Starting phenix.real_space_refine
on Tue Aug  4 21:31:37 2026 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/8y9l_39082/08_2026/8y9l_39082.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/8y9l_39082/08_2026/8y9l_39082.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=3.0
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/cci-nas-00/data/ceres_data/8y9l_39082/08_2026/8y9l_39082.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/8y9l_39082/08_2026/8y9l_39082.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/8y9l_39082/08_2026/8y9l_39082.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/8y9l_39082/08_2026/8y9l_39082.cif"
  }
  resolution = 3.0
  write_initial_geo_file = False
  refinement {
    macro_cycles = 10
  }


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

Validating inputs
Origin is already at (0, 0, 0), no shifts will be applied
-------------------------------------------------------------------------------
Processing inputs
*****************
Set random seed
  Set to: 0
Set model cs if undefined
Decide on map wrapping
  Map wrapping is set to: False
Normalize map: mean=0, sd=1
  Input map: mean=   0.000 sd=   0.077
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: 6
    Type Number    sf(0)   Gaussians
     P      41      5.49       5
     Mg      1      5.21       5
     S      25      5.16       5
     C    4299      2.51       5
     N    1241      2.21       5
     O    1401      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 21 residue(s): 0.01s

  Monomer Library directory:
    "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.2rc3-6140/lib/python3.11/site-packages/chem_data/mon_lib"
  Total number of atoms: 7008
  Number of models: 1
  Model: ""
    Number of chains: 3
    Chain: "A"
      Number of atoms: 6127
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 757, 6127
          Classifications: {'peptide': 757}
          Link IDs: {'PTRANS': 26, 'TRANS': 730}
          Chain breaks: 5
    Chain: "B"
      Number of atoms: 880
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 41, 880
          Classifications: {'RNA': 41}
          Modifications used: {'rna2p_pur': 3, 'rna2p_pyr': 2, 'rna3p_pur': 20, 'rna3p_pyr': 16}
          Link IDs: {'rna2p': 4, 'rna3p': 36}
    Chain: "A"
      Number of atoms: 1
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 1, 1
          Unusual residues: {' MG': 1}
          Classifications: {'undetermined': 1}
  Time building chain proxies: 1.75, per 1000 atoms: 0.25
  Number of scatterers: 7008
  At special positions: 0
  Unit cell: (86.355, 98.325, 101.745, 90, 90, 90)
  Space group: P 1 (No. 1)
  Number of sites at special positions: 0
  Number of scattering types: 6
    Type Number    sf(0)
     S      25     16.00
     P      41     15.00
     Mg      1     11.99
     O    1401      8.00
     N    1241      7.00
     C    4299      6.00
    sf(0) = scattering factor at diffraction angle 0.

  Number of disulfides: simple=0, symmetry=0

  Automatic linking
    Parameters for automatic linking
      Linking & cutoffs
        Metal                : Auto  - 3.00
        Amino acid           : True  - 1.90
        Carbohydrate         : True  - 1.99
        Ligands              : True  - 1.99
        Small molecules      : False - 1.98
        Amino acid - RNA/DNA : False
      
  Number of custom bonds: simple=0, symmetry=0
  Time building additional restraints: 0.63
  Conformation dependent library (CDL) restraints added in 306.8 milliseconds
  

  1490 Ramachandran restraints generated.
    745 Oldfield, 0 Emsley, 745 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  1418

  Finding SS restraints...
    Secondary structure from input PDB file:
      25 helices and 6 sheets defined
      47.0% alpha, 12.3% beta
      8 base pairs and 25 stacking pairs defined.
    Time for finding SS restraints: 0.47
  Creating SS restraints...
    Processing helix  chain 'A' and resid 20 through 42
      removed outlier: 3.667A  pdb=" N   TRP A  24 " --> pdb=" O   SER A  20 " (cutoff:3.500A)
      removed outlier: 3.894A  pdb=" N   SER A  37 " --> pdb=" O   LYS A  33 " (cutoff:3.500A)
      removed outlier: 3.888A  pdb=" N   LEU A  38 " --> pdb=" O   LYS A  34 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 49 through 53
      removed outlier: 3.976A  pdb=" N   ASP A  52 " --> pdb=" O   ALA A  49 " (cutoff:3.500A)
      removed outlier: 3.709A  pdb=" N   ASP A  53 " --> pdb=" O   ARG A  50 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'A' and resid 49 through 53'
    Processing helix  chain 'A' and resid 59 through 72
    Processing helix  chain 'A' and resid 74 through 88
      removed outlier: 3.588A  pdb=" N   ALA A  78 " --> pdb=" O   ALA A  74 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 89 through 94
      removed outlier: 3.801A  pdb=" N   SER A  94 " --> pdb=" O   ALA A  90 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 175 through 184
      removed outlier: 3.776A  pdb=" N   LEU A 179 " --> pdb=" O   LEU A 175 " (cutoff:3.500A)
      removed outlier: 3.801A  pdb=" N   ARG A 180 " --> pdb=" O   GLY A 176 " (cutoff:3.500A)
      removed outlier: 3.880A  pdb=" N   GLU A 181 " --> pdb=" O   LYS A 177 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 192 through 230
      removed outlier: 3.594A  pdb=" N   HIS A 210 " --> pdb=" O   GLN A 206 " (cutoff:3.500A)
      removed outlier: 3.637A  pdb=" N   GLU A 212 " --> pdb=" O   ARG A 208 " (cutoff:3.500A)
      removed outlier: 4.333A  pdb=" N   THR A 213 " --> pdb=" O   SER A 209 " (cutoff:3.500A)
      removed outlier: 3.766A  pdb=" N   VAL A 228 " --> pdb=" O   MET A 224 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 233 through 249
    Processing helix  chain 'A' and resid 254 through 266
      removed outlier: 3.913A  pdb=" N   LEU A 266 " --> pdb=" O   VAL A 262 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 276 through 282
    Processing helix  chain 'A' and resid 284 through 286
      No H-bonds generated for 'chain 'A' and resid 284 through 286'
    Processing helix  chain 'A' and resid 287 through 292
      removed outlier: 3.687A  pdb=" N   LEU A 291 " --> pdb=" O   PHE A 287 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 294 through 314
      removed outlier: 3.764A  pdb=" N   LYS A 299 " --> pdb=" O   TRP A 295 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 432 through 441
    Processing helix  chain 'A' and resid 448 through 455
      removed outlier: 3.627A  pdb=" N   ILE A 452 " --> pdb=" O   ASP A 448 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 508 through 511
    Processing helix  chain 'A' and resid 512 through 537
      removed outlier: 3.925A  pdb=" N   SER A 516 " --> pdb=" O   GLY A 512 " (cutoff:3.500A)
      removed outlier: 4.001A  pdb=" N   LEU A 517 " --> pdb=" O   GLU A 513 " (cutoff:3.500A)
      removed outlier: 4.519A  pdb=" N   LYS A 518 " --> pdb=" O   LEU A 514 " (cutoff:3.500A)
      removed outlier: 3.776A  pdb=" N   ALA A 533 " --> pdb=" O   LYS A 529 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 542 through 550
    Processing helix  chain 'A' and resid 560 through 584
      removed outlier: 3.786A  pdb=" N   GLN A 564 " --> pdb=" O   ARG A 560 " (cutoff:3.500A)
      removed outlier: 4.214A  pdb=" N   ARG A 566 " --> pdb=" O   MET A 562 " (cutoff:3.500A)
      removed outlier: 4.085A  pdb=" N   ASP A 569 " --> pdb=" O   SER A 565 " (cutoff:3.500A)
      removed outlier: 3.869A  pdb=" N   ARG A 572 " --> pdb=" O   ALA A 568 " (cutoff:3.500A)
      removed outlier: 3.942A  pdb=" N   GLU A 584 " --> pdb=" O   GLN A 580 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 591 through 610
      removed outlier: 3.773A  pdb=" N   LEU A 595 " --> pdb=" O   GLU A 591 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 632 through 649
      removed outlier: 3.801A  pdb=" N   TYR A 648 " --> pdb=" O   THR A 644 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 680 through 692
      removed outlier: 3.584A  pdb=" N   LEU A 684 " --> pdb=" O   ARG A 680 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 739 through 753
    Processing helix  chain 'A' and resid 779 through 790
    Processing helix  chain 'A' and resid 831 through 847
    Processing sheet with id=AA1, first strand: chain 'A' and resid 5 through 8
      removed outlier: 4.584A  pdb=" N   SER A 429 " --> pdb=" O   GLU A 404 " (cutoff:3.500A)
      removed outlier: 7.346A  pdb=" N   GLU A 404 " --> pdb=" O   SER A 429 " (cutoff:3.500A)
      removed outlier: 3.503A  pdb=" N   ARG A 377 " --> pdb=" O   HIS A 374 " (cutoff:3.500A)
    Processing sheet with id=AA2, first strand: chain 'A' and resid 329 through 332
      removed outlier: 4.919A  pdb=" N   PHE A 420 " --> pdb=" O   ILE A  14 " (cutoff:3.500A)
      removed outlier: 6.579A  pdb=" N   PHE A 359 " --> pdb=" O   LYS A  15 " (cutoff:3.500A)
      removed outlier: 4.448A  pdb=" N   TYR A  17 " --> pdb=" O   LYS A 357 " (cutoff:3.500A)
      removed outlier: 6.488A  pdb=" N   LYS A 357 " --> pdb=" O   TYR A  17 " (cutoff:3.500A)
      removed outlier: 3.856A  pdb=" N   GLY A 356 " --> pdb=" O   LEU A 352 " (cutoff:3.500A)
      removed outlier: 3.509A  pdb=" N   VAL A 349 " --> pdb=" O   GLU A 342 " (cutoff:3.500A)
      removed outlier: 3.518A  pdb=" N   GLU A 342 " --> pdb=" O   VAL A 349 " (cutoff:3.500A)
    Processing sheet with id=AA3, first strand: chain 'A' and resid 487 through 489
      removed outlier: 4.064A  pdb=" N   TYR A 494 " --> pdb=" O   GLY A 480 " (cutoff:3.500A)
      removed outlier: 6.938A  pdb=" N   VAL A 460 " --> pdb=" O   ILE A 654 " (cutoff:3.500A)
      removed outlier: 8.728A  pdb=" N   PHE A 656 " --> pdb=" O   VAL A 460 " (cutoff:3.500A)
      removed outlier: 7.100A  pdb=" N   GLY A 462 " --> pdb=" O   PHE A 656 " (cutoff:3.500A)
      removed outlier: 8.988A  pdb=" N   GLU A 658 " --> pdb=" O   GLY A 462 " (cutoff:3.500A)
    Processing sheet with id=AA4, first strand: chain 'A' and resid 717 through 718
    Processing sheet with id=AA5, first strand: chain 'A' and resid 760 through 761
      removed outlier: 3.569A  pdb=" N   GLU A 827 " --> pdb=" O   HIS A 824 " (cutoff:3.500A)
    Processing sheet with id=AA6, first strand: chain 'A' and resid 796 through 800
      removed outlier: 3.747A  pdb=" N   ARG A 796 " --> pdb=" O   THR A 808 " (cutoff:3.500A)

