Starting phenix.real_space_refine
on Sat May 10 14:44:57 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/8h3u_32828/05_2025/8h3u_32828.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/8h3u_32828/05_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_32828/05_2025/8h3u_32828.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/8h3u_32828/05_2025/8h3u_32828.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/8h3u_32828/05_2025/8h3u_32828.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/8h3u_32828/05_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-5687/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: 4.48, per 1000 atoms: 0.70
  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: 1.45
  Conformation dependent library (CDL) restraints added in 1.0 seconds
  

  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: 0.84
  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: 1.97

  Time building geometry restraints manager: 1.73 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:             0.960
  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:             0.000
  Extract box with map and model:          0.280
  Check model and map are aligned:         0.050
  Set scattering table:                    0.070
  Process input model:                     18.830
  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:2.720
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   23.000
-------------------------------------------------------------------------------
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   6557  Z= 0.131
  Angle     :  0.560   8.027   8932  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 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.28584 (  132)
  hydrogen bonds       : angle      10.77635 (  336)
  SS BOND              : bond        0.00098 (   14)
  SS BOND              : angle       0.39926 (   28)
  covalent geometry    : bond        0.00196 ( 6543)
  covalent geometry    : angle       0.56036 ( 8904)

*********************** 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  : 0.674 
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: 0.2299
  time to fit residues: 39.2951
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  : 0.654 
-------------------------------------------------------------------------------
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:    0.9980
   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:    3.9990
   chunk 24 optimal weight:    0.9990
   chunk 38 optimal weight:    0.5980
   chunk 47 optimal weight:    3.9990
   chunk 73 optimal weight:    0.0470
   overall best weight:    0.4492

-------------------------------------------------------------------------------
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 = 0.5388 r_free = 0.5388 target = 0.322902 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 57)----------------|
| r_work = 0.5323 r_free = 0.5323 target = 0.309543 restraints weight = 33921.936|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 37)----------------|
| r_work = 0.5323 r_free = 0.5323 target = 0.310468 restraints weight = 27516.947|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 32)----------------|
| r_work = 0.5339 r_free = 0.5339 target = 0.311404 restraints weight = 21807.440|
|-----------------------------------------------------------------------------|
r_work (final): 0.5052
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.3698
moved from start:          0.2125

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.068   6557  Z= 0.117
  Angle     :  0.550  10.527   8932  Z= 0.284
  Chirality :  0.044   0.166    961
  Planarity :  0.004   0.037   1179
  Dihedral  :  3.284  28.404    869
  Min Nonbonded Distance : 2.512

Molprobity Statistics.
  All-atom Clashscore : 9.58
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.28 %
    Favored  : 93.72 %
  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: -2.45 (0.27), residues: 812
  helix: -2.03 (0.63), residues: 50
  sheet: -0.62 (0.35), residues: 195
  loop : -2.11 (0.25), residues: 567

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.013   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   0.006   0.001   ARG B 872 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03644 (  132)
  hydrogen bonds       : angle       7.41779 (  336)
  SS BOND              : bond        0.00424 (   14)
  SS BOND              : angle       2.12225 (   28)
  covalent geometry    : bond        0.00266 ( 6543)
  covalent geometry    : angle       0.53831 ( 8904)

*********************** 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  : 0.685 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  529 GLU cc_start: 0.7346 (mp0) cc_final: 0.6470 (tm-30)
REVERT: A  555 ILE cc_start: 0.6515 (mt) cc_final: 0.6245 (tp)
REVERT: A  620 ASP cc_start: 0.8654 (m-30) cc_final: 0.8279 (m-30)
REVERT: A  647 HIS cc_start: 0.6530 (m-70) cc_final: 0.6250 (m-70)
REVERT: B  808 LEU cc_start: 0.6408 (mt) cc_final: 0.4875 (mt)
REVERT: B  809 LEU cc_start: 0.7540 (mt) cc_final: 0.5679 (mt)
REVERT: B  874 ASP cc_start: 0.7479 (p0) cc_final: 0.7066 (p0)
REVERT: B  942 GLN cc_start: 0.6687 (tp40) cc_final: 0.6353 (tp-100)
REVERT: B  955 ILE cc_start: 0.7596 (tt) cc_final: 0.7279 (pt)
REVERT: B  976 MET cc_start: 0.5621 (mpp) cc_final: 0.5078 (mpp)
REVERT: B 1004 TYR cc_start: 0.6980 (m-80) cc_final: 0.5987 (m-80)
  outliers start: 0
  outliers final: 0
  residues processed: 109
  average time/residue: 0.2159
  time to fit residues: 30.1674
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 
-------------------------------------------------------------------------------
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:    3.9990
   chunk 15 optimal weight:   20.0000
   chunk 3 optimal weight:    7.9990
   chunk 70 optimal weight:    0.0030
   chunk 28 optimal weight:    0.9990
   chunk 50 optimal weight:    0.7980
   chunk 47 optimal weight:    2.9990
   chunk 71 optimal weight:    1.9990
   chunk 24 optimal weight:    5.9990
   chunk 31 optimal weight:    1.9990
   overall best weight:    1.1596

