Starting phenix.real_space_refine
on Fri Jul  3 16:20:09 2026 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/8opt_17087/07_2026/8opt_17087.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/8opt_17087/07_2026/8opt_17087.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=3.65
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    model {
      file = "/net/cci-nas-00/data/ceres_data/8opt_17087/07_2026/8opt_17087.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/8opt_17087/07_2026/8opt_17087.cif"
    real_map_files = "/net/cci-nas-00/data/ceres_data/8opt_17087/07_2026/8opt_17087.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/8opt_17087/07_2026/8opt_17087.map"
  }
  resolution = 3.65
  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=   0.001 sd=   0.020
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: 7
    Type Number    sf(0)   Gaussians
     Zn      2      6.06       5
     P      54      5.49       5
     S      36      5.16       5
     C    4781      2.51       5
     N    1338      2.21       5
     O    1563      1.98       5
     H    7197      0.53       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 6 residue(s): 0.01s

  Monomer Library directory:
    "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/chem_data/mon_lib"
  Total number of atoms: 14971
  Number of models: 1
  Model: ""
    Number of chains: 5
    Chain: "A"
      Number of atoms: 12651
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 783, 12651
          Classifications: {'peptide': 783}
          Link IDs: {'PTRANS': 43, 'TRANS': 739}
          Chain breaks: 7
          Unresolved non-hydrogen bonds: 50
          Unresolved non-hydrogen angles: 57
          Unresolved non-hydrogen dihedrals: 45
          Unresolved non-hydrogen chiralities: 1
          Planarities with less than four sites: {'ASP:plan': 2, 'ARG:plan': 1, 'GLU:plan': 1, 'PHE:plan': 1}
          Unresolved non-hydrogen planarities: 21
    Chain: "D"
      Number of atoms: 1740
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 54, 1740
          Classifications: {'RNA': 54}
          Modifications used: {'3*END': 1, 'rna2p_pur': 6, 'rna2p_pyr': 4, 'rna3p_pur': 26, 'rna3p_pyr': 18}
          Link IDs: {'rna2p': 10, 'rna3p': 43}
    Chain: "B"
      Number of atoms: 578
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 42, 578
          Classifications: {'peptide': 42}
          Link IDs: {'PTRANS': 4, 'TRANS': 37}
          Unresolved non-hydrogen bonds: 20
          Unresolved non-hydrogen angles: 23
          Unresolved non-hydrogen dihedrals: 19
          Planarities with less than four sites: {'ARG:plan': 1, 'HIS:plan': 1}
          Unresolved non-hydrogen planarities: 10
    Chain: "A"
      Number of atoms: 1
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 1, 1
          Unusual residues: {' ZN': 1}
          Classifications: {'undetermined': 1}
    Chain: "B"
      Number of atoms: 1
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 1, 1
          Unusual residues: {' ZN': 1}
          Classifications: {'undetermined': 1}

List of CYS excluded from plausible disulfide bonds:
  (reason: may participate in coordination)
  ATOM   7018  SG  CYS A 965      30.740  58.816  80.274  1.00 76.39           S
  ATOM   7058  SG  CYS A 968      32.244  56.154  82.639  1.00 79.01           S
  ATOM   7229  SG  CYS A 978      28.562  56.027  81.831  1.00 71.28           S
  ATOM  14423  SG  CYS B 139      45.794  36.750  28.084  1.00101.21           S
  ATOM  14468  SG  CYS B 142      49.793  36.545  27.527  1.00103.47           S
  ATOM  14591  SG  CYS B 152      48.043  36.623  31.187  1.00 98.61           S

  Time building chain proxies: 3.08, per 1000 atoms: 0.21
  Number of scatterers: 14971
  At special positions: 0
  Unit cell: (81.084, 114.636, 142.596, 90, 90, 90)
  Space group: P 1 (No. 1)
  Number of sites at special positions: 0
  Number of scattering types: 7
    Type Number    sf(0)
     Zn      2     29.99
     S      36     16.00
     P      54     15.00
     O    1563      8.00
     N    1338      7.00
     C    4781      6.00
     H    7197      1.00
    sf(0) = scattering factor at diffraction angle 0.

  Number of disulfides: simple=1, symmetry=0
    Simple disulfide: pdb=" SG  CYS A 447 " - pdb=" SG  CYS A 621 " 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
  Time building additional restraints: 1.56
  Conformation dependent library (CDL) restraints added in 586.3 milliseconds
  
  Dynamic metal coordination
    Zn2+ tetrahedral coordination
      pdb="  ZN A1501 "
        pdb="ZN    ZN A1501 " - pdb=" ND1 HIS A 973 "
        pdb="ZN    ZN A1501 " - pdb=" SG  CYS A 978 "
        pdb="ZN    ZN A1501 " - pdb=" SG  CYS A 968 "
        pdb="ZN    ZN A1501 " - pdb=" SG  CYS A 965 "
      pdb="  ZN B 301 "
        pdb="ZN    ZN B 301 " - pdb=" SG  CYS B 152 "
        pdb="ZN    ZN B 301 " - pdb=" SG  CYS B 139 "
        pdb="ZN    ZN B 301 " - pdb=" SG  CYS B 142 "
      Number of angles added : 3


  1614 Ramachandran restraints generated.
    807 Oldfield, 0 Emsley, 807 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  1574

  Finding SS restraints...
    Secondary structure from input PDB file:
      25 helices and 6 sheets defined
      44.2% alpha, 9.8% beta
      6 base pairs and 16 stacking pairs defined.
    Time for finding SS restraints: 3.23
  Creating SS restraints...
    Processing helix  chain 'A' and resid 210 through 227
    Processing helix  chain 'A' and resid 255 through 265
      removed outlier: 3.673A  pdb=" N   LYS A 264 " --> pdb=" O   HIS A 260 " (cutoff:3.500A)
      removed outlier: 3.649A  pdb=" N   GLU A 265 " --> pdb=" O   LYS A 261 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 265 through 284
      removed outlier: 3.752A  pdb=" N   LYS A 269 " --> pdb=" O   GLU A 265 " (cutoff:3.500A)
      removed outlier: 3.750A  pdb=" N   LEU A 284 " --> pdb=" O   LEU A 280 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 288 through 307
    Processing helix  chain 'A' and resid 309 through 328
    Processing helix  chain 'A' and resid 340 through 345
    Processing helix  chain 'A' and resid 364 through 379
    Processing helix  chain 'A' and resid 416 through 430
    Processing helix  chain 'A' and resid 432 through 448
      removed outlier: 3.814A  pdb=" N   LEU A 436 " --> pdb=" O   LYS A 432 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 460 through 473
      removed outlier: 3.713A  pdb=" N   LEU A 464 " --> pdb=" O   TYR A 460 " (cutoff:3.500A)
      removed outlier: 4.043A  pdb=" N   LEU A 470 " --> pdb=" O   ALA A 466 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 491 through 495
      removed outlier: 3.890A  pdb=" N   GLY A 495 " --> pdb=" O   SER A 492 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 550 through 563
    Processing helix  chain 'A' and resid 611 through 630
    Processing helix  chain 'A' and resid 951 through 957
    Processing helix  chain 'A' and resid 994 through 1013
    Processing helix  chain 'A' and resid 1015 through 1037
      removed outlier: 4.213A  pdb=" N   ASP A1036 " --> pdb=" O   PHE A1032 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 1075 through 1090
      removed outlier: 3.591A  pdb=" N   LYS A1089 " --> pdb=" O   ARG A1085 " (cutoff:3.500A)
      removed outlier: 3.813A  pdb=" N   HIS A1090 " --> pdb=" O   VAL A1086 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 1124 through 1141
      removed outlier: 4.373A  pdb=" N   ASP A1141 " --> pdb=" O   TYR A1137 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 1141 through 1158
      removed outlier: 4.028A  pdb=" N   LYS A1145 " --> pdb=" O   ASP A1141 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 1169 through 1183
    Processing helix  chain 'A' and resid 1219 through 1224
      removed outlier: 3.731A  pdb=" N   TYR A1223 " --> pdb=" O   GLU A1219 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 1233 through 1247
    Processing helix  chain 'A' and resid 1266 through 1270
    Processing helix  chain 'A' and resid 1293 through 1311
    Processing helix  chain 'A' and resid 1324 through 1330
      removed outlier: 3.780A  pdb=" N   PHE A1329 " --> pdb=" O   LYS A1325 " (cutoff:3.500A)
    Processing sheet with id=AA1, first strand: chain 'A' and resid 229 through 230
    Processing sheet with id=AA2, first strand: chain 'A' and resid 335 through 339
      removed outlier: 4.555A  pdb=" N   ASN A 354 " --> pdb=" O   TYR A 339 " (cutoff:3.500A)
      removed outlier: 6.204A  pdb=" N   VAL A 353 " --> pdb=" O   LYS A 408 " (cutoff:3.500A)
      removed outlier: 7.321A  pdb=" N   SER A 410 " --> pdb=" O   VAL A 353 " (cutoff:3.500A)
      removed outlier: 6.074A  pdb=" N   ILE A 355 " --> pdb=" O   SER A 410 " (cutoff:3.500A)
      removed outlier: 3.997A  pdb=" N   ARG A 399 " --> pdb=" O   ASP A 384 " (cutoff:3.500A)
      removed outlier: 4.970A  pdb=" N   ASP A 384 " --> pdb=" O   ARG A 399 " (cutoff:3.500A)
    Processing sheet with id=AA3, first strand: chain 'A' and resid 498 through 503
      removed outlier: 5.455A  pdb=" N   LEU A 499 " --> pdb=" O   GLU A 510 " (cutoff:3.500A)
      removed outlier: 5.907A  pdb=" N   GLU A 510 " --> pdb=" O   LEU A 499 " (cutoff:3.500A)
    Processing sheet with id=AA4, first strand: chain 'A' and resid 596 through 597
      removed outlier: 4.492A  pdb=" N   ASP A 597 " --> pdb=" O   SER A 600 " (cutoff:3.500A)
    Processing sheet with id=AA5, first strand: chain 'A' and resid 1040 through 1045
      removed outlier: 3.844A  pdb=" N   ASP A1060 " --> pdb=" O   PHE A1045 " (cutoff:3.500A)
      removed outlier: 5.996A  pdb=" N   LEU A1059 " --> pdb=" O   ASP A1119 " (cutoff:3.500A)
      removed outlier: 7.493A  pdb=" N   SER A1121 " --> pdb=" O   LEU A1059 " (cutoff:3.500A)
      removed outlier: 6.559A  pdb=" N   VAL A1061 " --> pdb=" O   SER A1121 " (cutoff:3.500A)
      removed outlier: 4.788A  pdb=" N   PHE A1110 " --> pdb=" O   ASN A1095 " (cutoff:3.500A)
      removed outlier: 5.872A  pdb=" N   ASN A1095 " --> pdb=" O   PHE A1110 " (cutoff:3.500A)
    Processing sheet with id=AA6, first strand: chain 'A' and resid 1205 through 1206
      removed outlier: 3.677A  pdb=" N   TRP A1209 " --> pdb=" O   VAL A1206 " (cutoff:3.500A)

