Starting phenix.real_space_refine
on Tue Mar 11 14:30:08 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/7dcp_30638/03_2025/7dcp_30638.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/7dcp_30638/03_2025/7dcp_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 {
    real_map_files = "/net/cci-nas-00/data/ceres_data/7dcp_30638/03_2025/7dcp_30638.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/7dcp_30638/03_2025/7dcp_30638.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/7dcp_30638/03_2025/7dcp_30638.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/7dcp_30638/03_2025/7dcp_30638.cif"
  }
  resolution = 3.15
  write_initial_geo_file = False
  refinement {
    macro_cycles = 10
  }
  qi {
    qm_restraints {
      package {
        program = *test
      }
    }
  }


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

Validating inputs
Origin is already at (0, 0, 0), no shifts will be applied
-------------------------------------------------------------------------------
Processing inputs
*****************
Set random seed
  Set to: 0
Set model cs if undefined
Decide on map wrapping
  Map wrapping is set to: False
Normalize map: mean=0, sd=1
  Input map: mean=   0.000 sd=   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): 0.02s

  Monomer Library directory:
    "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5624/modules/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: 4.18, per 1000 atoms: 0.71
  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: 1.51
  Conformation dependent library (CDL) restraints added in 849.8 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: 0.81
  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: 2.11

  Time building geometry restraints manager: 1.79 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:             1.090
  Set stop_for_unknowns flag:              0.000
  Assert model is a single copy model:     0.000
  Assert all atoms have isotropic ADPs:    0.040
  Construct map_model_manager:             0.000
  Extract box with map and model:          0.270
  Check model and map are aligned:         0.040
  Set scattering table:                    0.070
  Process input model:                     18.190
  Find NCS groups from input model:        0.070
  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:             0.000
  Load rotamer database and sin/cos tables:2.920
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   22.720
-------------------------------------------------------------------------------
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= 0.318
  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 : 3.96
  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 (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -2.88 (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
 TRP   0.027   0.003   TRP x 723 
 HIS   0.006   0.002   HIS x 704 
 PHE   0.023   0.002   PHE x 308 
 TYR   0.029   0.003   TYR x 321 
 ARG   0.004   0.001   ARG x 289 

*********************** 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  : 0.643 
Fit side-chains
REVERT: x  280 ARG cc_start: 0.7505 (ttp-110) cc_final: 0.7126 (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: 0.8428 (m)
REVERT: x  560 LYS cc_start: 0.8202 (mttt) cc_final: 0.7979 (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: 0.2633
  time to fit residues: 54.5245
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  : 0.791 
-------------------------------------------------------------------------------
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 61 optimal weight:    1.9990
   chunk 55 optimal weight:    1.9990
   chunk 30 optimal weight:    2.9990
   chunk 18 optimal weight:    6.9990
   chunk 37 optimal weight:    3.9990
   chunk 29 optimal weight:    5.9990
   chunk 57 optimal weight:    0.9980
   chunk 22 optimal weight:    3.9990
   chunk 34 optimal weight:    0.9990
   chunk 42 optimal weight:    3.9990
   chunk 66 optimal weight:    2.9990
   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 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 = 0.3453 r_free = 0.3453 target = 0.133154 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 44)----------------|
| r_work = 0.3094 r_free = 0.3094 target = 0.105721 restraints weight = 6603.487|
|-----------------------------------------------------------------------------|
r_work (start): 0.3087 rms_B_bonded: 1.70
r_work: 0.2926 rms_B_bonded: 2.58 restraints_weight: 0.5000
r_work: 0.2768 rms_B_bonded: 4.18 restraints_weight: 0.2500
r_work (final): 0.2768
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8385
moved from start:          0.2585

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= 0.316
  Angle     :  0.692   8.647   8075  Z= 0.350
  Chirality :  0.046   0.173    931
  Planarity :  0.006   0.048   1018
  Dihedral  :  8.144 134.589    801
  Min Nonbonded Distance : 2.003

