Starting phenix.real_space_refine
on Tue Mar  3 23:07:18 2026 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/7rpi_24615/03_2026/7rpi_24615.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/7rpi_24615/03_2026/7rpi_24615.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=2.5
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    model {
      file = "/net/cci-nas-00/data/ceres_data/7rpi_24615/03_2026/7rpi_24615.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/7rpi_24615/03_2026/7rpi_24615.cif"
    real_map_files = "/net/cci-nas-00/data/ceres_data/7rpi_24615/03_2026/7rpi_24615.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/7rpi_24615/03_2026/7rpi_24615.map"
  }
  resolution = 2.5
  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=   0.005 sd=   0.579
Set stop_for_unknowns flag
  Set to: True
Assert model is a single copy model
Assert all atoms have isotropic ADPs
Construct map_model_manager
Extract box with map and model
Check model and map are aligned
Set scattering table
  Set to: electron
  Number of scattering types: 5
    Type Number    sf(0)   Gaussians
     S      65      5.16       5
     Na      2      4.78       5
     C    5741      2.51       5
     N    1184      2.21       5
     O    1534      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 24 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: 8526
  Number of models: 1
  Model: ""
    Number of chains: 2
    Chain: "A"
      Number of atoms: 7363
      Number of conformers: 2
      Conformer: "A"
        Number of residues, atoms: 926, 7358
          Classifications: {'peptide': 926}
          Link IDs: {'PCIS': 1, 'PTRANS': 39, 'TRANS': 885}
          Chain breaks: 3
      Conformer: "B"
        Number of residues, atoms: 926, 7358
          Classifications: {'peptide': 926}
          Link IDs: {'PCIS': 1, 'PTRANS': 39, 'TRANS': 885}
          Chain breaks: 3
          bond proxies already assigned to first conformer: 7550
    Chain: "A"
      Number of atoms: 1163
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 78, 1163
          Unusual residues: {' NA': 2, 'AV0': 2, 'NAG': 5, 'Y01': 26}
          Classifications: {'undetermined': 35, 'water': 43}
          Link IDs: {None: 77}
          Unresolved non-hydrogen bonds: 5
          Unresolved non-hydrogen angles: 10
          Unresolved non-hydrogen dihedrals: 15
          Unresolved non-hydrogen chiralities: 5
  Time building chain proxies: 2.98, per 1000 atoms: 0.35
  Number of scatterers: 8526
  At special positions: 0
  Unit cell: (86.005, 87.675, 127.755, 90, 90, 90)
  Space group: P 1 (No. 1)
  Number of sites at special positions: 0
  Number of scattering types: 5
    Type Number    sf(0)
     S      65     16.00
     Na      2     11.00
     O    1534      8.00
     N    1184      7.00
     C    5741      6.00
    sf(0) = scattering factor at diffraction angle 0.

  Number of disulfides: simple=8, symmetry=0
    Simple disulfide: pdb=" SG  CYS A 292 " - pdb=" SG  CYS A 348 " distance=2.03
    Simple disulfide: pdb=" SG  CYS A 322 " - pdb=" SG  CYS A 366 " distance=2.05
    Simple disulfide: pdb=" SG  CYS A 339 " - pdb=" SG  CYS A 347 " distance=2.03
    Simple disulfide: pdb=" SG  CYS A 384 " - pdb=" SG  CYS A 417 " distance=2.03
    Simple disulfide: pdb=" SG  CYS A 397 " - pdb=" SG  CYS A 410 " distance=2.03
    Simple disulfide: pdb=" SG  CYS A 829 " - pdb=" SG  CYS A 849 " distance=2.05
    Simple disulfide: pdb=" SG  CYS A 863 " - pdb=" SG  CYS A 872 " distance=2.04
    Simple disulfide: pdb=" SG  CYS A 871 " - pdb=" SG  CYS A 887 " distance=2.04

  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
  Links applied
    NAG-ASN
      " NAG A2129 " - " ASN A 915 "
      " NAG A2130 " - " ASN A 834 "
      " NAG A2131 " - " ASN A 475 "
      " NAG A2132 " - " ASN A 390 "
      " NAG A2133 " - " ASN A 362 "
  Time building additional restraints: 0.50
  Conformation dependent library (CDL) restraints added in 528.7 milliseconds
  

  1838 Ramachandran restraints generated.
    919 Oldfield, 0 Emsley, 919 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  1766

  Finding SS restraints...
    Secondary structure from input PDB file:
      41 helices and 2 sheets defined
      66.1% alpha, 4.9% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 0.20
  Creating SS restraints...
    Processing helix  chain 'A' and resid 179 through 187
    Processing helix  chain 'A' and resid 187 through 209
      removed outlier: 3.552A  pdb=" N   VAL A 191 " --> pdb=" O   TRP A 187 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 227 through 242
    Processing helix  chain 'A' and resid 253 through 262
      removed outlier: 3.827A  pdb=" N   GLU A 259 " --> pdb=" O   LYS A 255 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 314 through 329
      removed outlier: 3.564A  pdb=" N   CYS A 322 " --> pdb=" O   ILE A 318 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 334 through 339
      removed outlier: 3.630A  pdb=" N   LEU A 338 " --> pdb=" O   GLN A 334 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 352 through 361
    Processing helix  chain 'A' and resid 365 through 369
    Processing helix  chain 'A' and resid 370 through 390
      removed outlier: 5.239A  pdb=" N   LYS A 386 " --> pdb=" O   ARG A 382 " (cutoff:3.500A)
      removed outlier: 4.937A  pdb=" N   HIS A 387 " --> pdb=" O   THR A 383 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 421 through 430
    Processing helix  chain 'A' and resid 460 through 462
      No H-bonds generated for 'chain 'A' and resid 460 through 462'
    Processing helix  chain 'A' and resid 463 through 471
    Processing helix  chain 'A' and resid 490 through 502
      removed outlier: 3.827A  pdb=" N   GLN A 496 " --> pdb=" O   HIS A 492 " (cutoff:3.500A)
      removed outlier: 4.230A  pdb=" N   ASP A 497 " --> pdb=" O   SER A 493 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 503 through 522
    Processing helix  chain 'A' and resid 523 through 548
      removed outlier: 3.653A  pdb=" N   THR A 527 " --> pdb=" O   SER A 523 " (cutoff:3.500A)
      removed outlier: 3.761A  pdb=" N   LEU A 538 " --> pdb=" O   ILE A 534 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 555 through 559
    Processing helix  chain 'A' and resid 560 through 569
    Processing helix  chain 'A' and resid 570 through 587
      removed outlier: 3.642A  pdb=" N   VAL A 575 " --> pdb=" O   ASP A 571 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 591 through 620
      removed outlier: 5.557A  pdb=" N   LEU A 605 " --> pdb=" O   GLN A 601 " (cutoff:3.500A)
      removed outlier: 5.253A  pdb=" N   SER A 606 " --> pdb=" O   HIS A 602 " (cutoff:3.500A)
      removed outlier: 3.629A  pdb=" N   THR A 614 " --> pdb=" O   THR A 610 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 621 through 624
    Processing helix  chain 'A' and resid 626 through 648
    Processing helix  chain 'A' and resid 649 through 661
    Processing helix  chain 'A' and resid 661 through 666
    Processing helix  chain 'A' and resid 682 through 706
      removed outlier: 4.586A  pdb=" N   GLN A 687 " --> pdb=" O   ALA A 683 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 706 through 715
      removed outlier: 3.720A  pdb=" N   CYS A 710 " --> pdb=" O   LYS A 706 " (cutoff:3.500A)
      removed outlier: 3.587A  pdb=" N   PHE A 715 " --> pdb=" O   ILE A 711 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 715 through 736
    Processing helix  chain 'A' and resid 746 through 750
    Processing helix  chain 'A' and resid 757 through 765
      removed outlier: 3.689A  pdb=" N   ASP A 763 " --> pdb=" O   PHE A 759 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 766 through 769
    Processing helix  chain 'A' and resid 770 through 775
    Processing helix  chain 'A' and resid 818 through 833
    Processing helix  chain 'A' and resid 849 through 859
      removed outlier: 3.608A  pdb=" N   THR A 853 " --> pdb=" O   CYS A 849 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 865 through 869
    Processing helix  chain 'A' and resid 880 through 899
      removed outlier: 3.978A  pdb=" N   LYS A 889 " --> pdb=" O   GLU A 885 " (cutoff:3.500A)
      removed outlier: 4.151A  pdb=" N   ASP A 896 " --> pdb=" O   ILE A 892 " (cutoff:3.500A)
      removed outlier: 4.298A  pdb=" N   ARG A 897 " --> pdb=" O   MET A 893 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 934 through 954
    Processing helix  chain 'A' and resid 969 through 1002
    Processing helix  chain 'A' and resid 1003 through 1028
    Processing helix  chain 'A' and resid 1035 through 1061
      removed outlier: 3.590A  pdb=" N   ILE A1040 " --> pdb=" O   GLU A1036 " (cutoff:3.500A)
      removed outlier: 3.910A  pdb=" N   SER A1041 " --> pdb=" O   SER A1037 " (cutoff:3.500A)
      removed outlier: 3.952A  pdb=" N   VAL A1044 " --> pdb=" O   ILE A1040 " (cutoff:3.500A)
      removed outlier: 3.702A  pdb=" N   GLY A1045 " --> pdb=" O   SER A1041 " (cutoff:3.500A)
      removed outlier: 4.699A  pdb=" N   ASP A1049 " --> pdb=" O   GLY A1045 " (cutoff:3.500A)
      removed outlier: 4.917A  pdb=" N   PHE A1050 " --> pdb=" O   LEU A1046 " (cutoff:3.500A)
      removed outlier: 4.767A  pdb=" N   ALA A1051 " --> pdb=" O   SER A1047 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 1065 through 1094
      removed outlier: 5.434A  pdb=" N   SER A1079 " --> pdb=" O   SER A1075 " (cutoff:3.500A)
      removed outlier: 5.914A  pdb=" N   ALA A1080 " --> pdb=" O   ARG A1076 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 1100 through 1123
    Processing helix  chain 'A' and resid 1123 through 1133
    Processing sheet with id=AA1, first strand: chain 'A' and resid 450 through 458
      removed outlier: 4.013A  pdb=" N   SER A 300 " --> pdb=" O   SER A 455 " (cutoff:3.500A)
      removed outlier: 6.543A  pdb=" N   ALA A 305 " --> pdb=" O   VAL A 483 " (cutoff:3.500A)
      removed outlier: 5.295A  pdb=" N   VAL A 483 " --> pdb=" O   ALA A 305 " (cutoff:3.500A)
    Processing sheet with id=AA2, first strand: chain 'A' and resid 909 through 912
      removed outlier: 3.577A  pdb=" N   ALA A 920 " --> pdb=" O   ARG A 911 " (cutoff:3.500A)
      removed outlier: 8.051A  pdb=" N   LEU A 923 " --> pdb=" O   TRP A 789 " (cutoff:3.500A)
      removed outlier: 7.919A  pdb=" N   TRP A 789 " --> pdb=" O   LEU A 923 " (cutoff:3.500A)
      removed outlier: 7.996A  pdb=" N   PHE A 925 " --> pdb=" O   VAL A 787 " (cutoff:3.500A)
      removed outlier: 7.726A  pdb=" N   VAL A 787 " --> pdb=" O   PHE A 925 " (cutoff:3.500A)
      removed outlier: 7.163A  pdb=" N   SER A 927 " --> pdb=" O   ILE A 785 " (cutoff:3.500A)
      removed outlier: 7.685A  pdb=" N   ILE A 785 " --> pdb=" O   SER A 927 " (cutoff:3.500A)
      removed outlier: 6.083A  pdb=" N   PHE A 929 " --> pdb=" O   MET A 783 " (cutoff:3.500A)

