Starting phenix.real_space_refine
on Tue Mar 11 20:48:16 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/8ubv_42106/03_2025/8ubv_42106.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/8ubv_42106/03_2025/8ubv_42106.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=4.1
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/cci-nas-00/data/ceres_data/8ubv_42106/03_2025/8ubv_42106.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/8ubv_42106/03_2025/8ubv_42106.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/8ubv_42106/03_2025/8ubv_42106.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/8ubv_42106/03_2025/8ubv_42106.cif"
  }
  resolution = 4.1
  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=   0.008
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      56      5.16       5
     C    4210      2.51       5
     N    1085      2.21       5
     O    1252      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 11 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: 6603
  Number of models: 1
  Model: ""
    Number of chains: 4
    Chain: "B"
      Number of atoms: 2509
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 324, 2509
          Classifications: {'peptide': 324}
          Link IDs: {'PTRANS': 4, 'TRANS': 319}
          Unresolved non-hydrogen bonds: 46
          Unresolved non-hydrogen angles: 74
          Unresolved non-hydrogen dihedrals: 32
          Planarities with less than four sites: {'ARG:plan': 16}
          Unresolved non-hydrogen planarities: 44
    Chain: "C"
      Number of atoms: 792
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 102, 792
          Classifications: {'peptide': 102}
          Link IDs: {'CIS': 1, 'PTRANS': 2, 'TRANS': 98}
          Unresolved non-hydrogen bonds: 12
          Unresolved non-hydrogen angles: 19
          Unresolved non-hydrogen dihedrals: 7
          Planarities with less than four sites: {'ARG:plan': 5}
          Unresolved non-hydrogen planarities: 12
    Chain: "H"
      Number of atoms: 2500
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 323, 2500
          Classifications: {'peptide': 323}
          Link IDs: {'PTRANS': 4, 'TRANS': 318}
          Unresolved non-hydrogen bonds: 44
          Unresolved non-hydrogen angles: 71
          Unresolved non-hydrogen dihedrals: 31
          Planarities with less than four sites: {'ARG:plan': 15}
          Unresolved non-hydrogen planarities: 42
    Chain: "I"
      Number of atoms: 802
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 103, 802
          Classifications: {'peptide': 103}
          Link IDs: {'CIS': 1, 'PTRANS': 2, 'TRANS': 99}
          Unresolved non-hydrogen bonds: 12
          Unresolved non-hydrogen angles: 19
          Unresolved non-hydrogen dihedrals: 7
          Planarities with less than four sites: {'ARG:plan': 5}
          Unresolved non-hydrogen planarities: 12
  Time building chain proxies: 6.12, per 1000 atoms: 0.93
  Number of scatterers: 6603
  At special positions: 0
  Unit cell: (89.16, 121.852, 67.613, 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      56     16.00
     O    1252      8.00
     N    1085      7.00
     C    4210      6.00
    sf(0) = scattering factor at diffraction angle 0.

  Number of disulfides: simple=4, symmetry=0
    Simple disulfide: pdb=" SG  CYS B 396 " - pdb=" SG  CYS B 422 " distance=2.03
    Simple disulfide: pdb=" SG  CYS C 107 " - pdb=" SG  CYS I 109 " distance=2.03
    Simple disulfide: pdb=" SG  CYS C 109 " - pdb=" SG  CYS I 107 " distance=2.05
    Simple disulfide: pdb=" SG  CYS H 396 " - pdb=" SG  CYS H 422 " 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: 1.46
  Conformation dependent library (CDL) restraints added in 950.5 milliseconds
  

  1688 Ramachandran restraints generated.
    844 Oldfield, 0 Emsley, 844 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  1624

