.691    869
  Min Nonbonded Distance : 2.528

Molprobity Statistics.
  All-atom Clashscore : 9.66
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.03 %
    Favored  : 93.97 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  2.54 %
    Favored  : 97.46 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -2.45 (0.27), residues: 812
  helix: -2.04 (0.63), residues: 50
  sheet: -0.61 (0.35), residues: 195
  loop : -2.10 (0.25), residues: 567

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.012   0.001   TRP B1013 
 HIS   0.004   0.001   HIS A 700 
 PHE   0.014   0.001   PHE A 681 
 TYR   0.010   0.001   TYR B 920 
 ARG   0.005   0.001   ARG B 807 

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

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

  1624 Ramachandran restraints generated.
    812 Oldfield, 0 Emsley, 812 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1624 Ramachandran restraints generated.
    812 Oldfield, 0 Emsley, 812 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  109 residues out of total 708 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 109
  time to evaluate  : 0.698 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  529 GLU cc_start: 0.7342 (mp0) cc_final: 0.6527 (tm-30)
REVERT: A  555 ILE cc_start: 0.6509 (mt) cc_final: 0.6141 (tp)
REVERT: A  591 LEU cc_start: 0.6884 (mp) cc_final: 0.6613 (mp)
REVERT: A  620 ASP cc_start: 0.8687 (m-30) cc_final: 0.8312 (m-30)
REVERT: A  647 HIS cc_start: 0.6530 (m-70) cc_final: 0.6239 (m-70)
REVERT: B  809 LEU cc_start: 0.7524 (mt) cc_final: 0.7237 (mt)
REVERT: B  873 LYS cc_start: 0.7899 (mtmt) cc_final: 0.7671 (tppt)
REVERT: B  874 ASP cc_start: 0.7472 (p0) cc_final: 0.7128 (p0)
REVERT: B  942 GLN cc_start: 0.6655 (tp40) cc_final: 0.6341 (tp-100)
REVERT: B  955 ILE cc_start: 0.7622 (tt) cc_final: 0.7315 (pt)
REVERT: B  976 MET cc_start: 0.5622 (mpp) cc_final: 0.5048 (mpp)
REVERT: B 1004 TYR cc_start: 0.6983 (m-80) cc_final: 0.5955 (m-80)
  outliers start: 0
  outliers final: 0
  residues processed: 109
  average time/residue: 0.2299
  time to fit residues: 32.1878
Evaluate side-chains
  95 residues out of total 708 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 95
  time to evaluate  : 0.706 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 81
   random chunks:
   chunk 39 optimal weight:    5.9990
   chunk 58 optimal weight:    0.9990
   chunk 15 optimal weight:   20.0000
   chunk 3 optimal weight:    6.9990
   chunk 70 optimal weight:    0.0870
   chunk 28 optimal weight:    0.9990
   chunk 50 optimal weight:    0.7980
   chunk 47 optimal weight:    2.9990
   chunk 71 optimal weight:    6.9990
   chunk 24 optimal weight:    5.9990
   chunk 31 optimal weight:    0.9990
   overall best weight:    0.7764

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

Flipped N/Q/H residues before XYZ refinement:
A 404 GLN
A 649 GLN
** A 660 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 700 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 713 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 768 ASN
B 844 HIS
B 875 ASN
** B 929 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
B 980 ASN

Total number of N/Q/H flips: 6

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.5161 r_free = 0.5161 target = 0.280903 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 63)----------------|
| r_work = 0.4718 r_free = 0.4718 target = 0.230780 restraints weight = 21801.801|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 42)----------------|
| r_work = 0.4775 r_free = 0.4775 target = 0.236332 restraints weight = 16742.755|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 36)----------------|
| r_work = 0.4816 r_free = 0.4816 target = 0.240416 restraints weight = 13561.337|
|-----------------------------------------------------------------------------|
r_work (final): 0.4802
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.4509
moved from start:          0.2901

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.060   6543  Z= 0.210
  Angle     :  0.543   7.294   8904  Z= 0.284
  Chirality :  0.044   0.155    961
  Planarity :  0.004   0.037   1179
  Dihedral  :  3.572  25.146    869
  Min Nonbonded Distance : 2.567

Molprobity Statistics.
  All-atom Clashscore : 10.87
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  7.39 %
    Favored  : 92.61 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  2.12 %
    Favored  : 97.88 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -2.09 (0.28), residues: 812
  helix: -1.82 (0.71), residues: 42
  sheet: -0.43 (0.37), residues: 194
  loop : -1.83 (0.25), residues: 576

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.019   0.001   TRP A 699 
 HIS   0.005   0.001   HIS A 700 
 PHE   0.009   0.001   PHE A 631 
 TYR   0.017   0.001   TYR B 920 
 ARG   0.007   0.001   ARG B 872 

