Starting phenix.real_space_refine
on Fri Jul  3 03:27:03 2026 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/9k4e_62056/07_2026/9k4e_62056.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/9k4e_62056/07_2026/9k4e_62056.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=3.3
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/cci-nas-00/data/ceres_data/9k4e_62056/07_2026/9k4e_62056.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/9k4e_62056/07_2026/9k4e_62056.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/9k4e_62056/07_2026/9k4e_62056.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/9k4e_62056/07_2026/9k4e_62056.cif"
  }
  resolution = 3.3
  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=   0.006 sd=   0.154
Set stop_for_unknowns flag
  Set to: True
Assert model is a single copy model
Assert all atoms have isotropic ADPs
Construct map_model_manager
Extract box with map and model
Check model and map are aligned
Set scattering table
  Set to: electron
  Number of scattering types: 5
    Type Number    sf(0)   Gaussians
     P     112      5.49       5
     S      19      5.16       5
     C    7001      2.51       5
     N    2044      2.21       5
     O    2491      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 1 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: 11667
  Number of models: 1
  Model: ""
    Number of chains: 4
    Chain: "A"
      Number of atoms: 9247
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 1134, 9247
          Classifications: {'peptide': 1134}
          Modifications used: {'COO': 1}
          Link IDs: {'PTRANS': 30, 'TRANS': 1103}
          Chain breaks: 2
    Chain: "B"
      Number of atoms: 282
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 14, 282
          Classifications: {'DNA': 14}
          Modifications used: {'5*END': 1}
          Link IDs: {'rna3p': 13}
    Chain: "C"
      Number of atoms: 286
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 14, 286
          Classifications: {'DNA': 14}
          Modifications used: {'5*END': 1}
          Link IDs: {'rna3p': 13}
    Chain: "D"
      Number of atoms: 1852
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 87, 1852
          Classifications: {'RNA': 87}
          Modifications used: {'5*END': 1, 'rna2p_pur': 6, 'rna2p_pyr': 5, 'rna3p_pur': 42, 'rna3p_pyr': 33}
          Link IDs: {'rna2p': 11, 'rna3p': 75}
          Unresolved non-hydrogen bonds: 1
          Unresolved non-hydrogen angles: 1
          Unresolved non-hydrogen dihedrals: 1
  Time building chain proxies: 2.56, per 1000 atoms: 0.22
  Number of scatterers: 11667
  At special positions: 0
  Unit cell: (118.26, 105.12, 130.305, 90, 90, 90)
  Space group: P 1 (No. 1)
  Number of sites at special positions: 0
  Number of scattering types: 5
    Type Number    sf(0)
     S      19     16.00
     P     112     15.00
     O    2491      8.00
     N    2044      7.00
     C    7001      6.00
    sf(0) = scattering factor at diffraction angle 0.

  Number of disulfides: simple=0, symmetry=0

  Automatic linking
    Parameters for automatic linking
      Linking & cutoffs
        Metal                : Auto  - 3.00
        Amino acid           : True  - 1.90
        Carbohydrate         : True  - 1.99
        Ligands              : True  - 1.99
        Small molecules      : False - 1.98
        Amino acid - RNA/DNA : False
      
  Number of custom bonds: simple=0, symmetry=0
  Time building additional restraints: 1.04
  Conformation dependent library (CDL) restraints added in 477.6 milliseconds
  

  2256 Ramachandran restraints generated.
    1128 Oldfield, 0 Emsley, 1128 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  2156