  Finding SS restraints...
    Secondary structure from input PDB file:
      36 helices and 6 sheets defined
      40.0% alpha, 5.2% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 0.63
  Creating SS restraints...
    Processing helix  chain 'B' and resid 377 through 382
      removed outlier: 4.156A  pdb=" N   ILE B 381 " --> pdb=" O   LEU B 377 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 400 through 409
      removed outlier: 4.724A  pdb=" N   LEU B 407 " --> pdb=" O   GLY B 403 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 426 through 436
      removed outlier: 3.967A  pdb=" N   ILE B 430 " --> pdb=" O   SER B 426 " (cutoff:3.500A)
      removed outlier: 3.529A  pdb=" N   HIS B 436 " --> pdb=" O   ALA B 432 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 453 through 463
      removed outlier: 3.557A  pdb=" N   CYS B 463 " --> pdb=" O   LEU B 459 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 479 through 488
      removed outlier: 4.209A  pdb=" N   GLY B 488 " --> pdb=" O   VAL B 484 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 505 through 510
      removed outlier: 3.721A  pdb=" N   LYS B 509 " --> pdb=" O   ASP B 505 " (cutoff:3.500A)
      removed outlier: 3.674A  pdb=" N   ALA B 510 " --> pdb=" O   GLN B 506 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'B' and resid 505 through 510'
    Processing helix  chain 'B' and resid 529 through 534
      removed outlier: 3.679A  pdb=" N   VAL B 533 " --> pdb=" O   THR B 529 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 535 through 538
    Processing helix  chain 'B' and resid 554 through 565
    Processing helix  chain 'B' and resid 580 through 588
      removed outlier: 4.354A  pdb=" N   VAL B 584 " --> pdb=" O   ASN B 580 " (cutoff:3.500A)
      removed outlier: 4.029A  pdb=" N   ALA B 588 " --> pdb=" O   VAL B 584 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 607 through 616
      removed outlier: 3.509A  pdb=" N   ALA B 611 " --> pdb=" O   TYR B 607 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 631 through 642
      removed outlier: 3.758A  pdb=" N   ALA B 635 " --> pdb=" O   THR B 631 " (cutoff:3.500A)
      removed outlier: 3.898A  pdb=" N   GLN B 640 " --> pdb=" O   THR B 636 " (cutoff:3.500A)
      removed outlier: 3.932A  pdb=" N   SER B 642 " --> pdb=" O   ILE B 638 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 659 through 668
      removed outlier: 4.533A  pdb=" N   VAL B 665 " --> pdb=" O   VAL B 661 " (cutoff:3.500A)
      removed outlier: 5.040A  pdb=" N   GLN B 666 " --> pdb=" O   GLU B 662 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 680 through 686
    Processing helix  chain 'C' and resid 18 through 29
    Processing helix  chain 'C' and resid 49 through 56
      removed outlier: 3.611A  pdb=" N   ALA C  53 " --> pdb=" O   ARG C  49 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 56 through 64
      removed outlier: 3.600A  pdb=" N   ARG C  62 " --> pdb=" O   TYR C  58 " (cutoff:3.500A)
      removed outlier: 3.667A  pdb=" N   VAL C  64 " --> pdb=" O   HIS C  60 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 80 through 94
      Proline residue:  C  86  - end of helix
      removed outlier: 4.179A  pdb=" N   GLN C  89 " --> pdb=" O   GLU C  85 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 103 through 107
    Processing helix  chain 'H' and resid 377 through 382
      removed outlier: 3.840A  pdb=" N   ILE H 381 " --> pdb=" O   LEU H 377 " (cutoff:3.500A)
    Processing helix  chain 'H' and resid 400 through 409
      removed outlier: 4.632A  pdb=" N   LEU H 407 " --> pdb=" O   GLY H 403 " (cutoff:3.500A)
    Processing helix  chain 'H' and resid 427 through 436
    Processing helix  chain 'H' and resid 452 through 463
      removed outlier: 4.060A  pdb=" N   LEU H 456 " --> pdb=" O   THR H 452 " (cutoff:3.500A)
      removed outlier: 3.566A  pdb=" N   LYS H 457 " --> pdb=" O   ASP H 453 " (cutoff:3.500A)
    Processing helix  chain 'H' and resid 479 through 488
      removed outlier: 3.545A  pdb=" N   ILE H 483 " --> pdb=" O   ASP H 479 " (cutoff:3.500A)
      removed outlier: 4.138A  pdb=" N   GLY H 488 " --> pdb=" O   VAL H 484 " (cutoff:3.500A)
    Processing helix  chain 'H' and resid 504 through 508
    Processing helix  chain 'H' and resid 529 through 536
      removed outlier: 4.038A  pdb=" N   VAL H 533 " --> pdb=" O   THR H 529 " (cutoff:3.500A)
      removed outlier: 3.688A  pdb=" N   LEU H 536 " --> pdb=" O   GLY H 532 " (cutoff:3.500A)
    Processing helix  chain 'H' and resid 554 through 565
    Processing helix  chain 'H' and resid 580 through 591
      removed outlier: 4.494A  pdb=" N   VAL H 584 " --> pdb=" O   ASN H 580 " (cutoff:3.500A)
      removed outlier: 3.663A  pdb=" N   ALA H 588 " --> pdb=" O   VAL H 584 " (cutoff:3.500A)
      removed outlier: 3.945A  pdb=" N   LYS H 589 " --> pdb=" O   GLU H 585 " (cutoff:3.500A)
      removed outlier: 3.547A  pdb=" N   GLU H 590 " --> pdb=" O   VAL H 586 " (cutoff:3.500A)
    Processing helix  chain 'H' and resid 607 through 616
      removed outlier: 3.908A  pdb=" N   ALA H 611 " --> pdb=" O   TYR H 607 " (cutoff:3.500A)
    Processing helix  chain 'H' and resid 631 through 642
      removed outlier: 3.679A  pdb=" N   ALA H 635 " --> pdb=" O   THR H 631 " (cutoff:3.500A)
      removed outlier: 3.775A  pdb=" N   GLN H 640 " --> pdb=" O   THR H 636 " (cutoff:3.500A)
      removed outlier: 3.981A  pdb=" N   SER H 642 " --> pdb=" O   ILE H 638 " (cutoff:3.500A)
    Processing helix  chain 'H' and resid 659 through 668
      removed outlier: 5.122A  pdb=" N   VAL H 665 " --> pdb=" O   VAL H 661 " (cutoff:3.500A)
      removed outlier: 5.218A  pdb=" N   GLN H 666 " --> pdb=" O   GLU H 662 " (cutoff:3.500A)
    Processing helix  chain 'I' and resid 17 through 29
    Processing helix  chain 'I' and resid 49 through 56
      removed outlier: 3.740A  pdb=" N   ALA I  53 " --> pdb=" O   ARG I  49 " (cutoff:3.500A)
    Processing helix  chain 'I' and resid 56 through 65
      removed outlier: 3.702A  pdb=" N   SER I  61 " --> pdb=" O   SER I  57 " (cutoff:3.500A)
      removed outlier: 3.747A  pdb=" N   ARG I  62 " --> pdb=" O   TYR I  58 " (cutoff:3.500A)
      removed outlier: 4.385A  pdb=" N   GLY I  65 " --> pdb=" O   SER I  61 " (cutoff:3.500A)
    Processing helix  chain 'I' and resid 80 through 94
      Proline residue:  I  86  - end of helix
    Processing helix  chain 'I' and resid 103 through 107
    Processing sheet with id=AA1, first strand: chain 'B' and resid 570 through 571
      removed outlier: 3.600A  pdb=" N   LEU B 597 " --> pdb=" O   THR B 621 " (cutoff:3.500A)
    Processing sheet with id=AA2, first strand: chain 'C' and resid 43 through 47
    Processing sheet with id=AA3, first strand: chain 'C' and resid 95 through 96
      removed outlier: 3.718A  pdb=" N   LEU I  98 " --> pdb=" O   LEU C  96 " (cutoff:3.500A)
    Processing sheet with id=AA4, first strand: chain 'H' and resid 443 through 444
      removed outlier: 4.204A  pdb=" N   HIS H 470 " --> pdb=" O   VAL H 443 " (cutoff:3.500A)
  No H-bonds generated for sheet with id=AA4
    Processing sheet with id=AA5, first strand: chain 'H' and resid 494 through 496
      removed outlier: 6.265A  pdb=" N   ILE H 495 " --> pdb=" O   GLY H 522 " (cutoff:3.500A)
      removed outlier: 3.874A  pdb=" N   LEU H 571 " --> pdb=" O   GLU H 596 " (cutoff:3.500A)
      removed outlier: 3.718A  pdb=" N   TYR H 598 " --> pdb=" O   LEU H 571 " (cutoff:3.500A)
      removed outlier: 6.319A  pdb=" N   LEU H 597 " --> pdb=" O   ASP H 623 " (cutoff:3.500A)
    Processing sheet with id=AA6, first strand: chain 'I' and resid 43 through 47

    177 hydrogen bonds defined for protein.
    495 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: 1.66

