Starting phenix.real_space_refine
on Tue Mar  3 14:23:43 2026 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/7dcp_30638/03_2026/7dcp_30638.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/7dcp_30638/03_2026/7dcp_30638.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=3.15
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    model {
      file = "/net/cci-nas-00/data/ceres_data/7dcp_30638/03_2026/7dcp_30638.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/7dcp_30638/03_2026/7dcp_30638.cif"
    real_map_files = "/net/cci-nas-00/data/ceres_data/7dcp_30638/03_2026/7dcp_30638.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/7dcp_30638/03_2026/7dcp_30638.map"
  }
  resolution = 3.15
  write_initial_geo_file = False
  refinement {
    macro_cycles = 10
  }


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

Validating inputs
Origin is already at (0, 0, 0), no shifts will be applied
-------------------------------------------------------------------------------
Processing inputs
*****************
Set random seed
  Set to: 0
Set model cs if undefined
Decide on map wrapping
  Map wrapping is set to: False
Normalize map: mean=0, sd=1
  Input map: mean=   0.000 sd=   0.002
Set stop_for_unknowns flag
  Set to: True
Assert model is a single copy model
Assert all atoms have isotropic ADPs
  Anisotropic ADP refinement not supported. Converting 168 atoms to isotropic.
Construct map_model_manager
Extract box with map and model
Check model and map are aligned
Set scattering table
  Set to: electron
  Number of scattering types: 6
    Type Number    sf(0)   Gaussians
     P       2      5.49       5
     Mg      1      5.21       5
     S      35      5.16       5
     C    3741      2.51       5
     N    1001      2.21       5
     O    1088      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 5 residue(s): 0.01s

  Monomer Library directory:
    "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-5986/lib/python3.9/site-packages/chem_data/mon_lib"
  Total number of atoms: 5868
  Number of models: 1
  Model: ""
    Number of chains: 3
    Chain: "x"
      Number of atoms: 5355
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 670, 5355
          Classifications: {'peptide': 670}
          Link IDs: {'PCIS': 1, 'PTRANS': 32, 'TRANS': 636}
          Chain breaks: 2
    Chain: "y"
      Number of atoms: 485
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 62, 485
          Classifications: {'peptide': 62}
          Incomplete info: {'truncation_to_alanine': 1}
          Link IDs: {'PTRANS': 4, 'TRANS': 57}
          Chain breaks: 3
          Unresolved non-hydrogen bonds: 4
          Unresolved non-hydrogen angles: 4
          Unresolved non-hydrogen dihedrals: 4
    Chain: "x"
      Number of atoms: 28
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 2, 28
          Unusual residues: {' MG': 1, 'ADP': 1}
          Classifications: {'undetermined': 2}
          Link IDs: {None: 1}
  Time building chain proxies: 1.43, per 1000 atoms: 0.24
  Number of scatterers: 5868
  At special positions: 0
  Unit cell: (92.75, 90.7625, 83.475, 90, 90, 90)
  Space group: P 1 (No. 1)
  Number of sites at special positions: 0
  Number of scattering types: 6
    Type Number    sf(0)
     S      35     16.00
     P       2     15.00
     Mg      1     11.99
     O    1088      8.00
     N    1001      7.00
     C    3741      6.00
    sf(0) = scattering factor at diffraction angle 0.

  Number of disulfides: simple=0, symmetry=0

  Automatic linking
    Parameters for automatic linking
      Linking & cutoffs
        Metal                : Auto  - 3.00
        Amino acid           : True  - 1.90
        Carbohydrate         : True  - 1.99
        Ligands              : True  - 1.99
        Small molecules      : False - 1.98
        Amino acid - RNA/DNA : False
      
  Number of custom bonds: simple=0, symmetry=0
  Time building additional restraints: 0.45
  Conformation dependent library (CDL) restraints added in 276.1 milliseconds
  

  1436 Ramachandran restraints generated.
    718 Oldfield, 0 Emsley, 718 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  1382