    441 hydrogen bonds defined for protein.
    1287 hydrogen bond angles defined for protein.
    Restraints generated for nucleic acids:
      0 hydrogen bonds
      0 hydrogen bond angles
      0 basepair planarities
      0 basepair parallelities
      0 stacking parallelities
  Total time for adding SS restraints: 1.44

  Time building geometry restraints manager: 0.70 seconds

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

  Histogram of bond lengths:
        1.19 -     1.32: 1340
        1.32 -     1.45: 2192
        1.45 -     1.58: 5065
        1.58 -     1.70: 69
        1.70 -     1.83: 98
  Bond restraints: 8764
  Sorted by residual:
  bond pdb=" N   MET A 557 "
       pdb=" CA BMET A 557 "
    ideal  model  delta    sigma   weight residual
    1.458  1.357  0.102 1.27e-02 6.20e+03 6.43e+01
  bond pdb=" N   GLU A1031 "
       pdb=" CA  GLU A1031 "
    ideal  model  delta    sigma   weight residual
    1.454  1.400  0.053 1.23e-02 6.61e+03 1.86e+01
  bond pdb=" C   ASP A 578 "
       pdb=" O   ASP A 578 "
    ideal  model  delta    sigma   weight residual
    1.236  1.189  0.047 1.15e-02 7.56e+03 1.66e+01
  bond pdb=" CA  GLU A1031 "
       pdb=" CB  GLU A1031 "
    ideal  model  delta    sigma   weight residual
    1.535  1.462  0.073 1.93e-02 2.68e+03 1.42e+01
  bond pdb=" CB  THR A1122 "
       pdb=" OG1 THR A1122 "
    ideal  model  delta    sigma   weight residual
    1.433  1.373  0.060 1.60e-02 3.91e+03 1.42e+01
  ... (remaining 8759 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     2.65: 10331
        2.65 -     5.31: 1646
        5.31 -     7.96: 76
        7.96 -    10.61: 8
       10.61 -    13.26: 1
  Bond angle restraints: 12062
  Sorted by residual:
  angle pdb=" N   ARG A 341 "
        pdb=" CA  ARG A 341 "
        pdb=" C   ARG A 341 "
      ideal   model   delta    sigma   weight residual
     108.76  122.02  -13.26 1.69e+00 3.50e-01 6.16e+01
  angle pdb=" N   MET A 557 "
        pdb=" CA BMET A 557 "
        pdb=" C   MET A 557 "
      ideal   model   delta    sigma   weight residual
     111.75  120.36   -8.61 1.28e+00 6.10e-01 4.52e+01
  angle pdb=" CA  PHE A 759 "
        pdb=" CB  PHE A 759 "
        pdb=" CG  PHE A 759 "
      ideal   model   delta    sigma   weight residual
     113.80  120.40   -6.60 1.00e+00 1.00e+00 4.36e+01
  angle pdb=" CA  PHE A 549 "
        pdb=" CB  PHE A 549 "
        pdb=" CG  PHE A 549 "
      ideal   model   delta    sigma   weight residual
     113.80  120.17   -6.37 1.00e+00 1.00e+00 4.06e+01
  angle pdb=" CA  ASP A 293 "
        pdb=" CB  ASP A 293 "
        pdb=" CG  ASP A 293 "
      ideal   model   delta    sigma   weight residual
     112.60  118.82   -6.22 1.00e+00 1.00e+00 3.87e+01
  ... (remaining 12057 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    26.89: 6362
       26.89 -    53.79: 229
       53.79 -    80.68: 41
       80.68 -   107.57: 21
      107.57 -   134.47: 6
  Dihedral angle restraints: 6659
    sinusoidal: 3931
      harmonic: 2728
  Sorted by residual:
  dihedral pdb=" CA  VAL A1048 "
           pdb=" C   VAL A1048 "
           pdb=" N   ASP A1049 "
           pdb=" CA  ASP A1049 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00 -150.68  -29.32     0      5.00e+00 4.00e-02 3.44e+01
  dihedral pdb=" CA  TYR A 420 "
           pdb=" C   TYR A 420 "
           pdb=" N   ASN A 421 "
           pdb=" CA  ASN A 421 "
      ideal   model   delta  harmonic     sigma   weight residual
    -180.00 -153.68  -26.32     0      5.00e+00 4.00e-02 2.77e+01
  dihedral pdb=" CA  TYR A 443 "
           pdb=" C   TYR A 443 "
           pdb=" N   ALA A 444 "
           pdb=" CA  ALA A 444 "
      ideal   model   delta  harmonic     sigma   weight residual
    -180.00 -155.33  -24.67     0      5.00e+00 4.00e-02 2.43e+01
  ... (remaining 6656 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.095: 922
       0.095 -    0.191: 432
       0.191 -    0.286: 69
       0.286 -    0.381: 15
       0.381 -    0.477: 3
  Chirality restraints: 1441
  Sorted by residual:
  chirality pdb=" CA  GLU A1031 "
            pdb=" N   GLU A1031 "
            pdb=" C   GLU A1031 "
            pdb=" CB  GLU A1031 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.03    0.48 2.00e-01 2.50e+01 5.68e+00
  chirality pdb=" CA BMET A 557 "
            pdb=" N   MET A 557 "
            pdb=" C   MET A 557 "
            pdb=" CB BMET A 557 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.06    0.45 2.00e-01 2.50e+01 5.08e+00
  chirality pdb=" CA  ASP A 916 "
            pdb=" N   ASP A 916 "
            pdb=" C   ASP A 916 "
            pdb=" CB  ASP A 916 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.12    0.39 2.00e-01 2.50e+01 3.86e+00
  ... (remaining 1438 not shown)