  Time building geometry restraints manager: 1.78 seconds

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

  Histogram of bond lengths:
        1.22 -     1.34: 2155
        1.34 -     1.47: 1353
        1.47 -     1.59: 3104
        1.59 -     1.71: 0
        1.71 -     1.83: 70
  Bond restraints: 6682
  Sorted by residual:
  bond pdb=" CD2 TRP H 577 "
       pdb=" CE2 TRP H 577 "
    ideal  model  delta    sigma   weight residual
    1.409  1.445 -0.036 1.70e-02 3.46e+03 4.60e+00
  bond pdb=" CD2 TRP H 626 "
       pdb=" CE2 TRP H 626 "
    ideal  model  delta    sigma   weight residual
    1.409  1.445 -0.036 1.70e-02 3.46e+03 4.37e+00
  bond pdb=" CD2 TRP B 577 "
       pdb=" CE2 TRP B 577 "
    ideal  model  delta    sigma   weight residual
    1.409  1.444 -0.035 1.70e-02 3.46e+03 4.24e+00
  bond pdb=" CD2 TRP B 626 "
       pdb=" CE2 TRP B 626 "
    ideal  model  delta    sigma   weight residual
    1.409  1.444 -0.035 1.70e-02 3.46e+03 4.20e+00
  bond pdb=" CD2 TRP H 577 "
       pdb=" CE3 TRP H 577 "
    ideal  model  delta    sigma   weight residual
    1.398  1.429 -0.031 1.60e-02 3.91e+03 3.74e+00
  ... (remaining 6677 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     4.08: 8909
        4.08 -     8.16: 61
        8.16 -    12.24: 4
       12.24 -    16.32: 3
       16.32 -    20.40: 1
  Bond angle restraints: 8978
  Sorted by residual:
  angle pdb=" C   VAL C 115 "
        pdb=" N   HIS C 116 "
        pdb=" CA  HIS C 116 "
      ideal   model   delta    sigma   weight residual
     121.70  142.10  -20.40 1.80e+00 3.09e-01 1.28e+02
  angle pdb=" N   VAL C 110 "
        pdb=" CA  VAL C 110 "
        pdb=" C   VAL C 110 "
      ideal   model   delta    sigma   weight residual
     112.29  104.74    7.55 9.40e-01 1.13e+00 6.45e+01
  angle pdb=" C   VAL I 115 "
        pdb=" N   HIS I 116 "
        pdb=" CA  HIS I 116 "
      ideal   model   delta    sigma   weight residual
     121.70  135.92  -14.22 1.80e+00 3.09e-01 6.24e+01
  angle pdb=" N   VAL H 373 "
        pdb=" CA  VAL H 373 "
        pdb=" C   VAL H 373 "
      ideal   model   delta    sigma   weight residual
     113.53  107.63    5.90 9.80e-01 1.04e+00 3.63e+01
  angle pdb=" N   ILE H 389 "
        pdb=" CA  ILE H 389 "
        pdb=" C   ILE H 389 "
      ideal   model   delta    sigma   weight residual
     113.71  109.15    4.56 9.50e-01 1.11e+00 2.30e+01
  ... (remaining 8973 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    17.56: 3545
       17.56 -    35.13: 445
       35.13 -    52.69: 119
       52.69 -    70.25: 22
       70.25 -    87.81: 11
  Dihedral angle restraints: 4142
    sinusoidal: 1670
      harmonic: 2472
  Sorted by residual:
  dihedral pdb=" CB  CYS B 396 "
           pdb=" SG  CYS B 396 "
           pdb=" SG  CYS B 422 "
           pdb=" CB  CYS B 422 "
      ideal   model   delta sinusoidal    sigma   weight residual
      93.00  165.99  -72.99     1      1.00e+01 1.00e-02 6.79e+01
  dihedral pdb=" CB  CYS H 396 "
           pdb=" SG  CYS H 396 "
           pdb=" SG  CYS H 422 "
           pdb=" CB  CYS H 422 "
      ideal   model   delta sinusoidal    sigma   weight residual
      93.00  160.39  -67.39     1      1.00e+01 1.00e-02 5.91e+01
  dihedral pdb=" CA  ILE B 485 "
           pdb=" C   ILE B 485 "
           pdb=" N   ALA B 486 "
           pdb=" CA  ALA B 486 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  145.21   34.79     0      5.00e+00 4.00e-02 4.84e+01
  ... (remaining 4139 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.048: 748
       0.048 -    0.096: 266
       0.096 -    0.144: 67
       0.144 -    0.192: 10
       0.192 -    0.239: 1
  Chirality restraints: 1092
  Sorted by residual:
  chirality pdb=" CB  ILE B 578 "
            pdb=" CA  ILE B 578 "
            pdb=" CG1 ILE B 578 "
            pdb=" CG2 ILE B 578 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.64    2.41    0.24 2.00e-01 2.50e+01 1.43e+00
  chirality pdb=" CA  GLU C 111 "
            pdb=" N   GLU C 111 "
            pdb=" C   GLU C 111 "
            pdb=" CB  GLU C 111 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.33    0.18 2.00e-01 2.50e+01 8.01e-01
  chirality pdb=" CA  LYS H 450 "
            pdb=" N   LYS H 450 "
            pdb=" C   LYS H 450 "
            pdb=" CB  LYS H 450 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.34    0.17 2.00e-01 2.50e+01 7.56e-01
  ... (remaining 1089 not shown)

  Planarity restraints: 1117
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  GLU I  41 "    0.008 2.00e-02 2.50e+03   1.52e-02 2.31e+00
        pdb=" C   GLU I  41 "   -0.026 2.00e-02 2.50e+03
        pdb=" O   GLU I  41 "    0.010 2.00e-02 2.50e+03
        pdb=" N   GLY I  42 "    0.009 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  VAL I 106 "    0.007 2.00e-02 2.50e+03   1.48e-02 2.18e+00
        pdb=" C   VAL I 106 "   -0.026 2.00e-02 2.50e+03
        pdb=" O   VAL I 106 "    0.009 2.00e-02 2.50e+03
        pdb=" N   CYS I 107 "    0.009 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  GLU C 111 "    0.007 2.00e-02 2.50e+03   1.43e-02 2.05e+00
        pdb=" C   GLU C 111 "   -0.025 2.00e-02 2.50e+03
        pdb=" O   GLU C 111 "    0.009 2.00e-02 2.50e+03
        pdb=" N   PHE C 112 "    0.008 2.00e-02 2.50e+03
  ... (remaining 1114 not shown)

  Histogram of nonbonded interaction distances:
        1.96 -     2.54: 71
        2.54 -     3.13: 5632
        3.13 -     3.72: 10034
        3.72 -     4.31: 13698
        4.31 -     4.90: 21477
  Nonbonded interactions: 50912
  Sorted by model distance:
  nonbonded pdb=" O   GLN H 592 "
            pdb=" OG1 THR H 618 "
     model   vdw
     1.956 3.040
  nonbonded pdb=" O   ILE B 619 "
            pdb=" OG  SER B 644 "
     model   vdw
     2.076 3.040
  nonbonded pdb=" OD1 ASN C  25 "
            pdb=" NZ  LYS C  29 "
     model   vdw
     2.086 3.120
  nonbonded pdb=" OG1 THR H 452 "
            pdb=" OE1 GLU H 454 "
     model   vdw
     2.105 3.040
  nonbonded pdb=" O   LYS H 566 "
            pdb=" ND2 ASN H 593 "
     model   vdw
     2.117 3.120
  ... (remaining 50907 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
Found NCS groups:
ncs_group {
  reference = (chain 'B' and resid 363 through 685)
  selection = chain 'H'
}
ncs_group {
  reference = chain 'C'
  selection = (chain 'I' and resid 17 through 118)
}

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:             7.610
  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:          0.280
  Check model and map are aligned:         0.050
  Set scattering table:                    0.070
  Process input model:                     20.080
  Find NCS groups from input model:        0.300
  Set up NCS constraints:                  0.030
  Set refine NCS operators:                0.000
  Adjust number of macro_cycles:           0.000
  Reset NCS operators:                     0.000
  Extract rigid body selections:           0.000
  Check and reset occupancies:             0.010
  Load rotamer database and sin/cos tables:2.730
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   31.170
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.5692
moved from start:          0.0000

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.037   6682  Z= 0.329
  Angle     :  1.001  20.400   8978  Z= 0.562
  Chirality :  0.051   0.239   1092
  Planarity :  0.003   0.023   1117
  Dihedral  : 17.196  87.815   2506
  Min Nonbonded Distance : 1.956

Molprobity Statistics.
  All-atom Clashscore : 24.13
  Ramachandran Plot:
    Outliers :  0.12 %
    Allowed  : 16.00 %
    Favored  : 83.89 %
  Rotamer:
    Outliers :  3.88 %
    Allowed  :  1.94 %
    Favored  : 94.19 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.12 %
    Twisted Proline : 0.00 %
    Twisted General : 0.24 %

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: -3.69 (0.26), residues: 844
  helix: -1.64 (0.30), residues: 257
  sheet: -2.52 (0.58), residues: 73
  loop : -3.02 (0.25), residues: 514

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.009   0.002   TRP B 577 
 HIS   0.008   0.002   HIS H 514 
 PHE   0.015   0.002   PHE C 112 
 TYR   0.015   0.002   TYR H 420 
 ARG   0.000   0.000   ARG H 397 