  Finding SS restraints...
    Secondary structure from input PDB file:
      34 helices and 5 sheets defined
      51.0% alpha, 12.6% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 0.21
  Creating SS restraints...
    Processing helix  chain 'x' and resid 12 through 16
      removed outlier: 3.774A  pdb=" N   THR x  16 " --> pdb=" O   VAL x  13 " (cutoff:3.500A)
    Processing helix  chain 'x' and resid 216 through 222
      removed outlier: 3.720A  pdb=" N   ARG x 220 " --> pdb=" O   ILE x 216 " (cutoff:3.500A)
      removed outlier: 3.877A  pdb=" N   LYS x 221 " --> pdb=" O   GLN x 217 " (cutoff:3.500A)
      removed outlier: 3.890A  pdb=" N   LEU x 222 " --> pdb=" O   GLU x 218 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'x' and resid 216 through 222'
    Processing helix  chain 'x' and resid 228 through 239
      removed outlier: 3.515A  pdb=" N   GLN x 234 " --> pdb=" O   ASP x 230 " (cutoff:3.500A)
    Processing helix  chain 'x' and resid 251 through 264
      removed outlier: 3.573A  pdb=" N   LEU x 256 " --> pdb=" O   LYS x 252 " (cutoff:3.500A)
      Proline residue:  x 257  - end of helix
    Processing helix  chain 'x' and resid 279 through 295
      removed outlier: 3.584A  pdb=" N   VAL x 286 " --> pdb=" O   ALA x 282 " (cutoff:3.500A)
      removed outlier: 3.507A  pdb=" N   ALA x 287 " --> pdb=" O   ALA x 283 " (cutoff:3.500A)
    Processing helix  chain 'x' and resid 324 through 334
      removed outlier: 3.759A  pdb=" N   LEU x 328 " --> pdb=" O   ASP x 324 " (cutoff:3.500A)
      removed outlier: 3.688A  pdb=" N   PHE x 331 " --> pdb=" O   LEU x 327 " (cutoff:3.500A)
      removed outlier: 4.183A  pdb=" N   LEU x 332 " --> pdb=" O   LEU x 328 " (cutoff:3.500A)
      removed outlier: 4.012A  pdb=" N   THR x 333 " --> pdb=" O   ARG x 329 " (cutoff:3.500A)
    Processing helix  chain 'x' and resid 348 through 351
    Processing helix  chain 'x' and resid 352 through 369
      removed outlier: 3.736A  pdb=" N   ASP x 364 " --> pdb=" O   GLY x 360 " (cutoff:3.500A)
      removed outlier: 3.601A  pdb=" N   ILE x 365 " --> pdb=" O   LEU x 361 " (cutoff:3.500A)
      Proline residue:  x 367  - end of helix
    Processing helix  chain 'x' and resid 383 through 390
    Processing helix  chain 'x' and resid 416 through 432
      removed outlier: 3.628A  pdb=" N   THR x 431 " --> pdb=" O   GLN x 427 " (cutoff:3.500A)
    Processing helix  chain 'x' and resid 444 through 463
    Processing helix  chain 'x' and resid 479 through 484
      removed outlier: 3.773A  pdb=" N   LEU x 484 " --> pdb=" O   GLN x 480 " (cutoff:3.500A)
    Processing helix  chain 'x' and resid 502 through 507
      removed outlier: 3.875A  pdb=" N   THR x 506 " --> pdb=" O   ASN x 502 " (cutoff:3.500A)
    Processing helix  chain 'x' and resid 542 through 551
    Processing helix  chain 'x' and resid 552 through 555
      removed outlier: 3.843A  pdb=" N   ARG x 555 " --> pdb=" O   ARG x 552 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'x' and resid 552 through 555'
    Processing helix  chain 'x' and resid 567 through 572
      removed outlier: 3.675A  pdb=" N   HIS x 572 " --> pdb=" O   TRP x 568 " (cutoff:3.500A)
    Processing helix  chain 'x' and resid 580 through 584
    Processing helix  chain 'x' and resid 587 through 598
    Processing helix  chain 'x' and resid 612 through 626
    Processing helix  chain 'x' and resid 636 through 643
    Processing helix  chain 'x' and resid 648 through 661
      removed outlier: 3.602A  pdb=" N   ALA x 659 " --> pdb=" O   LEU x 655 " (cutoff:3.500A)
    Processing helix  chain 'x' and resid 667 through 680
      removed outlier: 3.605A  pdb=" N   THR x 673 " --> pdb=" O   GLU x 669 " (cutoff:3.500A)
      removed outlier: 3.537A  pdb=" N   HIS x 679 " --> pdb=" O   VAL x 675 " (cutoff:3.500A)
      removed outlier: 4.022A  pdb=" N   GLU x 680 " --> pdb=" O   SER x 676 " (cutoff:3.500A)
    Processing helix  chain 'x' and resid 681 through 684
    Processing helix  chain 'x' and resid 688 through 697
      removed outlier: 3.766A  pdb=" N   ALA x 692 " --> pdb=" O   GLN x 688 " (cutoff:3.500A)
      removed outlier: 3.573A  pdb=" N   SER x 695 " --> pdb=" O   ASP x 691 " (cutoff:3.500A)
    Processing helix  chain 'x' and resid 702 through 717
      removed outlier: 3.536A  pdb=" N   PHE x 711 " --> pdb=" O   TYR x 707 " (cutoff:3.500A)
    Processing helix  chain 'x' and resid 720 through 728
      removed outlier: 3.919A  pdb=" N   CYS x 724 " --> pdb=" O   SER x 720 " (cutoff:3.500A)
      removed outlier: 3.501A  pdb=" N   GLN x 725 " --> pdb=" O   ARG x 721 " (cutoff:3.500A)
    Processing helix  chain 'x' and resid 730 through 752
      removed outlier: 3.646A  pdb=" N   ARG x 736 " --> pdb=" O   LYS x 732 " (cutoff:3.500A)
    Processing helix  chain 'x' and resid 752 through 765
      removed outlier: 3.501A  pdb=" N   LYS x 763 " --> pdb=" O   GLN x 759 " (cutoff:3.500A)
      removed outlier: 3.653A  pdb=" N   GLY x 765 " --> pdb=" O   ARG x 761 " (cutoff:3.500A)
    Processing helix  chain 'x' and resid 767 through 783
      removed outlier: 4.015A  pdb=" N   ASN x 772 " --> pdb=" O   ALA x 768 " (cutoff:3.500A)
      removed outlier: 4.082A  pdb=" N   ALA x 773 " --> pdb=" O   GLY x 769 " (cutoff:3.500A)
    Processing helix  chain 'x' and resid 813 through 822
      removed outlier: 3.518A  pdb=" N   VAL x 817 " --> pdb=" O   SER x 813 " (cutoff:3.500A)
    Processing helix  chain 'x' and resid 852 through 859
      removed outlier: 3.872A  pdb=" N   ILE x 856 " --> pdb=" O   GLU x 852 " (cutoff:3.500A)
    Processing helix  chain 'x' and resid 859 through 867
      removed outlier: 5.709A  pdb=" N   ASP x 865 " --> pdb=" O   GLN x 861 " (cutoff:3.500A)
      removed outlier: 3.695A  pdb=" N   LEU x 866 " --> pdb=" O   ILE x 862 " (cutoff:3.500A)
    Processing helix  chain 'y' and resid 95 through 100
    Processing helix  chain 'y' and resid 101 through 114
      removed outlier: 3.779A  pdb=" N   GLY y 106 " --> pdb=" O   VAL y 102 " (cutoff:3.500A)
      removed outlier: 3.976A  pdb=" N   ASP y 107 " --> pdb=" O   GLU y 103 " (cutoff:3.500A)
      removed outlier: 3.534A  pdb=" N   GLY y 112 " --> pdb=" O   ALA y 108 " (cutoff:3.500A)
    Processing sheet with id=AA1, first strand: chain 'x' and resid 171 through 172
      removed outlier: 5.572A  pdb=" N   TYR x 171 " --> pdb=" O   VAL y 167 " (cutoff:3.500A)
  No H-bonds generated for sheet with id=AA1
    Processing sheet with id=AA2, first strand: chain 'x' and resid 310 through 311
      removed outlier: 6.270A  pdb=" N   ILE x 273 " --> pdb=" O   LYS x 320 " (cutoff:3.500A)
      removed outlier: 7.273A  pdb=" N   MET x 322 " --> pdb=" O   ILE x 273 " (cutoff:3.500A)
      removed outlier: 6.175A  pdb=" N   ILE x 275 " --> pdb=" O   MET x 322 " (cutoff:3.500A)
      removed outlier: 6.001A  pdb=" N   GLN x 272 " --> pdb=" O   TYR x 340 " (cutoff:3.500A)
      removed outlier: 3.932A  pdb=" N   CYS x 342 " --> pdb=" O   GLN x 272 " (cutoff:3.500A)
      removed outlier: 6.876A  pdb=" N   SER x 341 " --> pdb=" O   LYS x 373 " (cutoff:3.500A)
      removed outlier: 8.315A  pdb=" N   LEU x 375 " --> pdb=" O   SER x 341 " (cutoff:3.500A)
      removed outlier: 6.682A  pdb=" N   ILE x 343 " --> pdb=" O   LEU x 375 " (cutoff:3.500A)
      removed outlier: 7.728A  pdb=" N   SER x 377 " --> pdb=" O   ILE x 343 " (cutoff:3.500A)
      removed outlier: 6.377A  pdb=" N   ILE x 345 " --> pdb=" O   SER x 377 " (cutoff:3.500A)
      removed outlier: 8.031A  pdb=" N   PHE x 396 " --> pdb=" O   VAL x 241 " (cutoff:3.500A)
      removed outlier: 6.178A  pdb=" N   ILE x 243 " --> pdb=" O   PHE x 396 " (cutoff:3.500A)
      removed outlier: 7.437A  pdb=" N   VAL x 398 " --> pdb=" O   ILE x 243 " (cutoff:3.500A)
      removed outlier: 6.565A  pdb=" N   MET x 245 " --> pdb=" O   VAL x 398 " (cutoff:3.500A)
    Processing sheet with id=AA3, first strand: chain 'x' and resid 405 through 408
      removed outlier: 6.224A  pdb=" N   ASP x 406 " --> pdb=" O   CYS x 561 " (cutoff:3.500A)
      removed outlier: 7.495A  pdb=" N   ARG x 563 " --> pdb=" O   ASP x 406 " (cutoff:3.500A)
      removed outlier: 6.213A  pdb=" N   HIS x 408 " --> pdb=" O   ARG x 563 " (cutoff:3.500A)
      removed outlier: 5.694A  pdb=" N   ASP x 437 " --> pdb=" O   ILE x 513 " (cutoff:3.500A)
      removed outlier: 6.466A  pdb=" N   ILE x 438 " --> pdb=" O   VAL x 498 " (cutoff:3.500A)
      removed outlier: 7.467A  pdb=" N   ALA x 500 " --> pdb=" O   ILE x 438 " (cutoff:3.500A)
      removed outlier: 5.981A  pdb=" N   VAL x 440 " --> pdb=" O   ALA x 500 " (cutoff:3.500A)
      removed outlier: 6.524A  pdb=" N   GLN x 468 " --> pdb=" O   ARG x 495 " (cutoff:3.500A)
      removed outlier: 7.308A  pdb=" N   VAL x 497 " --> pdb=" O   GLN x 468 " (cutoff:3.500A)
      removed outlier: 6.000A  pdb=" N   ILE x 470 " --> pdb=" O   VAL x 497 " (cutoff:3.500A)
      removed outlier: 6.934A  pdb=" N   LEU x 499 " --> pdb=" O   ILE x 470 " (cutoff:3.500A)
      removed outlier: 6.186A  pdb=" N   THR x 472 " --> pdb=" O   LEU x 499 " (cutoff:3.500A)
    Processing sheet with id=AA4, first strand: chain 'x' and resid 521 through 528
      removed outlier: 3.639A  pdb=" N   MET x 533 " --> pdb=" O   VAL x 528 " (cutoff:3.500A)
      removed outlier: 7.102A  pdb=" N   THR x 534 " --> pdb=" O   LEU x 835 " (cutoff:3.500A)
      removed outlier: 7.852A  pdb=" N   LEU x 837 " --> pdb=" O   THR x 534 " (cutoff:3.500A)
      removed outlier: 6.775A  pdb=" N   LEU x 536 " --> pdb=" O   LEU x 837 " (cutoff:3.500A)
    Processing sheet with id=AA5, first strand: chain 'x' and resid 795 through 797
      removed outlier: 3.980A  pdb=" N   TYR x 829 " --> pdb=" O   ILE x 849 " (cutoff:3.500A)

    239 hydrogen bonds defined for protein.
    693 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: 0.83