    296 hydrogen bonds defined for protein.
    846 hydrogen bond angles defined for protein.
    Restraints generated for nucleic acids:
      19 hydrogen bonds
      34 hydrogen bond angles
      0 basepair planarities
      8 basepair parallelities
      25 stacking parallelities
  Total time for adding SS restraints: 1.03

  Time building geometry restraints manager: 0.73 seconds

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

  Histogram of bond lengths:
        1.14 -     1.27: 1042
        1.27 -     1.41: 1928
        1.41 -     1.54: 4114
        1.54 -     1.68: 115
        1.68 -     1.81: 39
  Bond restraints: 7238
  Sorted by residual:
  bond pdb=" C   PRO A   7 "
       pdb=" O   PRO A   7 "
    ideal  model  delta    sigma   weight residual
    1.233  1.135  0.098 1.13e-02 7.83e+03 7.52e+01
  bond pdb=" O3'   C B   0 "
       pdb=" P     A B   1 "
    ideal  model  delta    sigma   weight residual
    1.607  1.515  0.092 1.20e-02 6.94e+03 5.91e+01
  bond pdb=" O3'   U B   2 "
       pdb=" P     A B   3 "
    ideal  model  delta    sigma   weight residual
    1.607  1.523  0.084 1.20e-02 6.94e+03 4.95e+01
  bond pdb=" O3'   A B   1 "
       pdb=" P     U B   2 "
    ideal  model  delta    sigma   weight residual
    1.607  1.529  0.078 1.20e-02 6.94e+03 4.24e+01
  bond pdb=" P     U B   2 "
       pdb=" OP2   U B   2 "
    ideal  model  delta    sigma   weight residual
    1.485  1.376  0.109 2.00e-02 2.50e+03 2.98e+01
  ... (remaining 7233 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     4.33: 9892
        4.33 -     8.65: 47
        8.65 -    12.98: 8
       12.98 -    17.31: 3
       17.31 -    21.64: 2
  Bond angle restraints: 9952
  Sorted by residual:
  angle pdb=" CA  ILE A   6 "
        pdb=" C   ILE A   6 "
        pdb=" O   ILE A   6 "
      ideal   model   delta    sigma   weight residual
     119.15  111.19    7.96 5.90e-01 2.87e+00 1.82e+02
  angle pdb=" C   PRO A   7 "
        pdb=" CA  PRO A   7 "
        pdb=" CB  PRO A   7 "
      ideal   model   delta    sigma   weight residual
     111.46   97.82   13.64 1.21e+00 6.83e-01 1.27e+02
  angle pdb=" O5'   A B   3 "
        pdb=" C5'   A B   3 "
        pdb=" C4'   A B   3 "
      ideal   model   delta    sigma   weight residual
     109.40  117.36   -7.96 8.00e-01 1.56e+00 9.89e+01
  angle pdb=" CA  ILE A   6 "
        pdb=" C   ILE A   6 "
        pdb=" N   PRO A   7 "
      ideal   model   delta    sigma   weight residual
     119.22  125.85   -6.63 7.80e-01 1.64e+00 7.23e+01
  angle pdb=" O4'   A B   1 "
        pdb=" C1'   A B   1 "
        pdb=" C2'   A B   1 "
      ideal   model   delta    sigma   weight residual
     105.80   97.91    7.89 1.00e+00 1.00e+00 6.22e+01
  ... (remaining 9947 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    29.02: 4137
       29.02 -    58.05: 232
       58.05 -    87.07: 61
       87.07 -   116.10: 2
      116.10 -   145.12: 1
  Dihedral angle restraints: 4433
    sinusoidal: 2229
      harmonic: 2204
  Sorted by residual:
  dihedral pdb=" O4'   U B -18 "
           pdb=" C1'   U B -18 "
           pdb=" N1    U B -18 "
           pdb=" C2    U B -18 "
      ideal   model   delta sinusoidal    sigma   weight residual
     200.00   54.88  145.12     1      1.50e+01 4.44e-03 7.77e+01
  dihedral pdb=" O4'   U B   5 "
           pdb=" C1'   U B   5 "
           pdb=" N1    U B   5 "
           pdb=" C2    U B   5 "
      ideal   model   delta sinusoidal    sigma   weight residual
    -128.00  -23.43 -104.57     1      1.70e+01 3.46e-03 4.16e+01
  dihedral pdb=" C3'   U B   5 "
           pdb=" C4'   U B   5 "
           pdb=" O4'   U B   5 "
           pdb=" C1'   U B   5 "
      ideal   model   delta sinusoidal    sigma   weight residual
      -2.00   40.96  -42.96     1      8.00e+00 1.56e-02 4.02e+01
  ... (remaining 4430 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.181: 1095
       0.181 -    0.362: 15
       0.362 -    0.544: 3
       0.544 -    0.725: 0
       0.725 -    0.906: 1
  Chirality restraints: 1114
  Sorted by residual:
  chirality pdb=" C2'   A B   3 "
            pdb=" C3'   A B   3 "
            pdb=" O2'   A B   3 "
            pdb=" C1'   A B   3 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.62   -1.71   -0.91 2.00e-01 2.50e+01 2.05e+01
  chirality pdb=" CA  ILE A   6 "
            pdb=" N   ILE A   6 "
            pdb=" C   ILE A   6 "
            pdb=" CB  ILE A   6 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.43    2.96   -0.53 2.00e-01 2.50e+01 6.92e+00
  chirality pdb=" P     U B   2 "
            pdb=" OP1   U B   2 "
            pdb=" OP2   U B   2 "
            pdb=" O5'   U B   2 "
    both_signs  ideal   model   delta    sigma   weight residual
      True       2.41   -1.89    0.52 2.00e-01 2.50e+01 6.78e+00
  ... (remaining 1111 not shown)