-------------------------------------------------------------------------------
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 742 ASN
A 768 ASN
** B 844 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
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 = 0.5130 r_free = 0.5130 target = 0.272232 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 60)----------------|
| r_work = 0.4690 r_free = 0.4690 target = 0.223283 restraints weight = 20043.189|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 36)----------------|
| r_work = 0.4746 r_free = 0.4746 target = 0.228872 restraints weight = 15432.547|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 45)----------------|
| r_work = 0.4785 r_free = 0.4785 target = 0.232945 restraints weight = 12519.068|
|-----------------------------------------------------------------------------|
r_work (final): 0.4765
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.4536
moved from start:          0.3079

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.059   6557  Z= 0.173
  Angle     :  0.610   7.031   8932  Z= 0.317
  Chirality :  0.045   0.160    961
  Planarity :  0.004   0.044   1179
  Dihedral  :  3.902  24.033    869
  Min Nonbonded Distance : 2.557

Molprobity Statistics.
  All-atom Clashscore : 14.17
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  7.76 %
    Favored  : 92.24 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  3.25 %
    Favored  : 96.75 %
  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: -2.13 (0.28), residues: 812
  helix: -1.88 (0.71), residues: 42
  sheet: -0.42 (0.37), residues: 190
  loop : -1.86 (0.25), residues: 580

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.019   0.002   TRP A 699 
 HIS   0.007   0.001   HIS A 700 
 PHE   0.015   0.001   PHE B 904 
 TYR   0.021   0.002   TYR B 920 
 ARG   0.007   0.001   ARG B 908 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04025 (  132)
  hydrogen bonds       : angle       7.40722 (  336)
  SS BOND              : bond        0.00646 (   14)
  SS BOND              : angle       1.50241 (   28)
  covalent geometry    : bond        0.00385 ( 6543)
  covalent geometry    : angle       0.60520 ( 8904)

*********************** 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
  100 residues out of total 708 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 100
  time to evaluate  : 0.654 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  565 GLN cc_start: 0.7651 (tm-30) cc_final: 0.7183 (tm-30)
REVERT: A  620 ASP cc_start: 0.8723 (m-30) cc_final: 0.8384 (m-30)
REVERT: A  764 ARG cc_start: 0.8389 (tpp80) cc_final: 0.7672 (tpp80)
REVERT: B  808 LEU cc_start: 0.6809 (mt) cc_final: 0.6331 (mm)
REVERT: B  884 PHE cc_start: 0.7057 (m-80) cc_final: 0.6711 (m-80)
REVERT: B  954 MET cc_start: 0.7668 (mtp) cc_final: 0.7451 (mtp)
REVERT: B  955 ILE cc_start: 0.8161 (tt) cc_final: 0.7334 (pt)
REVERT: B  976 MET cc_start: 0.5725 (mpp) cc_final: 0.5077 (mpp)
REVERT: B  984 PHE cc_start: 0.5436 (m-80) cc_final: 0.5025 (m-80)
REVERT: B 1004 TYR cc_start: 0.7187 (m-80) cc_final: 0.5935 (m-80)
  outliers start: 0
  outliers final: 0
  residues processed: 100
  average time/residue: 0.2321
  time to fit residues: 29.3373
Evaluate side-chains
  86 residues out of total 708 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 86
  time to evaluate  : 0.584 
-------------------------------------------------------------------------------
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:    2.9990
   chunk 21 optimal weight:    5.9990
   chunk 67 optimal weight:    0.9980
   chunk 23 optimal weight:    2.9990
   chunk 73 optimal weight:    4.9990
   chunk 60 optimal weight:    0.6980
   chunk 62 optimal weight:    0.4980
   chunk 42 optimal weight:    0.9980
   chunk 1 optimal weight:    7.9990
   chunk 52 optimal weight:    0.5980
   overall best weight:    0.7580