  Planarity restraints: 1344
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CB  ASN A 834 "   -0.102 2.00e-02 2.50e+03   1.05e-01 1.37e+02
        pdb=" CG  ASN A 834 "    0.066 2.00e-02 2.50e+03
        pdb=" OD1 ASN A 834 "    0.004 2.00e-02 2.50e+03
        pdb=" ND2 ASN A 834 "    0.157 2.00e-02 2.50e+03
        pdb=" C1  NAG A2130 "   -0.125 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CB  TRP A 313 "    0.145 2.00e-02 2.50e+03   7.20e-02 1.30e+02
        pdb=" CG  TRP A 313 "   -0.030 2.00e-02 2.50e+03
        pdb=" CD1 TRP A 313 "   -0.061 2.00e-02 2.50e+03
        pdb=" CD2 TRP A 313 "   -0.051 2.00e-02 2.50e+03
        pdb=" NE1 TRP A 313 "   -0.032 2.00e-02 2.50e+03
        pdb=" CE2 TRP A 313 "    0.004 2.00e-02 2.50e+03
        pdb=" CE3 TRP A 313 "   -0.090 2.00e-02 2.50e+03
        pdb=" CZ2 TRP A 313 "    0.084 2.00e-02 2.50e+03
        pdb=" CZ3 TRP A 313 "   -0.043 2.00e-02 2.50e+03
        pdb=" CH2 TRP A 313 "    0.075 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CB  ASN A 915 "   -0.091 2.00e-02 2.50e+03   1.01e-01 1.28e+02
        pdb=" CG  ASN A 915 "    0.045 2.00e-02 2.50e+03
        pdb=" OD1 ASN A 915 "    0.001 2.00e-02 2.50e+03
        pdb=" ND2 ASN A 915 "    0.164 2.00e-02 2.50e+03
        pdb=" C1  NAG A2129 "   -0.119 2.00e-02 2.50e+03
  ... (remaining 1341 not shown)

  Histogram of nonbonded interaction distances:
        2.17 -     2.72: 140
        2.72 -     3.26: 8270
        3.26 -     3.81: 12726
        3.81 -     4.35: 18480
        4.35 -     4.90: 29510
  Nonbonded interactions: 69126
  Sorted by model distance:
  nonbonded pdb=" OD1 ASP A1049 "
            pdb="NA    NA A2134 "
     model   vdw
     2.170 2.470
  nonbonded pdb=" O   GLY A1045 "
            pdb="NA    NA A2134 "
     model   vdw
     2.205 2.470
  nonbonded pdb=" OD1 ASP A 572 "
            pdb="NA    NA A2135 "
     model   vdw
     2.213 2.470
  nonbonded pdb=" OD2 ASP A 572 "
            pdb="NA    NA A2135 "
     model   vdw
     2.245 2.470
  nonbonded pdb="NA    NA A2135 "
            pdb=" O   HOH A2231 "
     model   vdw
     2.261 2.470
  ... (remaining 69121 not shown)

  NOTE: a complete listing of the restraints can be obtained by requesting
        output of .geo file.
Find NCS groups from input model
========== 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=0.50 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:                         0.010
  Set model cs if undefined:               0.000
  Decide on map wrapping:                  0.000
  Normalize map: mean=0, sd=1:             2.100
  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:          0.170
  Check model and map are aligned:         0.030
  Set scattering table:                    0.030
  Process input model:                     9.880
  Find NCS groups from input model:        0.040
  Set up NCS constraints:                  0.020
  Set refine NCS operators:                0.000
  Adjust number of macro_cycles:           0.000
  Reset NCS operators:                     0.000
  Extract rigid body selections:           0.000
  Check and reset occupancies:             0.000
  Load rotamer database and sin/cos tables:6.450
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   18.740
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7006
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      :  0.016   0.102   8777  Z= 0.895
  Angle     :  1.828  13.262  12093  Z= 1.186
  Chirality :  0.106   0.477   1441
  Planarity :  0.014   0.100   1339
  Dihedral  : 14.731 134.467   4869
  Min Nonbonded Distance : 2.170

Molprobity Statistics.
  All-atom Clashscore : 0.93
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.96 %
    Favored  : 98.04 %
  Rotamer:
    Outliers :  0.12 %
    Allowed  :  1.72 %
    Favored  : 98.16 %
  Cbeta Deviations :  0.23 %
  Peptide Plane:
    Cis-proline     : 2.50 %
    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: -0.69 (0.25), residues: 919
  helix: -0.43 (0.19), residues: 558
  sheet:  0.48 (0.94), residues: 29
  loop : -0.29 (0.35), residues: 332

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.007   0.001   ARG A 301 
 TYR   0.114   0.021   TYR A 635 
 PHE   0.063   0.014   PHE A1109 
 TRP   0.145   0.028   TRP A 313 
 HIS   0.008   0.003   HIS A 332 

Details of bonding type rmsd
  covalent geometry    : bond        0.01586 ( 8764)
  covalent geometry    : angle       1.81803 (12062)
  SS BOND              : bond        0.01033 (    8)
  SS BOND              : angle       1.43047 (   16)
  hydrogen bonds       : bond        0.19508 (  441)
  hydrogen bonds       : angle       7.16071 ( 1287)
  link_NAG-ASN         : bond        0.01743 (    5)
  link_NAG-ASN         : angle       5.71678 (   15)

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

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

  1838 Ramachandran restraints generated.
    919 Oldfield, 0 Emsley, 919 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1838 Ramachandran restraints generated.
    919 Oldfield, 0 Emsley, 919 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  130 residues out of total 812 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 129
  time to evaluate  : 0.238 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  187 TRP cc_start: 0.7100 (m-10) cc_final: 0.6769 (m-10)
REVERT: A  194 MET cc_start: 0.5966 (mtp) cc_final: 0.5583 (mmp)
REVERT: A  647 MET cc_start: 0.7973 (mmp) cc_final: 0.7606 (mmt)
REVERT: A  698 GLU cc_start: 0.6845 (mm-30) cc_final: 0.6555 (mm-30)
REVERT: A  700 SER cc_start: 0.7653 (t) cc_final: 0.7056 (m)
REVERT: A  701 ARG cc_start: 0.7019 (mmt90) cc_final: 0.6546 (tpm170)
REVERT: A  702 ILE cc_start: 0.6853 (mm) cc_final: 0.6584 (mm)
REVERT: A  860 ASN cc_start: 0.7009 (m-40) cc_final: 0.6679 (t0)
REVERT: A  937 LYS cc_start: 0.7678 (mtmt) cc_final: 0.7445 (mtmm)
REVERT: A  943 LYS cc_start: 0.7334 (mtpp) cc_final: 0.6813 (mmmt)
REVERT: A  997 MET cc_start: 0.7552 (mtm) cc_final: 0.7263 (mtp)
  outliers start: 1
  outliers final: 0
  residues processed: 129
  average time/residue: 0.5842
  time to fit residues: 79.9896
Evaluate side-chains
  87 residues out of total 812 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 87
  time to evaluate  : 0.308 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 92
   random chunks:
   chunk 49 optimal weight:    1.9990
   chunk 53 optimal weight:    0.7980
   chunk 5 optimal weight:    0.9980
   chunk 33 optimal weight:    0.8980
   chunk 65 optimal weight:    9.9990
   chunk 62 optimal weight:    1.9990
   chunk 51 optimal weight:    1.9990
   chunk 38 optimal weight:    4.9990
   chunk 61 optimal weight:    0.8980
   chunk 45 optimal weight:    0.0870
   chunk 74 optimal weight:    0.9990
   overall best weight:    0.7358

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

Flipped N/Q/H residues before XYZ refinement:
A 284 ASN
A 340 GLN
A 421 ASN
A 465 ASN
A 470 ASN
A 856 GLN

Total number of N/Q/H flips: 6

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4175 r_free = 0.4175 target = 0.188684 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 37)----------------|
| r_work = 0.3591 r_free = 0.3591 target = 0.132825 restraints weight = 8664.358|
|-----------------------------------------------------------------------------|
r_work (start): 0.3561 rms_B_bonded: 2.07
r_work: 0.3401 rms_B_bonded: 3.08 restraints_weight: 0.5000
r_work: 0.3256 rms_B_bonded: 4.81 restraints_weight: 0.2500
r_work (final): 0.3256
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3260
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3260 r_free = 0.3260    target_work(ls_wunit_k1) = 0.106         |
| occupancies: max = 1.00  min = 0.50   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3260 r_free = 0.3260    target_work(ls_wunit_k1) = 0.106         |
| occupancies: max = 1.00  min = 0.42   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.3260
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8025
moved from start:          0.2214

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.035   8777  Z= 0.140
  Angle     :  0.715   9.675  12093  Z= 0.337
  Chirality :  0.043   0.229   1441
  Planarity :  0.004   0.033   1339
  Dihedral  : 11.608 167.517   3198
  Min Nonbonded Distance : 2.221

Molprobity Statistics.
  All-atom Clashscore : 4.05
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  0.87 %
    Favored  : 99.13 %
  Rotamer:
    Outliers :  1.47 %
    Allowed  :  6.39 %
    Favored  : 92.14 %
  Cbeta Deviations :  0.11 %
  Peptide Plane:
    Cis-proline     : 2.50 %
    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:  1.63 (0.28), residues: 919
  helix:  1.59 (0.21), residues: 568
  sheet:  0.71 (0.90), residues: 29
  loop :  0.34 (0.36), residues: 322

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.001   ARG A 691 
 TYR   0.014   0.002   TYR A 619 
 PHE   0.017   0.002   PHE A 608 
 TRP   0.015   0.002   TRP A 789 
 HIS   0.007   0.001   HIS A 827 

Details of bonding type rmsd
  covalent geometry    : bond        0.00297 ( 8764)
  covalent geometry    : angle       0.69710 (12062)
  SS BOND              : bond        0.00621 (    8)
  SS BOND              : angle       1.20655 (   16)
  hydrogen bonds       : bond        0.05246 (  441)
  hydrogen bonds       : angle       4.63227 ( 1287)
  link_NAG-ASN         : bond        0.01077 (    5)
  link_NAG-ASN         : angle       4.48687 (   15)