    298 hydrogen bonds defined for protein.
    861 hydrogen bond angles defined for protein.
    Restraints generated for nucleic acids:
      14 hydrogen bonds
      24 hydrogen bond angles
      0 basepair planarities
      6 basepair parallelities
      16 stacking parallelities
  Total time for adding SS restraints: 3.68

  Time building geometry restraints manager: 2.13 seconds

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

  Histogram of bond lengths:
        0.84 -     1.03: 7179
        1.03 -     1.23: 55
        1.23 -     1.43: 3475
        1.43 -     1.62: 4502
        1.62 -     1.82: 46
  Bond restraints: 15257
  Sorted by residual:
  bond pdb=" N9    G D  45 "
       pdb=" C4    G D  45 "
    ideal  model  delta    sigma   weight residual
    1.375  1.386 -0.011 8.00e-03 1.56e+04 1.85e+00
  bond pdb=" CB  LYS A 270 "
       pdb=" CG  LYS A 270 "
    ideal  model  delta    sigma   weight residual
    1.520  1.547 -0.027 3.00e-02 1.11e+03 7.90e-01
  bond pdb=" CA  ARG A1184 "
       pdb=" CB  ARG A1184 "
    ideal  model  delta    sigma   weight residual
    1.533  1.519  0.014 1.66e-02 3.63e+03 7.17e-01
  bond pdb=" CB  GLU A 222 "
       pdb=" CG  GLU A 222 "
    ideal  model  delta    sigma   weight residual
    1.520  1.545 -0.025 3.00e-02 1.11e+03 6.93e-01
  bond pdb=" C   GLN A1183 "
       pdb=" N   ARG A1184 "
    ideal  model  delta    sigma   weight residual
    1.331  1.341 -0.010 1.24e-02 6.50e+03 6.77e-01
  ... (remaining 15252 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     1.78: 27260
        1.78 -     3.57: 326
        3.57 -     5.35: 19
        5.35 -     7.14: 1
        7.14 -     8.92: 1
  Bond angle restraints: 27607
  Sorted by residual:
  angle pdb=" C1'   G D  45 "
        pdb=" N9    G D  45 "
        pdb=" C4    G D  45 "
      ideal   model   delta    sigma   weight residual
     126.50  130.50   -4.00 1.30e+00 5.92e-01 9.49e+00
  angle pdb=" CB  LYS A 270 "
        pdb=" CG  LYS A 270 "
        pdb=" CD  LYS A 270 "
      ideal   model   delta    sigma   weight residual
     111.30  117.96   -6.66 2.30e+00 1.89e-01 8.39e+00
  angle pdb=" C1'   C D  18 "
        pdb=" N1    C D  18 "
        pdb=" C2    C D  18 "
      ideal   model   delta    sigma   weight residual
     118.80  115.68    3.12 1.10e+00 8.26e-01 8.03e+00
  angle pdb=" C1'   C D  18 "
        pdb=" N1    C D  18 "
        pdb=" C6    C D  18 "
      ideal   model   delta    sigma   weight residual
     120.80  124.15   -3.35 1.20e+00 6.94e-01 7.79e+00
  angle pdb=" N9    G D  45 "
        pdb=" C4    G D  45 "
        pdb=" N3    G D  45 "
      ideal   model   delta    sigma   weight residual
     126.00  127.59   -1.59 6.00e-01 2.78e+00 7.03e+00
  ... (remaining 27602 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    25.09: 6598
       25.09 -    50.18: 475
       50.18 -    75.27: 151
       75.27 -   100.35: 12
      100.35 -   125.44: 3
  Dihedral angle restraints: 7239
    sinusoidal: 4355
      harmonic: 2884
  Sorted by residual:
  dihedral pdb=" C4'   C D  48 "
           pdb=" C3'   C D  48 "
           pdb=" O3'   C D  48 "
           pdb=" P     A D  49 "
      ideal   model   delta sinusoidal    sigma   weight residual
    -110.00   10.20 -120.20     1      3.50e+01 8.16e-04 1.18e+01
  dihedral pdb=" CA  ASP A 587 "
           pdb=" CB  ASP A 587 "
           pdb=" CG  ASP A 587 "
           pdb=" OD1 ASP A 587 "
      ideal   model   delta sinusoidal    sigma   weight residual
     -30.00  -88.33   58.33     1      2.00e+01 2.50e-03 1.14e+01
  dihedral pdb=" O4'   G D  45 "
           pdb=" C1'   G D  45 "
           pdb=" N9    G D  45 "
           pdb=" C4    G D  45 "
      ideal   model   delta sinusoidal    sigma   weight residual
      68.00  115.46  -47.46     1      1.70e+01 3.46e-03 1.08e+01
  ... (remaining 7236 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.026: 852
       0.026 -    0.051: 300
       0.051 -    0.077: 69
       0.077 -    0.103: 41
       0.103 -    0.129: 37
  Chirality restraints: 1299
  Sorted by residual:
  chirality pdb=" CA  VAL A 393 "
            pdb=" N   VAL A 393 "
            pdb=" C   VAL A 393 "
            pdb=" CB  VAL A 393 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.44    2.57   -0.13 2.00e-01 2.50e+01 4.14e-01
  chirality pdb=" CA  ILE A 229 "
            pdb=" N   ILE A 229 "
            pdb=" C   ILE A 229 "
            pdb=" CB  ILE A 229 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.43    2.56   -0.12 2.00e-01 2.50e+01 3.89e-01
  chirality pdb=" CA  ILE A1204 "
            pdb=" N   ILE A1204 "
            pdb=" C   ILE A1204 "
            pdb=" CB  ILE A1204 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.43    2.56   -0.12 2.00e-01 2.50e+01 3.75e-01
  ... (remaining 1296 not shown)

  Planarity restraints: 2016
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CB  ASP A1207 "   -0.009 2.00e-02 2.50e+03   1.82e-02 3.30e+00
        pdb=" CG  ASP A1207 "    0.031 2.00e-02 2.50e+03
        pdb=" OD1 ASP A1207 "   -0.011 2.00e-02 2.50e+03
        pdb=" OD2 ASP A1207 "   -0.011 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  ASP A1207 "    0.008 2.00e-02 2.50e+03   1.55e-02 2.40e+00
        pdb=" C   ASP A1207 "   -0.027 2.00e-02 2.50e+03
        pdb=" O   ASP A1207 "    0.010 2.00e-02 2.50e+03
        pdb=" N   GLY A1208 "    0.009 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   SER A1013 "   -0.024 5.00e-02 4.00e+02   3.72e-02 2.21e+00
        pdb=" N   PRO A1014 "    0.064 5.00e-02 4.00e+02
        pdb=" CA  PRO A1014 "   -0.019 5.00e-02 4.00e+02
        pdb=" CD  PRO A1014 "   -0.021 5.00e-02 4.00e+02
  ... (remaining 2013 not shown)