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

Flipped N/Q/H residues before XYZ refinement:
** A 660 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 682 ASN
** A 700 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
B 844 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 = 0.5148 r_free = 0.5148 target = 0.274072 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 67)----------------|
| r_work = 0.4702 r_free = 0.4702 target = 0.224826 restraints weight = 21548.731|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 42)----------------|
| r_work = 0.4762 r_free = 0.4762 target = 0.230785 restraints weight = 16422.854|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 28)----------------|
| r_work = 0.4800 r_free = 0.4800 target = 0.234589 restraints weight = 13228.275|
|-----------------------------------------------------------------------------|
r_work (final): 0.4763
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.4571
moved from start:          0.3559

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.050   6557  Z= 0.128
  Angle     :  0.538   5.088   8932  Z= 0.280
  Chirality :  0.045   0.331    961
  Planarity :  0.004   0.037   1179
  Dihedral  :  3.906  26.402    869
  Min Nonbonded Distance : 2.448

Molprobity Statistics.
  All-atom Clashscore : 12.16
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  7.27 %
    Favored  : 92.73 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  1.98 %
    Favored  : 98.02 %
  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: -1.72 (0.69), residues: 40
  sheet: -0.26 (0.38), residues: 189
  loop : -1.62 (0.25), residues: 583

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.012   0.001   TRP B 819 
 HIS   0.003   0.001   HIS A 700 
 PHE   0.012   0.001   PHE A 479 
 TYR   0.008   0.001   TYR B 920 
 ARG   0.007   0.001   ARG B 872 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03120 (  132)
  hydrogen bonds       : angle       6.73165 (  336)
  SS BOND              : bond        0.00462 (   14)
  SS BOND              : angle       1.48264 (   28)
  covalent geometry    : bond        0.00296 ( 6543)
  covalent geometry    : angle       0.53270 ( 8904)

*********************** 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
  101 residues out of total 708 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 101
  time to evaluate  : 0.713 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  565 GLN cc_start: 0.7650 (tm-30) cc_final: 0.7139 (tm-30)
REVERT: A  620 ASP cc_start: 0.8701 (m-30) cc_final: 0.8351 (m-30)
REVERT: B  789 SER cc_start: 0.5800 (t) cc_final: 0.5456 (p)
REVERT: B  874 ASP cc_start: 0.7401 (p0) cc_final: 0.7174 (p0)
REVERT: B  884 PHE cc_start: 0.7096 (m-80) cc_final: 0.6717 (m-80)
REVERT: B  976 MET cc_start: 0.5821 (mpp) cc_final: 0.5183 (mpp)
REVERT: B  984 PHE cc_start: 0.5348 (m-80) cc_final: 0.4961 (m-80)
REVERT: B 1004 TYR cc_start: 0.7273 (m-80) cc_final: 0.5944 (m-80)
  outliers start: 0
  outliers final: 0
  residues processed: 101
  average time/residue: 0.2485
  time to fit residues: 31.5977
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  : 0.641 
-------------------------------------------------------------------------------
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:    7.9990
   chunk 48 optimal weight:    2.9990
   chunk 76 optimal weight:    0.7980
   chunk 61 optimal weight:    0.9990
   chunk 34 optimal weight:    4.9990
   chunk 46 optimal weight:    0.9990
   chunk 49 optimal weight:    0.9990
   chunk 63 optimal weight:    1.9990
   chunk 67 optimal weight:    0.9980
   chunk 21 optimal weight:    8.9990
   chunk 57 optimal weight:    0.9980
   overall best weight:    0.9584

-------------------------------------------------------------------------------
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**
** 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: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.5132 r_free = 0.5132 target = 0.274626 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 61)----------------|
| r_work = 0.4677 r_free = 0.4677 target = 0.212726 restraints weight = 18775.619|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 26)----------------|
| r_work = 0.4699 r_free = 0.4699 target = 0.215297 restraints weight = 16028.068|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 27)----------------|
| r_work = 0.4720 r_free = 0.4720 target = 0.217612 restraints weight = 14558.483|
|-----------------------------------------------------------------------------|
r_work (final): 0.4690
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.4904
moved from start:          0.4151

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.065   6557  Z= 0.155
  Angle     :  0.588   6.521   8932  Z= 0.305
  Chirality :  0.046   0.315    961
  Planarity :  0.004   0.056   1179
  Dihedral  :  4.237  25.141    869
  Min Nonbonded Distance : 2.431

Molprobity Statistics.
  All-atom Clashscore : 14.01
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  8.87 %
    Favored  : 91.13 %
  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: -1.79 (0.29), residues: 812
  helix: -1.96 (0.68), residues: 40
  sheet: -0.30 (0.39), residues: 191
  loop : -1.54 (0.26), residues: 581