  Finding SS restraints...
    Secondary structure from input PDB file:
      55 helices and 7 sheets defined
      55.8% alpha, 8.6% beta
      37 base pairs and 73 stacking pairs defined.
    Time for finding SS restraints: 1.48
  Creating SS restraints...
    Processing helix  chain 'A' and resid 59 through 94
      removed outlier: 4.701A  pdb=" N   ASN A  88 " --> pdb=" O   GLU A  84 " (cutoff:3.500A)
      removed outlier: 5.237A  pdb=" N   GLU A  89 " --> pdb=" O   ILE A  85 " (cutoff:3.500A)
      removed outlier: 4.268A  pdb=" N   LYS A  92 " --> pdb=" O   ASN A  88 " (cutoff:3.500A)
      removed outlier: 3.790A  pdb=" N   VAL A  93 " --> pdb=" O   GLU A  89 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 96 through 103
    Processing helix  chain 'A' and resid 104 through 106
      No H-bonds generated for 'chain 'A' and resid 104 through 106'
    Processing helix  chain 'A' and resid 121 through 132
    Processing helix  chain 'A' and resid 134 through 145
      removed outlier: 3.776A  pdb=" N   LEU A 138 " --> pdb=" O   THR A 134 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 150 through 164
    Processing helix  chain 'A' and resid 180 through 196
    Processing helix  chain 'A' and resid 207 through 213
    Processing helix  chain 'A' and resid 217 through 228
    Processing helix  chain 'A' and resid 236 through 247
    Processing helix  chain 'A' and resid 252 through 257
    Processing helix  chain 'A' and resid 270 through 283
    Processing helix  chain 'A' and resid 286 through 306
    Processing helix  chain 'A' and resid 315 through 343
    Processing helix  chain 'A' and resid 346 through 352
    Processing helix  chain 'A' and resid 358 through 364
    Processing helix  chain 'A' and resid 368 through 382
      Proline residue:  A 378  - end of helix
    Processing helix  chain 'A' and resid 386 through 396
    Processing helix  chain 'A' and resid 404 through 410
      removed outlier: 3.522A  pdb=" N   ASN A 407 " --> pdb=" O   THR A 404 " (cutoff:3.500A)
      removed outlier: 3.732A  pdb=" N   GLY A 408 " --> pdb=" O   PHE A 405 " (cutoff:3.500A)
      removed outlier: 3.535A  pdb=" N   SER A 409 " --> pdb=" O   ASP A 406 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 411 through 427
      removed outlier: 4.055A  pdb=" N   HIS A 415 " --> pdb=" O   PRO A 411 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 430 through 436
      removed outlier: 3.587A  pdb=" N   LYS A 434 " --> pdb=" O   TYR A 430 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 436 through 446
    Processing helix  chain 'A' and resid 477 through 482
    Processing helix  chain 'A' and resid 483 through 496
      removed outlier: 3.529A  pdb=" N   THR A 496 " --> pdb=" O   ILE A 492 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 512 through 526
      removed outlier: 4.230A  pdb=" N   LYS A 526 " --> pdb=" O   ASN A 522 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 541 through 552
    Processing helix  chain 'A' and resid 560 through 568
    Processing helix  chain 'A' and resid 591 through 602
    Processing helix  chain 'A' and resid 603 through 609
    Processing helix  chain 'A' and resid 612 through 626
    Processing helix  chain 'A' and resid 628 through 637
    Processing helix  chain 'A' and resid 638 through 640