  Histogram of nonbonded interaction distances:
        1.12 -     1.81: 25
        1.81 -     2.51: 11068
        2.51 -     3.21: 45244
        3.21 -     3.90: 57311
        3.90 -     4.60: 87927
  Nonbonded interactions: 201575
  Sorted by model distance:
  nonbonded pdb=" HE1 HIS A 973 "
            pdb="ZN    ZN A1501 "
     model   vdw
     1.116 1.408
  nonbonded pdb=" OE1 GLU A1219 "
            pdb=" H   GLU A1219 "
     model   vdw
     1.613 2.450
  nonbonded pdb=" OD1 ASN A 567 "
            pdb=" H   ASP A 570 "
     model   vdw
     1.620 2.450
  nonbonded pdb=" O   LEU A 214 "
            pdb="HE21 GLN A 218 "
     model   vdw
     1.628 2.450
  nonbonded pdb=" HZ2 LYS A 976 "
            pdb=" OD1 ASP A 977 "
     model   vdw
     1.633 2.450
  ... (remaining 201570 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 group one per residue
Make a string to write initial .geo file
Internal consistency checks
Time:
  Set random seed:                         0.000
  Set model cs if undefined:               0.000
  Decide on map wrapping:                  0.000
  Normalize map: mean=0, sd=1:             4.570
  Set stop_for_unknowns flag:              0.000
  Assert model is a single copy model:     0.000
  Assert all atoms have isotropic ADPs:    0.010
  Construct map_model_manager:             0.120
  Extract box with map and model:          0.280
  Check model and map are aligned:         0.050
  Set scattering table:                    0.030
  Process input model:                     23.090
  Find NCS groups from input model:        0.060
  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:1.610
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   29.840
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6006
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      :  0.002   0.031   8068  Z= 0.104
  Angle     :  0.479   8.923  11174  Z= 0.275
  Chirality :  0.035   0.129   1299
  Planarity :  0.003   0.037   1217
  Dihedral  : 19.509 125.444   3359
  Min Nonbonded Distance : 1.982

Molprobity Statistics.
  All-atom Clashscore : 7.00
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.35 %
    Favored  : 97.65 %
  Rotamer:
    Outliers :  0.14 %
    Allowed  : 19.27 %
    Favored  : 80.60 %
  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:  1.92 (0.30), residues: 807
  helix:  2.97 (0.28), residues: 337
  sheet:  0.08 (0.56), residues: 86
  loop :  0.04 (0.30), residues: 384

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.000   ARG A 970 
 TYR   0.010   0.001   TYR A1245 
 PHE   0.007   0.001   PHE A 955 
 TRP   0.005   0.001   TRP A 555 
 HIS   0.002   0.001   HIS A 422 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00219 /  0.10 ( 8060)
  covalent geometry    : angle       0.47783 /  0.27 (11169)
  SS BOND              : bond        0.00464 /  0.31 (    1)
  SS BOND              : angle       0.86277 /  0.58 (    2)
  hydrogen bonds       : bond        0.12020 /  8.29 (  312)
  hydrogen bonds       : angle       5.09320 /  3.96 (  885)
  metal coordination   : bond        0.00541 /  0.28 (    7)
  metal coordination   : angle       1.87773 /  1.34 (    3)

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

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

  1614 Ramachandran restraints generated.
    807 Oldfield, 0 Emsley, 807 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1614 Ramachandran restraints generated.
    807 Oldfield, 0 Emsley, 807 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Residue LYS  212 is missing expected H atoms. Skipping.
Residue LYS  401 is missing expected H atoms. Skipping.
Residue LEU  478 is missing expected H atoms. Skipping.
Residue LYS  504 is missing expected H atoms. Skipping.
Residue LYS  591 is missing expected H atoms. Skipping.
Residue MET 1063 is missing expected H atoms. Skipping.
Residue LYS 1325 is missing expected H atoms. Skipping.
Residue LYS  150 is missing expected H atoms. Skipping.
Residue LYS  160 is missing expected H atoms. Skipping.
Evaluate side-chains
  108 residues out of total 754 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 107
  time to evaluate  : 0.384 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
  outliers start: 1
  outliers final: 1
  residues processed: 107
  average time/residue: 0.2020
  time to fit residues: 29.5446
Evaluate side-chains
  108 residues out of total 754 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 107
  time to evaluate  : 0.378 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  580 LEU
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 87
   random chunks:
   chunk 49 optimal weight:    4.9990
   chunk 53 optimal weight:    4.9990
   chunk 5 optimal weight:    0.9990
   chunk 33 optimal weight:    1.9990
   chunk 65 optimal weight:    0.8980
   chunk 62 optimal weight:    0.9990
   chunk 51 optimal weight:    0.5980
   chunk 38 optimal weight:    1.9990
   chunk 61 optimal weight:    0.9980
   chunk 45 optimal weight:    0.7980
   chunk 74 optimal weight:    0.9990
   overall best weight:    0.8582

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
A 413 ASN
A1193 GLN
B 157 GLN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4731 r_free = 0.4731 target = 0.217317 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 58)----------------|
| r_work = 0.4345 r_free = 0.4345 target = 0.184613 restraints weight = 40127.268|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 53)----------------|
| r_work = 0.4400 r_free = 0.4400 target = 0.189293 restraints weight = 18417.121|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 68)----------------|
| r_work = 0.4436 r_free = 0.4436 target = 0.192297 restraints weight = 11053.411|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 55)----------------|
| r_work = 0.4459 r_free = 0.4459 target = 0.194183 restraints weight = 7937.511|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 34)----------------|
| r_work = 0.4468 r_free = 0.4468 target = 0.195038 restraints weight = 6506.251|
|-----------------------------------------------------------------------------|
r_work (final): 0.4404
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6027
moved from start:          0.0646

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.038   8068  Z= 0.195
  Angle     :  0.538   6.431  11174  Z= 0.290
  Chirality :  0.038   0.132   1299
  Planarity :  0.004   0.045   1217
  Dihedral  : 18.964 122.760   1711
  Min Nonbonded Distance : 2.308

Molprobity Statistics.
  All-atom Clashscore : 6.93
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.10 %
    Favored  : 96.90 %
  Rotamer:
    Outliers :  1.09 %
    Allowed  : 18.45 %
    Favored  : 80.46 %
  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:  1.40 (0.29), residues: 807
  helix:  2.45 (0.28), residues: 341
  sheet: -0.26 (0.54), residues: 86
  loop : -0.17 (0.30), residues: 380

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.001   ARG A 583 
 TYR   0.012   0.002   TYR A 562 
 PHE   0.017   0.001   PHE A1154 
 TRP   0.007   0.001   TRP A 555 
 HIS   0.004   0.001   HIS A 390 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00437 /  0.20 ( 8060)
  covalent geometry    : angle       0.53467 /  0.29 (11169)
  SS BOND              : bond        0.00825 /  0.55 (    1)
  SS BOND              : angle       1.46216 /  0.83 (    2)
  hydrogen bonds       : bond        0.04803 /  3.20 (  312)
  hydrogen bonds       : angle       4.74906 /  3.65 (  885)
  metal coordination   : bond        0.00706 /  0.39 (    7)
  metal coordination   : angle       3.75392 /  2.74 (    3)

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

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

  1614 Ramachandran restraints generated.
    807 Oldfield, 0 Emsley, 807 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1614 Ramachandran restraints generated.
    807 Oldfield, 0 Emsley, 807 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Residue LYS  212 is missing expected H atoms. Skipping.
Residue LYS  401 is missing expected H atoms. Skipping.
Residue LEU  478 is missing expected H atoms. Skipping.
Residue LYS  504 is missing expected H atoms. Skipping.
Residue LYS  591 is missing expected H atoms. Skipping.
Residue MET 1063 is missing expected H atoms. Skipping.
Residue LYS 1325 is missing expected H atoms. Skipping.
Residue LYS  150 is missing expected H atoms. Skipping.
Residue LYS  160 is missing expected H atoms. Skipping.
Evaluate side-chains
  124 residues out of total 754 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 8
    poor density    : 116
  time to evaluate  : 0.385 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  222 GLU cc_start: 0.7265 (tm-30) cc_final: 0.7062 (tm-30)
REVERT: A 1141 ASP cc_start: 0.5745 (OUTLIER) cc_final: 0.4103 (m-30)
  outliers start: 8
  outliers final: 6
  residues processed: 121
  average time/residue: 0.2071
  time to fit residues: 33.8863
Evaluate side-chains
  122 residues out of total 754 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 7
    poor density    : 115
  time to evaluate  : 0.458 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  268 HIS
Chi-restraints excluded: chain A residue  351 SER
Chi-restraints excluded: chain A residue  503 GLU
Chi-restraints excluded: chain A residue 1140 ILE
Chi-restraints excluded: chain A residue 1141 ASP
Chi-restraints excluded: chain A residue 1276 ILE
Chi-restraints excluded: chain A residue 1292 LEU
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 87
   random chunks:
   chunk 77 optimal weight:    0.9990
   chunk 24 optimal weight:    0.9980
   chunk 29 optimal weight:    1.9990
   chunk 75 optimal weight:    0.9990
   chunk 51 optimal weight:   10.0000
   chunk 19 optimal weight:    0.3980
   chunk 14 optimal weight:    0.9990
   chunk 0 optimal weight:    3.9990
   chunk 8 optimal weight:    0.0370
   chunk 79 optimal weight:    6.9990
   chunk 10 optimal weight:    0.6980
   overall best weight:    0.6260