Molprobity Statistics.
  All-atom Clashscore : 6.40
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.18 %
    Favored  : 95.82 %
  Rotamer:
    Outliers :  2.13 %
    Allowed  :  9.30 %
    Favored  : 88.57 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.78 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -0.75 (0.29), residues: 718
  helix: -0.57 (0.25), residues: 314
  sheet:  0.25 (0.45), residues: 107
  loop : -0.49 (0.36), residues: 297

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.015   0.002   TRP x 723 
 HIS   0.006   0.001   HIS x 704 
 PHE   0.024   0.002   PHE x 426 
 TYR   0.013   0.002   TYR x 171 
 ARG   0.004   0.001   ARG x 514 

*********************** 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
  104 residues out of total 657 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 90
  time to evaluate  : 0.643 
Fit side-chains
REVERT: x  335 SER cc_start: 0.8401 (m) cc_final: 0.8084 (p)
REVERT: x  357 ILE cc_start: 0.8698 (OUTLIER) cc_final: 0.8489 (mm)
REVERT: x  560 LYS cc_start: 0.8424 (mttt) cc_final: 0.8200 (mtpp)
REVERT: x  632 LYS cc_start: 0.8801 (mptm) cc_final: 0.8506 (mmtm)
  outliers start: 14
  outliers final: 10
  residues processed: 99
  average time/residue: 0.2182
  time to fit residues: 27.4085
Evaluate side-chains
  88 residues out of total 657 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 77
  time to evaluate  : 0.722 
-------------------------------------------------------------------------------
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  357 ILE
Chi-restraints excluded: chain x residue  374 LEU
Chi-restraints excluded: chain x residue  502 ASN
Chi-restraints excluded: chain x residue  509 THR
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=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 73
   random chunks:
   chunk 26 optimal weight:    0.7980
   chunk 34 optimal weight:    0.6980
   chunk 31 optimal weight:    3.9990
   chunk 58 optimal weight:    3.9990
   chunk 29 optimal weight:    2.9990
   chunk 49 optimal weight:    6.9990
   chunk 28 optimal weight:    2.9990
   chunk 48 optimal weight:    0.8980
   chunk 33 optimal weight:    0.4980
   chunk 41 optimal weight:    5.9990
   chunk 18 optimal weight:    7.9990
   overall best weight:    1.1782

-------------------------------------------------------------------------------
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 445 GLN
** x 502 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
x 622 ASN
x 727 HIS
x 759 GLN

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3447 r_free = 0.3447 target = 0.132895 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 38)----------------|
| r_work = 0.3088 r_free = 0.3088 target = 0.105579 restraints weight = 6589.508|
|-----------------------------------------------------------------------------|
r_work (start): 0.3112 rms_B_bonded: 1.69
r_work: 0.2951 rms_B_bonded: 2.59 restraints_weight: 0.5000
r_work: 0.2801 rms_B_bonded: 4.13 restraints_weight: 0.2500
r_work (final): 0.2801
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8374
moved from start:          0.2954

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.030   5975  Z= 0.229
  Angle     :  0.602   8.656   8075  Z= 0.303
  Chirality :  0.044   0.181    931
  Planarity :  0.005   0.043   1018
  Dihedral  :  7.188 119.373    801
  Min Nonbonded Distance : 1.915

Molprobity Statistics.
  All-atom Clashscore : 6.40
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.18 %
    Favored  : 95.82 %
  Rotamer:
    Outliers :  2.59 %
    Allowed  :  9.60 %
    Favored  : 87.80 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.78 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.13 (0.30), residues: 718
  helix:  0.68 (0.28), residues: 312
  sheet:  0.26 (0.45), residues: 104
  loop : -0.48 (0.36), residues: 302

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.009   0.002   TRP x 568 
 HIS   0.004   0.001   HIS x 704 
 PHE   0.017   0.002   PHE x 426 
 TYR   0.014   0.002   TYR x 171 
 ARG   0.003   0.000   ARG x 514 