  Time building geometry restraints manager: 0.61 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: 1869
        1.34 -     1.46: 828
        1.46 -     1.57: 3217
        1.57 -     1.69: 4
        1.69 -     1.81: 57
  Bond restraints: 5975
  Sorted by residual:
  bond pdb=" CA  ARG x 584 "
       pdb=" CB  ARG x 584 "
    ideal  model  delta    sigma   weight residual
    1.527  1.607 -0.080 2.48e-02 1.63e+03 1.04e+01
  bond pdb=" N   LEU x 375 "
       pdb=" CA  LEU x 375 "
    ideal  model  delta    sigma   weight residual
    1.456  1.487 -0.031 1.21e-02 6.83e+03 6.56e+00
  bond pdb=" N   LEU x 374 "
       pdb=" CA  LEU x 374 "
    ideal  model  delta    sigma   weight residual
    1.456  1.487 -0.030 1.21e-02 6.83e+03 6.26e+00
  bond pdb=" N   LYS x 373 "
       pdb=" CA  LYS x 373 "
    ideal  model  delta    sigma   weight residual
    1.456  1.486 -0.030 1.21e-02 6.83e+03 5.99e+00
  bond pdb=" CA  THR y  93 "
       pdb=" CB  THR y  93 "
    ideal  model  delta    sigma   weight residual
    1.532  1.568 -0.035 2.01e-02 2.48e+03 3.11e+00
  ... (remaining 5970 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     2.01: 7749
        2.01 -     4.02: 269
        4.02 -     6.03: 33
        6.03 -     8.04: 17
        8.04 -    10.05: 7
  Bond angle restraints: 8075
  Sorted by residual:
  angle pdb=" C   THR x 838 "
        pdb=" N   SER x 839 "
        pdb=" CA  SER x 839 "
      ideal   model   delta    sigma   weight residual
     121.54  130.30   -8.76 1.91e+00 2.74e-01 2.10e+01
  angle pdb=" CA  ARG x 584 "
        pdb=" CB  ARG x 584 "
        pdb=" CG  ARG x 584 "
      ideal   model   delta    sigma   weight residual
     114.10  123.00   -8.90 2.00e+00 2.50e-01 1.98e+01
  angle pdb=" C   VAL y  92 "
        pdb=" N   THR y  93 "
        pdb=" CA  THR y  93 "
      ideal   model   delta    sigma   weight residual
     122.19  132.24  -10.05 2.30e+00 1.89e-01 1.91e+01
  angle pdb=" C   VAL x 174 "
        pdb=" N   PHE x 175 "
        pdb=" CA  PHE x 175 "
      ideal   model   delta    sigma   weight residual
     121.70  129.33   -7.63 1.80e+00 3.09e-01 1.80e+01
  angle pdb=" C   ASP x 601 "
        pdb=" N   LEU x 602 "
        pdb=" CA  LEU x 602 "
      ideal   model   delta    sigma   weight residual
     121.54  128.61   -7.07 1.91e+00 2.74e-01 1.37e+01
  ... (remaining 8070 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    28.63: 3593
       28.63 -    57.25: 66
       57.25 -    85.88: 8
       85.88 -   114.51: 1
      114.51 -   143.14: 1
  Dihedral angle restraints: 3669
    sinusoidal: 1538
      harmonic: 2131
  Sorted by residual:
  dihedral pdb=" O1B ADP x1001 "
           pdb=" O3A ADP x1001 "
           pdb=" PB  ADP x1001 "
           pdb=" PA  ADP x1001 "
      ideal   model   delta sinusoidal    sigma   weight residual
     300.00  156.86  143.14     1      2.00e+01 2.50e-03 4.32e+01
  dihedral pdb=" O2A ADP x1001 "
           pdb=" O3A ADP x1001 "
           pdb=" PA  ADP x1001 "
           pdb=" PB  ADP x1001 "
      ideal   model   delta sinusoidal    sigma   weight residual
     -60.00   33.71  -93.71     1      2.00e+01 2.50e-03 2.56e+01
  dihedral pdb=" CA  ALA y 161 "
           pdb=" C   ALA y 161 "
           pdb=" N   SER y 162 "
           pdb=" CA  SER y 162 "
      ideal   model   delta  harmonic     sigma   weight residual
    -180.00 -158.60  -21.40     0      5.00e+00 4.00e-02 1.83e+01
  ... (remaining 3666 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.038: 582
       0.038 -    0.076: 220
       0.076 -    0.115: 80
       0.115 -    0.153: 44
       0.153 -    0.191: 5
  Chirality restraints: 931
  Sorted by residual:
  chirality pdb=" CB  ILE x 635 "
            pdb=" CA  ILE x 635 "
            pdb=" CG1 ILE x 635 "
            pdb=" CG2 ILE x 635 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.64    2.45    0.19 2.00e-01 2.50e+01 9.13e-01
  chirality pdb=" CB  THR x 538 "
            pdb=" CA  THR x 538 "
            pdb=" OG1 THR x 538 "
            pdb=" CG2 THR x 538 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.55    2.36    0.19 2.00e-01 2.50e+01 8.77e-01
  chirality pdb=" CA  ILE x 767 "
            pdb=" N   ILE x 767 "
            pdb=" C   ILE x 767 "
            pdb=" CB  ILE x 767 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.43    2.61   -0.18 2.00e-01 2.50e+01 7.97e-01
  ... (remaining 928 not shown)

  Planarity restraints: 1018
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   MET x 577 "    0.040 5.00e-02 4.00e+02   6.00e-02 5.75e+00
        pdb=" N   PRO x 578 "   -0.104 5.00e-02 4.00e+02
        pdb=" CA  PRO x 578 "    0.031 5.00e-02 4.00e+02
        pdb=" CD  PRO x 578 "    0.033 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   ASP x 518 "    0.036 5.00e-02 4.00e+02   5.43e-02 4.72e+00
        pdb=" N   PRO x 519 "   -0.094 5.00e-02 4.00e+02
        pdb=" CA  PRO x 519 "    0.028 5.00e-02 4.00e+02
        pdb=" CD  PRO x 519 "    0.030 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   HIS x 810 "   -0.035 5.00e-02 4.00e+02   5.24e-02 4.40e+00
        pdb=" N   PRO x 811 "    0.091 5.00e-02 4.00e+02
        pdb=" CA  PRO x 811 "   -0.027 5.00e-02 4.00e+02
        pdb=" CD  PRO x 811 "   -0.029 5.00e-02 4.00e+02
  ... (remaining 1015 not shown)

  Histogram of nonbonded interaction distances:
        2.09 -     2.65: 76
        2.65 -     3.21: 5022
        3.21 -     3.78: 8772
        3.78 -     4.34: 12538
        4.34 -     4.90: 20329
  Nonbonded interactions: 46737
  Sorted by model distance:
  nonbonded pdb=" O3B ADP x1001 "
            pdb="MG    MG x1002 "
     model   vdw
     2.092 2.170
  nonbonded pdb=" OG1 THR x 253 "
            pdb="MG    MG x1002 "
     model   vdw
     2.094 2.170
  nonbonded pdb=" O   GLN x 427 "
            pdb=" OG1 THR x 431 "
     model   vdw
     2.262 3.040
  nonbonded pdb=" O   GLU x 581 "
            pdb=" OG1 THR x 585 "
     model   vdw
     2.273 3.040
  nonbonded pdb=" O   SER x 530 "
            pdb=" OG  SER x 801 "
     model   vdw
     2.284 3.040
  ... (remaining 46732 not shown)

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

  No NCS relation were found !!!

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

Found NCS groups:
  found none.
Set up NCS constraints
  No NCS constraints will be used in refinement.
Set refine NCS operators
Adjust number of macro_cycles
  Number of macro_cycles: 10
Reset NCS operators
Extract rigid body selections
Check and reset occupancies
  Occupancies: min=1.00 max=1.00 mean=1.00
Load rotamer database and sin/cos tables
Set ADP refinement strategy
  ADPs will be refined as individual isotropic
Make a string to write initial .geo file
Internal consistency checks
Time:
  Set random seed:                         0.000
  Set model cs if undefined:               0.000
  Decide on map wrapping:                  0.000
  Normalize map: mean=0, sd=1:             1.850
  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:          0.130
  Check model and map are aligned:         0.010
  Set scattering table:                    0.030
  Process input model:                     7.000
  Find NCS groups from input model:        0.030
  Set up NCS constraints:                  0.010
  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:1.300
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   10.370
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7941
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   0.080   5975  Z= 0.220
  Angle     :  0.917  10.046   8075  Z= 0.478
  Chirality :  0.052   0.191    931
  Planarity :  0.007   0.060   1018
  Dihedral  : 11.275 143.137   2287
  Min Nonbonded Distance : 2.092

Molprobity Statistics.
  All-atom Clashscore : 3.88
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.92 %
    Favored  : 97.08 %
  Rotamer:
    Outliers :  0.61 %
    Allowed  :  3.51 %
    Favored  : 95.88 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.78 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -2.88 (0.25), residues: 718
  helix: -3.17 (0.15), residues: 294
  sheet:  0.94 (0.49), residues: 106
  loop : -1.50 (0.31), residues: 318