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
A1193 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4709 r_free = 0.4709 target = 0.211841 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 40)----------------|
| r_work = 0.4366 r_free = 0.4366 target = 0.181903 restraints weight = 40143.328|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 30)----------------|
| r_work = 0.4387 r_free = 0.4387 target = 0.184989 restraints weight = 18922.721|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 33)----------------|
| r_work = 0.4406 r_free = 0.4406 target = 0.186405 restraints weight = 12766.791|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 25)----------------|
| r_work = 0.4409 r_free = 0.4409 target = 0.186625 restraints weight = 8759.819|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 29)----------------|
| r_work = 0.4411 r_free = 0.4411 target = 0.186888 restraints weight = 8765.237|
|-----------------------------------------------------------------------------|
r_work (final): 0.4367
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6095
moved from start:          0.0851

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.028   8068  Z= 0.143
  Angle     :  0.498   9.034  11174  Z= 0.265
  Chirality :  0.037   0.129   1299
  Planarity :  0.004   0.038   1217
  Dihedral  : 18.954 122.198   1709
  Min Nonbonded Distance : 2.291

Molprobity Statistics.
  All-atom Clashscore : 6.47
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.85 %
    Favored  : 97.15 %
  Rotamer:
    Outliers :  1.36 %
    Allowed  : 18.18 %
    Favored  : 80.46 %
  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:  1.22 (0.29), residues: 807
  helix:  2.22 (0.28), residues: 348
  sheet: -0.34 (0.55), residues: 86
  loop : -0.23 (0.30), residues: 373

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG A 267 
 TYR   0.009   0.002   TYR A1245 
 PHE   0.016   0.001   PHE A1154 
 TRP   0.008   0.001   TRP A 555 
 HIS   0.004   0.001   HIS A 973 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00323 /  0.14 ( 8060)
  covalent geometry    : angle       0.49482 /  0.26 (11169)
  SS BOND              : bond        0.00629 /  0.42 (    1)
  SS BOND              : angle       1.17446 /  0.69 (    2)
  hydrogen bonds       : bond        0.04626 /  3.11 (  312)
  hydrogen bonds       : angle       4.57799 /  3.53 (  885)
  metal coordination   : bond        0.00909 /  0.46 (    7)
  metal coordination   : angle       3.45457 /  2.44 (    3)

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

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

  1614 Ramachandran restraints generated.
    807 Oldfield, 0 Emsley, 807 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1614 Ramachandran restraints generated.
    807 Oldfield, 0 Emsley, 807 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Residue LYS  212 is missing expected H atoms. Skipping.
Residue LYS  401 is missing expected H atoms. Skipping.
Residue LEU  478 is missing expected H atoms. Skipping.
Residue LYS  504 is missing expected H atoms. Skipping.
Residue LYS  591 is missing expected H atoms. Skipping.
Residue MET 1063 is missing expected H atoms. Skipping.
Residue LYS 1325 is missing expected H atoms. Skipping.
Residue LYS  150 is missing expected H atoms. Skipping.
Residue LYS  160 is missing expected H atoms. Skipping.
Evaluate side-chains
  128 residues out of total 754 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 118
  time to evaluate  : 0.392 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  222 GLU cc_start: 0.7134 (tm-30) cc_final: 0.6877 (tm-30)
REVERT: A  263 ILE cc_start: 0.8158 (pt) cc_final: 0.7733 (tt)
REVERT: A 1141 ASP cc_start: 0.5738 (OUTLIER) cc_final: 0.4140 (m-30)
REVERT: A 1248 GLU cc_start: 0.7200 (OUTLIER) cc_final: 0.6985 (tm-30)
  outliers start: 10
  outliers final: 7
  residues processed: 125
  average time/residue: 0.1948
  time to fit residues: 33.0169
Evaluate side-chains
  124 residues out of total 754 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 9
    poor density    : 115
  time to evaluate  : 0.353 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  329 HIS
Chi-restraints excluded: chain A residue  420 THR
Chi-restraints excluded: chain A residue  503 GLU
Chi-restraints excluded: chain A residue 1140 ILE
Chi-restraints excluded: chain A residue 1141 ASP
Chi-restraints excluded: chain A residue 1206 VAL
Chi-restraints excluded: chain A residue 1220 LEU
Chi-restraints excluded: chain A residue 1248 GLU
Chi-restraints excluded: chain A residue 1292 LEU
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 87
   random chunks:
   chunk 19 optimal weight:    1.9990
   chunk 50 optimal weight:    7.9990
   chunk 63 optimal weight:    0.9980
   chunk 39 optimal weight:    0.8980
   chunk 22 optimal weight:    1.9990
   chunk 38 optimal weight:    0.2980
   chunk 12 optimal weight:    0.8980
   chunk 4 optimal weight:    3.9990
   chunk 62 optimal weight:    1.9990
   chunk 53 optimal weight:    3.9990
   chunk 28 optimal weight:    0.9990
   overall best weight:    0.8182

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
A 218 GLN
A1193 GLN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4648 r_free = 0.4648 target = 0.201926 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 34)----------------|
| r_work = 0.4299 r_free = 0.4299 target = 0.172185 restraints weight = 40680.728|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 30)----------------|
| r_work = 0.4317 r_free = 0.4317 target = 0.174893 restraints weight = 18992.228|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 33)----------------|
| r_work = 0.4337 r_free = 0.4337 target = 0.176400 restraints weight = 12763.973|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 32)----------------|
| r_work = 0.4350 r_free = 0.4350 target = 0.177405 restraints weight = 8930.947|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 27)----------------|
| r_work = 0.4350 r_free = 0.4350 target = 0.177443 restraints weight = 8982.649|
|-----------------------------------------------------------------------------|
r_work (final): 0.4324
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6171
moved from start:          0.1274

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.036   8068  Z= 0.188
  Angle     :  0.537   8.832  11174  Z= 0.287
  Chirality :  0.038   0.146   1299
  Planarity :  0.004   0.044   1217
  Dihedral  : 18.965 123.626   1709
  Min Nonbonded Distance : 2.214

Molprobity Statistics.
  All-atom Clashscore : 7.73
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.72 %
    Favored  : 96.28 %
  Rotamer:
    Outliers :  2.44 %
    Allowed  : 18.18 %
    Favored  : 79.38 %
  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:  0.80 (0.29), residues: 807
  helix:  1.73 (0.27), residues: 354
  sheet: -0.17 (0.57), residues: 81
  loop : -0.44 (0.30), residues: 372

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARG A 560 
 TYR   0.017   0.002   TYR A 562 
 PHE   0.016   0.002   PHE A1154 
 TRP   0.008   0.001   TRP A 555 
 HIS   0.005   0.001   HIS A 973 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00423 /  0.19 ( 8060)
  covalent geometry    : angle       0.53206 /  0.29 (11169)
  SS BOND              : bond        0.00885 /  0.59 (    1)
  SS BOND              : angle       1.68968 /  0.95 (    2)
  hydrogen bonds       : bond        0.04685 /  3.15 (  312)
  hydrogen bonds       : angle       4.58186 /  3.50 (  885)
  metal coordination   : bond        0.00858 /  0.45 (    7)
  metal coordination   : angle       4.37262 /  3.13 (    3)