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

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

  1838 Ramachandran restraints generated.
    919 Oldfield, 0 Emsley, 919 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1838 Ramachandran restraints generated.
    919 Oldfield, 0 Emsley, 919 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  112 residues out of total 812 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 100
  time to evaluate  : 0.346 
Fit side-chains
   revert: symmetry clash
REVERT: A  194 MET cc_start: 0.7487 (mtp) cc_final: 0.6763 (mmp)
REVERT: A  223 GLU cc_start: 0.8278 (tt0) cc_final: 0.7434 (pm20)
REVERT: A  340 GLN cc_start: 0.7313 (tt0) cc_final: 0.7049 (mt0)
REVERT: A  363 ARG cc_start: 0.7154 (mpt90) cc_final: 0.6950 (mpt90)
REVERT: A  515 LEU cc_start: 0.7965 (mt) cc_final: 0.7688 (tp)
REVERT: A  698 GLU cc_start: 0.7107 (mm-30) cc_final: 0.6548 (mm-30)
REVERT: A  700 SER cc_start: 0.7983 (t) cc_final: 0.7477 (m)
REVERT: A  701 ARG cc_start: 0.7485 (mmt90) cc_final: 0.6880 (tpm170)
REVERT: A  746 GLU cc_start: 0.7450 (mt-10) cc_final: 0.7222 (mm-30)
REVERT: A  756 SER cc_start: 0.8955 (OUTLIER) cc_final: 0.8645 (p)
REVERT: A  771 MET cc_start: 0.7700 (mpp) cc_final: 0.7452 (mmp)
REVERT: A  887 CYS cc_start: 0.7630 (m) cc_final: 0.7207 (m)
REVERT: A  962 ARG cc_start: 0.7624 (OUTLIER) cc_final: 0.7021 (mtm110)
  outliers start: 12
  outliers final: 5
  residues processed: 108
  average time/residue: 0.5862
  time to fit residues: 67.4822
Evaluate side-chains
  90 residues out of total 812 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 7
    poor density    : 83
  time to evaluate  : 0.298 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  336 SER
Chi-restraints excluded: chain A residue  436 MET
Chi-restraints excluded: chain A residue  756 SER
Chi-restraints excluded: chain A residue  792 SER
Chi-restraints excluded: chain A residue  848 SER
Chi-restraints excluded: chain A residue  851 ILE
Chi-restraints excluded: chain A residue  962 ARG
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 92
   random chunks:
   chunk 75 optimal weight:    2.9990
   chunk 0 optimal weight:   10.0000
   chunk 30 optimal weight:    1.9990
   chunk 74 optimal weight:    0.9980
   chunk 14 optimal weight:    0.1980
   chunk 8 optimal weight:    4.9990
   chunk 83 optimal weight:    0.7980
   chunk 5 optimal weight:    0.9980
   chunk 24 optimal weight:    4.9990
   chunk 31 optimal weight:    0.9990
   chunk 19 optimal weight:    1.9990
   overall best weight:    0.7982

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4156 r_free = 0.4156 target = 0.187217 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 34)----------------|
| r_work = 0.3603 r_free = 0.3603 target = 0.132230 restraints weight = 10530.143|
|-----------------------------------------------------------------------------|
r_work (start): 0.3557 rms_B_bonded: 2.08
r_work: 0.3369 rms_B_bonded: 3.18 restraints_weight: 0.5000
r_work: 0.3225 rms_B_bonded: 4.96 restraints_weight: 0.2500
r_work (final): 0.3225
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3228
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3228 r_free = 0.3228    target_work(ls_wunit_k1) = 0.104         |
| occupancies: max = 1.00  min = 0.42   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3228 r_free = 0.3228    target_work(ls_wunit_k1) = 0.104         |
| occupancies: max = 1.00  min = 0.38   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.3228
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8049
moved from start:          0.2514

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.032   8777  Z= 0.130
  Angle     :  0.657   9.090  12093  Z= 0.304
  Chirality :  0.043   0.410   1441
  Planarity :  0.004   0.044   1339
  Dihedral  : 11.031 178.869   3198
  Min Nonbonded Distance : 2.230

Molprobity Statistics.
  All-atom Clashscore : 4.40
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.74 %
    Favored  : 98.26 %
  Rotamer:
    Outliers :  1.35 %
    Allowed  :  9.21 %
    Favored  : 89.43 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.50 %
    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:  1.95 (0.28), residues: 919
  helix:  1.92 (0.22), residues: 573
  sheet:  0.86 (0.94), residues: 29
  loop :  0.27 (0.37), residues: 317

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.000   ARG A 341 
 TYR   0.014   0.002   TYR A 619 
 PHE   0.018   0.001   PHE A 608 
 TRP   0.014   0.001   TRP A 650 
 HIS   0.004   0.001   HIS A 827 

Details of bonding type rmsd
  covalent geometry    : bond        0.00281 ( 8764)
  covalent geometry    : angle       0.64267 (12062)
  SS BOND              : bond        0.00375 (    8)
  SS BOND              : angle       0.92548 (   16)
  hydrogen bonds       : bond        0.05278 (  441)
  hydrogen bonds       : angle       4.44016 ( 1287)
  link_NAG-ASN         : bond        0.01035 (    5)
  link_NAG-ASN         : angle       3.85189 (   15)

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

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

  1838 Ramachandran restraints generated.
    919 Oldfield, 0 Emsley, 919 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1838 Ramachandran restraints generated.
    919 Oldfield, 0 Emsley, 919 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  110 residues out of total 812 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 99
  time to evaluate  : 0.313 
Fit side-chains
   revert: symmetry clash
REVERT: A  194 MET cc_start: 0.7437 (mtp) cc_final: 0.6678 (mmp)
REVERT: A  223 GLU cc_start: 0.8322 (tt0) cc_final: 0.7477 (pm20)
REVERT: A  339 CYS cc_start: 0.7482 (p) cc_final: 0.7051 (p)
REVERT: A  340 GLN cc_start: 0.7217 (tt0) cc_final: 0.6997 (tt0)
REVERT: A  515 LEU cc_start: 0.7942 (mt) cc_final: 0.7672 (tt)
REVERT: A  700 SER cc_start: 0.7978 (t) cc_final: 0.7454 (m)
REVERT: A  701 ARG cc_start: 0.7481 (mmt90) cc_final: 0.6856 (tpm170)
REVERT: A  746 GLU cc_start: 0.7347 (mt-10) cc_final: 0.7143 (mm-30)
REVERT: A  771 MET cc_start: 0.7689 (mpp) cc_final: 0.7439 (mmp)
REVERT: A  887 CYS cc_start: 0.7604 (m) cc_final: 0.7197 (m)
  outliers start: 11
  outliers final: 5
  residues processed: 105
  average time/residue: 0.5243
  time to fit residues: 58.9932
Evaluate side-chains
  93 residues out of total 812 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 5
    poor density    : 88
  time to evaluate  : 0.255 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  190 VAL
Chi-restraints excluded: chain A residue  306 SER
Chi-restraints excluded: chain A residue  475 ASN
Chi-restraints excluded: chain A residue  792 SER
Chi-restraints excluded: chain A residue  851 ILE
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 92
   random chunks:
   chunk 57 optimal weight:    0.0270
   chunk 45 optimal weight:    0.8980
   chunk 47 optimal weight:    5.9990
   chunk 17 optimal weight:    6.9990
   chunk 84 optimal weight:    0.8980
   chunk 36 optimal weight:    3.9990
   chunk 30 optimal weight:    0.8980
   chunk 64 optimal weight:    0.6980
   chunk 1 optimal weight:    0.9980
   chunk 82 optimal weight:    2.9990
   chunk 60 optimal weight:    5.9990
   overall best weight:    0.6838

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

Flipped N/Q/H residues before XYZ refinement:
A 968 ASN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4219 r_free = 0.4219 target = 0.191756 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.3731 r_free = 0.3731 target = 0.140185 restraints weight = 12565.811|
|-----------------------------------------------------------------------------|
r_work (start): 0.3686 rms_B_bonded: 2.03
r_work: 0.3529 rms_B_bonded: 3.10 restraints_weight: 0.5000
r_work: 0.3400 rms_B_bonded: 4.86 restraints_weight: 0.2500
r_work (final): 0.3400
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3374
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3374 r_free = 0.3374    target_work(ls_wunit_k1) = 0.113         |
| occupancies: max = 1.00  min = 0.38   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3374 r_free = 0.3374    target_work(ls_wunit_k1) = 0.113         |
| occupancies: max = 1.00  min = 0.38   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.3374
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8037
moved from start:          0.2770

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.037   8777  Z= 0.120
  Angle     :  0.607   7.553  12093  Z= 0.285
  Chirality :  0.041   0.383   1441
  Planarity :  0.004   0.044   1339
  Dihedral  : 10.527 175.093   3198
  Min Nonbonded Distance : 2.249