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.021   0.002   TRP A 699 
 HIS   0.006   0.001   HIS A 700 
 PHE   0.013   0.001   PHE B 991 
 TYR   0.015   0.001   TYR B 920 
 ARG   0.008   0.001   ARG B 872 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03292 (  132)
  hydrogen bonds       : angle       6.68685 (  336)
  SS BOND              : bond        0.00547 (   14)
  SS BOND              : angle       1.49669 (   28)
  covalent geometry    : bond        0.00353 ( 6543)
  covalent geometry    : angle       0.58316 ( 8904)

*********************** 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
  94 residues out of total 708 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 94
  time to evaluate  : 0.612 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  620 ASP cc_start: 0.8572 (m-30) cc_final: 0.8194 (m-30)
REVERT: A  764 ARG cc_start: 0.8186 (tpp80) cc_final: 0.7662 (tpp80)
REVERT: B  789 SER cc_start: 0.5710 (t) cc_final: 0.5345 (p)
REVERT: B  884 PHE cc_start: 0.7283 (m-80) cc_final: 0.6822 (m-80)
REVERT: B  954 MET cc_start: 0.7310 (mtp) cc_final: 0.7095 (mtp)
REVERT: B  976 MET cc_start: 0.5871 (mpp) cc_final: 0.5171 (mpp)
REVERT: B  982 ARG cc_start: 0.6019 (mtp180) cc_final: 0.5722 (mtp85)
REVERT: B  984 PHE cc_start: 0.5615 (m-80) cc_final: 0.5314 (m-80)
REVERT: B 1004 TYR cc_start: 0.7228 (m-80) cc_final: 0.5810 (m-80)
  outliers start: 0
  outliers final: 0
  residues processed: 94
  average time/residue: 0.2456
  time to fit residues: 29.1551
Evaluate side-chains
  85 residues out of total 708 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 85
  time to evaluate  : 0.684 
-------------------------------------------------------------------------------
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:    0.0770
   chunk 61 optimal weight:    0.9990
   chunk 14 optimal weight:    0.8980
   chunk 44 optimal weight:    5.9990
   chunk 31 optimal weight:    0.9980
   chunk 70 optimal weight:    0.0570
   chunk 37 optimal weight:    3.9990
   chunk 2 optimal weight:    0.7980
   chunk 52 optimal weight:    2.9990
   chunk 75 optimal weight:    0.8980
   chunk 71 optimal weight:    0.6980
   overall best weight:    0.5056

-------------------------------------------------------------------------------
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**

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.5359 r_free = 0.5359 target = 0.318938 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 70)----------------|
| r_work = 0.5315 r_free = 0.5315 target = 0.305544 restraints weight = 32989.567|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 33)----------------|
| r_work = 0.5288 r_free = 0.5288 target = 0.306507 restraints weight = 28249.126|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 29)----------------|
| r_work = 0.5305 r_free = 0.5305 target = 0.307471 restraints weight = 20815.011|
|-----------------------------------------------------------------------------|
r_work (final): 0.4998
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.3944
moved from start:          0.4304

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.051   6557  Z= 0.107
  Angle     :  0.527   5.678   8932  Z= 0.273
  Chirality :  0.044   0.309    961
  Planarity :  0.004   0.042   1179
  Dihedral  :  4.065  27.104    869
  Min Nonbonded Distance : 2.474

Molprobity Statistics.
  All-atom Clashscore : 11.11
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  7.76 %
    Favored  : 92.24 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  0.99 %
    Favored  : 99.01 %
  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: -1.64 (0.29), residues: 812
  helix: -1.42 (0.75), residues: 38
  sheet: -0.23 (0.40), residues: 191
  loop : -1.45 (0.26), residues: 583

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.012   0.001   TRP A 699 
 HIS   0.002   0.000   HIS A 700 
 PHE   0.012   0.001   PHE B 991 
 TYR   0.016   0.001   TYR B 959 
 ARG   0.009   0.001   ARG B 872 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.02682 (  132)
  hydrogen bonds       : angle       6.20266 (  336)
  SS BOND              : bond        0.00293 (   14)
  SS BOND              : angle       1.22567 (   28)
  covalent geometry    : bond        0.00249 ( 6543)
  covalent geometry    : angle       0.52314 ( 8904)