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

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

  1688 Ramachandran restraints generated.
    844 Oldfield, 0 Emsley, 844 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1688 Ramachandran restraints generated.
    844 Oldfield, 0 Emsley, 844 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  193 residues out of total 774 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 30
    poor density    : 163
  time to evaluate  : 0.785 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: B  399 MET cc_start: 0.0872 (pmm) cc_final: 0.0136 (ptp)
REVERT: B  554 ASP cc_start: 0.7503 (t0) cc_final: 0.7185 (t70)
REVERT: H  375 ASP cc_start: 0.5060 (p0) cc_final: 0.4718 (p0)
REVERT: H  439 LEU cc_start: 0.7060 (tp) cc_final: 0.6219 (pp)
REVERT: H  449 ASP cc_start: 0.6818 (m-30) cc_final: 0.6613 (m-30)
REVERT: H  471 PHE cc_start: 0.7028 (m-80) cc_final: 0.6621 (m-10)
REVERT: H  524 MET cc_start: 0.5915 (ptp) cc_final: 0.5334 (ptp)
REVERT: H  645 LEU cc_start: 0.8286 (mm) cc_final: 0.8070 (mm)
REVERT: I   70 GLU cc_start: 0.6926 (tt0) cc_final: 0.6531 (tm-30)
  outliers start: 30
  outliers final: 30
  residues processed: 188
  average time/residue: 0.1635
  time to fit residues: 42.2177
Evaluate side-chains
  126 residues out of total 774 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 30
    poor density    : 96
  time to evaluate  : 0.740 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 84
   random chunks:
   chunk 70 optimal weight:    7.9990
   chunk 63 optimal weight:    1.9990
   chunk 35 optimal weight:    2.9990
   chunk 21 optimal weight:    0.2980
   chunk 42 optimal weight:   10.0000
   chunk 34 optimal weight:    1.9990
   chunk 65 optimal weight:    0.4980
   chunk 25 optimal weight:    4.9990
   chunk 40 optimal weight:    0.0970
   chunk 49 optimal weight:    4.9990
   chunk 76 optimal weight:    0.9980
   overall best weight:    0.7780

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

Flipped N/Q/H residues before XYZ refinement:
B 372 GLN
B 473 GLN
B 541 ASN
** B 593 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
H 441 GLN
** H 447 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** H 572 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** H 576 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4914 r_free = 0.4914 target = 0.214302 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 51)----------------|
| r_work = 0.4575 r_free = 0.4575 target = 0.187207 restraints weight = 19906.031|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 36)----------------|
| r_work = 0.4593 r_free = 0.4593 target = 0.188637 restraints weight = 17984.447|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 43)----------------|
| r_work = 0.4594 r_free = 0.4594 target = 0.188582 restraints weight = 15546.518|
|-----------------------------------------------------------------------------|
r_work (final): 0.4541
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.5563
moved from start:          0.2996

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.037   6682  Z= 0.222
  Angle     :  0.753  10.412   8978  Z= 0.402
  Chirality :  0.046   0.198   1092
  Planarity :  0.004   0.077   1117
  Dihedral  :  5.815  35.873    848
  Min Nonbonded Distance : 2.463

Molprobity Statistics.
  All-atom Clashscore : 15.31
  Ramachandran Plot:
    Outliers :  0.12 %
    Allowed  : 11.26 %
    Favored  : 88.63 %
  Rotamer:
    Outliers :  3.75 %
    Allowed  :  8.91 %
    Favored  : 87.34 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.12 %
    Twisted Proline : 0.00 %
    Twisted General : 0.24 %

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: -3.50 (0.27), residues: 844
  helix: -1.48 (0.29), residues: 283
  sheet: -2.39 (0.58), residues: 71
  loop : -2.97 (0.26), residues: 490

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.006   0.001   TRP B 626 
 HIS   0.006   0.002   HIS H 470 
 PHE   0.013   0.002   PHE H 511 
 TYR   0.013   0.001   TYR H 598 
 ARG   0.000   0.000   ARG H 416 

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

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

  1688 Ramachandran restraints generated.
    844 Oldfield, 0 Emsley, 844 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1688 Ramachandran restraints generated.
    844 Oldfield, 0 Emsley, 844 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  155 residues out of total 774 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 29
    poor density    : 126
  time to evaluate  : 0.763 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: B  399 MET cc_start: 0.1074 (pmm) cc_final: 0.0629 (ptp)
REVERT: B  524 MET cc_start: 0.5896 (tmm) cc_final: 0.5302 (ttp)
REVERT: B  578 ILE cc_start: 0.6324 (mp) cc_final: 0.5241 (mp)
REVERT: H  439 LEU cc_start: 0.6536 (tp) cc_final: 0.6318 (tp)
REVERT: H  440 LEU cc_start: 0.6762 (mt) cc_final: 0.6450 (mt)
REVERT: H  509 LYS cc_start: 0.7030 (mttt) cc_final: 0.6704 (mmtm)
REVERT: H  617 MET cc_start: 0.3179 (pmm) cc_final: 0.2784 (pmm)
  outliers start: 29
  outliers final: 28
  residues processed: 145
  average time/residue: 0.1488
  time to fit residues: 30.4883
Evaluate side-chains
  117 residues out of total 774 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 28
    poor density    : 89
  time to evaluate  : 0.755 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 84
   random chunks:
   chunk 45 optimal weight:    0.9980
   chunk 51 optimal weight:    0.9990
   chunk 26 optimal weight:    1.9990
   chunk 48 optimal weight:    0.9980
   chunk 66 optimal weight:    0.7980
   chunk 37 optimal weight:    3.9990
   chunk 9 optimal weight:    2.9990
   chunk 70 optimal weight:    0.0870
   chunk 24 optimal weight:    2.9990
   chunk 55 optimal weight:    4.9990
   chunk 67 optimal weight:    9.9990
   overall best weight:    0.7760

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

Flipped N/Q/H residues before XYZ refinement:
** B 593 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
H 424 GLN
** H 447 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** H 572 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** H 576 ASN ** 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 = 0.4855 r_free = 0.4855 target = 0.209150 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 49)----------------|
| r_work = 0.4513 r_free = 0.4513 target = 0.180713 restraints weight = 18148.189|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 33)----------------|
| r_work = 0.4512 r_free = 0.4512 target = 0.180760 restraints weight = 14839.598|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 31)----------------|
| r_work = 0.4516 r_free = 0.4516 target = 0.181083 restraints weight = 13332.096|
|-----------------------------------------------------------------------------|
r_work (final): 0.4520
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.5591
moved from start:          0.3912

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.037   6682  Z= 0.223
  Angle     :  0.741  10.721   8978  Z= 0.393
  Chirality :  0.045   0.164   1092
  Planarity :  0.003   0.055   1117
  Dihedral  :  5.643  35.915    848
  Min Nonbonded Distance : 2.494

Molprobity Statistics.
  All-atom Clashscore : 15.68
  Ramachandran Plot:
    Outliers :  0.12 %
    Allowed  : 13.51 %
    Favored  : 86.37 %
  Rotamer:
    Outliers :  4.01 %
    Allowed  :  7.88 %
    Favored  : 88.11 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.12 %
    Twisted Proline : 0.00 %
    Twisted General : 0.36 %