      No H-bonds generated for 'chain 'A' and resid 638 through 640'
    Processing helix  chain 'A' and resid 644 through 654
    Processing helix  chain 'A' and resid 664 through 669
    Processing helix  chain 'A' and resid 678 through 685
    Processing helix  chain 'A' and resid 692 through 699
    Processing helix  chain 'A' and resid 703 through 712
    Processing helix  chain 'A' and resid 723 through 727
    Processing helix  chain 'A' and resid 730 through 751
    Processing helix  chain 'A' and resid 926 through 940
    Processing helix  chain 'A' and resid 959 through 970
      removed outlier: 4.054A  pdb=" N   VAL A 963 " --> pdb=" O   LYS A 959 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 981 through 1001
    Processing helix  chain 'A' and resid 1076 through 1088
    Processing helix  chain 'A' and resid 1127 through 1132
    Processing helix  chain 'A' and resid 1170 through 1177
    Processing helix  chain 'A' and resid 1177 through 1185
    Processing helix  chain 'A' and resid 1191 through 1195
    Processing helix  chain 'A' and resid 1207 through 1209
      No H-bonds generated for 'chain 'A' and resid 1207 through 1209'
    Processing helix  chain 'A' and resid 1229 through 1241
    Processing helix  chain 'A' and resid 1248 through 1262
    Processing helix  chain 'A' and resid 1264 through 1281
    Processing helix  chain 'A' and resid 1283 through 1297
    Processing helix  chain 'A' and resid 1301 through 1313
      removed outlier: 3.898A  pdb=" N   HIS A1311 " --> pdb=" O   GLU A1307 " (cutoff:3.500A)
      removed outlier: 3.663A  pdb=" N   PHE A1313 " --> pdb=" O   ILE A1309 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 1340 through 1344
      removed outlier: 4.010A  pdb=" N   ASP A1344 " --> pdb=" O   GLU A1341 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 1363 through 1365
      No H-bonds generated for 'chain 'A' and resid 1363 through 1365'
    Processing sheet with id=AA1, first strand: chain 'A' and resid 954 through 957
      removed outlier: 4.178A  pdb=" N   ASN A 758 " --> pdb=" O   TYR A   5 " (cutoff:3.500A)
    Processing sheet with id=AA2, first strand: chain 'A' and resid 29 through 33
    Processing sheet with id=AA3, first strand: chain 'A' and resid 35 through 36
      removed outlier: 6.384A  pdb=" N   LEU A  35 " --> pdb=" O   ARG A1359 " (cutoff:3.500A)
      removed outlier: 7.857A  pdb=" N   ASP A1361 " --> pdb=" O   LEU A  35 " (cutoff:3.500A)
      removed outlier: 4.345A  pdb=" N   LEU A1203 " --> pdb=" O   ILE A1348 " (cutoff:3.500A)
      removed outlier: 4.096A  pdb=" N   SER A1202 " --> pdb=" O   LEU A1214 " (cutoff:3.500A)
      removed outlier: 6.505A  pdb=" N   GLU A1219 " --> pdb=" O   ALA A1215 " (cutoff:3.500A)
    Processing sheet with id=AA4, first strand: chain 'A' and resid 507 through 509
      removed outlier: 5.432A  pdb=" N   LEU A 508 " --> pdb=" O   GLY A 660 " (cutoff:3.500A)
    Processing sheet with id=AA5, first strand: chain 'A' and resid 538 through 539
    Processing sheet with id=AA6, first strand: chain 'A' and resid 1156 through 1167
      removed outlier: 3.552A  pdb=" N   LYS A1156 " --> pdb=" O   LYS A1151 " (cutoff:3.500A)
      removed outlier: 3.809A  pdb=" N   ILE A1196 " --> pdb=" O   LEU A1144 " (cutoff:3.500A)
    Processing sheet with id=AA7, first strand: chain 'A' and resid 1324 through 1326