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.001   ARG x 289 
 TYR   0.029   0.003   TYR x 321 
 PHE   0.023   0.002   PHE x 308 
 TRP   0.027   0.003   TRP x 723 
 HIS   0.006   0.002   HIS x 704 

Details of bonding type rmsd
  covalent geometry    : bond        0.00477 ( 5975)
  covalent geometry    : angle       0.91725 ( 8075)
  hydrogen bonds       : bond        0.30459 (  239)
  hydrogen bonds       : angle       7.93667 (  693)

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

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

  1436 Ramachandran restraints generated.
    718 Oldfield, 0 Emsley, 718 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1436 Ramachandran restraints generated.
    718 Oldfield, 0 Emsley, 718 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  172 residues out of total 657 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 4
    poor density    : 168
  time to evaluate  : 0.251 
Fit side-chains
REVERT: x  280 ARG cc_start: 0.7505 (ttp-110) cc_final: 0.7125 (ttm110)
REVERT: x  335 SER cc_start: 0.8158 (m) cc_final: 0.7907 (p)
REVERT: x  341 SER cc_start: 0.8794 (t) cc_final: 0.8257 (p)
REVERT: x  534 THR cc_start: 0.8690 (t) cc_final: 0.8427 (m)
REVERT: x  560 LYS cc_start: 0.8202 (mttt) cc_final: 0.7980 (mtpp)
REVERT: x  575 GLU cc_start: 0.7257 (mm-30) cc_final: 0.7048 (mp0)
REVERT: x  632 LYS cc_start: 0.8573 (mptm) cc_final: 0.8299 (mmtt)
REVERT: x  770 TYR cc_start: 0.6622 (m-10) cc_final: 0.6395 (m-80)
  outliers start: 4
  outliers final: 1
  residues processed: 171
  average time/residue: 0.1183
  time to fit residues: 24.5766
Evaluate side-chains
  95 residues out of total 657 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 94
  time to evaluate  : 0.245 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain x residue  374 LEU
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 73
   random chunks:
   chunk 49 optimal weight:    0.9980
   chunk 53 optimal weight:    0.9980
   chunk 5 optimal weight:    0.7980
   chunk 33 optimal weight:    0.9990
   chunk 65 optimal weight:    2.9990
   chunk 62 optimal weight:    5.9990
   chunk 51 optimal weight:    0.7980
   chunk 38 optimal weight:    2.9990
   chunk 61 optimal weight:    1.9990
   chunk 45 optimal weight:    2.9990
   chunk 27 optimal weight:    1.9990
   overall best weight:    0.9182

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

Flipped N/Q/H residues before XYZ refinement:
x 255 GLN
x 258 GLN
x 382 ASN
x 408 HIS
x 419 HIS
x 427 GLN
x 429 HIS
** x 502 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
x 548 GLN
x 663 GLN
x 834 GLN

Total number of N/Q/H flips: 10

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3490 r_free = 0.3490 target = 0.136526 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 42)----------------|
| r_work = 0.3149 r_free = 0.3149 target = 0.109925 restraints weight = 6647.020|
|-----------------------------------------------------------------------------|
r_work (start): 0.3137 rms_B_bonded: 1.66
r_work: 0.2973 rms_B_bonded: 2.64 restraints_weight: 0.5000
r_work: 0.2821 rms_B_bonded: 4.24 restraints_weight: 0.2500
r_work (final): 0.2821
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8332
moved from start:          0.2360

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.033   5975  Z= 0.145
  Angle     :  0.643   8.811   8075  Z= 0.327
  Chirality :  0.044   0.177    931
  Planarity :  0.005   0.041   1018
  Dihedral  :  8.113 140.633    801
  Min Nonbonded Distance : 2.016

Molprobity Statistics.
  All-atom Clashscore : 5.90
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.20 %
    Favored  : 96.80 %
  Rotamer:
    Outliers :  1.83 %
    Allowed  :  9.76 %
    Favored  : 88.41 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.78 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -0.51 (0.29), residues: 718
  helix: -0.26 (0.26), residues: 310
  sheet:  0.46 (0.46), residues: 108
  loop : -0.54 (0.36), residues: 300

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARG x 514 
 TYR   0.011   0.001   TYR x 171 
 PHE   0.016   0.002   PHE x 426 
 TRP   0.012   0.001   TRP x 723 
 HIS   0.003   0.001   HIS x 704 

Details of bonding type rmsd
  covalent geometry    : bond        0.00327 ( 5975)
  covalent geometry    : angle       0.64267 ( 8075)
  hydrogen bonds       : bond        0.05523 (  239)
  hydrogen bonds       : angle       4.66667 (  693)

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

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

  1436 Ramachandran restraints generated.
    718 Oldfield, 0 Emsley, 718 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1436 Ramachandran restraints generated.
    718 Oldfield, 0 Emsley, 718 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  108 residues out of total 657 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 96
  time to evaluate  : 0.210 
Fit side-chains
REVERT: x  335 SER cc_start: 0.8408 (m) cc_final: 0.8082 (p)
REVERT: x  575 GLU cc_start: 0.8084 (mm-30) cc_final: 0.7708 (mp0)
REVERT: x  632 LYS cc_start: 0.8780 (mptm) cc_final: 0.8429 (mmtm)
  outliers start: 12
  outliers final: 8
  residues processed: 104
  average time/residue: 0.0791
  time to fit residues: 10.7414
Evaluate side-chains
  88 residues out of total 657 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 8
    poor density    : 80
  time to evaluate  : 0.143 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain x residue  297 VAL
Chi-restraints excluded: chain x residue  323 THR
Chi-restraints excluded: chain x residue  333 THR
Chi-restraints excluded: chain x residue  374 LEU
Chi-restraints excluded: chain x residue  509 THR
Chi-restraints excluded: chain x residue  585 THR
Chi-restraints excluded: chain x residue  859 VAL
Chi-restraints excluded: chain x residue  865 ASP
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 73
   random chunks:
   chunk 27 optimal weight:    1.9990
   chunk 67 optimal weight:    9.9990
   chunk 23 optimal weight:    0.9990
   chunk 17 optimal weight:    0.9980
   chunk 64 optimal weight:    3.9990
   chunk 14 optimal weight:    2.9990
   chunk 40 optimal weight:    7.9990
   chunk 71 optimal weight:   10.0000
   chunk 12 optimal weight:    2.9990
   chunk 21 optimal weight:    5.9990
   chunk 45 optimal weight:    1.9990
   overall best weight:    1.7988

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

Flipped N/Q/H residues before XYZ refinement:
** x 239 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** x 502 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
x 622 ASN
x 727 HIS

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3431 r_free = 0.3431 target = 0.131611 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 43)----------------|
| r_work = 0.3069 r_free = 0.3069 target = 0.104159 restraints weight = 6617.901|
|-----------------------------------------------------------------------------|
r_work (start): 0.3084 rms_B_bonded: 1.70
r_work: 0.2925 rms_B_bonded: 2.55 restraints_weight: 0.5000
r_work: 0.2772 rms_B_bonded: 4.10 restraints_weight: 0.2500
r_work (final): 0.2772
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8403
moved from start:          0.3023

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.041   5975  Z= 0.196
  Angle     :  0.656   8.521   8075  Z= 0.330
  Chirality :  0.046   0.199    931
  Planarity :  0.005   0.039   1018
  Dihedral  :  7.384 120.835    801
  Min Nonbonded Distance : 1.920

Molprobity Statistics.
  All-atom Clashscore : 6.57
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.46 %
    Favored  : 95.54 %
  Rotamer:
    Outliers :  2.59 %
    Allowed  : 10.37 %
    Favored  : 87.04 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.78 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  0.15 (0.30), residues: 718
  helix:  0.70 (0.28), residues: 313
  sheet:  0.38 (0.45), residues: 106
  loop : -0.54 (0.36), residues: 299

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.001   ARG x 514 
 TYR   0.016   0.002   TYR x 171 
 PHE   0.024   0.002   PHE x 426 
 TRP   0.010   0.002   TRP x 568 
 HIS   0.006   0.001   HIS x 704 

Details of bonding type rmsd
  covalent geometry    : bond        0.00477 ( 5975)
  covalent geometry    : angle       0.65616 ( 8075)
  hydrogen bonds       : bond        0.05000 (  239)
  hydrogen bonds       : angle       4.47226 (  693)