  Planarity restraints: 1115
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  LYS A 838 "   -0.029 2.00e-02 2.50e+03   5.95e-02 3.54e+01
        pdb=" C   LYS A 838 "    0.103 2.00e-02 2.50e+03
        pdb=" O   LYS A 838 "   -0.039 2.00e-02 2.50e+03
        pdb=" N   ASP A 839 "   -0.034 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CD  ARG A 852 "   -0.430 9.50e-02 1.11e+02   1.93e-01 2.28e+01
        pdb=" NE  ARG A 852 "    0.023 2.00e-02 2.50e+03
        pdb=" CZ  ARG A 852 "    0.011 2.00e-02 2.50e+03
        pdb=" NH1 ARG A 852 "    0.002 2.00e-02 2.50e+03
        pdb=" NH2 ARG A 852 "   -0.017 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CD  ARG A 853 "   -0.330 9.50e-02 1.11e+02   1.48e-01 1.35e+01
        pdb=" NE  ARG A 853 "    0.018 2.00e-02 2.50e+03
        pdb=" CZ  ARG A 853 "    0.008 2.00e-02 2.50e+03
        pdb=" NH1 ARG A 853 "    0.002 2.00e-02 2.50e+03
        pdb=" NH2 ARG A 853 "   -0.013 2.00e-02 2.50e+03
  ... (remaining 1112 not shown)

  Histogram of nonbonded interaction distances:
        1.95 -     2.54: 48
        2.54 -     3.13: 5128
        3.13 -     3.72: 10538
        3.72 -     4.31: 15108
        4.31 -     4.90: 24814
  Nonbonded interactions: 55636
  Sorted by model distance:
  nonbonded pdb=" O2'   C B   0 "
            pdb=" OP1   U B   2 "
     model   vdw
     1.953 3.040
  nonbonded pdb=" OD2 ASP A 465 "
            pdb="MG    MG A 901 "
     model   vdw
     2.114 2.170
  nonbonded pdb=" ND1 HIS A   4 "
            pdb=" O   HIS A 430 "
     model   vdw
     2.175 3.120
  nonbonded pdb=" OD2 ASP A  31 "
            pdb=" OH  TYR A 195 "
     model   vdw
     2.185 3.040
  nonbonded pdb=" ND2 ASN A 753 "
            pdb=" O   PHE A 867 "
     model   vdw
     2.216 3.120
  ... (remaining 55631 not shown)

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

  No NCS relation were found !!!

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

Found NCS groups:
  found none.
Set up NCS constraints
  No NCS constraints will be used in refinement.
Set refine NCS operators
Adjust number of macro_cycles
  Number of macro_cycles: 10
Reset NCS operators
Extract rigid body selections
Check and reset occupancies
  Occupancies: min=1.00 max=1.00 mean=1.00
Load rotamer database and sin/cos tables
Set ADP refinement strategy
  ADPs will be refined as individual isotropic
Make a string to write initial .geo file
Internal consistency checks
Time:
  Set random seed:                         0.000
  Set model cs if undefined:               0.000
  Decide on map wrapping:                  0.000
  Normalize map: mean=0, sd=1:             1.120
  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:          0.150
  Check model and map are aligned:         0.030
  Set scattering table:                    0.020
  Process input model:                     7.810
  Find NCS groups from input model:        0.030
  Set up NCS constraints:                  0.010
  Set refine NCS operators:                0.000
  Adjust number of macro_cycles:           0.000
  Reset NCS operators:                     0.000
  Extract rigid body selections:           0.000
  Check and reset occupancies:             0.000
  Load rotamer database and sin/cos tables:7.050
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   16.230
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7753
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      :  0.006   0.109   7238  Z= 0.395
  Angle     :  0.939  21.637   9952  Z= 0.600
  Chirality :  0.068   0.906   1114
  Planarity :  0.009   0.193   1115
  Dihedral  : 17.888 145.122   3015
  Min Nonbonded Distance : 1.953

Molprobity Statistics.
  All-atom Clashscore : 10.21
  Ramachandran Plot:
    Outliers :  0.13 %
    Allowed  :  3.76 %
    Favored  : 96.11 %
  Rotamer:
    Outliers :  1.52 %
    Allowed  :  0.91 %
    Favored  : 97.57 %
  Cbeta Deviations :  0.42 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    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: -0.24 (0.30), residues: 745
  helix:  0.37 (0.28), residues: 352
  sheet:  0.03 (0.47), residues: 124
  loop : -0.81 (0.37), residues: 269

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.006   0.001   ARG A 852 
 TYR   0.014   0.001   TYR A 214 
 PHE   0.026   0.002   PHE A 785 
 TRP   0.027   0.002   TRP A 323 
 HIS   0.012   0.001   HIS A   4 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00593 /  0.39 ( 7238)
  covalent geometry    : angle       0.93925 /  0.60 ( 9952)
  hydrogen bonds       : bond        0.19183 / 13.61 (  315)
  hydrogen bonds       : angle       7.30116 /  5.17 (  880)