Molprobity Statistics.
  All-atom Clashscore : 4.34
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.20 %
    Favored  : 98.80 %
  Rotamer:
    Outliers :  1.72 %
    Allowed  : 10.07 %
    Favored  : 88.21 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.50 %
    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:  2.11 (0.28), residues: 919
  helix:  2.18 (0.22), residues: 567
  sheet:  0.89 (0.90), residues: 29
  loop :  0.09 (0.36), residues: 323

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.000   ARG A 774 
 TYR   0.012   0.001   TYR A 545 
 PHE   0.016   0.001   PHE A 608 
 TRP   0.012   0.001   TRP A 650 
 HIS   0.002   0.001   HIS A 827 

Details of bonding type rmsd
  covalent geometry    : bond        0.00257 ( 8764)
  covalent geometry    : angle       0.59857 (12062)
  SS BOND              : bond        0.00357 (    8)
  SS BOND              : angle       1.04349 (   16)
  hydrogen bonds       : bond        0.04752 (  441)
  hydrogen bonds       : angle       4.32476 ( 1287)
  link_NAG-ASN         : bond        0.01158 (    5)
  link_NAG-ASN         : angle       2.81097 (   15)

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

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

  1838 Ramachandran restraints generated.
    919 Oldfield, 0 Emsley, 919 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1838 Ramachandran restraints generated.
    919 Oldfield, 0 Emsley, 919 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  108 residues out of total 812 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 94
  time to evaluate  : 0.286 
Fit side-chains
   revert: symmetry clash
REVERT: A  194 MET cc_start: 0.7423 (mtp) cc_final: 0.6683 (mmp)
REVERT: A  223 GLU cc_start: 0.8262 (tt0) cc_final: 0.7430 (pm20)
REVERT: A  340 GLN cc_start: 0.7307 (tt0) cc_final: 0.6937 (tt0)
REVERT: A  363 ARG cc_start: 0.7464 (mpt90) cc_final: 0.7178 (mtt-85)
REVERT: A  515 LEU cc_start: 0.7864 (mt) cc_final: 0.7625 (tt)
REVERT: A  700 SER cc_start: 0.8031 (t) cc_final: 0.7522 (m)
REVERT: A  701 ARG cc_start: 0.7407 (mmt90) cc_final: 0.6866 (tpm170)
REVERT: A  746 GLU cc_start: 0.7302 (mt-10) cc_final: 0.7020 (pt0)
REVERT: A  771 MET cc_start: 0.7701 (mpp) cc_final: 0.7362 (mmp)
REVERT: A  887 CYS cc_start: 0.7579 (m) cc_final: 0.7144 (m)
REVERT: A  943 LYS cc_start: 0.8159 (OUTLIER) cc_final: 0.7616 (tptt)
  outliers start: 14
  outliers final: 4
  residues processed: 103
  average time/residue: 0.5491
  time to fit residues: 60.3717
Evaluate side-chains
  93 residues out of total 812 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 5
    poor density    : 88
  time to evaluate  : 0.259 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  475 ASN
Chi-restraints excluded: chain A residue  792 SER
Chi-restraints excluded: chain A residue  848 SER
Chi-restraints excluded: chain A residue  851 ILE
Chi-restraints excluded: chain A residue  943 LYS
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 92
   random chunks:
   chunk 34 optimal weight:    0.9990
   chunk 15 optimal weight:    6.9990
   chunk 69 optimal weight:    0.9990
   chunk 31 optimal weight:    0.9990
   chunk 49 optimal weight:    0.5980
   chunk 90 optimal weight:    2.9990
   chunk 27 optimal weight:    8.9990
   chunk 71 optimal weight:    3.9990
   chunk 85 optimal weight:    1.9990
   chunk 36 optimal weight:    3.9990
   chunk 29 optimal weight:    2.9990
   overall best weight:    1.1188

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

Flipped N/Q/H residues before XYZ refinement:
A 421 ASN
A 968 ASN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4195 r_free = 0.4195 target = 0.188919 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 34)----------------|
| r_work = 0.3696 r_free = 0.3696 target = 0.137092 restraints weight = 10758.831|
|-----------------------------------------------------------------------------|
r_work (start): 0.3651 rms_B_bonded: 1.98
r_work: 0.3497 rms_B_bonded: 2.99 restraints_weight: 0.5000
r_work: 0.3367 rms_B_bonded: 4.69 restraints_weight: 0.2500
r_work (final): 0.3367
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3329
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3329 r_free = 0.3329    target_work(ls_wunit_k1) = 0.110         |
| occupancies: max = 1.00  min = 0.38   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3329 r_free = 0.3329    target_work(ls_wunit_k1) = 0.110         |
| occupancies: max = 1.00  min = 0.40   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.3329
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8078
moved from start:          0.2745

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.036   8777  Z= 0.145
  Angle     :  0.640   7.331  12093  Z= 0.302
  Chirality :  0.043   0.368   1441
  Planarity :  0.004   0.041   1339
  Dihedral  : 10.648 171.492   3198
  Min Nonbonded Distance : 2.215

Molprobity Statistics.
  All-atom Clashscore : 4.57
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.53 %
    Favored  : 98.47 %
  Rotamer:
    Outliers :  2.09 %
    Allowed  : 10.57 %
    Favored  : 87.35 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.50 %
    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:  1.98 (0.28), residues: 919
  helix:  2.09 (0.22), residues: 568
  sheet:  0.81 (0.89), residues: 29
  loop : -0.01 (0.36), residues: 322

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARG A 754 
 TYR   0.014   0.002   TYR A 644 
 PHE   0.019   0.002   PHE A 608 
 TRP   0.013   0.001   TRP A 650 
 HIS   0.002   0.001   HIS A 602 

Details of bonding type rmsd
  covalent geometry    : bond        0.00326 ( 8764)
  covalent geometry    : angle       0.63198 (12062)
  SS BOND              : bond        0.00362 (    8)
  SS BOND              : angle       0.96024 (   16)
  hydrogen bonds       : bond        0.05592 (  441)
  hydrogen bonds       : angle       4.44095 ( 1287)
  link_NAG-ASN         : bond        0.01106 (    5)
  link_NAG-ASN         : angle       2.79496 (   15)

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

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

  1838 Ramachandran restraints generated.
    919 Oldfield, 0 Emsley, 919 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1838 Ramachandran restraints generated.
    919 Oldfield, 0 Emsley, 919 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  110 residues out of total 812 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 17
    poor density    : 93
  time to evaluate  : 0.329 
Fit side-chains
   revert: symmetry clash
REVERT: A  194 MET cc_start: 0.7349 (mtp) cc_final: 0.6593 (mmp)
REVERT: A  223 GLU cc_start: 0.8367 (tt0) cc_final: 0.7632 (pm20)
REVERT: A  340 GLN cc_start: 0.7308 (tt0) cc_final: 0.6941 (tt0)
REVERT: A  363 ARG cc_start: 0.7416 (mpt90) cc_final: 0.7104 (mtt-85)
REVERT: A  515 LEU cc_start: 0.7912 (mt) cc_final: 0.7616 (tt)
REVERT: A  700 SER cc_start: 0.8025 (t) cc_final: 0.7504 (m)
REVERT: A  701 ARG cc_start: 0.7340 (mmt90) cc_final: 0.6786 (tpm170)
REVERT: A  771 MET cc_start: 0.7605 (mpp) cc_final: 0.7248 (mmp)
REVERT: A  887 CYS cc_start: 0.7524 (m) cc_final: 0.7132 (m)
REVERT: A  937 LYS cc_start: 0.8032 (OUTLIER) cc_final: 0.7376 (mmpt)
REVERT: A  943 LYS cc_start: 0.8137 (OUTLIER) cc_final: 0.7587 (tptt)
  outliers start: 17
  outliers final: 7
  residues processed: 103
  average time/residue: 0.5439
  time to fit residues: 59.9135
Evaluate side-chains
  102 residues out of total 812 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 9
    poor density    : 93
  time to evaluate  : 0.299 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  190 VAL
Chi-restraints excluded: chain A residue  306 SER
Chi-restraints excluded: chain A residue  336 SER
Chi-restraints excluded: chain A residue  341 ARG
Chi-restraints excluded: chain A residue  792 SER
Chi-restraints excluded: chain A residue  848 SER
Chi-restraints excluded: chain A residue  851 ILE
Chi-restraints excluded: chain A residue  937 LYS
Chi-restraints excluded: chain A residue  943 LYS
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 92
   random chunks:
   chunk 35 optimal weight:    0.9990
   chunk 55 optimal weight:    0.9980
   chunk 20 optimal weight:    0.9990
   chunk 45 optimal weight:    2.9990
   chunk 51 optimal weight:    0.8980
   chunk 42 optimal weight:    0.9990
   chunk 78 optimal weight:    1.9990
   chunk 19 optimal weight:    0.9980
   chunk 87 optimal weight:    0.6980
   chunk 3 optimal weight:    0.5980
   chunk 65 optimal weight:    9.9990
   overall best weight:    0.8380