*********************** 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
  101 residues out of total 657 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 17
    poor density    : 84
  time to evaluate  : 0.998 
Fit side-chains
REVERT: x  335 SER cc_start: 0.8303 (m) cc_final: 0.7991 (p)
REVERT: x  341 SER cc_start: 0.9030 (t) cc_final: 0.8510 (p)
REVERT: x  357 ILE cc_start: 0.8699 (OUTLIER) cc_final: 0.8498 (mm)
REVERT: x  560 LYS cc_start: 0.8447 (mttt) cc_final: 0.8180 (mtmt)
REVERT: x  632 LYS cc_start: 0.8790 (mptm) cc_final: 0.8533 (mmtm)
REVERT: x  637 ARG cc_start: 0.8251 (mtp180) cc_final: 0.7910 (mmm-85)
  outliers start: 17
  outliers final: 13
  residues processed: 96
  average time/residue: 0.1966
  time to fit residues: 24.6873
Evaluate side-chains
  89 residues out of total 657 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 75
  time to evaluate  : 0.747 
-------------------------------------------------------------------------------
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  357 ILE
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  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 46 optimal weight:    0.0010
   chunk 30 optimal weight:    3.9990
   chunk 22 optimal weight:    3.9990
   chunk 68 optimal weight:    8.9990
   chunk 58 optimal weight:    0.8980
   chunk 2 optimal weight:    0.0770
   chunk 23 optimal weight:    0.7980
   chunk 24 optimal weight:    0.6980
   chunk 29 optimal weight:    4.9990
   chunk 5 optimal weight:    1.9990
   chunk 12 optimal weight:    4.9990
   overall best weight:    0.4944

-------------------------------------------------------------------------------
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 = 0.3497 r_free = 0.3497 target = 0.137110 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 47)----------------|
| r_work = 0.3149 r_free = 0.3149 target = 0.109942 restraints weight = 6674.152|
|-----------------------------------------------------------------------------|
r_work (start): 0.3130 rms_B_bonded: 1.70
r_work: 0.2963 rms_B_bonded: 2.64 restraints_weight: 0.5000
r_work: 0.2817 rms_B_bonded: 4.12 restraints_weight: 0.2500
r_work (final): 0.2817
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8334
moved from start:          0.3173

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.029   5975  Z= 0.148
  Angle     :  0.543   8.157   8075  Z= 0.271
  Chirality :  0.042   0.184    931
  Planarity :  0.004   0.041   1018
  Dihedral  :  6.621 109.999    799
  Min Nonbonded Distance : 1.971

Molprobity Statistics.
  All-atom Clashscore : 6.40
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.04 %
    Favored  : 95.96 %
  Rotamer:
    Outliers :  2.59 %
    Allowed  : 12.80 %
    Favored  : 84.60 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.78 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.74 (0.31), residues: 718
  helix:  1.41 (0.29), residues: 314
  sheet:  0.10 (0.46), residues: 108
  loop : -0.25 (0.37), residues: 296

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.005   0.001   TRP y 115 
 HIS   0.002   0.001   HIS x 727 
 PHE   0.011   0.001   PHE x 426 
 TYR   0.011   0.001   TYR x 171 
 ARG   0.003   0.000   ARG x 514 

*********************** 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
  99 residues out of total 657 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 17
    poor density    : 82
  time to evaluate  : 0.641 
Fit side-chains
REVERT: x  335 SER cc_start: 0.8242 (m) cc_final: 0.7970 (p)
REVERT: x  560 LYS cc_start: 0.8412 (mttt) cc_final: 0.8196 (mtpp)
REVERT: x  615 THR cc_start: 0.8345 (m) cc_final: 0.8053 (m)
REVERT: x  632 LYS cc_start: 0.8802 (mptm) cc_final: 0.8500 (mmtm)
REVERT: x  637 ARG cc_start: 0.8230 (mtp180) cc_final: 0.7924 (mmm-85)
  outliers start: 17
  outliers final: 11
  residues processed: 96
  average time/residue: 0.1901
  time to fit residues: 23.7479
Evaluate side-chains
  87 residues out of total 657 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 76
  time to evaluate  : 0.638 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain x residue  297 VAL
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  603 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=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 73
   random chunks:
   chunk 21 optimal weight:    5.9990
   chunk 1 optimal weight:   10.0000
   chunk 61 optimal weight:    0.9990
   chunk 41 optimal weight:    5.9990
   chunk 72 optimal weight:    0.5980
   chunk 36 optimal weight:    1.9990
   chunk 26 optimal weight:    0.9980
   chunk 62 optimal weight:    3.9990
   chunk 7 optimal weight:    0.9980
   chunk 13 optimal weight:    3.9990
   chunk 0 optimal weight:    4.9990
   overall best weight:    1.1184