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

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

  1624 Ramachandran restraints generated.
    812 Oldfield, 0 Emsley, 812 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1624 Ramachandran restraints generated.
    812 Oldfield, 0 Emsley, 812 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  104 residues out of total 708 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 104
  time to evaluate  : 0.669 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  529 GLU cc_start: 0.7211 (mp0) cc_final: 0.5999 (tm-30)
REVERT: A  555 ILE cc_start: 0.6532 (mt) cc_final: 0.6103 (tp)
REVERT: A  565 GLN cc_start: 0.7446 (tm-30) cc_final: 0.7000 (tm-30)
REVERT: A  620 ASP cc_start: 0.8735 (m-30) cc_final: 0.8363 (m-30)
REVERT: B  874 ASP cc_start: 0.7420 (p0) cc_final: 0.6864 (p0)
REVERT: B  884 PHE cc_start: 0.7104 (m-80) cc_final: 0.6726 (m-80)
REVERT: B  955 ILE cc_start: 0.7974 (tt) cc_final: 0.7243 (pt)
REVERT: B  976 MET cc_start: 0.5432 (mpp) cc_final: 0.4845 (mpp)
REVERT: B 1004 TYR cc_start: 0.7215 (m-80) cc_final: 0.5905 (m-80)
  outliers start: 0
  outliers final: 0
  residues processed: 104
  average time/residue: 0.2481
  time to fit residues: 32.7412
Evaluate side-chains
  92 residues out of total 708 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 92
  time to evaluate  : 0.677 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 81
   random chunks:
   chunk 4 optimal weight:    3.9990
   chunk 65 optimal weight:    3.9990
   chunk 21 optimal weight:    5.9990
   chunk 67 optimal weight:    2.9990
   chunk 23 optimal weight:    3.9990
   chunk 73 optimal weight:    3.9990
   chunk 60 optimal weight:    2.9990
   chunk 62 optimal weight:    0.3980
   chunk 42 optimal weight:    0.8980
   chunk 1 optimal weight:    5.9990
   chunk 52 optimal weight:    1.9990
   overall best weight:    1.8586

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

Flipped N/Q/H residues before XYZ refinement:
** A 565 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 682 ASN
** A 700 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 929 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
B 980 ASN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.5063 r_free = 0.5063 target = 0.263473 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 86)----------------|
| r_work = 0.4592 r_free = 0.4592 target = 0.198858 restraints weight = 18442.653|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 41)----------------|
| r_work = 0.4631 r_free = 0.4631 target = 0.202771 restraints weight = 15676.404|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 41)----------------|
| r_work = 0.4658 r_free = 0.4658 target = 0.205824 restraints weight = 13774.516|
|-----------------------------------------------------------------------------|
r_work (final): 0.4630
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.5096
moved from start:          0.4295

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.006   0.086   6543  Z= 0.392
  Angle     :  0.746  11.486   8904  Z= 0.392
  Chirality :  0.048   0.183    961
  Planarity :  0.006   0.112   1179
  Dihedral  :  4.960  23.567    869
  Min Nonbonded Distance : 2.388

Molprobity Statistics.
  All-atom Clashscore : 20.29
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  9.98 %
    Favored  : 90.02 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  3.53 %
    Favored  : 96.47 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -2.17 (0.28), residues: 812
  helix: -2.60 (0.58), residues: 46
  sheet: -0.45 (0.40), residues: 178
  loop : -1.79 (0.25), residues: 588

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.023   0.002   TRP A 707 
 HIS   0.010   0.002   HIS A 700 
 PHE   0.032   0.002   PHE B 904 
 TYR   0.017   0.002   TYR B 920 
 ARG   0.008   0.001   ARG B 872 