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

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

  1436 Ramachandran restraints generated.
    718 Oldfield, 0 Emsley, 718 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1436 Ramachandran restraints generated.
    718 Oldfield, 0 Emsley, 718 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  104 residues out of total 657 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 17
    poor density    : 87
  time to evaluate  : 0.176 
Fit side-chains
REVERT: x  335 SER cc_start: 0.8309 (m) cc_final: 0.7989 (p)
REVERT: x  341 SER cc_start: 0.9034 (t) cc_final: 0.8509 (p)
REVERT: x  560 LYS cc_start: 0.8460 (mttt) cc_final: 0.8182 (mtmt)
REVERT: x  632 LYS cc_start: 0.8805 (mptm) cc_final: 0.8531 (mmtm)
  outliers start: 17
  outliers final: 14
  residues processed: 97
  average time/residue: 0.0843
  time to fit residues: 10.7142
Evaluate side-chains
  92 residues out of total 657 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 78
  time to evaluate  : 0.136 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain x residue  254 THR
Chi-restraints excluded: chain x residue  297 VAL
Chi-restraints excluded: chain x residue  323 THR
Chi-restraints excluded: chain x residue  333 THR
Chi-restraints excluded: chain x residue  502 ASN
Chi-restraints excluded: chain x residue  509 THR
Chi-restraints excluded: chain x residue  534 THR
Chi-restraints excluded: chain x residue  537 LEU
Chi-restraints excluded: chain x residue  538 THR
Chi-restraints excluded: chain x residue  585 THR
Chi-restraints excluded: chain x residue  686 ILE
Chi-restraints excluded: chain x residue  722 SER
Chi-restraints excluded: chain x residue  859 VAL
Chi-restraints excluded: chain x residue  865 ASP
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 73
   random chunks:
   chunk 18 optimal weight:    7.9990
   chunk 50 optimal weight:    6.9990
   chunk 58 optimal weight:    0.7980
   chunk 12 optimal weight:    3.9990
   chunk 49 optimal weight:    3.9990
   chunk 38 optimal weight:    5.9990
   chunk 7 optimal weight:    0.8980
   chunk 34 optimal weight:    0.9980
   chunk 29 optimal weight:    0.8980
   chunk 48 optimal weight:    0.0370
   chunk 22 optimal weight:    3.9990
   overall best weight:    0.7258

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

Flipped N/Q/H residues before XYZ refinement:
** x 239 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
x 480 GLN
** x 502 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 = 0.3463 r_free = 0.3463 target = 0.134352 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 52)----------------|
| r_work = 0.3106 r_free = 0.3106 target = 0.106768 restraints weight = 6566.256|
|-----------------------------------------------------------------------------|
r_work (start): 0.3104 rms_B_bonded: 1.71
r_work: 0.2938 rms_B_bonded: 2.61 restraints_weight: 0.5000
r_work: 0.2780 rms_B_bonded: 4.20 restraints_weight: 0.2500
r_work (final): 0.2780
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8369
moved from start:          0.3151

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.029   5975  Z= 0.115
  Angle     :  0.564   8.404   8075  Z= 0.283
  Chirality :  0.043   0.187    931
  Planarity :  0.004   0.042   1018
  Dihedral  :  6.866 113.506    799
  Min Nonbonded Distance : 1.939

Molprobity Statistics.
  All-atom Clashscore : 5.98
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.32 %
    Favored  : 95.68 %
  Rotamer:
    Outliers :  2.74 %
    Allowed  : 13.11 %
    Favored  : 84.15 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.78 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  0.67 (0.31), residues: 718
  helix:  1.37 (0.29), residues: 313
  sheet:  0.24 (0.46), residues: 104
  loop : -0.38 (0.36), residues: 301

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG x 514 
 TYR   0.012   0.001   TYR x 171 
 PHE   0.013   0.001   PHE x 426 
 TRP   0.006   0.001   TRP x 568 
 HIS   0.002   0.001   HIS x 704 

Details of bonding type rmsd
  covalent geometry    : bond        0.00259 ( 5975)
  covalent geometry    : angle       0.56394 ( 8075)
  hydrogen bonds       : bond        0.03891 (  239)
  hydrogen bonds       : angle       4.27515 (  693)

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

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

  1436 Ramachandran restraints generated.
    718 Oldfield, 0 Emsley, 718 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1436 Ramachandran restraints generated.
    718 Oldfield, 0 Emsley, 718 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  101 residues out of total 657 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 18
    poor density    : 83
  time to evaluate  : 0.157 
Fit side-chains
REVERT: x  335 SER cc_start: 0.8262 (m) cc_final: 0.8003 (p)
REVERT: x  341 SER cc_start: 0.8999 (t) cc_final: 0.8484 (p)
REVERT: x  560 LYS cc_start: 0.8450 (mttt) cc_final: 0.8203 (mtpp)
REVERT: x  575 GLU cc_start: 0.8090 (mm-30) cc_final: 0.7698 (mp0)
REVERT: x  615 THR cc_start: 0.8386 (m) cc_final: 0.8118 (m)
REVERT: x  632 LYS cc_start: 0.8808 (mptm) cc_final: 0.8489 (mmtm)
REVERT: x  637 ARG cc_start: 0.8253 (mtp180) cc_final: 0.8014 (mmm-85)
REVERT: x  746 ARG cc_start: 0.7853 (mmp80) cc_final: 0.7628 (mpt180)
  outliers start: 18
  outliers final: 14
  residues processed: 97
  average time/residue: 0.0759
  time to fit residues: 9.6859
Evaluate side-chains
  93 residues out of total 657 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 79
  time to evaluate  : 0.224 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain x residue  254 THR
Chi-restraints excluded: chain x residue  297 VAL
Chi-restraints excluded: chain x residue  323 THR
Chi-restraints excluded: chain x residue  333 THR
Chi-restraints excluded: chain x residue  506 THR
Chi-restraints excluded: chain x residue  508 LEU
Chi-restraints excluded: chain x residue  509 THR
Chi-restraints excluded: chain x residue  534 THR
Chi-restraints excluded: chain x residue  537 LEU
Chi-restraints excluded: chain x residue  538 THR
Chi-restraints excluded: chain x residue  585 THR
Chi-restraints excluded: chain x residue  722 SER
Chi-restraints excluded: chain x residue  859 VAL
Chi-restraints excluded: chain x residue  865 ASP
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 73
   random chunks:
   chunk 17 optimal weight:    4.9990
   chunk 22 optimal weight:    3.9990
   chunk 14 optimal weight:    0.0980
   chunk 10 optimal weight:    3.9990
   chunk 61 optimal weight:    0.9980
   chunk 6 optimal weight:    0.9990
   chunk 42 optimal weight:    3.9990
   chunk 9 optimal weight:    5.9990
   chunk 62 optimal weight:    5.9990
   chunk 11 optimal weight:    3.9990
   chunk 51 optimal weight:    3.9990
   overall best weight:    2.0186

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

Flipped N/Q/H residues before XYZ refinement:
** x 239 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
x 480 GLN
** x 502 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 = 0.3423 r_free = 0.3423 target = 0.131123 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 48)----------------|
| r_work = 0.3065 r_free = 0.3065 target = 0.103833 restraints weight = 6652.344|
|-----------------------------------------------------------------------------|
r_work (start): 0.3034 rms_B_bonded: 1.69
r_work: 0.2865 rms_B_bonded: 2.59 restraints_weight: 0.5000
r_work: 0.2705 rms_B_bonded: 4.15 restraints_weight: 0.2500
r_work (final): 0.2705
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8439
moved from start:          0.3372

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.044   5975  Z= 0.210
  Angle     :  0.646   8.230   8075  Z= 0.323
  Chirality :  0.046   0.188    931
  Planarity :  0.005   0.040   1018
  Dihedral  :  6.948 103.533    799
  Min Nonbonded Distance : 1.875

Molprobity Statistics.
  All-atom Clashscore : 6.24
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.32 %
    Favored  : 95.68 %
  Rotamer:
    Outliers :  3.51 %
    Allowed  : 13.11 %
    Favored  : 83.38 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.78 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  0.67 (0.31), residues: 718
  helix:  1.31 (0.29), residues: 313
  sheet:  0.25 (0.44), residues: 126
  loop : -0.34 (0.38), residues: 279

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.001   ARG x 543 
 TYR   0.015   0.002   TYR x 171 
 PHE   0.025   0.002   PHE x 426 
 TRP   0.012   0.002   TRP x 568 
 HIS   0.005   0.001   HIS x 704 

Details of bonding type rmsd
  covalent geometry    : bond        0.00518 ( 5975)
  covalent geometry    : angle       0.64586 ( 8075)
  hydrogen bonds       : bond        0.04746 (  239)
  hydrogen bonds       : angle       4.45848 (  693)