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: -3.38 (0.27), residues: 844
  helix: -1.24 (0.30), residues: 275
  sheet: -2.73 (0.51), residues: 92
  loop : -2.86 (0.27), residues: 477

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.005   0.001   TRP B 626 
 HIS   0.007   0.001   HIS B 535 
 PHE   0.011   0.002   PHE H 511 
 TYR   0.011   0.001   TYR H 598 
 ARG   0.000   0.000   ARG H 646 

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

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

  1688 Ramachandran restraints generated.
    844 Oldfield, 0 Emsley, 844 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1688 Ramachandran restraints generated.
    844 Oldfield, 0 Emsley, 844 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  154 residues out of total 774 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 31
    poor density    : 123
  time to evaluate  : 0.779 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: B  399 MET cc_start: 0.0553 (pmm) cc_final: 0.0327 (ptp)
REVERT: B  524 MET cc_start: 0.6229 (tmm) cc_final: 0.5547 (ttp)
REVERT: B  534 ILE cc_start: 0.7637 (mm) cc_final: 0.7310 (mm)
REVERT: C  111 GLU cc_start: 0.7831 (pm20) cc_final: 0.7476 (pm20)
REVERT: H  399 MET cc_start: 0.3878 (mpp) cc_final: 0.2498 (ptp)
REVERT: H  509 LYS cc_start: 0.7153 (mttt) cc_final: 0.6659 (mmtm)
REVERT: H  617 MET cc_start: 0.3427 (pmm) cc_final: 0.3093 (pmm)
  outliers start: 31
  outliers final: 29
  residues processed: 144
  average time/residue: 0.1607
  time to fit residues: 32.6230
Evaluate side-chains
  128 residues out of total 774 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 29
    poor density    : 99
  time to evaluate  : 0.786 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 84
   random chunks:
   chunk 54 optimal weight:    0.6980
   chunk 39 optimal weight:    0.5980
   chunk 34 optimal weight:    0.7980
   chunk 29 optimal weight:    0.0870
   chunk 28 optimal weight:    4.9990
   chunk 52 optimal weight:    2.9990
   chunk 44 optimal weight:    4.9990
   chunk 42 optimal weight:    7.9990
   chunk 37 optimal weight:    1.9990
   chunk 3 optimal weight:   10.0000
   chunk 0 optimal weight:    7.9990
   overall best weight:    0.8360

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

Flipped N/Q/H residues before XYZ refinement:
B 473 GLN
** B 593 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
C  43 GLN
H 424 GLN
H 444 HIS
** H 447 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** H 572 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** H 576 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
H 592 GLN
I  89 GLN

Total number of N/Q/H flips: 6

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4828 r_free = 0.4828 target = 0.207372 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 58)----------------|
| r_work = 0.4465 r_free = 0.4465 target = 0.175679 restraints weight = 18165.490|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 42)----------------|
| r_work = 0.4490 r_free = 0.4490 target = 0.177578 restraints weight = 14149.962|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 48)----------------|
| r_work = 0.4503 r_free = 0.4503 target = 0.178691 restraints weight = 12044.558|
|-----------------------------------------------------------------------------|
r_work (final): 0.4505
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.5680
moved from start:          0.4546

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.037   6682  Z= 0.219
  Angle     :  0.734  10.101   8978  Z= 0.393
  Chirality :  0.046   0.176   1092
  Planarity :  0.003   0.048   1117
  Dihedral  :  5.648  37.934    848
  Min Nonbonded Distance : 2.509

Molprobity Statistics.
  All-atom Clashscore : 16.36
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  : 12.56 %
    Favored  : 87.44 %
  Rotamer:
    Outliers :  4.01 %
    Allowed  :  6.33 %
    Favored  : 89.66 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.12 %
    Twisted Proline : 0.00 %
    Twisted General : 0.36 %

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: -3.34 (0.27), residues: 844
  helix: -1.33 (0.30), residues: 278
  sheet: -2.10 (0.56), residues: 76
  loop : -2.90 (0.27), residues: 490

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.007   0.001   TRP H 626 
 HIS   0.006   0.001   HIS B 535 
 PHE   0.016   0.002   PHE I 112 
 TYR   0.009   0.001   TYR H 598 
 ARG   0.000   0.000   ARG H 421 

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

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

  1688 Ramachandran restraints generated.
    844 Oldfield, 0 Emsley, 844 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1688 Ramachandran restraints generated.
    844 Oldfield, 0 Emsley, 844 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  146 residues out of total 774 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 31
    poor density    : 115
  time to evaluate  : 0.827 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: B  399 MET cc_start: 0.0580 (pmm) cc_final: 0.0276 (ptp)
REVERT: B  485 ILE cc_start: 0.5058 (mp) cc_final: 0.4849 (mm)
REVERT: B  534 ILE cc_start: 0.7807 (mm) cc_final: 0.7451 (mm)
REVERT: B  578 ILE cc_start: 0.6779 (mp) cc_final: 0.6540 (mp)
REVERT: C   97 ILE cc_start: 0.7560 (pt) cc_final: 0.7325 (pt)
REVERT: H  439 LEU cc_start: 0.6373 (tp) cc_final: 0.5943 (pt)
REVERT: H  509 LYS cc_start: 0.7130 (mttt) cc_final: 0.6590 (mmtm)
REVERT: H  617 MET cc_start: 0.3577 (pmm) cc_final: 0.3342 (pmm)
  outliers start: 31
  outliers final: 29
  residues processed: 136
  average time/residue: 0.1501
  time to fit residues: 28.9811
Evaluate side-chains
  124 residues out of total 774 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 29
    poor density    : 95
  time to evaluate  : 0.778 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 84
   random chunks:
   chunk 19 optimal weight:    0.0050
   chunk 1 optimal weight:    0.8980
   chunk 10 optimal weight:    4.9990
   chunk 4 optimal weight:    2.9990
   chunk 57 optimal weight:    0.0770
   chunk 30 optimal weight:    0.5980
   chunk 43 optimal weight:    3.9990
   chunk 55 optimal weight:    0.7980
   chunk 76 optimal weight:    0.2980
   chunk 63 optimal weight:    2.9990
   chunk 18 optimal weight:    0.9980
   overall best weight:    0.3552

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

Flipped N/Q/H residues before XYZ refinement:
B 448 GLN
** B 593 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
H 424 GLN
** H 447 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
H 448 GLN
** H 572 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** H 576 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
I 116 HIS

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4854 r_free = 0.4854 target = 0.209994 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 55)----------------|
| r_work = 0.4575 r_free = 0.4575 target = 0.186009 restraints weight = 18183.737|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 27)----------------|
| r_work = 0.4539 r_free = 0.4539 target = 0.184275 restraints weight = 18062.115|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 24)----------------|
| r_work = 0.4556 r_free = 0.4556 target = 0.185620 restraints weight = 16418.301|
|-----------------------------------------------------------------------------|
r_work (final): 0.4557
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.5415
moved from start:          0.4910

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.037   6682  Z= 0.191
  Angle     :  0.723  10.954   8978  Z= 0.384
  Chirality :  0.045   0.173   1092
  Planarity :  0.003   0.051   1117
  Dihedral  :  5.589  35.862    848
  Min Nonbonded Distance : 2.479

Molprobity Statistics.
  All-atom Clashscore : 13.65
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  : 13.15 %
    Favored  : 86.85 %
  Rotamer:
    Outliers :  3.88 %
    Allowed  :  4.91 %
    Favored  : 91.21 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.12 %
    Twisted Proline : 0.00 %
    Twisted General : 0.36 %