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

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

  1614 Ramachandran restraints generated.
    807 Oldfield, 0 Emsley, 807 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1614 Ramachandran restraints generated.
    807 Oldfield, 0 Emsley, 807 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Residue LYS  212 is missing expected H atoms. Skipping.
Residue LYS  401 is missing expected H atoms. Skipping.
Residue LEU  478 is missing expected H atoms. Skipping.
Residue LYS  504 is missing expected H atoms. Skipping.
Residue LYS  591 is missing expected H atoms. Skipping.
Residue MET 1063 is missing expected H atoms. Skipping.
Residue LYS 1325 is missing expected H atoms. Skipping.
Residue LYS  150 is missing expected H atoms. Skipping.
Residue LYS  160 is missing expected H atoms. Skipping.
Evaluate side-chains
  138 residues out of total 754 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 18
    poor density    : 120
  time to evaluate  : 0.361 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  222 GLU cc_start: 0.7269 (tm-30) cc_final: 0.6958 (tm-30)
REVERT: A 1141 ASP cc_start: 0.5872 (OUTLIER) cc_final: 0.4183 (m-30)
  outliers start: 18
  outliers final: 13
  residues processed: 134
  average time/residue: 0.1884
  time to fit residues: 34.4492
Evaluate side-chains
  128 residues out of total 754 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 114
  time to evaluate  : 0.359 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  268 HIS
Chi-restraints excluded: chain A residue  272 ILE
Chi-restraints excluded: chain A residue  292 ILE
Chi-restraints excluded: chain A residue  329 HIS
Chi-restraints excluded: chain A residue  420 THR
Chi-restraints excluded: chain A residue  469 PHE
Chi-restraints excluded: chain A residue  503 GLU
Chi-restraints excluded: chain A residue 1140 ILE
Chi-restraints excluded: chain A residue 1141 ASP
Chi-restraints excluded: chain A residue 1153 VAL
Chi-restraints excluded: chain A residue 1206 VAL
Chi-restraints excluded: chain A residue 1220 LEU
Chi-restraints excluded: chain A residue 1292 LEU
Chi-restraints excluded: chain A residue 1322 TYR
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 87
   random chunks:
   chunk 9 optimal weight:    0.8980
   chunk 74 optimal weight:    1.9990
   chunk 41 optimal weight:    0.5980
   chunk 67 optimal weight:    0.6980
   chunk 85 optimal weight:    0.1980
   chunk 43 optimal weight:    0.9990
   chunk 69 optimal weight:    0.3980
   chunk 73 optimal weight:    0.7980
   chunk 14 optimal weight:    0.9980
   chunk 28 optimal weight:    0.0980
   chunk 11 optimal weight:    0.9990
   overall best weight:    0.3980

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
A 350 ASN
A1193 GLN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4702 r_free = 0.4702 target = 0.213034 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 38)----------------|
| r_work = 0.4365 r_free = 0.4365 target = 0.184047 restraints weight = 40240.938|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 28)----------------|
| r_work = 0.4383 r_free = 0.4383 target = 0.186834 restraints weight = 18949.848|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 35)----------------|
| r_work = 0.4400 r_free = 0.4400 target = 0.188155 restraints weight = 13070.282|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 25)----------------|
| r_work = 0.4404 r_free = 0.4404 target = 0.188516 restraints weight = 9011.035|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 27)----------------|
| r_work = 0.4407 r_free = 0.4407 target = 0.188758 restraints weight = 8928.214|
|-----------------------------------------------------------------------------|
r_work (final): 0.4348
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6123
moved from start:          0.1327

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.029   8068  Z= 0.120
  Angle     :  0.499   8.594  11174  Z= 0.264
  Chirality :  0.037   0.130   1299
  Planarity :  0.004   0.042   1217
  Dihedral  : 18.928 123.357   1709
  Min Nonbonded Distance : 2.233

Molprobity Statistics.
  All-atom Clashscore : 7.53
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.97 %
    Favored  : 97.03 %
  Rotamer:
    Outliers :  2.17 %
    Allowed  : 18.72 %
    Favored  : 79.10 %
  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:  1.02 (0.29), residues: 807
  helix:  2.04 (0.28), residues: 348
  sheet: -0.46 (0.55), residues: 86
  loop : -0.32 (0.31), residues: 373

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.000   ARG A 970 
 TYR   0.011   0.001   TYR A1245 
 PHE   0.014   0.001   PHE A 462 
 TRP   0.010   0.001   TRP A 555 
 HIS   0.003   0.001   HIS A 973 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00271 /  0.12 ( 8060)
  covalent geometry    : angle       0.49521 /  0.26 (11169)
  SS BOND              : bond        0.00631 /  0.42 (    1)
  SS BOND              : angle       1.14798 /  0.70 (    2)
  hydrogen bonds       : bond        0.04283 /  2.88 (  312)
  hydrogen bonds       : angle       4.43481 /  3.41 (  885)
  metal coordination   : bond        0.01162 /  0.57 (    7)
  metal coordination   : angle       3.63120 /  2.54 (    3)

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

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

  1614 Ramachandran restraints generated.
    807 Oldfield, 0 Emsley, 807 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1614 Ramachandran restraints generated.
    807 Oldfield, 0 Emsley, 807 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Residue LYS  212 is missing expected H atoms. Skipping.
Residue LYS  401 is missing expected H atoms. Skipping.
Residue LEU  478 is missing expected H atoms. Skipping.
Residue LYS  504 is missing expected H atoms. Skipping.
Residue LYS  591 is missing expected H atoms. Skipping.
Residue MET 1063 is missing expected H atoms. Skipping.
Residue LYS 1325 is missing expected H atoms. Skipping.
Residue LYS  150 is missing expected H atoms. Skipping.
Residue LYS  160 is missing expected H atoms. Skipping.
Evaluate side-chains
  132 residues out of total 754 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 116
  time to evaluate  : 0.338 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  222 GLU cc_start: 0.7060 (tm-30) cc_final: 0.6751 (tm-30)
REVERT: A  263 ILE cc_start: 0.8106 (pt) cc_final: 0.7667 (tt)
REVERT: A  384 ASP cc_start: 0.7570 (t0) cc_final: 0.7353 (t0)
REVERT: A  561 PHE cc_start: 0.6742 (t80) cc_final: 0.6344 (t80)
REVERT: A 1141 ASP cc_start: 0.5678 (OUTLIER) cc_final: 0.4004 (m-30)
  outliers start: 16
  outliers final: 12
  residues processed: 127
  average time/residue: 0.1904
  time to fit residues: 32.8162
Evaluate side-chains
  128 residues out of total 754 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 115
  time to evaluate  : 0.315 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  268 HIS
Chi-restraints excluded: chain A residue  292 ILE
Chi-restraints excluded: chain A residue  329 HIS
Chi-restraints excluded: chain A residue  350 ASN
Chi-restraints excluded: chain A residue  351 SER
Chi-restraints excluded: chain A residue  469 PHE
Chi-restraints excluded: chain A residue  503 GLU
Chi-restraints excluded: chain A residue 1140 ILE
Chi-restraints excluded: chain A residue 1141 ASP
Chi-restraints excluded: chain A residue 1153 VAL
Chi-restraints excluded: chain A residue 1206 VAL
Chi-restraints excluded: chain A residue 1292 LEU
Chi-restraints excluded: chain A residue 1322 TYR
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 87
   random chunks:
   chunk 28 optimal weight:    0.9990
   chunk 86 optimal weight:    0.0770
   chunk 22 optimal weight:    1.9990
   chunk 48 optimal weight:    0.0040
   chunk 51 optimal weight:    8.9990
   chunk 63 optimal weight:    0.9990
   chunk 50 optimal weight:    5.9990
   chunk 35 optimal weight:    0.9990
   chunk 7 optimal weight:    0.6980
   chunk 14 optimal weight:    0.7980
   chunk 77 optimal weight:    0.5980
   overall best weight:    0.4350

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
A 218 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4662 r_free = 0.4662 target = 0.202980 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 34)----------------|
| r_work = 0.4319 r_free = 0.4319 target = 0.173592 restraints weight = 40364.319|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 30)----------------|
| r_work = 0.4339 r_free = 0.4339 target = 0.176667 restraints weight = 18178.294|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 33)----------------|
| r_work = 0.4358 r_free = 0.4358 target = 0.178047 restraints weight = 12221.063|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 25)----------------|
| r_work = 0.4363 r_free = 0.4363 target = 0.178386 restraints weight = 8429.094|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 25)----------------|
| r_work = 0.4367 r_free = 0.4367 target = 0.178685 restraints weight = 8580.395|
|-----------------------------------------------------------------------------|
r_work (final): 0.4338
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6138
moved from start:          0.1397

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.076   8068  Z= 0.137
  Angle     :  0.507   8.595  11174  Z= 0.269
  Chirality :  0.037   0.149   1299
  Planarity :  0.004   0.044   1217
  Dihedral  : 18.920 123.026   1709
  Min Nonbonded Distance : 2.249

Molprobity Statistics.
  All-atom Clashscore : 8.07
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.35 %
    Favored  : 96.65 %
  Rotamer:
    Outliers :  2.31 %
    Allowed  : 18.45 %
    Favored  : 79.24 %
  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:  1.05 (0.29), residues: 807
  helix:  2.12 (0.28), residues: 348
  sheet: -0.48 (0.55), residues: 86
  loop : -0.35 (0.31), residues: 373

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG A 226 
 TYR   0.011   0.001   TYR A1245 
 PHE   0.013   0.001   PHE A 462 
 TRP   0.009   0.001   TRP A 555 
 HIS   0.003   0.001   HIS A 973 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00309 /  0.14 ( 8060)
  covalent geometry    : angle       0.50314 /  0.27 (11169)
  SS BOND              : bond        0.00629 /  0.42 (    1)
  SS BOND              : angle       1.18656 /  0.72 (    2)
  hydrogen bonds       : bond        0.04176 /  2.80 (  312)
  hydrogen bonds       : angle       4.37348 /  3.36 (  885)
  metal coordination   : bond        0.01010 /  0.50 (    7)
  metal coordination   : angle       3.53552 /  2.51 (    3)