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

Flipped N/Q/H residues before XYZ refinement:
A 968 ASN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4211 r_free = 0.4211 target = 0.190453 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 38)----------------|
| r_work = 0.3717 r_free = 0.3717 target = 0.139166 restraints weight = 9152.267|
|-----------------------------------------------------------------------------|
r_work (start): 0.3669 rms_B_bonded: 1.88
r_work: 0.3538 rms_B_bonded: 2.78 restraints_weight: 0.5000
r_work: 0.3412 rms_B_bonded: 4.32 restraints_weight: 0.2500
r_work (final): 0.3412
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3401
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3401 r_free = 0.3401    target_work(ls_wunit_k1) = 0.115         |
| occupancies: max = 1.00  min = 0.40   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3401 r_free = 0.3401    target_work(ls_wunit_k1) = 0.115         |
| occupancies: max = 1.00  min = 0.38   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.3401
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8034
moved from start:          0.2910

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.041   8777  Z= 0.126
  Angle     :  0.606   7.746  12093  Z= 0.285
  Chirality :  0.041   0.352   1441
  Planarity :  0.004   0.042   1339
  Dihedral  : 10.437 169.193   3198
  Min Nonbonded Distance : 2.234

Molprobity Statistics.
  All-atom Clashscore : 4.63
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.31 %
    Favored  : 98.69 %
  Rotamer:
    Outliers :  2.09 %
    Allowed  : 11.06 %
    Favored  : 86.86 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.50 %
    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:  2.04 (0.28), residues: 919
  helix:  2.17 (0.22), residues: 566
  sheet:  0.85 (0.90), residues: 29
  loop : -0.04 (0.36), residues: 324

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARG A 962 
 TYR   0.011   0.001   TYR A 545 
 PHE   0.017   0.001   PHE A 608 
 TRP   0.013   0.001   TRP A 650 
 HIS   0.002   0.000   HIS A 428 

Details of bonding type rmsd
  covalent geometry    : bond        0.00278 ( 8764)
  covalent geometry    : angle       0.59972 (12062)
  SS BOND              : bond        0.00341 (    8)
  SS BOND              : angle       0.80275 (   16)
  hydrogen bonds       : bond        0.04949 (  441)
  hydrogen bonds       : angle       4.34137 ( 1287)
  link_NAG-ASN         : bond        0.00924 (    5)
  link_NAG-ASN         : angle       2.57553 (   15)

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

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

  1838 Ramachandran restraints generated.
    919 Oldfield, 0 Emsley, 919 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1838 Ramachandran restraints generated.
    919 Oldfield, 0 Emsley, 919 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  108 residues out of total 812 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 17
    poor density    : 91
  time to evaluate  : 0.296 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  194 MET cc_start: 0.7297 (mtp) cc_final: 0.6567 (mmp)
REVERT: A  223 GLU cc_start: 0.8214 (tt0) cc_final: 0.7560 (pm20)
REVERT: A  340 GLN cc_start: 0.7403 (tt0) cc_final: 0.7024 (tt0)
REVERT: A  363 ARG cc_start: 0.7392 (mpt90) cc_final: 0.7086 (mtt-85)
REVERT: A  515 LEU cc_start: 0.7908 (mt) cc_final: 0.7653 (tt)
REVERT: A  700 SER cc_start: 0.8017 (t) cc_final: 0.7507 (m)
REVERT: A  701 ARG cc_start: 0.7320 (mmt90) cc_final: 0.6777 (tpm170)
REVERT: A  745 LEU cc_start: 0.8062 (OUTLIER) cc_final: 0.7414 (pt)
REVERT: A  887 CYS cc_start: 0.7488 (m) cc_final: 0.7088 (m)
REVERT: A  937 LYS cc_start: 0.7978 (OUTLIER) cc_final: 0.7338 (mmpt)
REVERT: A  943 LYS cc_start: 0.8124 (OUTLIER) cc_final: 0.7587 (tptt)
  outliers start: 17
  outliers final: 7
  residues processed: 99
  average time/residue: 0.5751
  time to fit residues: 60.6807
Evaluate side-chains
  97 residues out of total 812 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 87
  time to evaluate  : 0.283 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  190 VAL
Chi-restraints excluded: chain A residue  306 SER
Chi-restraints excluded: chain A residue  336 SER
Chi-restraints excluded: chain A residue  341 ARG
Chi-restraints excluded: chain A residue  475 ASN
Chi-restraints excluded: chain A residue  745 LEU
Chi-restraints excluded: chain A residue  792 SER
Chi-restraints excluded: chain A residue  851 ILE
Chi-restraints excluded: chain A residue  937 LYS
Chi-restraints excluded: chain A residue  943 LYS
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 92
   random chunks:
   chunk 89 optimal weight:    0.6980
   chunk 21 optimal weight:    0.1980
   chunk 51 optimal weight:    1.9990
   chunk 34 optimal weight:    0.4980
   chunk 19 optimal weight:    0.9980
   chunk 2 optimal weight:    1.9990
   chunk 20 optimal weight:    2.9990
   chunk 70 optimal weight:    0.8980
   chunk 9 optimal weight:    6.9990
   chunk 86 optimal weight:    1.9990
   chunk 49 optimal weight:    0.2980
   overall best weight:    0.5180

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

Flipped N/Q/H residues before XYZ refinement:
A 968 ASN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4230 r_free = 0.4230 target = 0.192608 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 44)----------------|
| r_work = 0.3756 r_free = 0.3756 target = 0.141964 restraints weight = 10919.548|
|-----------------------------------------------------------------------------|
r_work (start): 0.3702 rms_B_bonded: 1.98
r_work: 0.3548 rms_B_bonded: 3.09 restraints_weight: 0.5000
r_work: 0.3419 rms_B_bonded: 4.84 restraints_weight: 0.2500
r_work (final): 0.3419
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3390
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3390 r_free = 0.3390    target_work(ls_wunit_k1) = 0.115         |
| occupancies: max = 1.00  min = 0.38   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3390 r_free = 0.3390    target_work(ls_wunit_k1) = 0.115         |
| occupancies: max = 1.00  min = 0.36   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.3390
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8030
moved from start:          0.3124

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.040   8777  Z= 0.109
  Angle     :  0.573   8.971  12093  Z= 0.269
  Chirality :  0.040   0.339   1441
  Planarity :  0.004   0.043   1339
  Dihedral  : 10.176 168.126   3198
  Min Nonbonded Distance : 2.267

Molprobity Statistics.
  All-atom Clashscore : 4.92
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.31 %
    Favored  : 98.69 %
  Rotamer:
    Outliers :  1.35 %
    Allowed  : 11.67 %
    Favored  : 86.98 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.50 %
    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:  2.16 (0.29), residues: 919
  helix:  2.29 (0.22), residues: 566
  sheet:  0.91 (0.92), residues: 29
  loop : -0.04 (0.36), residues: 324

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARG A 962 
 TYR   0.011   0.001   TYR A 545 
 PHE   0.012   0.001   PHE A 608 
 TRP   0.013   0.001   TRP A 650 
 HIS   0.001   0.000   HIS A 428 

Details of bonding type rmsd
  covalent geometry    : bond        0.00231 ( 8764)
  covalent geometry    : angle       0.56695 (12062)
  SS BOND              : bond        0.00317 (    8)
  SS BOND              : angle       0.69195 (   16)
  hydrogen bonds       : bond        0.04338 (  441)
  hydrogen bonds       : angle       4.24355 ( 1287)
  link_NAG-ASN         : bond        0.00864 (    5)
  link_NAG-ASN         : angle       2.40270 (   15)

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

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

  1838 Ramachandran restraints generated.
    919 Oldfield, 0 Emsley, 919 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1838 Ramachandran restraints generated.
    919 Oldfield, 0 Emsley, 919 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  107 residues out of total 812 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 96
  time to evaluate  : 0.224 
Fit side-chains
REVERT: A  194 MET cc_start: 0.7421 (mtp) cc_final: 0.6695 (mmp)
REVERT: A  223 GLU cc_start: 0.8200 (tt0) cc_final: 0.7551 (pm20)
REVERT: A  363 ARG cc_start: 0.7405 (mpt90) cc_final: 0.7103 (mtt-85)
REVERT: A  515 LEU cc_start: 0.7851 (mt) cc_final: 0.7637 (tt)
REVERT: A  700 SER cc_start: 0.8029 (t) cc_final: 0.7521 (m)
REVERT: A  701 ARG cc_start: 0.7367 (mmt90) cc_final: 0.6796 (tpm170)
REVERT: A  887 CYS cc_start: 0.7494 (m) cc_final: 0.7064 (m)
REVERT: A  937 LYS cc_start: 0.7957 (OUTLIER) cc_final: 0.7321 (mmpt)
REVERT: A  943 LYS cc_start: 0.8185 (OUTLIER) cc_final: 0.7645 (tptt)
  outliers start: 11
  outliers final: 6
  residues processed: 102
  average time/residue: 0.5383
  time to fit residues: 58.6408
Evaluate side-chains
  95 residues out of total 812 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 8
    poor density    : 87
  time to evaluate  : 0.298 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  190 VAL
Chi-restraints excluded: chain A residue  306 SER
Chi-restraints excluded: chain A residue  341 ARG
Chi-restraints excluded: chain A residue  792 SER
Chi-restraints excluded: chain A residue  848 SER
Chi-restraints excluded: chain A residue  851 ILE
Chi-restraints excluded: chain A residue  937 LYS
Chi-restraints excluded: chain A residue  943 LYS
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 92
   random chunks:
   chunk 55 optimal weight:    0.8980
   chunk 38 optimal weight:    0.0270
   chunk 17 optimal weight:    6.9990
   chunk 86 optimal weight:    3.9990
   chunk 88 optimal weight:    0.5980
   chunk 40 optimal weight:    0.8980
   chunk 24 optimal weight:    6.9990
   chunk 35 optimal weight:    0.4980
   chunk 10 optimal weight:    0.6980
   chunk 31 optimal weight:    0.7980
   chunk 56 optimal weight:    1.9990
   overall best weight:    0.5238