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: -3.27 (0.27), residues: 844
  helix: -1.23 (0.30), residues: 275
  sheet: -2.25 (0.53), residues: 82
  loop : -2.84 (0.27), residues: 487

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.008   0.001   TRP B 577 
 HIS   0.006   0.001   HIS C 116 
 PHE   0.016   0.001   PHE I 112 
 TYR   0.010   0.001   TYR H 598 
 ARG   0.000   0.000   ARG H 421 

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

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

  1688 Ramachandran restraints generated.
    844 Oldfield, 0 Emsley, 844 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1688 Ramachandran restraints generated.
    844 Oldfield, 0 Emsley, 844 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  146 residues out of total 774 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 30
    poor density    : 116
  time to evaluate  : 0.977 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: B  507 SER cc_start: 0.7665 (p) cc_final: 0.7045 (m)
REVERT: B  524 MET cc_start: 0.6352 (ttp) cc_final: 0.5694 (ttp)
REVERT: C   88 ILE cc_start: 0.8527 (mm) cc_final: 0.8320 (mm)
REVERT: H  439 LEU cc_start: 0.6236 (tp) cc_final: 0.5951 (pt)
REVERT: H  509 LYS cc_start: 0.7174 (mttt) cc_final: 0.6326 (mmtt)
  outliers start: 30
  outliers final: 29
  residues processed: 137
  average time/residue: 0.1466
  time to fit residues: 28.8394
Evaluate side-chains
  127 residues out of total 774 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 29
    poor density    : 98
  time to evaluate  : 0.734 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 84
   random chunks:
   chunk 50 optimal weight:    1.9990
   chunk 73 optimal weight:    2.9990
   chunk 12 optimal weight:    4.9990
   chunk 70 optimal weight:    0.0050
   chunk 53 optimal weight:    3.9990
   chunk 79 optimal weight:    1.9990
   chunk 72 optimal weight:    0.4980
   chunk 35 optimal weight:    0.7980
   chunk 38 optimal weight:    4.9990
   chunk 34 optimal weight:    0.7980
   chunk 51 optimal weight:    3.9990
   overall best weight:    0.8196

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

Flipped N/Q/H residues before XYZ refinement:
** B 593 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
C  43 GLN
H 424 GLN
** H 447 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
H 567 ASN
** H 572 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** H 678 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4824 r_free = 0.4824 target = 0.207097 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 43)----------------|
| r_work = 0.4503 r_free = 0.4503 target = 0.179493 restraints weight = 18039.607|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 30)----------------|
| r_work = 0.4492 r_free = 0.4492 target = 0.179131 restraints weight = 16847.150|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 33)----------------|
| r_work = 0.4499 r_free = 0.4499 target = 0.179723 restraints weight = 14820.750|
|-----------------------------------------------------------------------------|
r_work (final): 0.4492
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.5697
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   0.037   6682  Z= 0.224
  Angle     :  0.763  10.353   8978  Z= 0.406
  Chirality :  0.046   0.186   1092
  Planarity :  0.003   0.043   1117
  Dihedral  :  5.729  35.768    848
  Min Nonbonded Distance : 2.349

Molprobity Statistics.
  All-atom Clashscore : 15.83
  Ramachandran Plot:
    Outliers :  0.12 %
    Allowed  : 14.22 %
    Favored  : 85.66 %
  Rotamer:
    Outliers :  4.13 %
    Allowed  :  3.88 %
    Favored  : 91.99 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.12 %
    Twisted Proline : 0.00 %
    Twisted General : 0.36 %

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: -3.32 (0.27), residues: 844
  helix: -1.18 (0.30), residues: 271
  sheet: -2.18 (0.55), residues: 77
  loop : -2.95 (0.27), residues: 496

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.007   0.001   TRP H 626 
 HIS   0.008   0.002   HIS B 535 
 PHE   0.015   0.002   PHE C 112 
 TYR   0.008   0.001   TYR H 420 
 ARG   0.000   0.000   ARG I  49 

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

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

  1688 Ramachandran restraints generated.
    844 Oldfield, 0 Emsley, 844 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1688 Ramachandran restraints generated.
    844 Oldfield, 0 Emsley, 844 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  148 residues out of total 774 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 32
    poor density    : 116
  time to evaluate  : 0.719 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: B  524 MET cc_start: 0.6645 (ttp) cc_final: 0.5860 (ttp)
REVERT: C   19 ASN cc_start: 0.6502 (t0) cc_final: 0.6225 (p0)
REVERT: H  439 LEU cc_start: 0.6326 (tp) cc_final: 0.5966 (pt)
REVERT: H  448 GLN cc_start: 0.5331 (tp40) cc_final: 0.4984 (tp40)
REVERT: H  509 LYS cc_start: 0.7552 (mttt) cc_final: 0.6395 (mmtt)
REVERT: H  610 ILE cc_start: 0.6377 (pt) cc_final: 0.6173 (mm)
REVERT: I  112 PHE cc_start: 0.6390 (m-80) cc_final: 0.5693 (m-80)
  outliers start: 32
  outliers final: 29
  residues processed: 140
  average time/residue: 0.1428
  time to fit residues: 28.4175
Evaluate side-chains
  126 residues out of total 774 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 29
    poor density    : 97
  time to evaluate  : 0.706 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 84
   random chunks:
   chunk 83 optimal weight:    0.5980
   chunk 44 optimal weight:    0.9990
   chunk 57 optimal weight:    0.0870
   chunk 46 optimal weight:    2.9990
   chunk 24 optimal weight:    1.9990
   chunk 22 optimal weight:    1.9990
   chunk 35 optimal weight:    0.1980
   chunk 56 optimal weight:    0.3980
   chunk 74 optimal weight:    4.9990
   chunk 21 optimal weight:    2.9990
   chunk 81 optimal weight:    0.9990
   overall best weight:    0.4560

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

Flipped N/Q/H residues before XYZ refinement:
H 424 GLN
** H 447 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
H 567 ASN
** H 572 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** H 576 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** H 593 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** H 678 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
I  89 GLN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4846 r_free = 0.4846 target = 0.209168 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 74)----------------|
| r_work = 0.4490 r_free = 0.4490 target = 0.177705 restraints weight = 18055.072|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 61)----------------|
| r_work = 0.4509 r_free = 0.4509 target = 0.179411 restraints weight = 14280.643|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 53)----------------|
| r_work = 0.4522 r_free = 0.4522 target = 0.180729 restraints weight = 12323.033|
|-----------------------------------------------------------------------------|
r_work (final): 0.4513
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.5652
moved from start:          0.5620

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.037   6682  Z= 0.190
  Angle     :  0.733  10.882   8978  Z= 0.392
  Chirality :  0.046   0.185   1092
  Planarity :  0.003   0.040   1117
  Dihedral  :  5.667  37.014    848
  Min Nonbonded Distance : 2.361

Molprobity Statistics.
  All-atom Clashscore : 14.40
  Ramachandran Plot:
    Outliers :  0.12 %
    Allowed  : 13.63 %
    Favored  : 86.26 %
  Rotamer:
    Outliers :  3.88 %
    Allowed  :  3.62 %
    Favored  : 92.51 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.12 %
    Twisted Proline : 0.00 %
    Twisted General : 0.24 %