-------------------------------------------------------------------------------
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 = 0.3447 r_free = 0.3447 target = 0.132988 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 44)----------------|
| r_work = 0.3090 r_free = 0.3090 target = 0.105503 restraints weight = 6530.525|
|-----------------------------------------------------------------------------|
r_work (start): 0.3071 rms_B_bonded: 1.70
r_work: 0.2900 rms_B_bonded: 2.63 restraints_weight: 0.5000
r_work: 0.2743 rms_B_bonded: 4.19 restraints_weight: 0.2500
r_work (final): 0.2743
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8384
moved from start:          0.3297

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.035   5975  Z= 0.214
  Angle     :  0.572   8.086   8075  Z= 0.285
  Chirality :  0.043   0.188    931
  Planarity :  0.004   0.037   1018
  Dihedral  :  6.481 101.009    799
  Min Nonbonded Distance : 1.914

Molprobity Statistics.
  All-atom Clashscore : 6.07
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.32 %
    Favored  : 95.68 %
  Rotamer:
    Outliers :  2.74 %
    Allowed  : 13.72 %
    Favored  : 83.54 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.78 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.86 (0.31), residues: 718
  helix:  1.59 (0.29), residues: 314
  sheet:  0.03 (0.47), residues: 106
  loop : -0.25 (0.36), residues: 298

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.007   0.001   TRP x 568 
 HIS   0.003   0.001   HIS x 704 
 PHE   0.016   0.002   PHE x 426 
 TYR   0.012   0.001   TYR x 171 
 ARG   0.002   0.000   ARG x 369 

*********************** 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
  96 residues out of total 657 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 18
    poor density    : 78
  time to evaluate  : 0.714 
Fit side-chains
REVERT: x  335 SER cc_start: 0.8270 (m) cc_final: 0.7994 (p)
REVERT: x  560 LYS cc_start: 0.8464 (mttt) cc_final: 0.8250 (mtmt)
REVERT: x  632 LYS cc_start: 0.8835 (mptm) cc_final: 0.8534 (mmtm)
  outliers start: 18
  outliers final: 16
  residues processed: 89
  average time/residue: 0.2118
  time to fit residues: 24.4262
Evaluate side-chains
  93 residues out of total 657 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 77
  time to evaluate  : 0.730 
-------------------------------------------------------------------------------
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  603 ILE
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=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 73
   random chunks:
   chunk 17 optimal weight:    3.9990
   chunk 67 optimal weight:    0.9980
   chunk 53 optimal weight:    0.8980
   chunk 40 optimal weight:    0.9980
   chunk 41 optimal weight:    2.9990
   chunk 64 optimal weight:    4.9990
   chunk 68 optimal weight:   10.0000
   chunk 19 optimal weight:    0.7980
   chunk 26 optimal weight:    0.9980
   chunk 2 optimal weight:    0.9990
   chunk 48 optimal weight:    0.6980
   overall best weight:    0.8780

-------------------------------------------------------------------------------
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 = 0.3470 r_free = 0.3470 target = 0.134999 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 51)----------------|
| r_work = 0.3119 r_free = 0.3119 target = 0.107780 restraints weight = 6532.111|
|-----------------------------------------------------------------------------|
r_work (start): 0.3087 rms_B_bonded: 1.68
r_work: 0.2920 rms_B_bonded: 2.61 restraints_weight: 0.5000
r_work: 0.2767 rms_B_bonded: 4.14 restraints_weight: 0.2500
r_work (final): 0.2767
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8368
moved from start:          0.3411

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.031   5975  Z= 0.181
  Angle     :  0.554   7.893   8075  Z= 0.275
  Chirality :  0.043   0.176    931
  Planarity :  0.004   0.038   1018
  Dihedral  :  6.248  94.669    799
  Min Nonbonded Distance : 1.927