*********************** 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  : 0.657 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  620 ASP cc_start: 0.8702 (m-30) cc_final: 0.8348 (m-30)
REVERT: B  789 SER cc_start: 0.5839 (t) cc_final: 0.5492 (p)
REVERT: B  831 ASN cc_start: 0.7915 (p0) cc_final: 0.7380 (t0)
REVERT: B  872 ARG cc_start: 0.8527 (mmm160) cc_final: 0.8237 (mmm160)
REVERT: B  884 PHE cc_start: 0.6949 (m-80) cc_final: 0.6582 (m-80)
REVERT: B  976 MET cc_start: 0.6171 (mpp) cc_final: 0.5520 (mpp)
REVERT: B  982 ARG cc_start: 0.5748 (mtp180) cc_final: 0.5546 (mtp85)
REVERT: B  984 PHE cc_start: 0.5032 (m-80) cc_final: 0.4627 (m-80)
REVERT: B 1004 TYR cc_start: 0.7175 (m-80) cc_final: 0.5876 (m-80)
  outliers start: 0
  outliers final: 0
  residues processed: 100
  average time/residue: 0.2460
  time to fit residues: 31.2791
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  : 0.663 
-------------------------------------------------------------------------------
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:    9.9990
   chunk 2 optimal weight:    0.9990
   chunk 48 optimal weight:    2.9990
   chunk 5 optimal weight:    9.9990
   chunk 80 optimal weight:    0.5980
   chunk 59 optimal weight:    1.9990
   chunk 17 optimal weight:    3.9990
   chunk 4 optimal weight:    0.7980
   chunk 40 optimal weight:    5.9990
   chunk 49 optimal weight:    0.6980
   overall best weight:    0.7982

-------------------------------------------------------------------------------
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**
** A 700 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
B 867 HIS
B 875 ASN
** 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 = 0.5122 r_free = 0.5122 target = 0.273165 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 66)----------------|
| r_work = 0.4653 r_free = 0.4653 target = 0.220818 restraints weight = 19858.809|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 45)----------------|
| r_work = 0.4706 r_free = 0.4706 target = 0.226164 restraints weight = 15766.660|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 31)----------------|
| r_work = 0.4744 r_free = 0.4744 target = 0.230132 restraints weight = 13090.433|
|-----------------------------------------------------------------------------|
r_work (final): 0.4700
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.4763
moved from start:          0.4700

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.059   6557  Z= 0.138
  Angle     :  0.567   5.960   8932  Z= 0.296
  Chirality :  0.045   0.302    961
  Planarity :  0.004   0.041   1179
  Dihedral  :  4.158  26.697    869
  Min Nonbonded Distance : 2.451

Molprobity Statistics.
  All-atom Clashscore : 13.69
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  9.36 %
    Favored  : 90.64 %
  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: -1.68 (0.30), residues: 812
  helix: -1.25 (0.76), residues: 38
  sheet: -0.61 (0.38), residues: 204
  loop : -1.36 (0.26), residues: 570

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.019   0.001   TRP A 699 
 HIS   0.006   0.001   HIS A 700 
 PHE   0.017   0.001   PHE B 991 
 TYR   0.014   0.001   TYR B 804 
 ARG   0.008   0.001   ARG B 807 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.02866 (  132)
  hydrogen bonds       : angle       6.36802 (  336)
  SS BOND              : bond        0.00389 (   14)
  SS BOND              : angle       1.35859 (   28)
  covalent geometry    : bond        0.00315 ( 6543)
  covalent geometry    : angle       0.56307 ( 8904)

*********************** 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
  92 residues out of total 708 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 92
  time to evaluate  : 0.681 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  620 ASP cc_start: 0.8667 (m-30) cc_final: 0.8297 (m-30)
REVERT: B  789 SER cc_start: 0.5840 (t) cc_final: 0.5436 (p)
REVERT: B  874 ASP cc_start: 0.7455 (p0) cc_final: 0.6973 (p0)
REVERT: B  877 ILE cc_start: 0.7511 (tt) cc_final: 0.7207 (tt)
REVERT: B  884 PHE cc_start: 0.7064 (m-80) cc_final: 0.6660 (m-80)
REVERT: B  976 MET cc_start: 0.5992 (mpp) cc_final: 0.5351 (mpp)
REVERT: B  981 ASN cc_start: 0.8214 (t0) cc_final: 0.7957 (t0)
REVERT: B 1004 TYR cc_start: 0.7144 (m-80) cc_final: 0.5956 (m-80)
REVERT: B 1010 PHE cc_start: 0.6555 (m-80) cc_final: 0.5884 (m-80)
  outliers start: 0
  outliers final: 0
  residues processed: 92
  average time/residue: 0.2418
  time to fit residues: 28.0961
Evaluate side-chains
  86 residues out of total 708 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 86
  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:    1.9990
   chunk 39 optimal weight:    5.9990
   chunk 10 optimal weight:    0.7980
   chunk 31 optimal weight:    5.9990
   chunk 69 optimal weight:    0.0770
   chunk 1 optimal weight:    2.9990
   chunk 23 optimal weight:    4.9990
   chunk 24 optimal weight:    3.9990
   chunk 5 optimal weight:    6.9990
   chunk 7 optimal weight:    0.9990
   chunk 72 optimal weight:    5.9990
   overall best weight:    1.3744