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

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

  1490 Ramachandran restraints generated.
    745 Oldfield, 0 Emsley, 745 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1490 Ramachandran restraints generated.
    745 Oldfield, 0 Emsley, 745 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  89 residues out of total 659 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 79
  time to evaluate  : 0.250 
Fit side-chains
REVERT: A   53 ASP cc_start: 0.7149 (m-30) cc_final: 0.6920 (t70)
REVERT: A  186 LYS cc_start: 0.8050 (ptmm) cc_final: 0.7819 (pttp)
REVERT: A  295 TRP cc_start: 0.6543 (t60) cc_final: 0.6342 (t60)
REVERT: A  399 ILE cc_start: 0.8192 (mp) cc_final: 0.7992 (mt)
  outliers start: 10
  outliers final: 6
  residues processed: 88
  average time/residue: 0.4817
  time to fit residues: 45.1007
Evaluate side-chains
  63 residues out of total 659 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 6
    poor density    : 57
  time to evaluate  : 0.269 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue    7 PRO
Chi-restraints excluded: chain A residue  703 ASP
Chi-restraints excluded: chain A residue  844 LEU
Chi-restraints excluded: chain A residue  845 VAL
Chi-restraints excluded: chain A residue  847 LYS
Chi-restraints excluded: chain A residue  853 ARG
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 79
   random chunks:
   chunk 49 optimal weight:    0.0970
   chunk 53 optimal weight:    1.9990
   chunk 5 optimal weight:    4.9990
   chunk 33 optimal weight:    3.9990
   chunk 65 optimal weight:    3.9990
   chunk 62 optimal weight:    9.9990
   chunk 51 optimal weight:    0.5980
   chunk 38 optimal weight:    4.9990
   chunk 61 optimal weight:    1.9990
   chunk 45 optimal weight:    0.5980
   chunk 74 optimal weight:    8.9990
   overall best weight:    1.0582

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
A 269 GLN
A 276 GLN
A 603 ASN
A 709 ASN

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4172 r_free = 0.4172 target = 0.191228 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 35)----------------|
| r_work = 0.3910 r_free = 0.3910 target = 0.163339 restraints weight = 8164.983|
|-----------------------------------------------------------------------------|
r_work (start): 0.3887 rms_B_bonded: 1.65
r_work: 0.3715 rms_B_bonded: 2.71 restraints_weight: 0.5000
r_work: 0.3588 rms_B_bonded: 4.59 restraints_weight: 0.2500
r_work (final): 0.3588
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8003
moved from start:          0.0971

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.026   7238  Z= 0.149
  Angle     :  0.569   7.271   9952  Z= 0.310
  Chirality :  0.041   0.229   1114
  Planarity :  0.004   0.047   1115
  Dihedral  : 17.966 149.251   1500
  Min Nonbonded Distance : 2.062

Molprobity Statistics.
  All-atom Clashscore : 7.12
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.09 %
    Favored  : 96.91 %
  Rotamer:
    Outliers :  1.82 %
    Allowed  :  7.28 %
    Favored  : 90.90 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    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:  0.17 (0.30), residues: 745
  helix:  0.79 (0.28), residues: 352
  sheet:  0.07 (0.48), residues: 119
  loop : -0.62 (0.36), residues: 274

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG A  50 
 TYR   0.013   0.001   TYR A 729 
 PHE   0.010   0.001   PHE A 531 
 TRP   0.024   0.002   TRP A 323 
 HIS   0.005   0.001   HIS A 824 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00315 /  0.15 ( 7238)
  covalent geometry    : angle       0.56861 /  0.31 ( 9952)
  hydrogen bonds       : bond        0.06392 /  4.20 (  315)
  hydrogen bonds       : angle       5.26753 /  3.71 (  880)

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

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

  1490 Ramachandran restraints generated.
    745 Oldfield, 0 Emsley, 745 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1490 Ramachandran restraints generated.
    745 Oldfield, 0 Emsley, 745 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  80 residues out of total 659 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 68
  time to evaluate  : 0.159 
Fit side-chains
REVERT: A   17 TYR cc_start: 0.8201 (OUTLIER) cc_final: 0.7916 (p90)
REVERT: A   53 ASP cc_start: 0.7535 (m-30) cc_final: 0.6659 (t70)
REVERT: A  186 LYS cc_start: 0.8224 (ptmm) cc_final: 0.7885 (pttp)
REVERT: A  295 TRP cc_start: 0.6214 (t60) cc_final: 0.5891 (t60)
REVERT: A  377 ARG cc_start: 0.7482 (ptt90) cc_final: 0.7004 (ptt-90)
REVERT: A  386 LEU cc_start: 0.8262 (OUTLIER) cc_final: 0.8003 (mp)
REVERT: A  725 GLU cc_start: 0.7121 (mt-10) cc_final: 0.6897 (mm-30)
  outliers start: 12
  outliers final: 2
  residues processed: 74
  average time/residue: 0.4457
  time to fit residues: 35.2819
Evaluate side-chains
  60 residues out of total 659 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 4
    poor density    : 56
  time to evaluate  : 0.244 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   17 TYR
Chi-restraints excluded: chain A residue  386 LEU
Chi-restraints excluded: chain A residue  678 SER
Chi-restraints excluded: chain A residue  763 THR
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 79
   random chunks:
   chunk 68 optimal weight:    7.9990
   chunk 9 optimal weight:    5.9990
   chunk 20 optimal weight:    0.6980
   chunk 22 optimal weight:    2.9990
   chunk 29 optimal weight:    3.9990
   chunk 70 optimal weight:    0.9990
   chunk 11 optimal weight:    0.8980
   chunk 36 optimal weight:    3.9990
   chunk 64 optimal weight:    6.9990
   chunk 48 optimal weight:    0.8980
   chunk 7 optimal weight:    8.9990
   overall best weight:    1.2984

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

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4188 r_free = 0.4188 target = 0.192907 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 35)----------------|
| r_work = 0.3938 r_free = 0.3938 target = 0.165864 restraints weight = 8242.810|
|-----------------------------------------------------------------------------|
r_work (start): 0.3893 rms_B_bonded: 1.61
r_work: 0.3696 rms_B_bonded: 2.88 restraints_weight: 0.5000
r_work: 0.3567 rms_B_bonded: 4.84 restraints_weight: 0.2500
r_work (final): 0.3567
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8020
moved from start:          0.1323

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.028   7238  Z= 0.146
  Angle     :  0.529   8.521   9952  Z= 0.287
  Chirality :  0.041   0.225   1114
  Planarity :  0.004   0.046   1115
  Dihedral  : 17.761 149.854   1484
  Min Nonbonded Distance : 2.048

Molprobity Statistics.
  All-atom Clashscore : 6.17
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.82 %
    Favored  : 97.18 %
  Rotamer:
    Outliers :  1.21 %
    Allowed  :  9.86 %
    Favored  : 88.92 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    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:  0.33 (0.30), residues: 745
  helix:  0.95 (0.28), residues: 353
  sheet:  0.11 (0.48), residues: 119
  loop : -0.56 (0.36), residues: 273

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG A 572 
 TYR   0.015   0.001   TYR A 214 
 PHE   0.009   0.001   PHE A 531 
 TRP   0.028   0.002   TRP A 323 
 HIS   0.007   0.001   HIS A 824 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00326 /  0.15 ( 7238)
  covalent geometry    : angle       0.52886 /  0.29 ( 9952)
  hydrogen bonds       : bond        0.05472 /  3.59 (  315)
  hydrogen bonds       : angle       4.76040 /  3.34 (  880)