Molprobity Statistics.
  All-atom Clashscore : 5.48
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.04 %
    Favored  : 95.96 %
  Rotamer:
    Outliers :  2.90 %
    Allowed  : 13.87 %
    Favored  : 83.23 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.78 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.98 (0.32), residues: 718
  helix:  1.73 (0.29), residues: 314
  sheet: -0.19 (0.47), residues: 109
  loop : -0.11 (0.37), residues: 295

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.007   0.001   TRP x 568 
 HIS   0.002   0.001   HIS x 704 
 PHE   0.014   0.001   PHE x 426 
 TYR   0.011   0.001   TYR x 171 
 ARG   0.002   0.000   ARG x 514 

*********************** 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
  95 residues out of total 657 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 19
    poor density    : 76
  time to evaluate  : 0.815 
Fit side-chains
REVERT: x  335 SER cc_start: 0.8232 (m) cc_final: 0.7985 (p)
REVERT: x  560 LYS cc_start: 0.8469 (mttt) cc_final: 0.8258 (mtmt)
REVERT: x  575 GLU cc_start: 0.8068 (mm-30) cc_final: 0.7666 (mp0)
REVERT: x  632 LYS cc_start: 0.8833 (mptm) cc_final: 0.8532 (mmtm)
  outliers start: 19
  outliers final: 15
  residues processed: 89
  average time/residue: 0.2162
  time to fit residues: 25.0798
Evaluate side-chains
  90 residues out of total 657 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 15
    poor density    : 75
  time to evaluate  : 0.663 
-------------------------------------------------------------------------------
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  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  603 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=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 73
   random chunks:
   chunk 4 optimal weight:    5.9990
   chunk 60 optimal weight:    6.9990
   chunk 39 optimal weight:    0.9990
   chunk 15 optimal weight:    4.9990
   chunk 19 optimal weight:    0.5980
   chunk 24 optimal weight:    4.9990
   chunk 44 optimal weight:    0.7980
   chunk 53 optimal weight:    0.6980
   chunk 42 optimal weight:    0.9980
   chunk 32 optimal weight:    0.9980
   chunk 43 optimal weight:    1.9990
   overall best weight:    0.8180

-------------------------------------------------------------------------------
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 = 0.3469 r_free = 0.3469 target = 0.135198 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 52)----------------|
| r_work = 0.3123 r_free = 0.3123 target = 0.108276 restraints weight = 6582.135|
|-----------------------------------------------------------------------------|
r_work (start): 0.3081 rms_B_bonded: 1.67
r_work: 0.2916 rms_B_bonded: 2.62 restraints_weight: 0.5000
r_work: 0.2756 rms_B_bonded: 4.23 restraints_weight: 0.2500
r_work (final): 0.2756
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8374
moved from start:          0.3487

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.028   5975  Z= 0.179
  Angle     :  0.560   7.831   8075  Z= 0.278
  Chirality :  0.043   0.186    931
  Planarity :  0.004   0.037   1018
  Dihedral  :  6.095  89.636    799
  Min Nonbonded Distance : 1.936

Molprobity Statistics.
  All-atom Clashscore : 4.97
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.46 %
    Favored  : 95.54 %
  Rotamer:
    Outliers :  2.59 %
    Allowed  : 14.79 %
    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 (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.02 (0.32), residues: 718
  helix:  1.79 (0.29), residues: 314
  sheet: -0.22 (0.48), residues: 109
  loop : -0.10 (0.37), residues: 295

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.007   0.001   TRP x 568 
 HIS   0.002   0.001   HIS x 727 
 PHE   0.014   0.001   PHE x 426 
 TYR   0.012   0.001   TYR x 829 
 ARG   0.002   0.000   ARG x 800 