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

Flipped N/Q/H residues before XYZ refinement:
A 541 ASN
** A 563 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 565 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 929 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
B 968 GLN
B 980 ASN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.5087 r_free = 0.5087 target = 0.267493 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 47)----------------|
| r_work = 0.4599 r_free = 0.4599 target = 0.207627 restraints weight = 17260.213|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 31)----------------|
| r_work = 0.4634 r_free = 0.4634 target = 0.210791 restraints weight = 14987.866|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 38)----------------|
| r_work = 0.4662 r_free = 0.4662 target = 0.211873 restraints weight = 13107.579|
|-----------------------------------------------------------------------------|
r_work (final): 0.4653
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.4943
moved from start:          0.5440

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.062   6557  Z= 0.203
  Angle     :  0.664   7.915   8932  Z= 0.351
  Chirality :  0.048   0.324    961
  Planarity :  0.005   0.078   1179
  Dihedral  :  4.774  26.460    869
  Min Nonbonded Distance : 2.458

Molprobity Statistics.
  All-atom Clashscore : 19.49
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  : 10.22 %
    Favored  : 89.78 %
  Rotamer:
    Outliers :  0.14 %
    Allowed  :  0.56 %
    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: -1.86 (0.29), residues: 812
  helix: -1.83 (0.71), residues: 40
  sheet: -0.66 (0.39), residues: 198
  loop : -1.48 (0.26), residues: 574

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.020   0.002   TRP A 707 
 HIS   0.006   0.001   HIS A 647 
 PHE   0.019   0.002   PHE B 984 
 TYR   0.016   0.002   TYR B 959 
 ARG   0.009   0.001   ARG B 872 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03668 (  132)
  hydrogen bonds       : angle       7.09028 (  336)
  SS BOND              : bond        0.00798 (   14)
  SS BOND              : angle       1.77082 (   28)
  covalent geometry    : bond        0.00451 ( 6543)
  covalent geometry    : angle       0.65748 ( 8904)

*********************** 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
  95 residues out of total 708 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 94
  time to evaluate  : 0.662 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  620 ASP cc_start: 0.8639 (m-30) cc_final: 0.8300 (m-30)
REVERT: A  770 LYS cc_start: 0.7790 (mtpp) cc_final: 0.7412 (mtpp)
REVERT: B  789 SER cc_start: 0.5817 (t) cc_final: 0.5345 (p)
REVERT: B  803 TYR cc_start: 0.7746 (m-10) cc_final: 0.7538 (m-10)
REVERT: B  809 LEU cc_start: 0.8218 (mt) cc_final: 0.7904 (mt)
REVERT: B  872 ARG cc_start: 0.8688 (mmm160) cc_final: 0.7974 (mmm-85)
REVERT: B  877 ILE cc_start: 0.7650 (tt) cc_final: 0.7243 (tt)
REVERT: B  884 PHE cc_start: 0.7300 (m-80) cc_final: 0.6825 (m-80)
REVERT: B  955 ILE cc_start: 0.8069 (tt) cc_final: 0.7789 (tt)
REVERT: B  976 MET cc_start: 0.5870 (mpp) cc_final: 0.5156 (mpp)
REVERT: B  981 ASN cc_start: 0.8536 (t0) cc_final: 0.8263 (t0)
REVERT: B 1004 TYR cc_start: 0.7151 (m-80) cc_final: 0.5905 (m-80)
REVERT: B 1010 PHE cc_start: 0.6690 (m-80) cc_final: 0.6114 (m-80)
  outliers start: 1
  outliers final: 0
  residues processed: 95
  average time/residue: 0.2265
  time to fit residues: 27.4643
Evaluate side-chains
  84 residues out of total 708 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 84
  time to evaluate  : 0.611 
-------------------------------------------------------------------------------
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:    0.0870
   chunk 75 optimal weight:    2.9990
   chunk 29 optimal weight:    0.7980
   chunk 64 optimal weight:    0.0770
   chunk 61 optimal weight:    1.9990
   chunk 19 optimal weight:   50.0000
   chunk 80 optimal weight:    0.1980
   chunk 57 optimal weight:    3.9990
   chunk 27 optimal weight:    0.7980
   chunk 34 optimal weight:    0.5980
   overall best weight:    0.3516