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

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

  1436 Ramachandran restraints generated.
    718 Oldfield, 0 Emsley, 718 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1436 Ramachandran restraints generated.
    718 Oldfield, 0 Emsley, 718 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  102 residues out of total 657 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 23
    poor density    : 79
  time to evaluate  : 0.222 
Fit side-chains
REVERT: x  335 SER cc_start: 0.8320 (m) cc_final: 0.8020 (p)
REVERT: x  341 SER cc_start: 0.9032 (t) cc_final: 0.8496 (p)
REVERT: x  560 LYS cc_start: 0.8514 (mttt) cc_final: 0.8273 (mtmt)
REVERT: x  632 LYS cc_start: 0.8816 (mptm) cc_final: 0.8503 (mmtm)
  outliers start: 23
  outliers final: 19
  residues processed: 95
  average time/residue: 0.0881
  time to fit residues: 10.9556
Evaluate side-chains
  96 residues out of total 657 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 19
    poor density    : 77
  time to evaluate  : 0.316 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain x residue  254 THR
Chi-restraints excluded: chain x residue  297 VAL
Chi-restraints excluded: chain x residue  322 MET
Chi-restraints excluded: chain x residue  323 THR
Chi-restraints excluded: chain x residue  333 THR
Chi-restraints excluded: chain x residue  502 ASN
Chi-restraints excluded: chain x residue  506 THR
Chi-restraints excluded: chain x residue  508 LEU
Chi-restraints excluded: chain x residue  509 THR
Chi-restraints excluded: chain x residue  534 THR
Chi-restraints excluded: chain x residue  537 LEU
Chi-restraints excluded: chain x residue  538 THR
Chi-restraints excluded: chain x residue  585 THR
Chi-restraints excluded: chain x residue  603 ILE
Chi-restraints excluded: chain x residue  686 ILE
Chi-restraints excluded: chain x residue  722 SER
Chi-restraints excluded: chain x residue  836 MET
Chi-restraints excluded: chain x residue  859 VAL
Chi-restraints excluded: chain x residue  865 ASP
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 73
   random chunks:
   chunk 62 optimal weight:    0.8980
   chunk 43 optimal weight:    0.9990
   chunk 61 optimal weight:    0.5980
   chunk 50 optimal weight:    3.9990
   chunk 66 optimal weight:    3.9990
   chunk 16 optimal weight:    1.9990
   chunk 29 optimal weight:    6.9990
   chunk 58 optimal weight:    0.9990
   chunk 48 optimal weight:    2.9990
   chunk 36 optimal weight:    5.9990
   chunk 72 optimal weight:    0.2980
   overall best weight:    0.7584

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

Flipped N/Q/H residues before XYZ refinement:
x 239 ASN
x 480 GLN
** x 502 ASN ** 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 = 0.3470 r_free = 0.3470 target = 0.135033 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 44)----------------|
| r_work = 0.3118 r_free = 0.3118 target = 0.107751 restraints weight = 6570.515|
|-----------------------------------------------------------------------------|
r_work (start): 0.3076 rms_B_bonded: 1.70
r_work: 0.2912 rms_B_bonded: 2.58 restraints_weight: 0.5000
r_work: 0.2751 rms_B_bonded: 4.19 restraints_weight: 0.2500
r_work (final): 0.2751
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8384
moved from start:          0.3462

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.027   5975  Z= 0.112
  Angle     :  0.556   8.341   8075  Z= 0.278
  Chirality :  0.042   0.186    931
  Planarity :  0.004   0.037   1018
  Dihedral  :  6.603 101.949    799
  Min Nonbonded Distance : 1.927

Molprobity Statistics.
  All-atom Clashscore : 5.56
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.04 %
    Favored  : 95.96 %
  Rotamer:
    Outliers :  2.59 %
    Allowed  : 14.48 %
    Favored  : 82.93 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.78 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  0.87 (0.31), residues: 718
  helix:  1.60 (0.29), residues: 314
  sheet:  0.06 (0.45), residues: 128
  loop : -0.27 (0.37), residues: 276

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG x 514 
 TYR   0.011   0.001   TYR x 171 
 PHE   0.014   0.001   PHE x 426 
 TRP   0.009   0.001   TRP x 568 
 HIS   0.002   0.001   HIS x 727 

Details of bonding type rmsd
  covalent geometry    : bond        0.00256 ( 5975)
  covalent geometry    : angle       0.55612 ( 8075)
  hydrogen bonds       : bond        0.03679 (  239)
  hydrogen bonds       : angle       4.26354 (  693)

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

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

  1436 Ramachandran restraints generated.
    718 Oldfield, 0 Emsley, 718 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1436 Ramachandran restraints generated.
    718 Oldfield, 0 Emsley, 718 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  97 residues out of total 657 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 17
    poor density    : 80
  time to evaluate  : 0.174 
Fit side-chains
REVERT: x  335 SER cc_start: 0.8248 (m) cc_final: 0.7982 (p)
REVERT: x  341 SER cc_start: 0.9001 (t) cc_final: 0.8488 (p)
REVERT: x  560 LYS cc_start: 0.8478 (mttt) cc_final: 0.8243 (mtmt)
REVERT: x  575 GLU cc_start: 0.8035 (mm-30) cc_final: 0.7638 (mp0)
REVERT: x  632 LYS cc_start: 0.8834 (mptm) cc_final: 0.8515 (mmtm)
  outliers start: 17
  outliers final: 14
  residues processed: 91
  average time/residue: 0.0896
  time to fit residues: 10.5376
Evaluate side-chains
  90 residues out of total 657 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 76
  time to evaluate  : 0.218 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain x residue  297 VAL
Chi-restraints excluded: chain x residue  322 MET
Chi-restraints excluded: chain x residue  333 THR
Chi-restraints excluded: chain x residue  506 THR
Chi-restraints excluded: chain x residue  508 LEU
Chi-restraints excluded: chain x residue  534 THR
Chi-restraints excluded: chain x residue  537 LEU
Chi-restraints excluded: chain x residue  538 THR
Chi-restraints excluded: chain x residue  585 THR
Chi-restraints excluded: chain x residue  686 ILE
Chi-restraints excluded: chain x residue  722 SER
Chi-restraints excluded: chain x residue  859 VAL
Chi-restraints excluded: chain x residue  862 ILE
Chi-restraints excluded: chain x residue  865 ASP
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 73
   random chunks:
   chunk 19 optimal weight:    3.9990
   chunk 27 optimal weight:    5.9990
   chunk 28 optimal weight:    1.9990
   chunk 32 optimal weight:    5.9990
   chunk 31 optimal weight:    1.9990
   chunk 52 optimal weight:    3.9990
   chunk 10 optimal weight:    4.9990
   chunk 20 optimal weight:    4.9990
   chunk 17 optimal weight:    3.9990
   chunk 33 optimal weight:    0.2980
   chunk 23 optimal weight:    2.9990
   overall best weight:    2.2588

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

Flipped N/Q/H residues before XYZ refinement:
** x 239 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
x 480 GLN
** x 502 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 = 0.3409 r_free = 0.3409 target = 0.130120 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 46)----------------|
| r_work = 0.3052 r_free = 0.3052 target = 0.103047 restraints weight = 6686.910|
|-----------------------------------------------------------------------------|
r_work (start): 0.3045 rms_B_bonded: 1.69
r_work: 0.2885 rms_B_bonded: 2.51 restraints_weight: 0.5000
r_work: 0.2725 rms_B_bonded: 4.09 restraints_weight: 0.2500
r_work (final): 0.2725
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8443
moved from start:          0.3580

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.045   5975  Z= 0.219
  Angle     :  0.652   8.060   8075  Z= 0.325
  Chirality :  0.047   0.204    931
  Planarity :  0.005   0.041   1018
  Dihedral  :  6.897  99.853    799
  Min Nonbonded Distance : 1.874

Molprobity Statistics.
  All-atom Clashscore : 6.24
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.18 %
    Favored  : 95.82 %
  Rotamer:
    Outliers :  3.35 %
    Allowed  : 14.02 %
    Favored  : 82.62 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.78 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  0.67 (0.31), residues: 718
  helix:  1.37 (0.29), residues: 313
  sheet:  0.11 (0.46), residues: 125
  loop : -0.35 (0.37), residues: 280

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG x 543 
 TYR   0.014   0.002   TYR x 171 
 PHE   0.024   0.002   PHE x 426 
 TRP   0.014   0.002   TRP x 568 
 HIS   0.005   0.001   HIS x 704 

Details of bonding type rmsd
  covalent geometry    : bond        0.00541 ( 5975)
  covalent geometry    : angle       0.65219 ( 8075)
  hydrogen bonds       : bond        0.04719 (  239)
  hydrogen bonds       : angle       4.47051 (  693)