    464 hydrogen bonds defined for protein.
    1356 hydrogen bond angles defined for protein.
    Restraints generated for nucleic acids:
      94 hydrogen bonds
      184 hydrogen bond angles
      0 basepair planarities
      37 basepair parallelities
      73 stacking parallelities
  Total time for adding SS restraints: 3.22

  Time building geometry restraints manager: 1.41 seconds

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

  Histogram of bond lengths:
        1.21 -     1.33: 2664
        1.33 -     1.45: 2956
        1.45 -     1.57: 6242
        1.57 -     1.69: 224
        1.69 -     1.81: 36
  Bond restraints: 12122
  Sorted by residual:
  bond pdb=" C3'  DG B   7 "
       pdb=" C2'  DG B   7 "
    ideal  model  delta    sigma   weight residual
    1.516  1.538 -0.022 8.00e-03 1.56e+04 7.89e+00
  bond pdb=" C3'  DG B  12 "
       pdb=" C2'  DG B  12 "
    ideal  model  delta    sigma   weight residual
    1.516  1.536 -0.020 8.00e-03 1.56e+04 6.27e+00
  bond pdb=" C3'  DG C   3 "
       pdb=" C2'  DG C   3 "
    ideal  model  delta    sigma   weight residual
    1.516  1.536 -0.020 8.00e-03 1.56e+04 6.17e+00
  bond pdb=" C3'  DC B  14 "
       pdb=" C2'  DC B  14 "
    ideal  model  delta    sigma   weight residual
    1.516  1.535 -0.019 8.00e-03 1.56e+04 5.87e+00
  bond pdb=" C3'  DT C   9 "
       pdb=" C2'  DT C   9 "
    ideal  model  delta    sigma   weight residual
    1.516  1.535 -0.019 8.00e-03 1.56e+04 5.69e+00
  ... (remaining 12117 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     1.91: 16658
        1.91 -     3.82: 187
        3.82 -     5.72: 10
        5.72 -     7.63: 1
        7.63 -     9.54: 1
  Bond angle restraints: 16857
  Sorted by residual:
  angle pdb=" N3   DT B  10 "
        pdb=" C4   DT B  10 "
        pdb=" O4   DT B  10 "
      ideal   model   delta    sigma   weight residual
     119.90  122.50   -2.60 6.00e-01 2.78e+00 1.88e+01
  angle pdb=" N3   DT C  12 "
        pdb=" C4   DT C  12 "
        pdb=" O4   DT C  12 "
      ideal   model   delta    sigma   weight residual
     119.90  122.37   -2.47 6.00e-01 2.78e+00 1.69e+01
  angle pdb=" N3   DT B   6 "
        pdb=" C4   DT B   6 "
        pdb=" O4   DT B   6 "
      ideal   model   delta    sigma   weight residual
     119.90  122.33   -2.43 6.00e-01 2.78e+00 1.64e+01
  angle pdb=" N3   DT B   4 "
        pdb=" C4   DT B   4 "
        pdb=" O4   DT B   4 "
      ideal   model   delta    sigma   weight residual
     119.90  122.30   -2.40 6.00e-01 2.78e+00 1.60e+01
  angle pdb=" N3   DT C   9 "
        pdb=" C4   DT C   9 "
        pdb=" O4   DT C   9 "
      ideal   model   delta    sigma   weight residual
     119.90  122.30   -2.40 6.00e-01 2.78e+00 1.59e+01
  ... (remaining 16852 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    30.03: 6992
       30.03 -    60.06: 329
       60.06 -    90.10: 69
       90.10 -   120.13: 0
      120.13 -   150.16: 1
  Dihedral angle restraints: 7391
    sinusoidal: 4060
      harmonic: 3331
  Sorted by residual:
  dihedral pdb=" CA  MET A 495 "
           pdb=" C   MET A 495 "
           pdb=" N   THR A 496 "
           pdb=" CA  THR A 496 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00 -160.61  -19.39     0      5.00e+00 4.00e-02 1.50e+01
  dihedral pdb=" C4'  DG B   7 "
           pdb=" C3'  DG B   7 "
           pdb=" O3'  DG B   7 "
           pdb=" P    DA B   8 "
      ideal   model   delta sinusoidal    sigma   weight residual
     220.00   69.84  150.16     1      3.50e+01 8.16e-04 1.46e+01
  dihedral pdb=" CG  ARG A1359 "
           pdb=" CD  ARG A1359 "
           pdb=" NE  ARG A1359 "
           pdb=" CZ  ARG A1359 "
      ideal   model   delta sinusoidal    sigma   weight residual
    -180.00 -135.21  -44.79     2      1.50e+01 4.44e-03 1.06e+01
  ... (remaining 7388 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.027: 1227
       0.027 -    0.054: 476
       0.054 -    0.081: 141
       0.081 -    0.108: 67
       0.108 -    0.135: 30
  Chirality restraints: 1941
  Sorted by residual:
  chirality pdb=" P    DA B   8 "
            pdb=" OP1  DA B   8 "
            pdb=" OP2  DA B   8 "
            pdb=" O5'  DA B   8 "
    both_signs  ideal   model   delta    sigma   weight residual
      True       2.34   -2.47   -0.13 2.00e-01 2.50e+01 4.54e-01
  chirality pdb=" C3'   C D  13 "
            pdb=" C4'   C D  13 "
            pdb=" O3'   C D  13 "
            pdb=" C2'   C D  13 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.48   -2.61    0.13 2.00e-01 2.50e+01 4.48e-01
  chirality pdb=" C3'  DC B  14 "
            pdb=" C4'  DC B  14 "
            pdb=" O3'  DC B  14 "
            pdb=" C2'  DC B  14 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.73   -2.60   -0.13 2.00e-01 2.50e+01 4.43e-01
  ... (remaining 1938 not shown)