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

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

  1614 Ramachandran restraints generated.
    807 Oldfield, 0 Emsley, 807 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1614 Ramachandran restraints generated.
    807 Oldfield, 0 Emsley, 807 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Residue LYS  212 is missing expected H atoms. Skipping.
Residue LYS  401 is missing expected H atoms. Skipping.
Residue LEU  478 is missing expected H atoms. Skipping.
Residue LYS  504 is missing expected H atoms. Skipping.
Residue LYS  591 is missing expected H atoms. Skipping.
Residue MET 1063 is missing expected H atoms. Skipping.
Residue LYS 1325 is missing expected H atoms. Skipping.
Residue LYS  150 is missing expected H atoms. Skipping.
Residue LYS  160 is missing expected H atoms. Skipping.
Evaluate side-chains
  131 residues out of total 754 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 17
    poor density    : 114
  time to evaluate  : 0.373 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  222 GLU cc_start: 0.7236 (tm-30) cc_final: 0.6893 (tm-30)
REVERT: A  263 ILE cc_start: 0.8141 (pt) cc_final: 0.7745 (tt)
REVERT: A  365 GLN cc_start: 0.8471 (OUTLIER) cc_final: 0.7344 (tp40)
REVERT: A  384 ASP cc_start: 0.7595 (t0) cc_final: 0.7358 (t0)
REVERT: A  561 PHE cc_start: 0.6736 (t80) cc_final: 0.6368 (t80)
REVERT: A 1141 ASP cc_start: 0.5661 (OUTLIER) cc_final: 0.3983 (m-30)
  outliers start: 17
  outliers final: 11
  residues processed: 127
  average time/residue: 0.1847
  time to fit residues: 31.6897
Evaluate side-chains
  125 residues out of total 754 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 112
  time to evaluate  : 0.379 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  268 HIS
Chi-restraints excluded: chain A residue  272 ILE
Chi-restraints excluded: chain A residue  292 ILE
Chi-restraints excluded: chain A residue  365 GLN
Chi-restraints excluded: chain A residue  420 THR
Chi-restraints excluded: chain A residue  469 PHE
Chi-restraints excluded: chain A residue  503 GLU
Chi-restraints excluded: chain A residue 1140 ILE
Chi-restraints excluded: chain A residue 1141 ASP
Chi-restraints excluded: chain A residue 1153 VAL
Chi-restraints excluded: chain A residue 1206 VAL
Chi-restraints excluded: chain A residue 1292 LEU
Chi-restraints excluded: chain A residue 1322 TYR
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 87
   random chunks:
   chunk 82 optimal weight:    5.9990
   chunk 24 optimal weight:    0.9990
   chunk 65 optimal weight:    0.0980
   chunk 54 optimal weight:    7.9990
   chunk 80 optimal weight:   20.0000
   chunk 79 optimal weight:    5.9990
   chunk 74 optimal weight:    1.9990
   chunk 46 optimal weight:    0.7980
   chunk 22 optimal weight:    1.9990
   chunk 55 optimal weight:    1.9990
   chunk 73 optimal weight:    0.2980
   overall best weight:    0.8384

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
A 413 ASN
A1193 GLN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4678 r_free = 0.4678 target = 0.212707 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 34)----------------|
| r_work = 0.4335 r_free = 0.4335 target = 0.183483 restraints weight = 39767.677|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 30)----------------|
| r_work = 0.4351 r_free = 0.4351 target = 0.186100 restraints weight = 18433.223|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 35)----------------|
| r_work = 0.4369 r_free = 0.4369 target = 0.187576 restraints weight = 12525.694|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 29)----------------|
| r_work = 0.4379 r_free = 0.4379 target = 0.188471 restraints weight = 8725.262|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 27)----------------|
| r_work = 0.4381 r_free = 0.4381 target = 0.188567 restraints weight = 8924.473|
|-----------------------------------------------------------------------------|
r_work (final): 0.4316
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6179
moved from start:          0.1657

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.036   8068  Z= 0.190
  Angle     :  0.548   8.177  11174  Z= 0.292
  Chirality :  0.038   0.150   1299
  Planarity :  0.004   0.048   1217
  Dihedral  : 18.978 123.944   1709
  Min Nonbonded Distance : 2.160

Molprobity Statistics.
  All-atom Clashscore : 9.27
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.84 %
    Favored  : 96.16 %
  Rotamer:
    Outliers :  1.90 %
    Allowed  : 19.13 %
    Favored  : 78.97 %
  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:  0.70 (0.29), residues: 807
  helix:  1.73 (0.28), residues: 354
  sheet: -0.33 (0.57), residues: 81
  loop : -0.56 (0.30), residues: 372

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARG A 623 
 TYR   0.015   0.002   TYR A 562 
 PHE   0.017   0.002   PHE A 462 
 TRP   0.009   0.001   TRP A 555 
 HIS   0.006   0.001   HIS A 973 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00431 /  0.19 ( 8060)
  covalent geometry    : angle       0.54324 /  0.29 (11169)
  SS BOND              : bond        0.00894 /  0.60 (    1)
  SS BOND              : angle       1.68813 /  0.96 (    2)
  hydrogen bonds       : bond        0.04667 /  3.13 (  312)
  hydrogen bonds       : angle       4.48952 /  3.42 (  885)
  metal coordination   : bond        0.01025 /  0.52 (    7)
  metal coordination   : angle       4.10160 /  2.96 (    3)

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

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

  1614 Ramachandran restraints generated.
    807 Oldfield, 0 Emsley, 807 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1614 Ramachandran restraints generated.
    807 Oldfield, 0 Emsley, 807 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Residue LYS  212 is missing expected H atoms. Skipping.
Residue LYS  401 is missing expected H atoms. Skipping.
Residue LEU  478 is missing expected H atoms. Skipping.
Residue LYS  504 is missing expected H atoms. Skipping.
Residue LYS  591 is missing expected H atoms. Skipping.
Residue MET 1063 is missing expected H atoms. Skipping.
Residue LYS 1325 is missing expected H atoms. Skipping.
Residue LYS  150 is missing expected H atoms. Skipping.
Residue LYS  160 is missing expected H atoms. Skipping.
Evaluate side-chains
  130 residues out of total 754 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 116
  time to evaluate  : 0.422 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  222 GLU cc_start: 0.7237 (tm-30) cc_final: 0.6889 (tm-30)
REVERT: A  263 ILE cc_start: 0.8176 (pt) cc_final: 0.7757 (tt)
REVERT: A  365 GLN cc_start: 0.8512 (OUTLIER) cc_final: 0.7464 (tp40)
REVERT: A  384 ASP cc_start: 0.7613 (t0) cc_final: 0.7397 (t0)
REVERT: A 1141 ASP cc_start: 0.5838 (OUTLIER) cc_final: 0.4102 (m-30)
REVERT: A 1298 ASN cc_start: 0.6622 (m-40) cc_final: 0.6405 (m110)
  outliers start: 14
  outliers final: 12
  residues processed: 126
  average time/residue: 0.2141
  time to fit residues: 35.9493
Evaluate side-chains
  130 residues out of total 754 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 116
  time to evaluate  : 0.375 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  268 HIS
Chi-restraints excluded: chain A residue  272 ILE
Chi-restraints excluded: chain A residue  292 ILE
Chi-restraints excluded: chain A residue  329 HIS
Chi-restraints excluded: chain A residue  350 ASN
Chi-restraints excluded: chain A residue  365 GLN
Chi-restraints excluded: chain A residue  420 THR
Chi-restraints excluded: chain A residue  469 PHE
Chi-restraints excluded: chain A residue  503 GLU
Chi-restraints excluded: chain A residue 1140 ILE
Chi-restraints excluded: chain A residue 1141 ASP
Chi-restraints excluded: chain A residue 1153 VAL
Chi-restraints excluded: chain A residue 1292 LEU
Chi-restraints excluded: chain A residue 1322 TYR
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 87
   random chunks:
   chunk 27 optimal weight:    0.2980
   chunk 38 optimal weight:    0.1980
   chunk 76 optimal weight:    0.9980
   chunk 59 optimal weight:    0.9990
   chunk 48 optimal weight:    0.9990
   chunk 43 optimal weight:    0.9990
   chunk 55 optimal weight:    2.9990
   chunk 75 optimal weight:    0.9990
   chunk 66 optimal weight:    0.8980
   chunk 68 optimal weight:    0.7980
   chunk 62 optimal weight:    0.9990
   overall best weight:    0.6380