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

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

  1436 Ramachandran restraints generated.
    718 Oldfield, 0 Emsley, 718 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1436 Ramachandran restraints generated.
    718 Oldfield, 0 Emsley, 718 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  101 residues out of total 657 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 22
    poor density    : 79
  time to evaluate  : 0.229 
Fit side-chains
REVERT: x  335 SER cc_start: 0.8308 (m) cc_final: 0.8019 (p)
REVERT: x  341 SER cc_start: 0.9036 (t) cc_final: 0.8511 (p)
REVERT: x  560 LYS cc_start: 0.8551 (mttt) cc_final: 0.8308 (mtmt)
REVERT: x  575 GLU cc_start: 0.8067 (mm-30) cc_final: 0.7659 (mp0)
REVERT: x  632 LYS cc_start: 0.8825 (mptm) cc_final: 0.8482 (mptt)
  outliers start: 22
  outliers final: 19
  residues processed: 90
  average time/residue: 0.0891
  time to fit residues: 10.4428
Evaluate side-chains
  97 residues out of total 657 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 19
    poor density    : 78
  time to evaluate  : 0.229 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain x residue  247 GLU
Chi-restraints excluded: chain x residue  297 VAL
Chi-restraints excluded: chain x residue  322 MET
Chi-restraints excluded: chain x residue  333 THR
Chi-restraints excluded: chain x residue  486 ILE
Chi-restraints excluded: chain x residue  502 ASN
Chi-restraints excluded: chain x residue  506 THR
Chi-restraints excluded: chain x residue  534 THR
Chi-restraints excluded: chain x residue  537 LEU
Chi-restraints excluded: chain x residue  538 THR
Chi-restraints excluded: chain x residue  585 THR
Chi-restraints excluded: chain x residue  603 ILE
Chi-restraints excluded: chain x residue  686 ILE
Chi-restraints excluded: chain x residue  722 SER
Chi-restraints excluded: chain x residue  762 MET
Chi-restraints excluded: chain x residue  836 MET
Chi-restraints excluded: chain x residue  859 VAL
Chi-restraints excluded: chain x residue  862 ILE
Chi-restraints excluded: chain x residue  865 ASP
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 73
   random chunks:
   chunk 45 optimal weight:    0.7980
   chunk 46 optimal weight:    0.6980
   chunk 3 optimal weight:    0.0050
   chunk 52 optimal weight:    1.9990
   chunk 44 optimal weight:    0.5980
   chunk 40 optimal weight:    1.9990
   chunk 0 optimal weight:   10.0000
   chunk 70 optimal weight:    5.9990
   chunk 21 optimal weight:    0.8980
   chunk 13 optimal weight:    0.8980
   chunk 38 optimal weight:    0.5980
   overall best weight:    0.5394

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

Flipped N/Q/H residues before XYZ refinement:
** x 239 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** x 502 ASN ** 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 = 0.3465 r_free = 0.3465 target = 0.134787 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 42)----------------|
| r_work = 0.3118 r_free = 0.3118 target = 0.107772 restraints weight = 6563.240|
|-----------------------------------------------------------------------------|
r_work (start): 0.3112 rms_B_bonded: 1.68
r_work: 0.2952 rms_B_bonded: 2.55 restraints_weight: 0.5000
r_work: 0.2793 rms_B_bonded: 4.14 restraints_weight: 0.2500
r_work (final): 0.2793
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8372
moved from start:          0.3639

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.034   5975  Z= 0.102
  Angle     :  0.553   8.424   8075  Z= 0.275
  Chirality :  0.042   0.184    931
  Planarity :  0.004   0.030   1018
  Dihedral  :  6.524  98.640    799
  Min Nonbonded Distance : 1.958

Molprobity Statistics.
  All-atom Clashscore : 5.56
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.76 %
    Favored  : 96.24 %
  Rotamer:
    Outliers :  2.29 %
    Allowed  : 15.40 %
    Favored  : 82.32 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.78 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  0.97 (0.32), residues: 718
  helix:  1.70 (0.29), residues: 314
  sheet:  0.06 (0.46), residues: 128
  loop : -0.22 (0.37), residues: 276

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG x 514 
 TYR   0.010   0.001   TYR x 304 
 PHE   0.012   0.001   PHE x 426 
 TRP   0.008   0.001   TRP x 568 
 HIS   0.004   0.001   HIS x 727 

Details of bonding type rmsd
  covalent geometry    : bond        0.00225 ( 5975)
  covalent geometry    : angle       0.55325 ( 8075)
  hydrogen bonds       : bond        0.03462 (  239)
  hydrogen bonds       : angle       4.26323 (  693)

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

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

  1436 Ramachandran restraints generated.
    718 Oldfield, 0 Emsley, 718 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1436 Ramachandran restraints generated.
    718 Oldfield, 0 Emsley, 718 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  92 residues out of total 657 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 15
    poor density    : 77
  time to evaluate  : 0.216 
Fit side-chains
REVERT: x  335 SER cc_start: 0.8213 (m) cc_final: 0.7964 (p)
REVERT: x  560 LYS cc_start: 0.8511 (mttt) cc_final: 0.8274 (mtmt)
REVERT: x  575 GLU cc_start: 0.8116 (mm-30) cc_final: 0.7709 (mp0)
REVERT: x  632 LYS cc_start: 0.8851 (mptm) cc_final: 0.8590 (mmtm)
  outliers start: 15
  outliers final: 11
  residues processed: 86
  average time/residue: 0.0891
  time to fit residues: 10.0094
Evaluate side-chains
  85 residues out of total 657 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 74
  time to evaluate  : 0.229 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain x residue  247 GLU
Chi-restraints excluded: chain x residue  297 VAL
Chi-restraints excluded: chain x residue  322 MET
Chi-restraints excluded: chain x residue  506 THR
Chi-restraints excluded: chain x residue  509 THR
Chi-restraints excluded: chain x residue  534 THR
Chi-restraints excluded: chain x residue  537 LEU
Chi-restraints excluded: chain x residue  538 THR
Chi-restraints excluded: chain x residue  585 THR
Chi-restraints excluded: chain x residue  859 VAL
Chi-restraints excluded: chain x residue  865 ASP
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 73
   random chunks:
   chunk 72 optimal weight:    1.9990
   chunk 34 optimal weight:    0.9990
   chunk 63 optimal weight:    5.9990
   chunk 50 optimal weight:    7.9990
   chunk 36 optimal weight:    1.9990
   chunk 3 optimal weight:    0.0970
   chunk 17 optimal weight:    0.9990
   chunk 49 optimal weight:    2.9990
   chunk 58 optimal weight:    0.5980
   chunk 66 optimal weight:    0.1980
   chunk 20 optimal weight:    0.2980
   overall best weight:    0.4380

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

Flipped N/Q/H residues before XYZ refinement:
** x 239 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** x 502 ASN ** 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 = 0.3484 r_free = 0.3484 target = 0.136413 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 43)----------------|
| r_work = 0.3141 r_free = 0.3141 target = 0.109499 restraints weight = 6623.621|
|-----------------------------------------------------------------------------|
r_work (start): 0.3131 rms_B_bonded: 1.69
r_work: 0.2971 rms_B_bonded: 2.59 restraints_weight: 0.5000
r_work: 0.2821 rms_B_bonded: 4.12 restraints_weight: 0.2500
r_work (final): 0.2821
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8347
moved from start:          0.3715

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.032   5975  Z= 0.096
  Angle     :  0.537   7.702   8075  Z= 0.266
  Chirality :  0.042   0.168    931
  Planarity :  0.004   0.029   1018
  Dihedral  :  6.073  87.284    799
  Min Nonbonded Distance : 1.973

Molprobity Statistics.
  All-atom Clashscore : 5.22
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.18 %
    Favored  : 95.82 %
  Rotamer:
    Outliers :  1.68 %
    Allowed  : 16.46 %
    Favored  : 81.86 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.78 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  1.22 (0.32), residues: 718
  helix:  1.90 (0.30), residues: 314
  sheet:  0.44 (0.48), residues: 123
  loop : -0.21 (0.37), residues: 281

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG x 514 
 TYR   0.010   0.001   TYR x 304 
 PHE   0.010   0.001   PHE x 426 
 TRP   0.005   0.001   TRP x 568 
 HIS   0.003   0.001   HIS x 727 

Details of bonding type rmsd
  covalent geometry    : bond        0.00210 ( 5975)
  covalent geometry    : angle       0.53680 ( 8075)
  hydrogen bonds       : bond        0.03214 (  239)
  hydrogen bonds       : angle       4.17684 (  693)