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

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

  1624 Ramachandran restraints generated.
    812 Oldfield, 0 Emsley, 812 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1624 Ramachandran restraints generated.
    812 Oldfield, 0 Emsley, 812 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  105 residues out of total 708 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 105
  time to evaluate  : 0.626 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  528 PHE cc_start: 0.7430 (m-10) cc_final: 0.7208 (m-10)
REVERT: A  620 ASP cc_start: 0.8835 (m-30) cc_final: 0.8523 (m-30)
REVERT: A  686 ASN cc_start: 0.8203 (t0) cc_final: 0.7827 (p0)
REVERT: A  764 ARG cc_start: 0.8319 (tpp80) cc_final: 0.7717 (tpp80)
REVERT: B  789 SER cc_start: 0.5422 (t) cc_final: 0.5042 (p)
REVERT: B  804 TYR cc_start: 0.6878 (t80) cc_final: 0.6543 (t80)
REVERT: B  809 LEU cc_start: 0.7869 (mt) cc_final: 0.7615 (mt)
REVERT: B  831 ASN cc_start: 0.8056 (p0) cc_final: 0.7629 (t0)
REVERT: B  874 ASP cc_start: 0.7416 (p0) cc_final: 0.7139 (p0)
REVERT: B  877 ILE cc_start: 0.7637 (tt) cc_final: 0.7320 (tt)
REVERT: B  880 MET cc_start: 0.7175 (mtm) cc_final: 0.6905 (mtm)
REVERT: B  884 PHE cc_start: 0.7122 (m-80) cc_final: 0.6711 (m-80)
REVERT: B  908 ARG cc_start: 0.5430 (mtt180) cc_final: 0.4678 (mtt-85)
REVERT: B  982 ARG cc_start: 0.6715 (mtp85) cc_final: 0.6382 (mtp85)
REVERT: B 1004 TYR cc_start: 0.7022 (m-80) cc_final: 0.5802 (m-80)
  outliers start: 0
  outliers final: 0
  residues processed: 105
  average time/residue: 0.2380
  time to fit residues: 32.0221
Evaluate side-chains
  92 residues out of total 708 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 92
  time to evaluate  : 0.616 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 81
   random chunks:
   chunk 29 optimal weight:    0.8980
   chunk 48 optimal weight:    0.7980
   chunk 76 optimal weight:    0.1980
   chunk 61 optimal weight:    0.1980
   chunk 34 optimal weight:    1.9990
   chunk 46 optimal weight:    0.6980
   chunk 49 optimal weight:    0.9990
   chunk 63 optimal weight:    0.8980
   chunk 67 optimal weight:    0.9980
   chunk 21 optimal weight:    7.9990
   chunk 57 optimal weight:    0.5980
   overall best weight:    0.4980

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

Flipped N/Q/H residues before XYZ refinement:
A 541 ASN
** A 565 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 660 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 700 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
B 867 HIS
** B 929 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
B 980 ASN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.5133 r_free = 0.5133 target = 0.274221 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 65)----------------|
| r_work = 0.4682 r_free = 0.4682 target = 0.223788 restraints weight = 20603.993|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 28)----------------|
| r_work = 0.4735 r_free = 0.4735 target = 0.229040 restraints weight = 16308.964|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 40)----------------|
| r_work = 0.4772 r_free = 0.4772 target = 0.232915 restraints weight = 13482.427|
|-----------------------------------------------------------------------------|
r_work (final): 0.4748
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.4662
moved from start:          0.4259

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.043   6543  Z= 0.179
  Angle     :  0.549   5.466   8904  Z= 0.286
  Chirality :  0.044   0.148    961
  Planarity :  0.004   0.044   1179
  Dihedral  :  4.259  27.951    869
  Min Nonbonded Distance : 2.417

Molprobity Statistics.
  All-atom Clashscore : 11.84
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  8.00 %
    Favored  : 92.00 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  1.55 %
    Favored  : 98.45 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -1.93 (0.29), residues: 812
  helix: -1.70 (0.68), residues: 39
  sheet: -0.61 (0.37), residues: 204
  loop : -1.60 (0.26), residues: 569

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.023   0.001   TRP A 699 
 HIS   0.002   0.001   HIS A 435 
 PHE   0.008   0.001   PHE A 452 
 TYR   0.014   0.001   TYR B 959 
 ARG   0.008   0.001   ARG B 872 