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
A 218 GLN
A 413 ASN
A1193 GLN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4636 r_free = 0.4636 target = 0.200963 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 34)----------------|
| r_work = 0.4292 r_free = 0.4292 target = 0.171640 restraints weight = 40312.480|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 34)----------------|
| r_work = 0.4310 r_free = 0.4310 target = 0.174317 restraints weight = 18466.150|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 35)----------------|
| r_work = 0.4329 r_free = 0.4329 target = 0.175792 restraints weight = 12506.584|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 32)----------------|
| r_work = 0.4340 r_free = 0.4340 target = 0.176624 restraints weight = 8718.877|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 27)----------------|
| r_work = 0.4341 r_free = 0.4341 target = 0.176739 restraints weight = 8874.061|
|-----------------------------------------------------------------------------|
r_work (final): 0.4317
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6179
moved from start:          0.1762

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.077   8068  Z= 0.151
  Angle     :  0.520   8.613  11174  Z= 0.276
  Chirality :  0.037   0.139   1299
  Planarity :  0.004   0.045   1217
  Dihedral  : 18.959 124.266   1709
  Min Nonbonded Distance : 2.149

Molprobity Statistics.
  All-atom Clashscore : 8.54
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.59 %
    Favored  : 96.41 %
  Rotamer:
    Outliers :  2.31 %
    Allowed  : 18.59 %
    Favored  : 79.10 %
  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:  0.73 (0.29), residues: 807
  helix:  1.78 (0.28), residues: 353
  sheet: -0.38 (0.57), residues: 81
  loop : -0.56 (0.30), residues: 373

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG A 623 
 TYR   0.013   0.002   TYR A 948 
 PHE   0.016   0.001   PHE A 462 
 TRP   0.010   0.001   TRP A 555 
 HIS   0.005   0.001   HIS A 973 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00352 /  0.15 ( 8060)
  covalent geometry    : angle       0.51578 /  0.28 (11169)
  SS BOND              : bond        0.00725 /  0.48 (    1)
  SS BOND              : angle       1.35972 /  0.82 (    2)
  hydrogen bonds       : bond        0.04480 /  3.01 (  312)
  hydrogen bonds       : angle       4.42159 /  3.37 (  885)
  metal coordination   : bond        0.01047 /  0.53 (    7)
  metal coordination   : angle       3.99160 /  2.83 (    3)

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

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

  1614 Ramachandran restraints generated.
    807 Oldfield, 0 Emsley, 807 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1614 Ramachandran restraints generated.
    807 Oldfield, 0 Emsley, 807 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Residue LYS  212 is missing expected H atoms. Skipping.
Residue LYS  401 is missing expected H atoms. Skipping.
Residue LEU  478 is missing expected H atoms. Skipping.
Residue LYS  504 is missing expected H atoms. Skipping.
Residue LYS  591 is missing expected H atoms. Skipping.
Residue MET 1063 is missing expected H atoms. Skipping.
Residue LYS 1325 is missing expected H atoms. Skipping.
Residue LYS  150 is missing expected H atoms. Skipping.
Residue LYS  160 is missing expected H atoms. Skipping.
Evaluate side-chains
  132 residues out of total 754 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 17
    poor density    : 115
  time to evaluate  : 0.378 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  222 GLU cc_start: 0.7229 (tm-30) cc_final: 0.6878 (tm-30)
REVERT: A  263 ILE cc_start: 0.8174 (pt) cc_final: 0.7759 (tt)
REVERT: A  365 GLN cc_start: 0.8496 (OUTLIER) cc_final: 0.7430 (tp40)
REVERT: A  561 PHE cc_start: 0.6769 (t80) cc_final: 0.6440 (t80)
REVERT: A 1141 ASP cc_start: 0.5813 (OUTLIER) cc_final: 0.4126 (m-30)
REVERT: A 1298 ASN cc_start: 0.6584 (m-40) cc_final: 0.6272 (m110)
  outliers start: 17
  outliers final: 11
  residues processed: 129
  average time/residue: 0.2249
  time to fit residues: 38.4099
Evaluate side-chains
  127 residues out of total 754 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 114
  time to evaluate  : 0.387 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  272 ILE
Chi-restraints excluded: chain A residue  292 ILE
Chi-restraints excluded: chain A residue  329 HIS
Chi-restraints excluded: chain A residue  365 GLN
Chi-restraints excluded: chain A residue  420 THR
Chi-restraints excluded: chain A residue  469 PHE
Chi-restraints excluded: chain A residue  502 ILE
Chi-restraints excluded: chain A residue  503 GLU
Chi-restraints excluded: chain A residue 1140 ILE
Chi-restraints excluded: chain A residue 1141 ASP
Chi-restraints excluded: chain A residue 1153 VAL
Chi-restraints excluded: chain A residue 1292 LEU
Chi-restraints excluded: chain A residue 1322 TYR
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 87
   random chunks:
   chunk 79 optimal weight:    7.9990
   chunk 4 optimal weight:    3.9990
   chunk 39 optimal weight:    0.7980
   chunk 17 optimal weight:    2.9990
   chunk 29 optimal weight:    0.9980
   chunk 35 optimal weight:    0.9990
   chunk 8 optimal weight:    0.1980
   chunk 13 optimal weight:    0.9990
   chunk 54 optimal weight:    9.9990
   chunk 11 optimal weight:    0.5980
   chunk 9 optimal weight:    0.0980
   overall best weight:    0.5380

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
A1193 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4684 r_free = 0.4684 target = 0.213319 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 40)----------------|
| r_work = 0.4343 r_free = 0.4343 target = 0.184089 restraints weight = 39727.161|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 30)----------------|
| r_work = 0.4365 r_free = 0.4365 target = 0.187333 restraints weight = 18229.818|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 29)----------------|
| r_work = 0.4382 r_free = 0.4382 target = 0.188575 restraints weight = 12082.254|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 25)----------------|
| r_work = 0.4385 r_free = 0.4385 target = 0.188861 restraints weight = 8471.983|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 27)----------------|
| r_work = 0.4388 r_free = 0.4388 target = 0.189135 restraints weight = 8516.765|
|-----------------------------------------------------------------------------|
r_work (final): 0.4322
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6167
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   0.028   8068  Z= 0.140
  Angle     :  0.516   8.809  11174  Z= 0.273
  Chirality :  0.037   0.135   1299
  Planarity :  0.004   0.046   1217
  Dihedral  : 18.951 124.009   1709
  Min Nonbonded Distance : 2.165

Molprobity Statistics.
  All-atom Clashscore : 8.40
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.47 %
    Favored  : 96.53 %
  Rotamer:
    Outliers :  2.04 %
    Allowed  : 18.32 %
    Favored  : 79.65 %
  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:  0.77 (0.29), residues: 807
  helix:  1.84 (0.28), residues: 353
  sheet: -0.41 (0.57), residues: 81
  loop : -0.55 (0.30), residues: 373

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.006   0.000   ARG A 970 
 TYR   0.014   0.002   TYR A 948 
 PHE   0.015   0.001   PHE A 462 
 TRP   0.011   0.001   TRP A 555 
 HIS   0.004   0.001   HIS A 973 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00320 /  0.14 ( 8060)
  covalent geometry    : angle       0.51138 /  0.27 (11169)
  SS BOND              : bond        0.00686 /  0.46 (    1)
  SS BOND              : angle       1.30470 /  0.80 (    2)
  hydrogen bonds       : bond        0.04332 /  2.89 (  312)
  hydrogen bonds       : angle       4.36534 /  3.33 (  885)
  metal coordination   : bond        0.00965 /  0.49 (    7)
  metal coordination   : angle       3.89989 /  2.74 (    3)