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: -3.37 (0.27), residues: 844
  helix: -1.29 (0.30), residues: 271
  sheet: -2.43 (0.53), residues: 87
  loop : -2.89 (0.27), residues: 486

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.006   0.001   TRP B 626 
 HIS   0.006   0.001   HIS C 116 
 PHE   0.019   0.001   PHE I 112 
 TYR   0.007   0.001   TYR H 598 
 ARG   0.000   0.000   ARG H 384 

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

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

  1688 Ramachandran restraints generated.
    844 Oldfield, 0 Emsley, 844 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1688 Ramachandran restraints generated.
    844 Oldfield, 0 Emsley, 844 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  142 residues out of total 774 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 30
    poor density    : 112
  time to evaluate  : 0.684 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: B  524 MET cc_start: 0.6679 (ttp) cc_final: 0.5758 (ttp)
REVERT: C   19 ASN cc_start: 0.6461 (t0) cc_final: 0.6180 (p0)
REVERT: H  439 LEU cc_start: 0.6395 (tp) cc_final: 0.5949 (pt)
REVERT: H  509 LYS cc_start: 0.7615 (mttt) cc_final: 0.6273 (mmtt)
REVERT: H  610 ILE cc_start: 0.6181 (pt) cc_final: 0.5959 (mm)
REVERT: I  112 PHE cc_start: 0.6314 (m-80) cc_final: 0.5752 (m-80)
  outliers start: 30
  outliers final: 29
  residues processed: 133
  average time/residue: 0.1390
  time to fit residues: 26.6594
Evaluate side-chains
  124 residues out of total 774 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 29
    poor density    : 95
  time to evaluate  : 0.685 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 84
   random chunks:
   chunk 32 optimal weight:    0.8980
   chunk 37 optimal weight:    0.6980
   chunk 38 optimal weight:    2.9990
   chunk 69 optimal weight:    6.9990
   chunk 60 optimal weight:    0.7980
   chunk 44 optimal weight:    0.0020
   chunk 6 optimal weight:    0.9990
   chunk 43 optimal weight:    0.1980
   chunk 31 optimal weight:    1.9990
   chunk 72 optimal weight:    4.9990
   chunk 13 optimal weight:    2.9990
   overall best weight:    0.5188

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

Flipped N/Q/H residues before XYZ refinement:
H 424 GLN
** H 447 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
H 567 ASN
** H 572 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** H 576 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** H 593 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** H 678 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4840 r_free = 0.4840 target = 0.207770 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 75)----------------|
| r_work = 0.4477 r_free = 0.4477 target = 0.176339 restraints weight = 17943.547|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 60)----------------|
| r_work = 0.4498 r_free = 0.4498 target = 0.178183 restraints weight = 14336.371|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 25)----------------|
| r_work = 0.4510 r_free = 0.4510 target = 0.179207 restraints weight = 12292.233|
|-----------------------------------------------------------------------------|
r_work (final): 0.4507
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.5689
moved from start:          0.5861

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.037   6682  Z= 0.197
  Angle     :  0.749  10.165   8978  Z= 0.398
  Chirality :  0.045   0.204   1092
  Planarity :  0.003   0.039   1117
  Dihedral  :  5.607  38.888    848
  Min Nonbonded Distance : 2.336

Molprobity Statistics.
  All-atom Clashscore : 14.93
  Ramachandran Plot:
    Outliers :  0.12 %
    Allowed  : 12.80 %
    Favored  : 87.09 %
  Rotamer:
    Outliers :  3.88 %
    Allowed  :  2.58 %
    Favored  : 93.54 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.12 %
    Twisted Proline : 0.00 %
    Twisted General : 0.24 %

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: -3.27 (0.28), residues: 844
  helix: -1.19 (0.30), residues: 278
  sheet: -2.40 (0.53), residues: 87
  loop : -2.84 (0.28), residues: 479

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.005   0.001   TRP B 626 
 HIS   0.007   0.001   HIS C 116 
 PHE   0.018   0.002   PHE I 112 
 TYR   0.007   0.001   TYR H 598 
 ARG   0.000   0.000   ARG H 464 

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

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

  1688 Ramachandran restraints generated.
    844 Oldfield, 0 Emsley, 844 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1688 Ramachandran restraints generated.
    844 Oldfield, 0 Emsley, 844 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  138 residues out of total 774 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 30
    poor density    : 108
  time to evaluate  : 0.715 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: B  524 MET cc_start: 0.6834 (ttp) cc_final: 0.5875 (ttp)
REVERT: C   19 ASN cc_start: 0.6436 (t0) cc_final: 0.6215 (p0)
REVERT: C   88 ILE cc_start: 0.8468 (mm) cc_final: 0.8263 (mm)
REVERT: H  439 LEU cc_start: 0.6301 (tp) cc_final: 0.5889 (pt)
REVERT: H  509 LYS cc_start: 0.7612 (mttt) cc_final: 0.6278 (mmtt)
REVERT: I  112 PHE cc_start: 0.6340 (m-80) cc_final: 0.5858 (m-80)
  outliers start: 30
  outliers final: 29
  residues processed: 130
  average time/residue: 0.1321
  time to fit residues: 25.2027
Evaluate side-chains
  125 residues out of total 774 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 29
    poor density    : 96
  time to evaluate  : 0.695 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 84
   random chunks:
   chunk 27 optimal weight:   10.0000
   chunk 55 optimal weight:    0.7980
   chunk 22 optimal weight:    0.7980
   chunk 25 optimal weight:    0.8980
   chunk 6 optimal weight:    0.7980
   chunk 79 optimal weight:    2.9990
   chunk 68 optimal weight:    3.9990
   chunk 39 optimal weight:    0.6980
   chunk 64 optimal weight:    0.7980
   chunk 11 optimal weight:    8.9990
   chunk 17 optimal weight:    1.9990
   overall best weight:    0.7780

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

Flipped N/Q/H residues before XYZ refinement:
B 514 HIS
** B 593 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
H 424 GLN
** H 447 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
H 567 ASN
** H 572 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** H 678 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4824 r_free = 0.4824 target = 0.205528 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 47)----------------|
| r_work = 0.4542 r_free = 0.4542 target = 0.183128 restraints weight = 17981.529|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 30)----------------|
| r_work = 0.4506 r_free = 0.4506 target = 0.180971 restraints weight = 19257.797|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 25)----------------|
| r_work = 0.4515 r_free = 0.4515 target = 0.181654 restraints weight = 17624.681|
|-----------------------------------------------------------------------------|
r_work (final): 0.4518
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.5543
moved from start:          0.6298

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.037   6682  Z= 0.224
  Angle     :  0.772  10.110   8978  Z= 0.408
  Chirality :  0.046   0.200   1092
  Planarity :  0.003   0.039   1117
  Dihedral  :  5.884  43.986    848
  Min Nonbonded Distance : 2.301

Molprobity Statistics.
  All-atom Clashscore : 16.81
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  : 14.34 %
    Favored  : 85.66 %
  Rotamer:
    Outliers :  3.88 %
    Allowed  :  2.20 %
    Favored  : 93.93 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.12 %
    Twisted Proline : 0.00 %
    Twisted General : 0.36 %

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: -3.24 (0.28), residues: 844
  helix: -1.23 (0.29), residues: 279
  sheet: -2.24 (0.56), residues: 82
  loop : -2.81 (0.28), residues: 483