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

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

  1624 Ramachandran restraints generated.
    812 Oldfield, 0 Emsley, 812 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1624 Ramachandran restraints generated.
    812 Oldfield, 0 Emsley, 812 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  102 residues out of total 708 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 102
  time to evaluate  : 0.650 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  620 ASP cc_start: 0.8686 (m-30) cc_final: 0.8335 (m-30)
REVERT: A  764 ARG cc_start: 0.8234 (tpp80) cc_final: 0.7600 (tpp80)
REVERT: B  789 SER cc_start: 0.5976 (t) cc_final: 0.5564 (p)
REVERT: B  804 TYR cc_start: 0.6634 (t80) cc_final: 0.5894 (t80)
REVERT: B  831 ASN cc_start: 0.7968 (p0) cc_final: 0.7482 (t0)
REVERT: B  872 ARG cc_start: 0.8411 (mmm160) cc_final: 0.8160 (mmm160)
REVERT: B  874 ASP cc_start: 0.7284 (p0) cc_final: 0.7040 (p0)
REVERT: B  877 ILE cc_start: 0.7623 (tt) cc_final: 0.7391 (tt)
REVERT: B  880 MET cc_start: 0.6983 (mtm) cc_final: 0.6776 (mtm)
REVERT: B  884 PHE cc_start: 0.7042 (m-80) cc_final: 0.6666 (m-80)
REVERT: B  908 ARG cc_start: 0.5534 (mtt180) cc_final: 0.4757 (mtt180)
REVERT: B  976 MET cc_start: 0.6109 (mpp) cc_final: 0.5537 (mpp)
REVERT: B  984 PHE cc_start: 0.5255 (m-80) cc_final: 0.4940 (m-80)
REVERT: B  991 PHE cc_start: 0.6008 (p90) cc_final: 0.5732 (p90)
REVERT: B 1004 TYR cc_start: 0.7164 (m-80) cc_final: 0.5894 (m-80)
  outliers start: 0
  outliers final: 0
  residues processed: 102
  average time/residue: 0.2593
  time to fit residues: 33.1308
Evaluate side-chains
  91 residues out of total 708 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 91
  time to evaluate  : 0.627 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 81
   random chunks:
   chunk 17 optimal weight:    2.9990
   chunk 61 optimal weight:    0.0980
   chunk 14 optimal weight:    5.9990
   chunk 44 optimal weight:    0.2980
   chunk 31 optimal weight:    0.6980
   chunk 70 optimal weight:    3.9990
   chunk 37 optimal weight:    4.9990
   chunk 2 optimal weight:    0.9990
   chunk 52 optimal weight:    2.9990
   chunk 75 optimal weight:    2.9990
   chunk 71 optimal weight:    0.8980
   overall best weight:    0.5982

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

Flipped N/Q/H residues before XYZ refinement:
A 480 ASN
** A 565 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 660 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 700 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 929 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
B 980 ASN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.5132 r_free = 0.5132 target = 0.271136 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 66)----------------|
| r_work = 0.4684 r_free = 0.4684 target = 0.221352 restraints weight = 19776.964|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 42)----------------|
| r_work = 0.4738 r_free = 0.4738 target = 0.226720 restraints weight = 15494.563|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 30)----------------|
| r_work = 0.4776 r_free = 0.4776 target = 0.230437 restraints weight = 12702.467|
|-----------------------------------------------------------------------------|
r_work (final): 0.4731
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.4682
moved from start:          0.4564

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.055   6543  Z= 0.188
  Angle     :  0.552   6.718   8904  Z= 0.286
  Chirality :  0.044   0.148    961
  Planarity :  0.004   0.041   1179
  Dihedral  :  4.149  27.536    869
  Min Nonbonded Distance : 2.442

Molprobity Statistics.
  All-atom Clashscore : 12.56
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  8.87 %
    Favored  : 91.13 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  1.13 %
    Favored  : 98.87 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -1.83 (0.29), residues: 812
  helix: -1.43 (0.73), residues: 38
  sheet: -0.54 (0.38), residues: 198
  loop : -1.53 (0.26), residues: 576

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.010   0.001   TRP B 819 
 HIS   0.004   0.001   HIS A 647 
 PHE   0.012   0.001   PHE A 693 
 TYR   0.013   0.001   TYR A 458 
 ARG   0.005   0.000   ARG B 872 

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

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

  1624 Ramachandran restraints generated.
    812 Oldfield, 0 Emsley, 812 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1624 Ramachandran restraints generated.
    812 Oldfield, 0 Emsley, 812 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  100 residues out of total 708 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 100
  time to evaluate  : 0.648 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  620 ASP cc_start: 0.8716 (m-30) cc_final: 0.8369 (m-30)
REVERT: A  678 VAL cc_start: 0.5743 (p) cc_final: 0.5110 (t)
REVERT: B  789 SER cc_start: 0.5953 (t) cc_final: 0.5519 (p)
REVERT: B  831 ASN cc_start: 0.8014 (p0) cc_final: 0.7676 (t0)
REVERT: B  868 TYR cc_start: 0.6924 (t80) cc_final: 0.6701 (t80)
REVERT: B  872 ARG cc_start: 0.8373 (mmm160) cc_final: 0.7742 (mmm160)
REVERT: B  874 ASP cc_start: 0.7373 (p0) cc_final: 0.7093 (p0)
REVERT: B  880 MET cc_start: 0.6939 (mtm) cc_final: 0.6691 (mtm)
REVERT: B  884 PHE cc_start: 0.7017 (m-80) cc_final: 0.6627 (m-80)
REVERT: B  954 MET cc_start: 0.7211 (mtp) cc_final: 0.6988 (mtp)
REVERT: B  976 MET cc_start: 0.6187 (mpp) cc_final: 0.5560 (mpp)
REVERT: B  981 ASN cc_start: 0.8233 (t0) cc_final: 0.7996 (t0)
REVERT: B  984 PHE cc_start: 0.5336 (m-80) cc_final: 0.5114 (m-80)
REVERT: B 1004 TYR cc_start: 0.7201 (m-80) cc_final: 0.5888 (m-80)
  outliers start: 0
  outliers final: 0
  residues processed: 100
  average time/residue: 0.2476
  time to fit residues: 31.2087
Evaluate side-chains
  87 residues out of total 708 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 87
  time to evaluate  : 0.680 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 81
   random chunks:
   chunk 3 optimal weight:    0.8980
   chunk 11 optimal weight:    3.9990
   chunk 2 optimal weight:    1.9990
   chunk 48 optimal weight:    0.9980
   chunk 5 optimal weight:    0.4980
   chunk 80 optimal weight:    0.9990
   chunk 59 optimal weight:    0.4980
   chunk 17 optimal weight:    5.9990
   chunk 4 optimal weight:    0.9990
   chunk 40 optimal weight:    1.9990
   chunk 49 optimal weight:    1.9990
   overall best weight:    0.7782