*********************** 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
  93 residues out of total 657 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 17
    poor density    : 76
  time to evaluate  : 0.707 
Fit side-chains
REVERT: x  335 SER cc_start: 0.8236 (m) cc_final: 0.7989 (p)
REVERT: x  560 LYS cc_start: 0.8465 (mttt) cc_final: 0.8254 (mtmt)
REVERT: x  575 GLU cc_start: 0.8076 (mm-30) cc_final: 0.7682 (mp0)
REVERT: x  632 LYS cc_start: 0.8822 (mptm) cc_final: 0.8477 (mptt)
  outliers start: 17
  outliers final: 14
  residues processed: 86
  average time/residue: 0.2030
  time to fit residues: 22.8114
Evaluate side-chains
  89 residues out of total 657 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 75
  time to evaluate  : 0.698 
-------------------------------------------------------------------------------
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  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  585 THR
Chi-restraints excluded: chain x residue  603 ILE
Chi-restraints excluded: chain x residue  722 SER
Chi-restraints excluded: chain x residue  746 ARG
Chi-restraints excluded: chain x residue  859 VAL
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 73
   random chunks:
   chunk 61 optimal weight:    0.9980
   chunk 11 optimal weight:    3.9990
   chunk 43 optimal weight:    1.9990
   chunk 10 optimal weight:    2.9990
   chunk 29 optimal weight:    5.9990
   chunk 6 optimal weight:    0.0980
   chunk 70 optimal weight:    0.7980
   chunk 33 optimal weight:    0.9990
   chunk 56 optimal weight:    4.9990
   chunk 63 optimal weight:    1.9990
   chunk 7 optimal weight:    0.8980
   overall best weight:    0.7582

-------------------------------------------------------------------------------
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 = 0.3457 r_free = 0.3457 target = 0.134060 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 55)----------------|
| r_work = 0.3109 r_free = 0.3109 target = 0.107042 restraints weight = 6531.380|
|-----------------------------------------------------------------------------|
r_work (start): 0.3118 rms_B_bonded: 1.68
r_work: 0.2956 rms_B_bonded: 2.59 restraints_weight: 0.5000
r_work: 0.2798 rms_B_bonded: 4.18 restraints_weight: 0.2500
r_work (final): 0.2798
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8363
moved from start:          0.3558

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.030   5975  Z= 0.168
  Angle     :  0.557   7.654   8075  Z= 0.275
  Chirality :  0.042   0.180    931
  Planarity :  0.004   0.032   1018
  Dihedral  :  5.863  81.731    799
  Min Nonbonded Distance : 1.949

Molprobity Statistics.
  All-atom Clashscore : 5.31
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.18 %
    Favored  : 95.82 %
  Rotamer:
    Outliers :  2.29 %
    Allowed  : 15.24 %
    Favored  : 82.47 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.78 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.08 (0.32), residues: 718
  helix:  1.85 (0.30), residues: 314
  sheet:  0.07 (0.50), residues: 104
  loop : -0.20 (0.37), residues: 300

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.007   0.001   TRP x 568 
 HIS   0.003   0.001   HIS x 727 
 PHE   0.013   0.001   PHE x 426 
 TYR   0.010   0.001   TYR x 171 
 ARG   0.001   0.000   ARG x 514 

*********************** 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
  97 residues out of total 657 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 15
    poor density    : 82
  time to evaluate  : 0.652 
Fit side-chains
REVERT: x  335 SER cc_start: 0.8229 (m) cc_final: 0.7993 (p)
REVERT: x  560 LYS cc_start: 0.8469 (mttt) cc_final: 0.8261 (mtmt)
REVERT: x  575 GLU cc_start: 0.8045 (mm-30) cc_final: 0.7656 (mp0)
REVERT: x  632 LYS cc_start: 0.8835 (mptm) cc_final: 0.8493 (mmtm)
REVERT: y  113 MET cc_start: 0.6733 (mtt) cc_final: 0.6494 (mtt)
  outliers start: 15
  outliers final: 13
  residues processed: 91
  average time/residue: 0.2101
  time to fit residues: 24.5501
Evaluate side-chains
  91 residues out of total 657 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 78
  time to evaluate  : 0.626 
-------------------------------------------------------------------------------
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  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  746 ARG
Chi-restraints excluded: chain x residue  859 VAL
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 73
   random chunks:
   chunk 48 optimal weight:    4.9990
   chunk 22 optimal weight:    4.9990
   chunk 16 optimal weight:    2.9990
   chunk 65 optimal weight:    0.9980
   chunk 62 optimal weight:    0.6980
   chunk 68 optimal weight:   10.0000
   chunk 24 optimal weight:    0.8980
   chunk 69 optimal weight:    0.9990
   chunk 13 optimal weight:    0.9990
   chunk 0 optimal weight:   10.0000
   chunk 1 optimal weight:   10.0000
   overall best weight:    0.9184