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

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

  1436 Ramachandran restraints generated.
    718 Oldfield, 0 Emsley, 718 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1436 Ramachandran restraints generated.
    718 Oldfield, 0 Emsley, 718 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  89 residues out of total 657 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 78
  time to evaluate  : 0.250 
Fit side-chains
REVERT: x  230 ASP cc_start: 0.8291 (t0) cc_final: 0.8081 (m-30)
REVERT: x  247 GLU cc_start: 0.7343 (OUTLIER) cc_final: 0.7072 (tt0)
REVERT: x  335 SER cc_start: 0.8170 (m) cc_final: 0.7956 (p)
REVERT: x  560 LYS cc_start: 0.8501 (mttt) cc_final: 0.8287 (mtmt)
REVERT: x  575 GLU cc_start: 0.8142 (mm-30) cc_final: 0.7732 (mp0)
REVERT: x  632 LYS cc_start: 0.8832 (mptm) cc_final: 0.8481 (mmtm)
REVERT: x  798 MET cc_start: 0.7626 (mtp) cc_final: 0.7421 (mtp)
REVERT: y  113 MET cc_start: 0.6804 (mtt) cc_final: 0.6550 (mtt)
  outliers start: 11
  outliers final: 9
  residues processed: 84
  average time/residue: 0.0860
  time to fit residues: 9.3888
Evaluate side-chains
  87 residues out of total 657 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 77
  time to evaluate  : 0.227 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain x residue  247 GLU
Chi-restraints excluded: chain x residue  297 VAL
Chi-restraints excluded: chain x residue  322 MET
Chi-restraints excluded: chain x residue  506 THR
Chi-restraints excluded: chain x residue  509 THR
Chi-restraints excluded: chain x residue  534 THR
Chi-restraints excluded: chain x residue  537 LEU
Chi-restraints excluded: chain x residue  538 THR
Chi-restraints excluded: chain x residue  585 THR
Chi-restraints excluded: chain x residue  859 VAL
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 73
   random chunks:
   chunk 6 optimal weight:    0.0050
   chunk 44 optimal weight:    0.0970
   chunk 36 optimal weight:    4.9990
   chunk 33 optimal weight:    0.0970
   chunk 11 optimal weight:    0.6980
   chunk 7 optimal weight:    1.9990
   chunk 5 optimal weight:    1.9990
   chunk 9 optimal weight:    4.9990
   chunk 56 optimal weight:    6.9990
   chunk 64 optimal weight:    0.9980
   chunk 42 optimal weight:    3.9990
   overall best weight:    0.3790

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

Flipped N/Q/H residues before XYZ refinement:
x 239 ASN
** x 502 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 = 0.3499 r_free = 0.3499 target = 0.137645 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 45)----------------|
| r_work = 0.3158 r_free = 0.3158 target = 0.110852 restraints weight = 6616.373|
|-----------------------------------------------------------------------------|
r_work (start): 0.3141 rms_B_bonded: 1.68
r_work: 0.2984 rms_B_bonded: 2.58 restraints_weight: 0.5000
r_work: 0.2830 rms_B_bonded: 4.18 restraints_weight: 0.2500
r_work (final): 0.2830
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8336
moved from start:          0.3770

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.031   5975  Z= 0.092
  Angle     :  0.526   7.911   8075  Z= 0.259
  Chirality :  0.042   0.174    931
  Planarity :  0.004   0.029   1018
  Dihedral  :  5.653  73.542    799
  Min Nonbonded Distance : 2.016

Molprobity Statistics.
  All-atom Clashscore : 5.14
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.76 %
    Favored  : 96.24 %
  Rotamer:
    Outliers :  1.83 %
    Allowed  : 16.92 %
    Favored  : 81.25 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.78 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  1.31 (0.32), residues: 718
  helix:  1.99 (0.30), residues: 315
  sheet:  0.51 (0.49), residues: 123
  loop : -0.20 (0.37), residues: 280

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG x 741 
 TYR   0.011   0.001   TYR x 304 
 PHE   0.009   0.001   PHE x 426 
 TRP   0.005   0.001   TRP x 568 
 HIS   0.003   0.001   HIS x 727 

Details of bonding type rmsd
  covalent geometry    : bond        0.00200 ( 5975)
  covalent geometry    : angle       0.52602 ( 8075)
  hydrogen bonds       : bond        0.03071 (  239)
  hydrogen bonds       : angle       4.12030 (  693)

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

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

  1436 Ramachandran restraints generated.
    718 Oldfield, 0 Emsley, 718 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1436 Ramachandran restraints generated.
    718 Oldfield, 0 Emsley, 718 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  91 residues out of total 657 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 79
  time to evaluate  : 0.233 
Fit side-chains
REVERT: x  230 ASP cc_start: 0.8248 (t0) cc_final: 0.8045 (m-30)
REVERT: x  247 GLU cc_start: 0.7269 (OUTLIER) cc_final: 0.7044 (tt0)
REVERT: x  560 LYS cc_start: 0.8496 (mttt) cc_final: 0.8282 (mtmt)
REVERT: x  575 GLU cc_start: 0.8116 (mm-30) cc_final: 0.7714 (mp0)
REVERT: x  632 LYS cc_start: 0.8818 (mptm) cc_final: 0.8487 (mmtm)
REVERT: x  798 MET cc_start: 0.7605 (mtp) cc_final: 0.7402 (mtp)
REVERT: y  113 MET cc_start: 0.6727 (mtt) cc_final: 0.6476 (mtt)
  outliers start: 12
  outliers final: 9
  residues processed: 86
  average time/residue: 0.0871
  time to fit residues: 9.7483
Evaluate side-chains
  86 residues out of total 657 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 76
  time to evaluate  : 0.266 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain x residue  247 GLU
Chi-restraints excluded: chain x residue  297 VAL
Chi-restraints excluded: chain x residue  322 MET
Chi-restraints excluded: chain x residue  506 THR
Chi-restraints excluded: chain x residue  509 THR
Chi-restraints excluded: chain x residue  534 THR
Chi-restraints excluded: chain x residue  537 LEU
Chi-restraints excluded: chain x residue  538 THR
Chi-restraints excluded: chain x residue  585 THR
Chi-restraints excluded: chain x residue  859 VAL
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 73
   random chunks:
   chunk 68 optimal weight:    8.9990
   chunk 21 optimal weight:    5.9990
   chunk 65 optimal weight:    0.7980
   chunk 4 optimal weight:    6.9990
   chunk 71 optimal weight:    0.9990
   chunk 15 optimal weight:    3.9990
   chunk 66 optimal weight:    0.7980
   chunk 67 optimal weight:    0.0770
   chunk 72 optimal weight:    0.0470
   chunk 18 optimal weight:    0.9980
   chunk 42 optimal weight:    0.8980
   overall best weight:    0.5236

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

Flipped N/Q/H residues before XYZ refinement:
** x 502 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
x 796 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3465 r_free = 0.3465 target = 0.134960 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 44)----------------|
| r_work = 0.3123 r_free = 0.3123 target = 0.108356 restraints weight = 6647.926|
|-----------------------------------------------------------------------------|
r_work (start): 0.3104 rms_B_bonded: 1.66
r_work: 0.2944 rms_B_bonded: 2.60 restraints_weight: 0.5000
r_work: 0.2788 rms_B_bonded: 4.21 restraints_weight: 0.2500
r_work (final): 0.2788
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8350
moved from start:          0.3798

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.026   5975  Z= 0.094
  Angle     :  0.522   8.019   8075  Z= 0.254
  Chirality :  0.041   0.129    931
  Planarity :  0.003   0.027   1018
  Dihedral  :  5.459  68.029    799
  Min Nonbonded Distance : 2.008

Molprobity Statistics.
  All-atom Clashscore : 5.14
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.76 %
    Favored  : 96.24 %
  Rotamer:
    Outliers :  1.52 %
    Allowed  : 17.23 %
    Favored  : 81.25 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.78 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  1.35 (0.32), residues: 718
  helix:  2.00 (0.30), residues: 315
  sheet:  0.55 (0.49), residues: 123
  loop : -0.16 (0.37), residues: 280

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG x 307 
 TYR   0.009   0.001   TYR x 304 
 PHE   0.010   0.001   PHE x 426 
 TRP   0.005   0.001   TRP x 568 
 HIS   0.003   0.001   HIS x 727 

Details of bonding type rmsd
  covalent geometry    : bond        0.00209 ( 5975)
  covalent geometry    : angle       0.52203 ( 8075)
  hydrogen bonds       : bond        0.03158 (  239)
  hydrogen bonds       : angle       4.09936 (  693)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 1752.93 seconds
wall clock time: 30 minutes 37.10 seconds (1837.10 seconds total)