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

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

  1490 Ramachandran restraints generated.
    745 Oldfield, 0 Emsley, 745 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1490 Ramachandran restraints generated.
    745 Oldfield, 0 Emsley, 745 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  67 residues out of total 659 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 8
    poor density    : 59
  time to evaluate  : 0.155 
Fit side-chains
REVERT: A   17 TYR cc_start: 0.8213 (OUTLIER) cc_final: 0.7828 (p90)
REVERT: A   53 ASP cc_start: 0.7662 (m-30) cc_final: 0.6706 (t70)
REVERT: A  186 LYS cc_start: 0.8310 (ptmm) cc_final: 0.8022 (pttp)
REVERT: A  377 ARG cc_start: 0.7515 (ptt90) cc_final: 0.7069 (ptt-90)
  outliers start: 8
  outliers final: 2
  residues processed: 63
  average time/residue: 0.3908
  time to fit residues: 26.7958
Evaluate side-chains
  58 residues out of total 659 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 3
    poor density    : 55
  time to evaluate  : 0.247 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   17 TYR
Chi-restraints excluded: chain A residue  678 SER
Chi-restraints excluded: chain A residue  763 THR
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 79
   random chunks:
   chunk 54 optimal weight:    0.5980
   chunk 11 optimal weight:    6.9990
   chunk 29 optimal weight:    3.9990
   chunk 18 optimal weight:    3.9990
   chunk 71 optimal weight:    0.8980
   chunk 48 optimal weight:    0.8980
   chunk 27 optimal weight:    5.9990
   chunk 2 optimal weight:    2.9990
   chunk 34 optimal weight:    2.9990
   chunk 9 optimal weight:    0.9990
   chunk 72 optimal weight:    1.9990
   overall best weight:    1.0784

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

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4113 r_free = 0.4113 target = 0.189891 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 31)----------------|
| r_work = 0.3827 r_free = 0.3827 target = 0.160495 restraints weight = 8506.680|
|-----------------------------------------------------------------------------|
r_work (start): 0.3816 rms_B_bonded: 1.88
r_work: 0.3648 rms_B_bonded: 2.81 restraints_weight: 0.5000
r_work: 0.3520 rms_B_bonded: 4.69 restraints_weight: 0.2500
r_work (final): 0.3520
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7946
moved from start:          0.1536

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.020   7238  Z= 0.127
  Angle     :  0.490   7.535   9952  Z= 0.267
  Chirality :  0.040   0.244   1114
  Planarity :  0.004   0.045   1115
  Dihedral  : 17.700 150.228   1484
  Min Nonbonded Distance : 2.063

Molprobity Statistics.
  All-atom Clashscore : 5.51
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.55 %
    Favored  : 97.45 %
  Rotamer:
    Outliers :  1.82 %
    Allowed  : 12.29 %
    Favored  : 85.89 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    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:  0.53 (0.31), residues: 745
  helix:  1.18 (0.28), residues: 350
  sheet:  0.20 (0.48), residues: 119
  loop : -0.55 (0.36), residues: 276

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG A 680 
 TYR   0.013   0.001   TYR A 729 
 PHE   0.007   0.001   PHE A 531 
 TRP   0.028   0.002   TRP A 323 
 HIS   0.007   0.001   HIS A 824 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00278 /  0.13 ( 7238)
  covalent geometry    : angle       0.49018 /  0.27 ( 9952)
  hydrogen bonds       : bond        0.04912 /  3.23 (  315)
  hydrogen bonds       : angle       4.51471 /  3.17 (  880)

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

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

  1490 Ramachandran restraints generated.
    745 Oldfield, 0 Emsley, 745 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1490 Ramachandran restraints generated.
    745 Oldfield, 0 Emsley, 745 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  72 residues out of total 659 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 60
  time to evaluate  : 0.253 
Fit side-chains
REVERT: A   17 TYR cc_start: 0.8147 (OUTLIER) cc_final: 0.7677 (p90)
REVERT: A  186 LYS cc_start: 0.8361 (ptmm) cc_final: 0.8092 (pttp)
REVERT: A  357 LYS cc_start: 0.7428 (ptpp) cc_final: 0.7056 (ptpt)
REVERT: A  377 ARG cc_start: 0.7488 (ptt90) cc_final: 0.7005 (ptt-90)
REVERT: A  795 VAL cc_start: 0.8483 (p) cc_final: 0.8253 (m)
  outliers start: 12
  outliers final: 3
  residues processed: 67
  average time/residue: 0.3934
  time to fit residues: 28.6700
Evaluate side-chains
  60 residues out of total 659 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 4
    poor density    : 56
  time to evaluate  : 0.255 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   17 TYR
Chi-restraints excluded: chain A residue  221 THR
Chi-restraints excluded: chain A residue  678 SER
Chi-restraints excluded: chain A residue  763 THR
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 79
   random chunks:
   chunk 46 optimal weight:    6.9990
   chunk 33 optimal weight:    3.9990
   chunk 32 optimal weight:   10.0000
   chunk 2 optimal weight:    2.9990
   chunk 9 optimal weight:    4.9990
   chunk 7 optimal weight:    2.9990
   chunk 63 optimal weight:    0.9980
   chunk 48 optimal weight:    0.2980
   chunk 8 optimal weight:    4.9990
   chunk 12 optimal weight:    0.9980
   chunk 43 optimal weight:    4.9990
   overall best weight:    1.6584

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

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4093 r_free = 0.4093 target = 0.187756 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 31)----------------|
| r_work = 0.3802 r_free = 0.3802 target = 0.158300 restraints weight = 8547.187|
|-----------------------------------------------------------------------------|
r_work (start): 0.3784 rms_B_bonded: 1.90
r_work: 0.3604 rms_B_bonded: 2.90 restraints_weight: 0.5000
r_work: 0.3476 rms_B_bonded: 4.81 restraints_weight: 0.2500
r_work (final): 0.3476
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7997
moved from start:          0.1614

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.026   7238  Z= 0.167
  Angle     :  0.563  14.771   9952  Z= 0.291
  Chirality :  0.041   0.241   1114
  Planarity :  0.004   0.045   1115
  Dihedral  : 17.751 150.739   1484
  Min Nonbonded Distance : 2.062

Molprobity Statistics.
  All-atom Clashscore : 6.17
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.82 %
    Favored  : 97.18 %
  Rotamer:
    Outliers :  1.21 %
    Allowed  : 15.02 %
    Favored  : 83.76 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    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:  0.42 (0.31), residues: 745
  helix:  1.06 (0.28), residues: 352
  sheet:  0.13 (0.47), residues: 119
  loop : -0.58 (0.36), residues: 274

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG A 820 
 TYR   0.019   0.001   TYR A 648 
 PHE   0.009   0.001   PHE A 867 
 TRP   0.029   0.002   TRP A 323 
 HIS   0.007   0.001   HIS A 824 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00377 /  0.17 ( 7238)
  covalent geometry    : angle       0.56350 /  0.29 ( 9952)
  hydrogen bonds       : bond        0.05412 /  3.58 (  315)
  hydrogen bonds       : angle       4.52924 /  3.18 (  880)