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

Flipped N/Q/H residues before XYZ refinement:
** A 565 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 660 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 929 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
B 980 ASN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.5114 r_free = 0.5114 target = 0.271145 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 51)----------------|
| r_work = 0.4640 r_free = 0.4640 target = 0.218177 restraints weight = 19391.921|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 47)----------------|
| r_work = 0.4696 r_free = 0.4696 target = 0.223719 restraints weight = 15287.237|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 31)----------------|
| r_work = 0.4735 r_free = 0.4735 target = 0.227559 restraints weight = 12573.278|
|-----------------------------------------------------------------------------|
r_work (final): 0.4692
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.4757
moved from start:          0.4922

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.058   6543  Z= 0.207
  Angle     :  0.566   7.070   8904  Z= 0.295
  Chirality :  0.045   0.144    961
  Planarity :  0.004   0.047   1179
  Dihedral  :  4.196  27.073    869
  Min Nonbonded Distance : 2.501

Molprobity Statistics.
  All-atom Clashscore : 14.50
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  9.36 %
    Favored  : 90.64 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  0.71 %
    Favored  : 99.29 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -1.79 (0.29), residues: 812
  helix: -1.39 (0.73), residues: 38
  sheet: -0.47 (0.39), residues: 192
  loop : -1.52 (0.26), residues: 582

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.018   0.001   TRP A 366 
 HIS   0.004   0.001   HIS A 647 
 PHE   0.027   0.001   PHE A 479 
 TYR   0.007   0.001   TYR A 276 
 ARG   0.006   0.001   ARG A 679 

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

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

  1624 Ramachandran restraints generated.
    812 Oldfield, 0 Emsley, 812 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1624 Ramachandran restraints generated.
    812 Oldfield, 0 Emsley, 812 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  97 residues out of total 708 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 97
  time to evaluate  : 0.688 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  555 ILE cc_start: 0.6063 (mp) cc_final: 0.5724 (mp)
REVERT: A  620 ASP cc_start: 0.8724 (m-30) cc_final: 0.8406 (m-30)
REVERT: A  678 VAL cc_start: 0.6063 (p) cc_final: 0.5506 (t)
REVERT: A  679 ARG cc_start: 0.7229 (ptt90) cc_final: 0.6972 (ptp-170)
REVERT: B  789 SER cc_start: 0.5892 (t) cc_final: 0.5511 (p)
REVERT: B  868 TYR cc_start: 0.6945 (t80) cc_final: 0.6699 (t80)
REVERT: B  872 ARG cc_start: 0.8392 (mmm160) cc_final: 0.7770 (mmm160)
REVERT: B  874 ASP cc_start: 0.7343 (p0) cc_final: 0.7069 (p0)
REVERT: B  880 MET cc_start: 0.7155 (mtm) cc_final: 0.6899 (mtm)
REVERT: B  884 PHE cc_start: 0.7047 (m-80) cc_final: 0.6663 (m-80)
REVERT: B  976 MET cc_start: 0.6021 (mpp) cc_final: 0.5443 (mpp)
REVERT: B  981 ASN cc_start: 0.8321 (t0) cc_final: 0.8091 (t0)
REVERT: B 1004 TYR cc_start: 0.7121 (m-80) cc_final: 0.5941 (m-80)
  outliers start: 0
  outliers final: 0
  residues processed: 97
  average time/residue: 0.2393
  time to fit residues: 29.5361
Evaluate side-chains
  91 residues out of total 708 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 91
  time to evaluate  : 0.641 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 81
   random chunks:
   chunk 11 optimal weight:    0.8980
   chunk 39 optimal weight:    0.8980
   chunk 10 optimal weight:    0.5980
   chunk 31 optimal weight:    0.9980
   chunk 69 optimal weight:    0.0980
   chunk 1 optimal weight:   20.0000
   chunk 23 optimal weight:    2.9990
   chunk 24 optimal weight:    7.9990
   chunk 5 optimal weight:    2.9990
   chunk 7 optimal weight:    0.6980
   chunk 72 optimal weight:    5.9990
   overall best weight:    0.6380