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

Flipped N/Q/H residues before XYZ refinement:
A 260 GLN
A 968 ASN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4230 r_free = 0.4230 target = 0.192449 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 34)----------------|
| r_work = 0.3754 r_free = 0.3754 target = 0.141686 restraints weight = 11196.518|
|-----------------------------------------------------------------------------|
r_work (start): 0.3699 rms_B_bonded: 2.04
r_work: 0.3546 rms_B_bonded: 3.08 restraints_weight: 0.5000
r_work: 0.3423 rms_B_bonded: 4.74 restraints_weight: 0.2500
r_work (final): 0.3423
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3395
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3395 r_free = 0.3395    target_work(ls_wunit_k1) = 0.115         |
| occupancies: max = 1.00  min = 0.36   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3395 r_free = 0.3395    target_work(ls_wunit_k1) = 0.115         |
| occupancies: max = 1.00  min = 0.35   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.3395
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8029
moved from start:          0.3193

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.044   8777  Z= 0.112
  Angle     :  0.592   9.188  12093  Z= 0.277
  Chirality :  0.040   0.328   1441
  Planarity :  0.004   0.044   1339
  Dihedral  : 10.052 167.253   3198
  Min Nonbonded Distance : 2.263

Molprobity Statistics.
  All-atom Clashscore : 5.33
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.42 %
    Favored  : 98.58 %
  Rotamer:
    Outliers :  1.47 %
    Allowed  : 11.79 %
    Favored  : 86.73 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.50 %
    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:  2.14 (0.29), residues: 919
  helix:  2.31 (0.22), residues: 566
  sheet:  0.87 (0.91), residues: 29
  loop : -0.11 (0.36), residues: 324

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARG A 754 
 TYR   0.011   0.001   TYR A 545 
 PHE   0.013   0.001   PHE A 608 
 TRP   0.013   0.001   TRP A 650 
 HIS   0.001   0.000   HIS A 428 

Details of bonding type rmsd
  covalent geometry    : bond        0.00241 ( 8764)
  covalent geometry    : angle       0.58526 (12062)
  SS BOND              : bond        0.00425 (    8)
  SS BOND              : angle       1.31646 (   16)
  hydrogen bonds       : bond        0.04382 (  441)
  hydrogen bonds       : angle       4.24483 ( 1287)
  link_NAG-ASN         : bond        0.00830 (    5)
  link_NAG-ASN         : angle       2.35372 (   15)

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

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

  1838 Ramachandran restraints generated.
    919 Oldfield, 0 Emsley, 919 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1838 Ramachandran restraints generated.
    919 Oldfield, 0 Emsley, 919 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  99 residues out of total 812 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 87
  time to evaluate  : 0.198 
Fit side-chains
REVERT: A  194 MET cc_start: 0.7454 (mtp) cc_final: 0.6737 (mmp)
REVERT: A  223 GLU cc_start: 0.8216 (tt0) cc_final: 0.7582 (pm20)
REVERT: A  363 ARG cc_start: 0.7381 (mpt90) cc_final: 0.7081 (mtt-85)
REVERT: A  515 LEU cc_start: 0.7855 (mt) cc_final: 0.7643 (tt)
REVERT: A  700 SER cc_start: 0.7962 (t) cc_final: 0.7459 (m)
REVERT: A  701 ARG cc_start: 0.7400 (mmt90) cc_final: 0.6806 (tpm170)
REVERT: A  825 ILE cc_start: 0.7542 (OUTLIER) cc_final: 0.7298 (mm)
REVERT: A  887 CYS cc_start: 0.7544 (m) cc_final: 0.7136 (m)
REVERT: A  937 LYS cc_start: 0.7954 (OUTLIER) cc_final: 0.7334 (mmpt)
REVERT: A  943 LYS cc_start: 0.8206 (OUTLIER) cc_final: 0.7664 (tptt)
  outliers start: 12
  outliers final: 5
  residues processed: 94
  average time/residue: 0.4878
  time to fit residues: 49.2169
Evaluate side-chains
  95 residues out of total 812 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 8
    poor density    : 87
  time to evaluate  : 0.280 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  306 SER
Chi-restraints excluded: chain A residue  792 SER
Chi-restraints excluded: chain A residue  825 ILE
Chi-restraints excluded: chain A residue  848 SER
Chi-restraints excluded: chain A residue  851 ILE
Chi-restraints excluded: chain A residue  937 LYS
Chi-restraints excluded: chain A residue  943 LYS
Chi-restraints excluded: chain A residue 1008 LEU
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 92
   random chunks:
   chunk 66 optimal weight:    2.9990
   chunk 32 optimal weight:    0.6980
   chunk 34 optimal weight:    0.7980
   chunk 74 optimal weight:    0.9980
   chunk 81 optimal weight:    0.0070
   chunk 6 optimal weight:    2.9990
   chunk 0 optimal weight:   10.0000
   chunk 14 optimal weight:    0.7980
   chunk 33 optimal weight:    0.6980
   chunk 43 optimal weight:    0.8980
   chunk 61 optimal weight:    0.9990
   overall best weight:    0.5998

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

Flipped N/Q/H residues before XYZ refinement:
A 860 ASN
A 968 ASN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4225 r_free = 0.4225 target = 0.192319 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 34)----------------|
| r_work = 0.3746 r_free = 0.3746 target = 0.140915 restraints weight = 11331.517|
|-----------------------------------------------------------------------------|
r_work (start): 0.3678 rms_B_bonded: 2.14
r_work: 0.3520 rms_B_bonded: 3.23 restraints_weight: 0.5000
r_work: 0.3395 rms_B_bonded: 5.00 restraints_weight: 0.2500
r_work (final): 0.3395
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3367
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3367 r_free = 0.3367    target_work(ls_wunit_k1) = 0.113         |
| occupancies: max = 1.00  min = 0.35   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3367 r_free = 0.3367    target_work(ls_wunit_k1) = 0.113         |
| occupancies: max = 1.00  min = 0.35   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.3367
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8060
moved from start:          0.3245

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.041   8777  Z= 0.114
  Angle     :  0.586   9.314  12093  Z= 0.275
  Chirality :  0.040   0.325   1441
  Planarity :  0.004   0.044   1339
  Dihedral  :  9.944 164.834   3198
  Min Nonbonded Distance : 2.254

Molprobity Statistics.
  All-atom Clashscore : 4.92
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.31 %
    Favored  : 98.69 %
  Rotamer:
    Outliers :  1.23 %
    Allowed  : 12.29 %
    Favored  : 86.49 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.50 %
    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:  2.10 (0.29), residues: 919
  helix:  2.30 (0.22), residues: 566
  sheet:  0.92 (0.91), residues: 29
  loop : -0.19 (0.36), residues: 324

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARG A 962 
 TYR   0.011   0.001   TYR A 545 
 PHE   0.014   0.001   PHE A 608 
 TRP   0.013   0.001   TRP A 650 
 HIS   0.001   0.000   HIS A 428 

Details of bonding type rmsd
  covalent geometry    : bond        0.00244 ( 8764)
  covalent geometry    : angle       0.58012 (12062)
  SS BOND              : bond        0.00380 (    8)
  SS BOND              : angle       0.85789 (   16)
  hydrogen bonds       : bond        0.04551 (  441)
  hydrogen bonds       : angle       4.26986 ( 1287)
  link_NAG-ASN         : bond        0.00797 (    5)
  link_NAG-ASN         : angle       2.33818 (   15)