-------------------------------------------------------------------------------
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 = 0.3459 r_free = 0.3459 target = 0.134503 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 40)----------------|
| r_work = 0.3112 r_free = 0.3112 target = 0.107463 restraints weight = 6613.978|
|-----------------------------------------------------------------------------|
r_work (start): 0.3109 rms_B_bonded: 1.69
r_work: 0.2945 rms_B_bonded: 2.60 restraints_weight: 0.5000
r_work: 0.2796 rms_B_bonded: 4.08 restraints_weight: 0.2500
r_work (final): 0.2796
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8376
moved from start:          0.3617

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.030   5975  Z= 0.187
  Angle     :  0.568   7.393   8075  Z= 0.280
  Chirality :  0.043   0.184    931
  Planarity :  0.004   0.029   1018
  Dihedral  :  5.721  71.784    799
  Min Nonbonded Distance : 1.946

Molprobity Statistics.
  All-atom Clashscore : 5.56
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.90 %
    Favored  : 96.10 %
  Rotamer:
    Outliers :  2.44 %
    Allowed  : 15.09 %
    Favored  : 82.47 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.78 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.06 (0.32), residues: 718
  helix:  1.84 (0.29), residues: 314
  sheet:  0.02 (0.50), residues: 104
  loop : -0.20 (0.37), residues: 300

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.009   0.001   TRP x 568 
 HIS   0.003   0.001   HIS x 704 
 PHE   0.015   0.001   PHE x 426 
 TYR   0.011   0.001   TYR x 171 
 ARG   0.002   0.000   ARG x 369 

*********************** 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
  95 residues out of total 657 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 79
  time to evaluate  : 0.716 
Fit side-chains
REVERT: x  326 MET cc_start: 0.8626 (mmp) cc_final: 0.8366 (mmt)
REVERT: x  335 SER cc_start: 0.8221 (m) cc_final: 0.7979 (p)
REVERT: x  459 MET cc_start: 0.7962 (mmm) cc_final: 0.7574 (mmt)
REVERT: x  560 LYS cc_start: 0.8499 (mttt) cc_final: 0.8293 (mtmt)
REVERT: x  575 GLU cc_start: 0.8091 (mm-30) cc_final: 0.7686 (mp0)
REVERT: x  632 LYS cc_start: 0.8833 (mptm) cc_final: 0.8504 (mmtm)
  outliers start: 16
  outliers final: 16
  residues processed: 88
  average time/residue: 0.1976
  time to fit residues: 22.7163
Evaluate side-chains
  95 residues out of total 657 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 79
  time to evaluate  : 0.620 
-------------------------------------------------------------------------------
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  323 THR
Chi-restraints excluded: chain x residue  333 THR
Chi-restraints excluded: chain x residue  486 ILE
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  746 ARG
Chi-restraints excluded: chain x residue  762 MET
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 58 optimal weight:    2.9990
   chunk 14 optimal weight:    0.6980
   chunk 59 optimal weight:    1.9990
   chunk 12 optimal weight:    0.8980
   chunk 33 optimal weight:    0.9980
   chunk 41 optimal weight:    0.7980
   chunk 7 optimal weight:    0.9980
   chunk 34 optimal weight:    0.8980
   chunk 60 optimal weight:    3.9990
   chunk 53 optimal weight:    0.7980
   chunk 56 optimal weight:    4.9990
   overall best weight:    0.8180

-------------------------------------------------------------------------------
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 = 0.3459 r_free = 0.3459 target = 0.134485 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 45)----------------|
| r_work = 0.3114 r_free = 0.3114 target = 0.107547 restraints weight = 6620.853|
|-----------------------------------------------------------------------------|
r_work (start): 0.3114 rms_B_bonded: 1.69
r_work: 0.2953 rms_B_bonded: 2.57 restraints_weight: 0.5000
r_work: 0.2796 rms_B_bonded: 4.14 restraints_weight: 0.2500
r_work (final): 0.2796
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8370
moved from start:          0.3670