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

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

  1490 Ramachandran restraints generated.
    745 Oldfield, 0 Emsley, 745 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1490 Ramachandran restraints generated.
    745 Oldfield, 0 Emsley, 745 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  72 residues out of total 659 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 8
    poor density    : 64
  time to evaluate  : 0.268 
Fit side-chains
REVERT: A   17 TYR cc_start: 0.8158 (OUTLIER) cc_final: 0.7657 (p90)
REVERT: A  186 LYS cc_start: 0.8441 (ptmm) cc_final: 0.8173 (pttp)
REVERT: A  357 LYS cc_start: 0.7463 (ptpp) cc_final: 0.7109 (ptpt)
REVERT: A  377 ARG cc_start: 0.7524 (ptt90) cc_final: 0.6997 (ptt-90)
REVERT: A  795 VAL cc_start: 0.8501 (p) cc_final: 0.8271 (m)
  outliers start: 8
  outliers final: 4
  residues processed: 68
  average time/residue: 0.4521
  time to fit residues: 33.1082
Evaluate side-chains
  66 residues out of total 659 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 5
    poor density    : 61
  time to evaluate  : 0.177 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   17 TYR
Chi-restraints excluded: chain A residue  185 ILE
Chi-restraints excluded: chain A residue  221 THR
Chi-restraints excluded: chain A residue  678 SER
Chi-restraints excluded: chain A residue  763 THR
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 79
   random chunks:
   chunk 35 optimal weight:    0.6980
   chunk 73 optimal weight:    6.9990
   chunk 47 optimal weight:    6.9990
   chunk 57 optimal weight:    3.9990
   chunk 19 optimal weight:    9.9990
   chunk 43 optimal weight:    4.9990
   chunk 48 optimal weight:    2.9990
   chunk 66 optimal weight:    0.9990
   chunk 39 optimal weight:    1.9990
   chunk 64 optimal weight:    2.9990
   chunk 71 optimal weight:    0.7980
   overall best weight:    1.4986

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

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4061 r_free = 0.4061 target = 0.185733 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 29)----------------|
| r_work = 0.3774 r_free = 0.3774 target = 0.155711 restraints weight = 8621.266|
|-----------------------------------------------------------------------------|
r_work (start): 0.3754 rms_B_bonded: 2.01
r_work: 0.3572 rms_B_bonded: 2.92 restraints_weight: 0.5000
r_work: 0.3438 rms_B_bonded: 4.85 restraints_weight: 0.2500
r_work (final): 0.3438
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7914
moved from start:          0.1737

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.038   7238  Z= 0.154
  Angle     :  0.548  14.120   9952  Z= 0.284
  Chirality :  0.041   0.223   1114
  Planarity :  0.004   0.044   1115
  Dihedral  : 17.781 150.831   1484
  Min Nonbonded Distance : 2.064

Molprobity Statistics.
  All-atom Clashscore : 5.87
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.09 %
    Favored  : 96.91 %
  Rotamer:
    Outliers :  1.82 %
    Allowed  : 15.48 %
    Favored  : 82.70 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    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:  0.47 (0.31), residues: 745
  helix:  1.08 (0.28), residues: 353
  sheet:  0.16 (0.47), residues: 119
  loop : -0.54 (0.36), residues: 273

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG A 680 
 TYR   0.017   0.001   TYR A 648 
 PHE   0.013   0.001   PHE A 531 
 TRP   0.035   0.002   TRP A 323 
 HIS   0.006   0.001   HIS A 824 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00350 /  0.15 ( 7238)
  covalent geometry    : angle       0.54814 /  0.28 ( 9952)
  hydrogen bonds       : bond        0.05209 /  3.44 (  315)
  hydrogen bonds       : angle       4.45727 /  3.13 (  880)

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

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

  1490 Ramachandran restraints generated.
    745 Oldfield, 0 Emsley, 745 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1490 Ramachandran restraints generated.
    745 Oldfield, 0 Emsley, 745 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  73 residues out of total 659 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 61
  time to evaluate  : 0.245 
Fit side-chains
REVERT: A   17 TYR cc_start: 0.8111 (OUTLIER) cc_final: 0.7625 (p90)
REVERT: A  186 LYS cc_start: 0.8439 (ptmm) cc_final: 0.8178 (pttp)
REVERT: A  357 LYS cc_start: 0.7391 (ptpp) cc_final: 0.7028 (ptpt)
REVERT: A  377 ARG cc_start: 0.7422 (ptt90) cc_final: 0.6867 (ptt-90)
REVERT: A  725 GLU cc_start: 0.7174 (mt-10) cc_final: 0.6830 (mp0)
REVERT: A  795 VAL cc_start: 0.8486 (p) cc_final: 0.8275 (m)
  outliers start: 12
  outliers final: 4
  residues processed: 66
  average time/residue: 0.4518
  time to fit residues: 32.1375
Evaluate side-chains
  66 residues out of total 659 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 5
    poor density    : 61
  time to evaluate  : 0.243 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   17 TYR
Chi-restraints excluded: chain A residue  185 ILE
Chi-restraints excluded: chain A residue  221 THR
Chi-restraints excluded: chain A residue  678 SER
Chi-restraints excluded: chain A residue  763 THR
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 79
   random chunks:
   chunk 19 optimal weight:    9.9990
   chunk 71 optimal weight:    1.9990
   chunk 12 optimal weight:    0.6980
   chunk 1 optimal weight:    0.8980
   chunk 53 optimal weight:    0.6980
   chunk 5 optimal weight:    1.9990
   chunk 45 optimal weight:    0.9980
   chunk 73 optimal weight:    3.9990
   chunk 47 optimal weight:    3.9990
   chunk 30 optimal weight:    2.9990
   chunk 61 optimal weight:    4.9990
   overall best weight:    1.0582

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

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4077 r_free = 0.4077 target = 0.187294 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 31)----------------|
| r_work = 0.3790 r_free = 0.3790 target = 0.157219 restraints weight = 8511.261|
|-----------------------------------------------------------------------------|
r_work (start): 0.3770 rms_B_bonded: 2.01
r_work: 0.3593 rms_B_bonded: 2.94 restraints_weight: 0.5000
r_work: 0.3459 rms_B_bonded: 4.88 restraints_weight: 0.2500
r_work (final): 0.3459
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7883
moved from start:          0.1847

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.026   7238  Z= 0.125
  Angle     :  0.507  13.355   9952  Z= 0.264
  Chirality :  0.039   0.184   1114
  Planarity :  0.004   0.044   1115
  Dihedral  : 17.797 150.977   1484
  Min Nonbonded Distance : 2.070

Molprobity Statistics.
  All-atom Clashscore : 5.80
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.68 %
    Favored  : 97.32 %
  Rotamer:
    Outliers :  1.37 %
    Allowed  : 16.08 %
    Favored  : 82.55 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    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:  0.62 (0.31), residues: 745
  helix:  1.25 (0.28), residues: 353
  sheet:  0.20 (0.47), residues: 119
  loop : -0.49 (0.36), residues: 273

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG A 680 
 TYR   0.015   0.001   TYR A 648 
 PHE   0.007   0.001   PHE A  35 
 TRP   0.036   0.002   TRP A 323 
 HIS   0.005   0.001   HIS A 824 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00278 /  0.13 ( 7238)
  covalent geometry    : angle       0.50749 /  0.26 ( 9952)
  hydrogen bonds       : bond        0.04696 /  3.10 (  315)
  hydrogen bonds       : angle       4.32268 /  3.03 (  880)