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.005   0.001   TRP H 626 
 HIS   0.007   0.002   HIS B 535 
 PHE   0.019   0.002   PHE I 112 
 TYR   0.007   0.001   TYR H 420 
 ARG   0.000   0.000   ARG B 416 

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

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

  1688 Ramachandran restraints generated.
    844 Oldfield, 0 Emsley, 844 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1688 Ramachandran restraints generated.
    844 Oldfield, 0 Emsley, 844 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  136 residues out of total 774 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 30
    poor density    : 106
  time to evaluate  : 0.722 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: B  524 MET cc_start: 0.6701 (ttp) cc_final: 0.5776 (ttp)
REVERT: H  439 LEU cc_start: 0.6043 (tp) cc_final: 0.5829 (pt)
REVERT: H  509 LYS cc_start: 0.7777 (mttt) cc_final: 0.6400 (mmtt)
REVERT: H  651 MET cc_start: 0.3988 (tmm) cc_final: 0.3512 (tmm)
REVERT: I  112 PHE cc_start: 0.6520 (m-80) cc_final: 0.6081 (m-80)
  outliers start: 30
  outliers final: 29
  residues processed: 127
  average time/residue: 0.1305
  time to fit residues: 24.4351
Evaluate side-chains
  117 residues out of total 774 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 29
    poor density    : 88
  time to evaluate  : 0.708 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 84
   random chunks:
   chunk 58 optimal weight:    0.9990
   chunk 61 optimal weight:    0.6980
   chunk 73 optimal weight:    0.0060
   chunk 53 optimal weight:    4.9990
   chunk 49 optimal weight:    6.9990
   chunk 41 optimal weight:    0.9980
   chunk 23 optimal weight:    0.7980
   chunk 20 optimal weight:    0.8980
   chunk 43 optimal weight:    0.1980
   chunk 10 optimal weight:    0.8980
   chunk 9 optimal weight:    5.9990
   overall best weight:    0.5196

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

Flipped N/Q/H residues before XYZ refinement:
** B 593 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** C  25 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
H 424 GLN
** H 447 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
H 567 ASN
** H 572 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** H 576 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** H 593 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** H 678 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4836 r_free = 0.4836 target = 0.206690 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 35)----------------|
| r_work = 0.4536 r_free = 0.4536 target = 0.181718 restraints weight = 18047.830|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 27)----------------|
| r_work = 0.4496 r_free = 0.4496 target = 0.179744 restraints weight = 19316.080|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 29)----------------|
| r_work = 0.4517 r_free = 0.4517 target = 0.181417 restraints weight = 16347.158|
|-----------------------------------------------------------------------------|
r_work (final): 0.4523
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.5537
moved from start:          0.6486

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.037   6682  Z= 0.197
  Angle     :  0.762  13.367   8978  Z= 0.397
  Chirality :  0.046   0.190   1092
  Planarity :  0.003   0.038   1117
  Dihedral  :  5.738  41.346    848
  Min Nonbonded Distance : 2.301

Molprobity Statistics.
  All-atom Clashscore : 15.53
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  : 12.44 %
    Favored  : 87.56 %
  Rotamer:
    Outliers :  3.88 %
    Allowed  :  1.55 %
    Favored  : 94.57 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.12 %
    Twisted Proline : 0.00 %
    Twisted General : 0.24 %

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: -3.18 (0.28), residues: 844
  helix: -1.21 (0.29), residues: 282
  sheet: -2.22 (0.55), residues: 82
  loop : -2.77 (0.28), residues: 480

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.006   0.001   TRP B 626 
 HIS   0.010   0.001   HIS C 116 
 PHE   0.016   0.001   PHE H 523 
 TYR   0.012   0.001   TYR H 598 
 ARG   0.000   0.000   ARG H 646 

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

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

  1688 Ramachandran restraints generated.
    844 Oldfield, 0 Emsley, 844 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1688 Ramachandran restraints generated.
    844 Oldfield, 0 Emsley, 844 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  137 residues out of total 774 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 30
    poor density    : 107
  time to evaluate  : 0.677 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: B  482 MET cc_start: 0.3892 (mtm) cc_final: 0.3687 (ttp)
REVERT: B  524 MET cc_start: 0.6668 (ttp) cc_final: 0.5807 (ttp)
REVERT: C   88 ILE cc_start: 0.8247 (mm) cc_final: 0.7961 (mm)
REVERT: H  439 LEU cc_start: 0.6113 (tp) cc_final: 0.5858 (pt)
REVERT: H  509 LYS cc_start: 0.7774 (mttt) cc_final: 0.6340 (mmtt)
REVERT: H  651 MET cc_start: 0.3918 (tmm) cc_final: 0.3596 (tmm)
REVERT: I  112 PHE cc_start: 0.6528 (m-80) cc_final: 0.6165 (m-80)
  outliers start: 30
  outliers final: 29
  residues processed: 128
  average time/residue: 0.1291
  time to fit residues: 24.2766
Evaluate side-chains
  120 residues out of total 774 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 29
    poor density    : 91
  time to evaluate  : 0.765 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 84
   random chunks:
   chunk 22 optimal weight:    0.7980
   chunk 36 optimal weight:    0.3980
   chunk 30 optimal weight:    3.9990
   chunk 70 optimal weight:    1.9990
   chunk 15 optimal weight:    0.9990
   chunk 4 optimal weight:    0.9990
   chunk 81 optimal weight:    0.9980
   chunk 34 optimal weight:    0.6980
   chunk 3 optimal weight:    5.9990
   chunk 26 optimal weight:    3.9990
   chunk 77 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:
** B 593 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
H 424 GLN
** H 447 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
H 567 ASN
** H 572 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** H 678 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4817 r_free = 0.4817 target = 0.204452 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 35)----------------|
| r_work = 0.4518 r_free = 0.4518 target = 0.179370 restraints weight = 18014.855|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 25)----------------|
| r_work = 0.4477 r_free = 0.4477 target = 0.177340 restraints weight = 18348.962|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 27)----------------|
| r_work = 0.4494 r_free = 0.4494 target = 0.178701 restraints weight = 16535.638|
|-----------------------------------------------------------------------------|
r_work (final): 0.4495
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.5624
moved from start:          0.6788

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.037   6682  Z= 0.220
  Angle     :  0.788  12.058   8978  Z= 0.411
  Chirality :  0.047   0.184   1092
  Planarity :  0.003   0.038   1117
  Dihedral  :  5.838  41.555    848
  Min Nonbonded Distance : 2.298

Molprobity Statistics.
  All-atom Clashscore : 17.72
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  : 14.10 %
    Favored  : 85.90 %
  Rotamer:
    Outliers :  3.88 %
    Allowed  :  1.81 %
    Favored  : 94.32 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.12 %
    Twisted Proline : 0.00 %
    Twisted General : 0.24 %

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: -3.27 (0.28), residues: 844
  helix: -1.25 (0.29), residues: 280
  sheet: -2.34 (0.55), residues: 82
  loop : -2.82 (0.28), residues: 482

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.006   0.001   TRP H 626 
 HIS   0.010   0.001   HIS C 116 
 PHE   0.018   0.002   PHE C 112 
 TYR   0.011   0.001   TYR H 598 
 ARG   0.000   0.000   ARG H 548 
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 2469.73 seconds
wall clock time: 43 minutes 43.03 seconds (2623.03 seconds total)