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

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

  1614 Ramachandran restraints generated.
    807 Oldfield, 0 Emsley, 807 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1614 Ramachandran restraints generated.
    807 Oldfield, 0 Emsley, 807 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Residue LYS  212 is missing expected H atoms. Skipping.
Residue LYS  401 is missing expected H atoms. Skipping.
Residue LEU  478 is missing expected H atoms. Skipping.
Residue LYS  504 is missing expected H atoms. Skipping.
Residue LYS  591 is missing expected H atoms. Skipping.
Residue MET 1063 is missing expected H atoms. Skipping.
Residue LYS 1325 is missing expected H atoms. Skipping.
Residue LYS  150 is missing expected H atoms. Skipping.
Residue LYS  160 is missing expected H atoms. Skipping.
Evaluate side-chains
  128 residues out of total 754 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 15
    poor density    : 113
  time to evaluate  : 0.397 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  222 GLU cc_start: 0.7161 (tm-30) cc_final: 0.6816 (tm-30)
REVERT: A  263 ILE cc_start: 0.8162 (pt) cc_final: 0.7726 (tt)
REVERT: A  365 GLN cc_start: 0.8488 (OUTLIER) cc_final: 0.7421 (tp40)
REVERT: A  561 PHE cc_start: 0.6799 (t80) cc_final: 0.6471 (t80)
REVERT: A 1141 ASP cc_start: 0.5725 (OUTLIER) cc_final: 0.4865 (m-30)
REVERT: A 1298 ASN cc_start: 0.6481 (m-40) cc_final: 0.6259 (m110)
  outliers start: 15
  outliers final: 12
  residues processed: 125
  average time/residue: 0.2109
  time to fit residues: 35.2364
Evaluate side-chains
  124 residues out of total 754 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 110
  time to evaluate  : 0.457 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  268 HIS
Chi-restraints excluded: chain A residue  272 ILE
Chi-restraints excluded: chain A residue  292 ILE
Chi-restraints excluded: chain A residue  350 ASN
Chi-restraints excluded: chain A residue  365 GLN
Chi-restraints excluded: chain A residue  420 THR
Chi-restraints excluded: chain A residue  469 PHE
Chi-restraints excluded: chain A residue  502 ILE
Chi-restraints excluded: chain A residue  503 GLU
Chi-restraints excluded: chain A residue 1140 ILE
Chi-restraints excluded: chain A residue 1141 ASP
Chi-restraints excluded: chain A residue 1153 VAL
Chi-restraints excluded: chain A residue 1292 LEU
Chi-restraints excluded: chain A residue 1322 TYR
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 87
   random chunks:
   chunk 28 optimal weight:    0.0670
   chunk 47 optimal weight:    0.0970
   chunk 35 optimal weight:    0.8980
   chunk 62 optimal weight:    0.0030
   chunk 22 optimal weight:    1.9990
   chunk 83 optimal weight:    0.2980
   chunk 64 optimal weight:    0.2980
   chunk 8 optimal weight:    0.0070
   chunk 46 optimal weight:    0.7980
   chunk 17 optimal weight:    0.0270
   chunk 54 optimal weight:    9.9990
   overall best weight:    0.0402

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
A1193 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4666 r_free = 0.4666 target = 0.203642 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 34)----------------|
| r_work = 0.4328 r_free = 0.4328 target = 0.174341 restraints weight = 40543.149|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 30)----------------|
| r_work = 0.4352 r_free = 0.4352 target = 0.177826 restraints weight = 18155.026|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 33)----------------|
| r_work = 0.4372 r_free = 0.4372 target = 0.179207 restraints weight = 11785.041|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 25)----------------|
| r_work = 0.4373 r_free = 0.4373 target = 0.179277 restraints weight = 8069.066|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 27)----------------|
| r_work = 0.4377 r_free = 0.4377 target = 0.179572 restraints weight = 8290.746|
|-----------------------------------------------------------------------------|
r_work (final): 0.4350
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6116
moved from start:          0.1802

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.032   8068  Z= 0.100
  Angle     :  0.493   9.724  11174  Z= 0.258
  Chirality :  0.037   0.144   1299
  Planarity :  0.004   0.042   1217
  Dihedral  : 18.894 122.658   1709
  Min Nonbonded Distance : 2.252

Molprobity Statistics.
  All-atom Clashscore : 7.07
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.85 %
    Favored  : 97.15 %
  Rotamer:
    Outliers :  1.22 %
    Allowed  : 18.86 %
    Favored  : 79.92 %
  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:  1.09 (0.29), residues: 807
  helix:  2.14 (0.28), residues: 353
  sheet: -0.28 (0.58), residues: 81
  loop : -0.40 (0.31), residues: 373

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.006   0.000   ARG A 970 
 TYR   0.012   0.001   TYR A 948 
 PHE   0.012   0.001   PHE A 440 
 TRP   0.014   0.001   TRP A 555 
 HIS   0.003   0.001   HIS A 422 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00228 /  0.10 ( 8060)
  covalent geometry    : angle       0.49049 /  0.26 (11169)
  SS BOND              : bond        0.00441 /  0.29 (    1)
  SS BOND              : angle       0.97239 /  0.69 (    2)
  hydrogen bonds       : bond        0.03792 /  2.51 (  312)
  hydrogen bonds       : angle       4.18071 /  3.21 (  885)
  metal coordination   : bond        0.01165 /  0.60 (    7)
  metal coordination   : angle       3.23984 /  2.25 (    3)

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

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

  1614 Ramachandran restraints generated.
    807 Oldfield, 0 Emsley, 807 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1614 Ramachandran restraints generated.
    807 Oldfield, 0 Emsley, 807 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Residue LYS  212 is missing expected H atoms. Skipping.
Residue LYS  401 is missing expected H atoms. Skipping.
Residue LEU  478 is missing expected H atoms. Skipping.
Residue LYS  504 is missing expected H atoms. Skipping.
Residue LYS  591 is missing expected H atoms. Skipping.
Residue MET 1063 is missing expected H atoms. Skipping.
Residue LYS 1325 is missing expected H atoms. Skipping.
Residue LYS  150 is missing expected H atoms. Skipping.
Residue LYS  160 is missing expected H atoms. Skipping.
Evaluate side-chains
  118 residues out of total 754 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 9
    poor density    : 109
  time to evaluate  : 0.363 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  222 GLU cc_start: 0.7139 (tm-30) cc_final: 0.6780 (tm-30)
REVERT: A  263 ILE cc_start: 0.8123 (pt) cc_final: 0.7717 (tt)
REVERT: A  561 PHE cc_start: 0.6738 (t80) cc_final: 0.6440 (t80)
REVERT: A 1298 ASN cc_start: 0.6354 (m-40) cc_final: 0.6118 (m110)
  outliers start: 9
  outliers final: 8
  residues processed: 116
  average time/residue: 0.1936
  time to fit residues: 30.6643
Evaluate side-chains
  116 residues out of total 754 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 8
    poor density    : 108
  time to evaluate  : 0.358 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  268 HIS
Chi-restraints excluded: chain A residue  272 ILE
Chi-restraints excluded: chain A residue  292 ILE
Chi-restraints excluded: chain A residue  350 ASN
Chi-restraints excluded: chain A residue  469 PHE
Chi-restraints excluded: chain A residue  502 ILE
Chi-restraints excluded: chain A residue  503 GLU
Chi-restraints excluded: chain A residue 1141 ASP
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 87
   random chunks:
   chunk 4 optimal weight:    2.9990
   chunk 22 optimal weight:    1.9990
   chunk 14 optimal weight:    0.9980
   chunk 1 optimal weight:    3.9990
   chunk 61 optimal weight:    0.9990
   chunk 58 optimal weight:    0.9980
   chunk 71 optimal weight:    0.0370
   chunk 44 optimal weight:    0.6980
   chunk 37 optimal weight:    0.7980
   chunk 84 optimal weight:    0.0980
   chunk 60 optimal weight:    0.9990
   overall best weight:    0.5258

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
A 413 ASN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4645 r_free = 0.4645 target = 0.201799 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 34)----------------|
| r_work = 0.4303 r_free = 0.4303 target = 0.172483 restraints weight = 40088.822|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 30)----------------|
| r_work = 0.4324 r_free = 0.4324 target = 0.175555 restraints weight = 18307.703|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 33)----------------|
| r_work = 0.4343 r_free = 0.4343 target = 0.176907 restraints weight = 12196.889|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 25)----------------|
| r_work = 0.4347 r_free = 0.4347 target = 0.177238 restraints weight = 8431.706|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 25)----------------|
| r_work = 0.4351 r_free = 0.4351 target = 0.177507 restraints weight = 8579.094|
|-----------------------------------------------------------------------------|
r_work (final): 0.4324
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6162
moved from start:          0.1879

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.030   8068  Z= 0.137
  Angle     :  0.506   9.173  11174  Z= 0.267
  Chirality :  0.037   0.133   1299
  Planarity :  0.004   0.048   1217
  Dihedral  : 18.921 122.426   1709
  Min Nonbonded Distance : 2.234

Molprobity Statistics.
  All-atom Clashscore : 8.20
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.59 %
    Favored  : 96.41 %
  Rotamer:
    Outliers :  1.09 %
    Allowed  : 19.13 %
    Favored  : 79.78 %
  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:  1.02 (0.29), residues: 807
  helix:  2.07 (0.28), residues: 353
  sheet: -0.30 (0.58), residues: 81
  loop : -0.44 (0.31), residues: 373

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.006   0.000   ARG A 970 
 TYR   0.011   0.001   TYR A1245 
 PHE   0.021   0.001   PHE A 955 
 TRP   0.010   0.001   TRP A 555 
 HIS   0.003   0.001   HIS A 973 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00316 /  0.14 ( 8060)
  covalent geometry    : angle       0.50249 /  0.27 (11169)
  SS BOND              : bond        0.00659 /  0.44 (    1)
  SS BOND              : angle       1.29547 /  0.78 (    2)
  hydrogen bonds       : bond        0.04050 /  2.69 (  312)
  hydrogen bonds       : angle       4.22305 /  3.22 (  885)
  metal coordination   : bond        0.00840 /  0.43 (    7)
  metal coordination   : angle       3.45121 /  2.47 (    3)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 2933.96 seconds
wall clock time: 50 minutes 45.99 seconds (3045.99 seconds total)