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

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

  1838 Ramachandran restraints generated.
    919 Oldfield, 0 Emsley, 919 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1838 Ramachandran restraints generated.
    919 Oldfield, 0 Emsley, 919 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  101 residues out of total 812 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 91
  time to evaluate  : 0.314 
Fit side-chains
REVERT: A  194 MET cc_start: 0.7447 (mtp) cc_final: 0.6719 (mmp)
REVERT: A  223 GLU cc_start: 0.8238 (tt0) cc_final: 0.7595 (pm20)
REVERT: A  363 ARG cc_start: 0.7345 (mpt90) cc_final: 0.7030 (mtt-85)
REVERT: A  515 LEU cc_start: 0.7873 (mt) cc_final: 0.7648 (tt)
REVERT: A  700 SER cc_start: 0.7934 (t) cc_final: 0.7423 (m)
REVERT: A  701 ARG cc_start: 0.7365 (mmt90) cc_final: 0.6786 (tpm170)
REVERT: A  825 ILE cc_start: 0.7539 (OUTLIER) cc_final: 0.7281 (mm)
REVERT: A  887 CYS cc_start: 0.7583 (m) cc_final: 0.7157 (m)
REVERT: A  937 LYS cc_start: 0.7915 (OUTLIER) cc_final: 0.7299 (mmpt)
REVERT: A  943 LYS cc_start: 0.8215 (OUTLIER) cc_final: 0.7676 (tptt)
REVERT: A 1096 MET cc_start: 0.8406 (mmm) cc_final: 0.8188 (mmp)
  outliers start: 10
  outliers final: 5
  residues processed: 97
  average time/residue: 0.4623
  time to fit residues: 48.3844
Evaluate side-chains
  97 residues out of total 812 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 8
    poor density    : 89
  time to evaluate  : 0.277 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  306 SER
Chi-restraints excluded: chain A residue  792 SER
Chi-restraints excluded: chain A residue  825 ILE
Chi-restraints excluded: chain A residue  848 SER
Chi-restraints excluded: chain A residue  851 ILE
Chi-restraints excluded: chain A residue  937 LYS
Chi-restraints excluded: chain A residue  943 LYS
Chi-restraints excluded: chain A residue 1008 LEU
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 92
   random chunks:
   chunk 78 optimal weight:    1.9990
   chunk 59 optimal weight:    6.9990
   chunk 73 optimal weight:    0.8980
   chunk 36 optimal weight:    0.5980
   chunk 91 optimal weight:    0.9980
   chunk 9 optimal weight:    0.0870
   chunk 81 optimal weight:    0.2980
   chunk 75 optimal weight:    0.9990
   chunk 48 optimal weight:    3.9990
   chunk 32 optimal weight:    2.9990
   chunk 8 optimal weight:    4.9990
   overall best weight:    0.5758

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

Flipped N/Q/H residues before XYZ refinement:
A 968 ASN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4227 r_free = 0.4227 target = 0.192474 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 34)----------------|
| r_work = 0.3750 r_free = 0.3750 target = 0.141801 restraints weight = 12712.656|
|-----------------------------------------------------------------------------|
r_work (start): 0.3696 rms_B_bonded: 2.02
r_work: 0.3540 rms_B_bonded: 3.12 restraints_weight: 0.5000
r_work: 0.3411 rms_B_bonded: 4.91 restraints_weight: 0.2500
r_work (final): 0.3411
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3381
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3381 r_free = 0.3381    target_work(ls_wunit_k1) = 0.114         |
| occupancies: max = 1.00  min = 0.35   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3381 r_free = 0.3381    target_work(ls_wunit_k1) = 0.114         |
| occupancies: max = 1.00  min = 0.35   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.3381
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8104
moved from start:          0.3288

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.050   8777  Z= 0.113
  Angle     :  0.585   9.454  12093  Z= 0.274
  Chirality :  0.040   0.320   1441
  Planarity :  0.004   0.044   1339
  Dihedral  :  9.896 165.045   3198
  Min Nonbonded Distance : 2.257

Molprobity Statistics.
  All-atom Clashscore : 4.98
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.53 %
    Favored  : 98.47 %
  Rotamer:
    Outliers :  1.11 %
    Allowed  : 13.02 %
    Favored  : 85.87 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.50 %
    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:  2.11 (0.29), residues: 919
  helix:  2.31 (0.22), residues: 566
  sheet:  0.98 (0.90), residues: 29
  loop : -0.19 (0.36), residues: 324

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARG A 962 
 TYR   0.011   0.001   TYR A 545 
 PHE   0.013   0.001   PHE A 608 
 TRP   0.013   0.001   TRP A 650 
 HIS   0.001   0.000   HIS A 428 

Details of bonding type rmsd
  covalent geometry    : bond        0.00243 ( 8764)
  covalent geometry    : angle       0.57865 (12062)
  SS BOND              : bond        0.00358 (    8)
  SS BOND              : angle       0.88181 (   16)
  hydrogen bonds       : bond        0.04457 (  441)
  hydrogen bonds       : angle       4.25386 ( 1287)
  link_NAG-ASN         : bond        0.00779 (    5)
  link_NAG-ASN         : angle       2.32214 (   15)

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

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

  1838 Ramachandran restraints generated.
    919 Oldfield, 0 Emsley, 919 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1838 Ramachandran restraints generated.
    919 Oldfield, 0 Emsley, 919 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  96 residues out of total 812 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 9
    poor density    : 87
  time to evaluate  : 0.278 
Fit side-chains
REVERT: A  194 MET cc_start: 0.7551 (mtp) cc_final: 0.6856 (mmp)
REVERT: A  223 GLU cc_start: 0.8234 (tt0) cc_final: 0.7656 (pm20)
REVERT: A  363 ARG cc_start: 0.7335 (mpt90) cc_final: 0.7020 (mtt-85)
REVERT: A  515 LEU cc_start: 0.7953 (mt) cc_final: 0.7747 (tt)
REVERT: A  700 SER cc_start: 0.8006 (t) cc_final: 0.7509 (m)
REVERT: A  701 ARG cc_start: 0.7393 (mmt90) cc_final: 0.6854 (tpm170)
REVERT: A  825 ILE cc_start: 0.7603 (OUTLIER) cc_final: 0.7338 (mm)
REVERT: A  887 CYS cc_start: 0.7600 (m) cc_final: 0.7218 (m)
REVERT: A  937 LYS cc_start: 0.7931 (OUTLIER) cc_final: 0.7352 (mmpt)
REVERT: A  943 LYS cc_start: 0.8272 (OUTLIER) cc_final: 0.7756 (tptt)
REVERT: A 1096 MET cc_start: 0.8428 (mmm) cc_final: 0.8224 (mmp)
  outliers start: 9
  outliers final: 5
  residues processed: 92
  average time/residue: 0.4708
  time to fit residues: 46.6022
Evaluate side-chains
  95 residues out of total 812 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 8
    poor density    : 87
  time to evaluate  : 0.293 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  306 SER
Chi-restraints excluded: chain A residue  792 SER
Chi-restraints excluded: chain A residue  825 ILE
Chi-restraints excluded: chain A residue  848 SER
Chi-restraints excluded: chain A residue  851 ILE
Chi-restraints excluded: chain A residue  937 LYS
Chi-restraints excluded: chain A residue  943 LYS
Chi-restraints excluded: chain A residue 1008 LEU
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 92
   random chunks:
   chunk 67 optimal weight:    3.9990
   chunk 45 optimal weight:    2.9990
   chunk 82 optimal weight:    2.9990
   chunk 12 optimal weight:    3.9990
   chunk 42 optimal weight:    0.9990
   chunk 46 optimal weight:    1.9990
   chunk 33 optimal weight:    2.9990
   chunk 86 optimal weight:    0.8980
   chunk 32 optimal weight:    1.9990
   chunk 90 optimal weight:    1.9990
   chunk 6 optimal weight:    2.9990
   overall best weight:    1.5788

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

Flipped N/Q/H residues before XYZ refinement:
A 968 ASN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4187 r_free = 0.4187 target = 0.187868 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 33)----------------|
| r_work = 0.3643 r_free = 0.3643 target = 0.133194 restraints weight = 16585.369|
|-----------------------------------------------------------------------------|
r_work (start): 0.3603 rms_B_bonded: 2.49
r_work: 0.3428 rms_B_bonded: 3.66 restraints_weight: 0.5000
r_work (final): 0.3428
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3397
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3397 r_free = 0.3397    target_work(ls_wunit_k1) = 0.116         |
| occupancies: max = 1.00  min = 0.35   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3397 r_free = 0.3397    target_work(ls_wunit_k1) = 0.116         |
| occupancies: max = 1.00  min = 0.38   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.3397
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8018
moved from start:          0.3088

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.044   8777  Z= 0.175
  Angle     :  0.679  10.693  12093  Z= 0.321
  Chirality :  0.044   0.329   1441
  Planarity :  0.004   0.043   1339
  Dihedral  : 10.448 164.026   3198
  Min Nonbonded Distance : 2.194

Molprobity Statistics.
  All-atom Clashscore : 4.63
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.63 %
    Favored  : 98.37 %
  Rotamer:
    Outliers :  1.23 %
    Allowed  : 12.90 %
    Favored  : 85.87 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.50 %
    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:  1.79 (0.28), residues: 919
  helix:  2.05 (0.22), residues: 568
  sheet:  0.93 (0.86), residues: 29
  loop : -0.34 (0.35), residues: 322

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.006   0.001   ARG A 754 
 TYR   0.015   0.002   TYR A 619 
 PHE   0.021   0.002   PHE A 608 
 TRP   0.012   0.001   TRP A 650 
 HIS   0.003   0.001   HIS A 332 

Details of bonding type rmsd
  covalent geometry    : bond        0.00413 ( 8764)
  covalent geometry    : angle       0.67287 (12062)
  SS BOND              : bond        0.00435 (    8)
  SS BOND              : angle       1.10443 (   16)
  hydrogen bonds       : bond        0.06033 (  441)
  hydrogen bonds       : angle       4.51643 ( 1287)
  link_NAG-ASN         : bond        0.00841 (    5)
  link_NAG-ASN         : angle       2.46649 (   15)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 4197.76 seconds
wall clock time: 71 minutes 49.17 seconds (4309.17 seconds total)