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

Flipped N/Q/H residues before XYZ refinement:
** A 563 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 565 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 660 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 929 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
B 980 ASN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.5120 r_free = 0.5120 target = 0.271600 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 65)----------------|
| r_work = 0.4680 r_free = 0.4680 target = 0.221145 restraints weight = 18661.659|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 30)----------------|
| r_work = 0.4727 r_free = 0.4727 target = 0.225936 restraints weight = 14974.764|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 27)----------------|
| r_work = 0.4756 r_free = 0.4756 target = 0.228985 restraints weight = 12576.238|
|-----------------------------------------------------------------------------|
r_work (final): 0.4703
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.4748
moved from start:          0.5123

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.055   6543  Z= 0.189
  Angle     :  0.559   8.783   8904  Z= 0.289
  Chirality :  0.044   0.142    961
  Planarity :  0.004   0.092   1179
  Dihedral  :  4.216  27.849    869
  Min Nonbonded Distance : 2.481

Molprobity Statistics.
  All-atom Clashscore : 14.01
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  8.87 %
    Favored  : 91.13 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  0.71 %
    Favored  : 99.29 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -1.80 (0.29), residues: 812
  helix: -1.13 (0.75), residues: 39
  sheet: -0.64 (0.39), residues: 196
  loop : -1.48 (0.26), residues: 577

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.033   0.002   TRP A 699 
 HIS   0.007   0.001   HIS A 700 
 PHE   0.011   0.001   PHE A 479 
 TYR   0.018   0.001   TYR B 959 
 ARG   0.004   0.000   ARG B 830 

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

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

  1624 Ramachandran restraints generated.
    812 Oldfield, 0 Emsley, 812 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1624 Ramachandran restraints generated.
    812 Oldfield, 0 Emsley, 812 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  92 residues out of total 708 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 92
  time to evaluate  : 0.625 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  620 ASP cc_start: 0.8687 (m-30) cc_final: 0.8462 (m-30)
REVERT: A  678 VAL cc_start: 0.5822 (p) cc_final: 0.5212 (t)
REVERT: A  679 ARG cc_start: 0.7076 (ptt90) cc_final: 0.6402 (ptp90)
REVERT: B  789 SER cc_start: 0.6015 (t) cc_final: 0.5596 (p)
REVERT: B  868 TYR cc_start: 0.6985 (t80) cc_final: 0.6709 (t80)
REVERT: B  874 ASP cc_start: 0.7255 (p0) cc_final: 0.7029 (p0)
REVERT: B  880 MET cc_start: 0.6982 (mtm) cc_final: 0.6746 (mtm)
REVERT: B  884 PHE cc_start: 0.6917 (m-80) cc_final: 0.6562 (m-80)
REVERT: B  908 ARG cc_start: 0.5140 (mtt180) cc_final: 0.4558 (mtt180)
REVERT: B  976 MET cc_start: 0.6020 (mpp) cc_final: 0.5480 (mpp)
REVERT: B  981 ASN cc_start: 0.8310 (t0) cc_final: 0.8050 (t0)
REVERT: B  991 PHE cc_start: 0.6209 (p90) cc_final: 0.5981 (p90)
REVERT: B 1004 TYR cc_start: 0.7141 (m-80) cc_final: 0.5876 (m-80)
  outliers start: 0
  outliers final: 0
  residues processed: 92
  average time/residue: 0.2373
  time to fit residues: 27.6146
Evaluate side-chains
  88 residues out of total 708 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 88
  time to evaluate  : 0.621 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 81
   random chunks:
   chunk 53 optimal weight:    1.9990
   chunk 66 optimal weight:    0.7980
   chunk 75 optimal weight:    0.0970
   chunk 29 optimal weight:    0.6980
   chunk 64 optimal weight:    0.8980
   chunk 61 optimal weight:    0.0070
   chunk 19 optimal weight:   50.0000
   chunk 80 optimal weight:    0.8980
   chunk 57 optimal weight:    3.9990
   chunk 27 optimal weight:    6.9990
   chunk 34 optimal weight:    0.7980
   overall best weight:    0.4796