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

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

  1490 Ramachandran restraints generated.
    745 Oldfield, 0 Emsley, 745 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1490 Ramachandran restraints generated.
    745 Oldfield, 0 Emsley, 745 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  75 residues out of total 659 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 9
    poor density    : 66
  time to evaluate  : 0.263 
Fit side-chains
REVERT: A   17 TYR cc_start: 0.8136 (OUTLIER) cc_final: 0.7623 (p90)
REVERT: A  186 LYS cc_start: 0.8490 (ptmm) cc_final: 0.8236 (pttp)
REVERT: A  357 LYS cc_start: 0.7344 (ptpp) cc_final: 0.6993 (ptpt)
REVERT: A  377 ARG cc_start: 0.7393 (ptt90) cc_final: 0.6847 (ptt-90)
REVERT: A  795 VAL cc_start: 0.8465 (p) cc_final: 0.8242 (m)
  outliers start: 9
  outliers final: 2
  residues processed: 72
  average time/residue: 0.4507
  time to fit residues: 34.9578
Evaluate side-chains
  64 residues out of total 659 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 3
    poor density    : 61
  time to evaluate  : 0.251 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   17 TYR
Chi-restraints excluded: chain A residue  221 THR
Chi-restraints excluded: chain A residue  678 SER
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 79
   random chunks:
   chunk 38 optimal weight:    7.9990
   chunk 23 optimal weight:    0.9980
   chunk 17 optimal weight:    5.9990
   chunk 51 optimal weight:    2.9990
   chunk 39 optimal weight:    2.9990
   chunk 26 optimal weight:    0.0370
   chunk 61 optimal weight:    5.9990
   chunk 54 optimal weight:    3.9990
   chunk 18 optimal weight:    0.8980
   chunk 73 optimal weight:    6.9990
   chunk 74 optimal weight:    2.9990
   overall best weight:    1.5862

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

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4053 r_free = 0.4053 target = 0.184861 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 33)----------------|
| r_work = 0.3765 r_free = 0.3765 target = 0.155166 restraints weight = 8574.973|
|-----------------------------------------------------------------------------|
r_work (start): 0.3749 rms_B_bonded: 1.98
r_work: 0.3566 rms_B_bonded: 2.92 restraints_weight: 0.5000
r_work: 0.3435 rms_B_bonded: 4.83 restraints_weight: 0.2500
r_work (final): 0.3435
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7922
moved from start:          0.1898

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.026   7238  Z= 0.162
  Angle     :  0.554  11.809   9952  Z= 0.285
  Chirality :  0.041   0.232   1114
  Planarity :  0.004   0.044   1115
  Dihedral  : 17.803 151.397   1484
  Min Nonbonded Distance : 2.062

Molprobity Statistics.
  All-atom Clashscore : 5.87
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.22 %
    Favored  : 96.78 %
  Rotamer:
    Outliers :  1.06 %
    Allowed  : 16.84 %
    Favored  : 82.09 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    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:  0.48 (0.31), residues: 745
  helix:  1.13 (0.28), residues: 353
  sheet:  0.10 (0.48), residues: 119
  loop : -0.54 (0.36), residues: 273

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG A 283 
 TYR   0.016   0.001   TYR A 214 
 PHE   0.009   0.001   PHE A  35 
 TRP   0.052   0.003   TRP A 323 
 HIS   0.007   0.001   HIS A 824 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00371 /  0.16 ( 7238)
  covalent geometry    : angle       0.55372 /  0.29 ( 9952)
  hydrogen bonds       : bond        0.05251 /  3.49 (  315)
  hydrogen bonds       : angle       4.42585 /  3.10 (  880)

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

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

  1490 Ramachandran restraints generated.
    745 Oldfield, 0 Emsley, 745 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1490 Ramachandran restraints generated.
    745 Oldfield, 0 Emsley, 745 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  69 residues out of total 659 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 7
    poor density    : 62
  time to evaluate  : 0.244 
Fit side-chains
REVERT: A   17 TYR cc_start: 0.8102 (OUTLIER) cc_final: 0.7569 (p90)
REVERT: A  186 LYS cc_start: 0.8523 (ptmm) cc_final: 0.8268 (pttp)
REVERT: A  357 LYS cc_start: 0.7371 (ptpp) cc_final: 0.7017 (ptpt)
REVERT: A  377 ARG cc_start: 0.7399 (ptt90) cc_final: 0.6859 (ptt-90)
REVERT: A  725 GLU cc_start: 0.7140 (mt-10) cc_final: 0.6791 (mp0)
REVERT: A  795 VAL cc_start: 0.8474 (p) cc_final: 0.8245 (m)
  outliers start: 7
  outliers final: 4
  residues processed: 65
  average time/residue: 0.4357
  time to fit residues: 30.3278
Evaluate side-chains
  65 residues out of total 659 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 5
    poor density    : 60
  time to evaluate  : 0.245 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   17 TYR
Chi-restraints excluded: chain A residue  185 ILE
Chi-restraints excluded: chain A residue  221 THR
Chi-restraints excluded: chain A residue  678 SER
Chi-restraints excluded: chain A residue  763 THR
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 79
   random chunks:
   chunk 9 optimal weight:    5.9990
   chunk 44 optimal weight:    1.9990
   chunk 42 optimal weight:    3.9990
   chunk 52 optimal weight:    0.8980
   chunk 46 optimal weight:    0.8980
   chunk 29 optimal weight:    2.9990
   chunk 70 optimal weight:    0.9990
   chunk 78 optimal weight:   10.0000
   chunk 28 optimal weight:    4.9990
   chunk 71 optimal weight:    5.9990
   chunk 77 optimal weight:   10.0000
   overall best weight:    1.5586

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

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4049 r_free = 0.4049 target = 0.184467 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 33)----------------|
| r_work = 0.3761 r_free = 0.3761 target = 0.154809 restraints weight = 8501.962|
|-----------------------------------------------------------------------------|
r_work (start): 0.3751 rms_B_bonded: 1.97
r_work: 0.3567 rms_B_bonded: 2.91 restraints_weight: 0.5000
r_work: 0.3436 rms_B_bonded: 4.82 restraints_weight: 0.2500
r_work (final): 0.3436
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7921
moved from start:          0.1948

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.026   7238  Z= 0.157
  Angle     :  0.541  10.574   9952  Z= 0.281
  Chirality :  0.041   0.268   1114
  Planarity :  0.004   0.043   1115
  Dihedral  : 17.810 151.403   1484
  Min Nonbonded Distance : 2.063

Molprobity Statistics.
  All-atom Clashscore : 6.09
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.09 %
    Favored  : 96.91 %
  Rotamer:
    Outliers :  0.91 %
    Allowed  : 16.69 %
    Favored  : 82.40 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    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:  0.47 (0.31), residues: 745
  helix:  1.14 (0.28), residues: 353
  sheet:  0.04 (0.48), residues: 119
  loop : -0.53 (0.36), residues: 273

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG A 820 
 TYR   0.015   0.001   TYR A 214 
 PHE   0.008   0.001   PHE A  35 
 TRP   0.054   0.003   TRP A 323 
 HIS   0.005   0.001   HIS A 824 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00359 /  0.16 ( 7238)
  covalent geometry    : angle       0.54080 /  0.28 ( 9952)
  hydrogen bonds       : bond        0.05206 /  3.45 (  315)
  hydrogen bonds       : angle       4.41608 /  3.09 (  880)