-------------------------------------------------------------------------------
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 = 0.5122 r_free = 0.5122 target = 0.272780 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 47)----------------|
| r_work = 0.4650 r_free = 0.4650 target = 0.220938 restraints weight = 20200.151|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 33)----------------|
| r_work = 0.4706 r_free = 0.4706 target = 0.226528 restraints weight = 15927.385|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 31)----------------|
| r_work = 0.4749 r_free = 0.4749 target = 0.230783 restraints weight = 13067.203|
|-----------------------------------------------------------------------------|
r_work (final): 0.4707
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.4721
moved from start:          0.5369

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.053   6557  Z= 0.112
  Angle     :  0.570   5.983   8932  Z= 0.298
  Chirality :  0.045   0.315    961
  Planarity :  0.004   0.045   1179
  Dihedral  :  4.412  28.644    869
  Min Nonbonded Distance : 2.484

Molprobity Statistics.
  All-atom Clashscore : 13.69
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  9.11 %
    Favored  : 90.89 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  0.42 %
    Favored  : 99.58 %
  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: -1.72 (0.30), residues: 812
  helix: -1.24 (0.76), residues: 41
  sheet: -0.46 (0.40), residues: 192
  loop : -1.46 (0.26), residues: 579

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.011   0.001   TRP B 983 
 HIS   0.003   0.001   HIS A 435 
 PHE   0.014   0.001   PHE B 991 
 TYR   0.011   0.001   TYR B 959 
 ARG   0.009   0.001   ARG B 872 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.02640 (  132)
  hydrogen bonds       : angle       6.38478 (  336)
  SS BOND              : bond        0.00335 (   14)
  SS BOND              : angle       1.29051 (   28)
  covalent geometry    : bond        0.00261 ( 6543)
  covalent geometry    : angle       0.56643 ( 8904)

*********************** 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
  97 residues out of total 708 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 97
  time to evaluate  : 0.741 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: B  789 SER cc_start: 0.6107 (t) cc_final: 0.5654 (p)
REVERT: B  872 ARG cc_start: 0.8434 (mmm160) cc_final: 0.8203 (mmm160)
REVERT: B  874 ASP cc_start: 0.7556 (p0) cc_final: 0.7046 (p0)
REVERT: B  877 ILE cc_start: 0.7467 (tt) cc_final: 0.7190 (tt)
REVERT: B  884 PHE cc_start: 0.7063 (m-80) cc_final: 0.6667 (m-80)
REVERT: B  976 MET cc_start: 0.6010 (mpp) cc_final: 0.5409 (mpp)
REVERT: B  981 ASN cc_start: 0.8233 (t0) cc_final: 0.7918 (t0)
REVERT: B 1004 TYR cc_start: 0.7074 (m-80) cc_final: 0.5937 (m-80)
REVERT: B 1010 PHE cc_start: 0.6383 (m-80) cc_final: 0.5829 (m-80)
  outliers start: 0
  outliers final: 0
  residues processed: 97
  average time/residue: 0.2303
  time to fit residues: 28.4258
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  : 0.630 
-------------------------------------------------------------------------------
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:    0.0970
   chunk 40 optimal weight:    0.9990
   chunk 71 optimal weight:    5.9990
   chunk 32 optimal weight:    0.0970
   chunk 18 optimal weight:   30.0000
   chunk 41 optimal weight:    0.7980
   chunk 73 optimal weight:    0.9980
   chunk 30 optimal weight:   10.0000
   chunk 65 optimal weight:    7.9990
   chunk 79 optimal weight:    0.9980
   chunk 64 optimal weight:    0.3980
   overall best weight:    0.4776

-------------------------------------------------------------------------------
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**
A 742 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 = 0.5131 r_free = 0.5131 target = 0.275218 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 69)----------------|
| r_work = 0.4682 r_free = 0.4682 target = 0.215107 restraints weight = 18410.727|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 39)----------------|
| r_work = 0.4719 r_free = 0.4719 target = 0.217884 restraints weight = 15895.465|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 43)----------------|
| r_work = 0.4742 r_free = 0.4742 target = 0.220515 restraints weight = 13869.287|
|-----------------------------------------------------------------------------|
r_work (final): 0.4708
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.4857
moved from start:          0.5488

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.056   6557  Z= 0.115
  Angle     :  0.570  10.275   8932  Z= 0.297
  Chirality :  0.045   0.299    961
  Planarity :  0.004   0.043   1179
  Dihedral  :  4.362  28.698    869
  Min Nonbonded Distance : 2.482

Molprobity Statistics.
  All-atom Clashscore : 12.24
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  8.99 %
    Favored  : 91.01 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  0.00 %
    Favored  : 100.00 %
  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: -1.68 (0.30), residues: 812
  helix: -1.14 (0.77), residues: 41
  sheet: -0.67 (0.39), residues: 200
  loop : -1.35 (0.26), residues: 571