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

Flipped N/Q/H residues before XYZ refinement:
** A 563 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 565 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 660 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
B 875 ASN
** B 929 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.5134 r_free = 0.5134 target = 0.272622 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 63)----------------|
| r_work = 0.4667 r_free = 0.4667 target = 0.220442 restraints weight = 19812.723|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 27)----------------|
| r_work = 0.4717 r_free = 0.4717 target = 0.225607 restraints weight = 15809.613|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 38)----------------|
| r_work = 0.4755 r_free = 0.4755 target = 0.229534 restraints weight = 13175.236|
|-----------------------------------------------------------------------------|
r_work (final): 0.4715
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.4724
moved from start:          0.5185

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.053   6543  Z= 0.169
  Angle     :  0.554   9.204   8904  Z= 0.285
  Chirality :  0.044   0.143    961
  Planarity :  0.004   0.051   1179
  Dihedral  :  4.167  28.066    869
  Min Nonbonded Distance : 2.483

Molprobity Statistics.
  All-atom Clashscore : 12.48
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  8.74 %
    Favored  : 91.26 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  0.14 %
    Favored  : 99.86 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -1.74 (0.30), residues: 812
  helix: -0.91 (0.80), residues: 39
  sheet: -0.46 (0.39), residues: 189
  loop : -1.51 (0.26), residues: 584

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.011   0.001   TRP A 366 
 HIS   0.005   0.001   HIS A 700 
 PHE   0.012   0.001   PHE A 479 
 TYR   0.010   0.001   TYR B 959 
 ARG   0.010   0.000   ARG B 872 

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

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

  1624 Ramachandran restraints generated.
    812 Oldfield, 0 Emsley, 812 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1624 Ramachandran restraints generated.
    812 Oldfield, 0 Emsley, 812 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  93 residues out of total 708 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 93
  time to evaluate  : 0.659 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  678 VAL cc_start: 0.5571 (p) cc_final: 0.5071 (t)
REVERT: A  679 ARG cc_start: 0.7136 (ptt90) cc_final: 0.6756 (ptp90)
REVERT: B  789 SER cc_start: 0.5820 (t) cc_final: 0.5427 (p)
REVERT: B  868 TYR cc_start: 0.6859 (t80) cc_final: 0.6598 (t80)
REVERT: B  872 ARG cc_start: 0.8507 (mmm160) cc_final: 0.7705 (mmm-85)
REVERT: B  874 ASP cc_start: 0.7321 (p0) cc_final: 0.6850 (p0)
REVERT: B  880 MET cc_start: 0.6901 (mtm) cc_final: 0.6696 (mtm)
REVERT: B  884 PHE cc_start: 0.6966 (m-80) cc_final: 0.6601 (m-80)
REVERT: B  908 ARG cc_start: 0.5049 (mtt180) cc_final: 0.4775 (mtt-85)
REVERT: B  976 MET cc_start: 0.6147 (mpp) cc_final: 0.5575 (mpp)
REVERT: B  981 ASN cc_start: 0.8365 (t0) cc_final: 0.8122 (t0)
REVERT: B 1004 TYR cc_start: 0.7117 (m-80) cc_final: 0.5941 (m-80)
  outliers start: 0
  outliers final: 0
  residues processed: 93
  average time/residue: 0.2523
  time to fit residues: 29.6326
Evaluate side-chains
  88 residues out of total 708 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 88
  time to evaluate  : 0.693 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 81
   random chunks:
   chunk 57 optimal weight:   10.0000
   chunk 40 optimal weight:    0.0970
   chunk 71 optimal weight:    0.8980
   chunk 32 optimal weight:    4.9990
   chunk 18 optimal weight:   20.0000
   chunk 41 optimal weight:    0.0870
   chunk 73 optimal weight:    1.9990
   chunk 30 optimal weight:   10.0000
   chunk 65 optimal weight:    0.7980
   chunk 79 optimal weight:    1.9990
   chunk 64 optimal weight:    0.7980
   overall best weight:    0.5356

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

Flipped N/Q/H residues before XYZ refinement:
** A 563 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 565 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 660 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 929 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.5128 r_free = 0.5128 target = 0.272583 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 55)----------------|
| r_work = 0.4687 r_free = 0.4687 target = 0.222486 restraints weight = 19096.224|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 37)----------------|
| r_work = 0.4737 r_free = 0.4737 target = 0.227557 restraints weight = 15276.311|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 36)----------------|
| r_work = 0.4774 r_free = 0.4774 target = 0.231411 restraints weight = 12671.631|
|-----------------------------------------------------------------------------|
r_work (final): 0.4725
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.4703
moved from start:          0.5320

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.054   6543  Z= 0.173
  Angle     :  0.550   8.662   8904  Z= 0.283
  Chirality :  0.044   0.144    961
  Planarity :  0.004   0.045   1179
  Dihedral  :  4.127  28.150    869
  Min Nonbonded Distance : 2.478