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

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

  1490 Ramachandran restraints generated.
    745 Oldfield, 0 Emsley, 745 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1490 Ramachandran restraints generated.
    745 Oldfield, 0 Emsley, 745 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  68 residues out of total 659 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 6
    poor density    : 62
  time to evaluate  : 0.244 
Fit side-chains
REVERT: A   17 TYR cc_start: 0.8125 (OUTLIER) cc_final: 0.7554 (p90)
REVERT: A  186 LYS cc_start: 0.8536 (ptmm) cc_final: 0.8290 (pttp)
REVERT: A  357 LYS cc_start: 0.7377 (ptpp) cc_final: 0.7025 (ptpt)
REVERT: A  377 ARG cc_start: 0.7390 (ptt90) cc_final: 0.6875 (ptt-90)
REVERT: A  725 GLU cc_start: 0.7137 (mt-10) cc_final: 0.6793 (mp0)
REVERT: A  795 VAL cc_start: 0.8501 (p) cc_final: 0.8270 (m)
  outliers start: 6
  outliers final: 5
  residues processed: 64
  average time/residue: 0.4638
  time to fit residues: 31.7857
Evaluate side-chains
  66 residues out of total 659 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 6
    poor density    : 60
  time to evaluate  : 0.240 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   17 TYR
Chi-restraints excluded: chain A residue  185 ILE
Chi-restraints excluded: chain A residue  221 THR
Chi-restraints excluded: chain A residue  539 LEU
Chi-restraints excluded: chain A residue  678 SER
Chi-restraints excluded: chain A residue  763 THR
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 79
   random chunks:
   chunk 50 optimal weight:    2.9990
   chunk 21 optimal weight:    9.9990
   chunk 44 optimal weight:    1.9990
   chunk 39 optimal weight:    4.9990
   chunk 16 optimal weight:    3.9990
   chunk 41 optimal weight:    0.8980
   chunk 75 optimal weight:    9.9990
   chunk 13 optimal weight:    3.9990
   chunk 78 optimal weight:    9.9990
   chunk 18 optimal weight:    0.0030
   chunk 56 optimal weight:    3.9990
   overall best weight:    1.9796

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
A 264 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4037 r_free = 0.4037 target = 0.183266 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 33)----------------|
| r_work = 0.3744 r_free = 0.3744 target = 0.153265 restraints weight = 8519.735|
|-----------------------------------------------------------------------------|
r_work (start): 0.3730 rms_B_bonded: 1.97
r_work: 0.3548 rms_B_bonded: 2.89 restraints_weight: 0.5000
r_work: 0.3415 rms_B_bonded: 4.80 restraints_weight: 0.2500
r_work (final): 0.3415
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7950
moved from start:          0.1991

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.032   7238  Z= 0.194
  Angle     :  0.588   9.710   9952  Z= 0.304
  Chirality :  0.043   0.251   1114
  Planarity :  0.004   0.044   1115
  Dihedral  : 17.856 151.603   1484
  Min Nonbonded Distance : 2.056

Molprobity Statistics.
  All-atom Clashscore : 6.02
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.49 %
    Favored  : 96.51 %
  Rotamer:
    Outliers :  1.06 %
    Allowed  : 16.39 %
    Favored  : 82.55 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    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:  0.27 (0.31), residues: 745
  helix:  0.97 (0.28), residues: 353
  sheet: -0.05 (0.48), residues: 119
  loop : -0.64 (0.36), residues: 273

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG A 820 
 TYR   0.019   0.002   TYR A 214 
 PHE   0.010   0.002   PHE A  35 
 TRP   0.061   0.003   TRP A 323 
 HIS   0.008   0.001   HIS A 824 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00451 /  0.19 ( 7238)
  covalent geometry    : angle       0.58783 /  0.30 ( 9952)
  hydrogen bonds       : bond        0.05787 /  3.84 (  315)
  hydrogen bonds       : angle       4.52245 /  3.17 (  880)

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

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

  1490 Ramachandran restraints generated.
    745 Oldfield, 0 Emsley, 745 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1490 Ramachandran restraints generated.
    745 Oldfield, 0 Emsley, 745 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  68 residues out of total 659 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 7
    poor density    : 61
  time to evaluate  : 0.293 
Fit side-chains
REVERT: A   17 TYR cc_start: 0.8129 (OUTLIER) cc_final: 0.7588 (p90)
REVERT: A  186 LYS cc_start: 0.8538 (ptmm) cc_final: 0.8294 (pttp)
REVERT: A  357 LYS cc_start: 0.7410 (ptpp) cc_final: 0.7065 (ptpt)
REVERT: A  377 ARG cc_start: 0.7401 (ptt90) cc_final: 0.6875 (ptt-90)
REVERT: A  391 ARG cc_start: 0.8596 (mmt180) cc_final: 0.8316 (tpm170)
REVERT: A  725 GLU cc_start: 0.7135 (mt-10) cc_final: 0.6792 (mp0)
REVERT: A  795 VAL cc_start: 0.8502 (p) cc_final: 0.8247 (m)
  outliers start: 7
  outliers final: 4
  residues processed: 64
  average time/residue: 0.5221
  time to fit residues: 35.7392
Evaluate side-chains
  65 residues out of total 659 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 5
    poor density    : 60
  time to evaluate  : 0.250 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   17 TYR
Chi-restraints excluded: chain A residue  179 LEU
Chi-restraints excluded: chain A residue  185 ILE
Chi-restraints excluded: chain A residue  221 THR
Chi-restraints excluded: chain A residue  763 THR
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 79
   random chunks:
   chunk 11 optimal weight:    4.9990
   chunk 45 optimal weight:    1.9990
   chunk 19 optimal weight:    0.4980
   chunk 46 optimal weight:    0.0470
   chunk 18 optimal weight:    1.9990
   chunk 73 optimal weight:    6.9990
   chunk 67 optimal weight:    5.9990
   chunk 9 optimal weight:    3.9990
   chunk 5 optimal weight:    4.9990
   chunk 6 optimal weight:    7.9990
   chunk 43 optimal weight:    3.9990
   overall best weight:    1.7084

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
A 264 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4046 r_free = 0.4046 target = 0.184074 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 33)----------------|
| r_work = 0.3756 r_free = 0.3756 target = 0.154305 restraints weight = 8506.406|
|-----------------------------------------------------------------------------|
r_work (start): 0.3740 rms_B_bonded: 1.95
r_work: 0.3558 rms_B_bonded: 2.88 restraints_weight: 0.5000
r_work: 0.3425 rms_B_bonded: 4.78 restraints_weight: 0.2500
r_work (final): 0.3425
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7932
moved from start:          0.2027

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.027   7238  Z= 0.169
  Angle     :  0.558   9.317   9952  Z= 0.290
  Chirality :  0.041   0.247   1114
  Planarity :  0.004   0.044   1115
  Dihedral  : 17.852 151.460   1484
  Min Nonbonded Distance : 2.057

Molprobity Statistics.
  All-atom Clashscore : 5.87
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.09 %
    Favored  : 96.91 %
  Rotamer:
    Outliers :  0.76 %
    Allowed  : 16.69 %
    Favored  : 82.55 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    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:  0.30 (0.31), residues: 745
  helix:  1.01 (0.28), residues: 353
  sheet: -0.09 (0.48), residues: 119
  loop : -0.62 (0.36), residues: 273

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG A 820 
 TYR   0.016   0.001   TYR A 214 
 PHE   0.008   0.001   PHE A 867 
 TRP   0.074   0.003   TRP A 323 
 HIS   0.007   0.001   HIS A 824 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00386 /  0.17 ( 7238)
  covalent geometry    : angle       0.55777 /  0.29 ( 9952)
  hydrogen bonds       : bond        0.05497 /  3.64 (  315)
  hydrogen bonds       : angle       4.47901 /  3.13 (  880)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 2244.68 seconds
wall clock time: 39 minutes 9.82 seconds (2349.82 seconds total)