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.020   0.001   TRP B 915 
 HIS   0.004   0.001   HIS A 700 
 PHE   0.014   0.001   PHE B 991 
 TYR   0.008   0.001   TYR B 959 
 ARG   0.009   0.000   ARG B 872 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.02543 (  132)
  hydrogen bonds       : angle       6.09206 (  336)
  SS BOND              : bond        0.00542 (   14)
  SS BOND              : angle       2.26601 (   28)
  covalent geometry    : bond        0.00271 ( 6543)
  covalent geometry    : angle       0.55621 ( 8904)

********************** 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
  96 residues out of total 708 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 96
  time to evaluate  : 0.645 
Fit side-chains
   revert: symmetry clash
REVERT: B  789 SER cc_start: 0.6085 (t) cc_final: 0.5693 (p)
REVERT: B  872 ARG cc_start: 0.8486 (mmm160) cc_final: 0.7660 (mmm-85)
REVERT: B  874 ASP cc_start: 0.7484 (p0) cc_final: 0.7079 (p0)
REVERT: B  877 ILE cc_start: 0.7394 (tt) cc_final: 0.7135 (tt)
REVERT: B  884 PHE cc_start: 0.7231 (m-80) cc_final: 0.6806 (m-80)
REVERT: B  908 ARG cc_start: 0.5181 (ptp-170) cc_final: 0.4872 (ptm160)
REVERT: B  976 MET cc_start: 0.6086 (mpp) cc_final: 0.5440 (mpp)
REVERT: B  981 ASN cc_start: 0.8384 (t0) cc_final: 0.8090 (t0)
REVERT: B  984 PHE cc_start: 0.4681 (m-80) cc_final: 0.4256 (m-80)
REVERT: B 1004 TYR cc_start: 0.7136 (m-80) cc_final: 0.5962 (m-80)
REVERT: B 1010 PHE cc_start: 0.6499 (m-80) cc_final: 0.5992 (m-80)
  outliers start: 0
  outliers final: 0
  residues processed: 96
  average time/residue: 0.2260
  time to fit residues: 27.8369
Evaluate side-chains
  90 residues out of total 708 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 90
  time to evaluate  : 0.668 
-------------------------------------------------------------------------------
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:    0.6980
   chunk 8 optimal weight:    1.9990
   chunk 43 optimal weight:    0.6980
   chunk 34 optimal weight:    0.8980
   chunk 51 optimal weight:    1.9990
   chunk 33 optimal weight:    3.9990
   chunk 22 optimal weight:    2.9990
   chunk 27 optimal weight:    2.9990
   chunk 44 optimal weight:    0.0670
   chunk 5 optimal weight:    9.9990
   chunk 56 optimal weight:    0.7980
   overall best weight:    0.6318

-------------------------------------------------------------------------------
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 = 0.5116 r_free = 0.5116 target = 0.272429 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 44)----------------|
| r_work = 0.4630 r_free = 0.4630 target = 0.211968 restraints weight = 18154.932|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 50)----------------|
| r_work = 0.4679 r_free = 0.4679 target = 0.214937 restraints weight = 16288.629|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 37)----------------|
| r_work = 0.4712 r_free = 0.4712 target = 0.217610 restraints weight = 14367.177|
|-----------------------------------------------------------------------------|
r_work (final): 0.4678
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.4860
moved from start:          0.5622

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.055   6557  Z= 0.120
  Angle     :  0.575   8.943   8932  Z= 0.299
  Chirality :  0.045   0.274    961
  Planarity :  0.004   0.044   1179
  Dihedral  :  4.313  28.536    869
  Min Nonbonded Distance : 2.488

Molprobity Statistics.
  All-atom Clashscore : 13.05
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  9.24 %
    Favored  : 90.76 %
  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: -1.70 (0.30), residues: 812
  helix: -1.38 (0.75), residues: 43
  sheet: -0.43 (0.40), residues: 191
  loop : -1.44 (0.26), residues: 578

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.010   0.001   TRP B 983 
 HIS   0.006   0.001   HIS A 700 
 PHE   0.008   0.001   PHE A 680 
 TYR   0.009   0.001   TYR B 959 
 ARG   0.011   0.001   ARG A 679 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.02609 (  132)
  hydrogen bonds       : angle       6.09786 (  336)
  SS BOND              : bond        0.00479 (   14)
  SS BOND              : angle       2.13855 (   28)
  covalent geometry    : bond        0.00281 ( 6543)
  covalent geometry    : angle       0.56331 ( 8904)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 2662.76 seconds
wall clock time: 47 minutes 9.85 seconds (2829.85 seconds total)