Molprobity Statistics.
  All-atom Clashscore : 11.92
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  8.87 %
    Favored  : 91.13 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  0.14 %
    Favored  : 99.86 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -1.73 (0.30), residues: 812
  helix: -1.13 (0.77), residues: 41
  sheet: -0.63 (0.39), residues: 195
  loop : -1.42 (0.26), residues: 576

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.059   0.002   TRP A 699 
 HIS   0.003   0.001   HIS A 647 
 PHE   0.010   0.001   PHE A 479 
 TYR   0.010   0.001   TYR B 959 
 ARG   0.011   0.001   ARG B 872 

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

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

  1624 Ramachandran restraints generated.
    812 Oldfield, 0 Emsley, 812 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1624 Ramachandran restraints generated.
    812 Oldfield, 0 Emsley, 812 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  92 residues out of total 708 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 92
  time to evaluate  : 0.816 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  678 VAL cc_start: 0.5891 (p) cc_final: 0.5256 (t)
REVERT: B  789 SER cc_start: 0.5898 (t) cc_final: 0.5476 (p)
REVERT: B  830 ARG cc_start: 0.6434 (mpt180) cc_final: 0.6070 (mmt-90)
REVERT: B  868 TYR cc_start: 0.6688 (t80) cc_final: 0.6399 (t80)
REVERT: B  872 ARG cc_start: 0.8436 (mmm160) cc_final: 0.7741 (mmm-85)
REVERT: B  874 ASP cc_start: 0.7286 (p0) cc_final: 0.6826 (p0)
REVERT: B  880 MET cc_start: 0.6839 (mtm) cc_final: 0.6639 (mtm)
REVERT: B  884 PHE cc_start: 0.6957 (m-80) cc_final: 0.6606 (m-80)
REVERT: B  908 ARG cc_start: 0.5239 (mtt180) cc_final: 0.4705 (mtt180)
REVERT: B  976 MET cc_start: 0.6027 (mpp) cc_final: 0.5446 (mpp)
REVERT: B  981 ASN cc_start: 0.8282 (t0) cc_final: 0.8063 (t0)
REVERT: B  991 PHE cc_start: 0.6166 (p90) cc_final: 0.5890 (p90)
REVERT: B 1004 TYR cc_start: 0.7209 (m-80) cc_final: 0.5967 (m-80)
  outliers start: 0
  outliers final: 0
  residues processed: 92
  average time/residue: 0.2728
  time to fit residues: 31.8739
Evaluate side-chains
  89 residues out of total 708 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 89
  time to evaluate  : 0.742 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 81
   random chunks:
   chunk 65 optimal weight:    5.9990
   chunk 8 optimal weight:    1.9990
   chunk 43 optimal weight:    0.9980
   chunk 34 optimal weight:    0.7980
   chunk 51 optimal weight:    3.9990
   chunk 33 optimal weight:    0.9980
   chunk 22 optimal weight:    0.0060
   chunk 27 optimal weight:    4.9990
   chunk 44 optimal weight:    1.9990
   chunk 5 optimal weight:   10.0000
   chunk 56 optimal weight:    0.9990
   overall best weight:    0.7598

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

Flipped N/Q/H residues before XYZ refinement:
** A 563 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 565 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 660 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 929 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.5114 r_free = 0.5114 target = 0.270897 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 64)----------------|
| r_work = 0.4638 r_free = 0.4638 target = 0.218173 restraints weight = 19640.607|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 36)----------------|
| r_work = 0.4690 r_free = 0.4690 target = 0.223389 restraints weight = 15612.937|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 37)----------------|
| r_work = 0.4730 r_free = 0.4730 target = 0.227502 restraints weight = 12961.481|
|-----------------------------------------------------------------------------|
r_work (final): 0.4678
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.4807
moved from start:          0.5571

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.056   6543  Z= 0.203
  Angle     :  0.577   8.617   8904  Z= 0.297
  Chirality :  0.045   0.153    961
  Planarity :  0.004   0.050   1179
  Dihedral  :  4.245  27.287    869
  Min Nonbonded Distance : 2.470

Molprobity Statistics.
  All-atom Clashscore : 13.69
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  9.73 %
    Favored  : 90.27 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  0.14 %
    Favored  : 99.86 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -1.79 (0.30), residues: 812
  helix: -1.11 (0.77), residues: 41
  sheet: -0.69 (0.39), residues: 194
  loop : -1.46 (0.26), residues: 577

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.042   0.002   TRP A 699 
 HIS   0.008   0.001   HIS A 700 
 PHE   0.012   0.001   PHE B 984 
 TYR   0.012   0.001   TYR B 959 
 ARG   0.010   0.001   ARG B 872 
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 2748.39 seconds
wall clock time: 47 minutes 57.70 seconds (2877.70 seconds total)