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.031   5975  Z= 0.175
  Angle     :  0.559   7.371   8075  Z= 0.276
  Chirality :  0.042   0.183    931
  Planarity :  0.004   0.029   1018
  Dihedral  :  5.546  63.808    799
  Min Nonbonded Distance : 1.975

Molprobity Statistics.
  All-atom Clashscore : 5.39
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.04 %
    Favored  : 95.96 %
  Rotamer:
    Outliers :  2.44 %
    Allowed  : 15.24 %
    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 (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.10 (0.32), residues: 718
  helix:  1.91 (0.30), residues: 314
  sheet:  0.07 (0.50), residues: 104
  loop : -0.23 (0.37), residues: 300

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.009   0.001   TRP x 568 
 HIS   0.002   0.001   HIS x 704 
 PHE   0.014   0.001   PHE x 426 
 TYR   0.010   0.001   TYR x 171 
 ARG   0.001   0.000   ARG x 514 

********************** 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
  97 residues out of total 657 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 81
  time to evaluate  : 0.754 
Fit side-chains
REVERT: x  335 SER cc_start: 0.8209 (m) cc_final: 0.7972 (p)
REVERT: x  459 MET cc_start: 0.7960 (mmm) cc_final: 0.7589 (mmt)
REVERT: x  560 LYS cc_start: 0.8476 (mttt) cc_final: 0.8266 (mtmt)
REVERT: x  575 GLU cc_start: 0.8126 (mm-30) cc_final: 0.7710 (mp0)
REVERT: x  632 LYS cc_start: 0.8840 (mptm) cc_final: 0.8524 (mmtm)
  outliers start: 16
  outliers final: 15
  residues processed: 90
  average time/residue: 0.2156
  time to fit residues: 25.2695
Evaluate side-chains
  93 residues out of total 657 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 15
    poor density    : 78
  time to evaluate  : 0.724 
-------------------------------------------------------------------------------
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  323 THR
Chi-restraints excluded: chain x residue  333 THR
Chi-restraints excluded: chain x residue  486 ILE
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  746 ARG
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 36 optimal weight:    5.9990
   chunk 20 optimal weight:    1.9990
   chunk 18 optimal weight:    3.9990
   chunk 37 optimal weight:    2.9990
   chunk 8 optimal weight:    0.7980
   chunk 53 optimal weight:    0.9980
   chunk 13 optimal weight:    2.9990
   chunk 48 optimal weight:    0.9980
   chunk 66 optimal weight:    0.6980
   chunk 32 optimal weight:    3.9990
   chunk 23 optimal weight:    0.0470
   overall best weight:    0.7078

-------------------------------------------------------------------------------
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 = 0.3463 r_free = 0.3463 target = 0.135302 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 43)----------------|
| r_work = 0.3119 r_free = 0.3119 target = 0.108176 restraints weight = 6683.474|
|-----------------------------------------------------------------------------|
r_work (start): 0.3128 rms_B_bonded: 1.70
r_work: 0.2971 rms_B_bonded: 2.59 restraints_weight: 0.5000
r_work: 0.2808 rms_B_bonded: 4.26 restraints_weight: 0.2500
r_work (final): 0.2808
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8364
moved from start:          0.3716

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.030   5975  Z= 0.164
  Angle     :  0.551   7.222   8075  Z= 0.273
  Chirality :  0.042   0.180    931
  Planarity :  0.004   0.029   1018
  Dihedral  :  5.349  64.320    799
  Min Nonbonded Distance : 1.996

Molprobity Statistics.
  All-atom Clashscore : 5.65
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.04 %
    Favored  : 95.96 %
  Rotamer:
    Outliers :  2.44 %
    Allowed  : 15.24 %
    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 (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.15 (0.32), residues: 718
  helix:  1.94 (0.30), residues: 314
  sheet:  0.10 (0.51), residues: 104
  loop : -0.20 (0.37), residues: 300

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.009   0.001   TRP x 568 
 HIS   0.002   0.001   HIS x 727 
 PHE   0.013   0.001   PHE x 426 
 TYR   0.010   0.001   TYR x 656 
 ARG   0.001   0.000   ARG x 514 
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 3439.39 seconds
wall clock time: 59 minutes 43.88 seconds (3583.88 seconds total)