  Planarity restraints: 1735
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C1'   A D  44 "    0.019 2.00e-02 2.50e+03   9.13e-03 2.29e+00
        pdb=" N9    A D  44 "   -0.022 2.00e-02 2.50e+03
        pdb=" C8    A D  44 "   -0.001 2.00e-02 2.50e+03
        pdb=" N7    A D  44 "    0.002 2.00e-02 2.50e+03
        pdb=" C5    A D  44 "    0.001 2.00e-02 2.50e+03
        pdb=" C6    A D  44 "    0.001 2.00e-02 2.50e+03
        pdb=" N6    A D  44 "    0.004 2.00e-02 2.50e+03
        pdb=" N1    A D  44 "    0.002 2.00e-02 2.50e+03
        pdb=" C2    A D  44 "   -0.001 2.00e-02 2.50e+03
        pdb=" N3    A D  44 "   -0.002 2.00e-02 2.50e+03
        pdb=" C4    A D  44 "   -0.002 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C1'   A D  49 "    0.016 2.00e-02 2.50e+03   7.54e-03 1.57e+00
        pdb=" N9    A D  49 "   -0.018 2.00e-02 2.50e+03
        pdb=" C8    A D  49 "   -0.001 2.00e-02 2.50e+03
        pdb=" N7    A D  49 "    0.002 2.00e-02 2.50e+03
        pdb=" C5    A D  49 "   -0.003 2.00e-02 2.50e+03
        pdb=" C6    A D  49 "    0.002 2.00e-02 2.50e+03
        pdb=" N6    A D  49 "    0.005 2.00e-02 2.50e+03
        pdb=" N1    A D  49 "    0.000 2.00e-02 2.50e+03
        pdb=" C2    A D  49 "   -0.001 2.00e-02 2.50e+03
        pdb=" N3    A D  49 "   -0.002 2.00e-02 2.50e+03
        pdb=" C4    A D  49 "    0.001 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C1'   A D  76 "   -0.015 2.00e-02 2.50e+03   7.05e-03 1.37e+00
        pdb=" N9    A D  76 "    0.018 2.00e-02 2.50e+03
        pdb=" C8    A D  76 "   -0.000 2.00e-02 2.50e+03
        pdb=" N7    A D  76 "   -0.000 2.00e-02 2.50e+03
        pdb=" C5    A D  76 "   -0.001 2.00e-02 2.50e+03
        pdb=" C6    A D  76 "   -0.001 2.00e-02 2.50e+03
        pdb=" N6    A D  76 "   -0.004 2.00e-02 2.50e+03
        pdb=" N1    A D  76 "   -0.000 2.00e-02 2.50e+03
        pdb=" C2    A D  76 "    0.000 2.00e-02 2.50e+03
        pdb=" N3    A D  76 "    0.002 2.00e-02 2.50e+03
        pdb=" C4    A D  76 "    0.001 2.00e-02 2.50e+03
  ... (remaining 1732 not shown)

  Histogram of nonbonded interaction distances:
        1.30 -     2.02: 2
        2.02 -     2.74: 969
        2.74 -     3.46: 15587
        3.46 -     4.18: 28908
        4.18 -     4.90: 48785
  Nonbonded interactions: 94251
  Sorted by model distance:
  nonbonded pdb=" NZ  LYS A 742 "
            pdb=" OP1   C D  69 "
     model   vdw
     1.296 3.120
  nonbonded pdb=" NH1 ARG A  71 "
            pdb=" N4    C D  20 "
     model   vdw
     1.351 3.200
  nonbonded pdb=" NH2 ARG A 400 "
            pdb=" OD2 ASP A 406 "
     model   vdw
     2.137 3.120
  nonbonded pdb=" O   ILE A 305 "
            pdb=" OG  SER A 320 "
     model   vdw
     2.150 3.040
  nonbonded pdb=" NH1 ARG A  71 "
            pdb=" C4    C D  20 "
     model   vdw
     2.153 3.340
  ... (remaining 94246 not shown)

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

  No NCS relation were found !!!

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

Found NCS groups:
  found none.
Set up NCS constraints
  No NCS constraints will be used in refinement.
Set refine NCS operators
Adjust number of macro_cycles
  Number of macro_cycles: 10
Reset NCS operators
Extract rigid body selections
Check and reset occupancies
  Occupancies: min=1.00 max=1.00 mean=1.00
Load rotamer database and sin/cos tables
Set ADP refinement strategy
  ADPs will be refined as individual isotropic
Make a string to write initial .geo file
Internal consistency checks
Time:
  Set random seed:                         0.010
  Set model cs if undefined:               0.000
  Decide on map wrapping:                  0.000
  Normalize map: mean=0, sd=1:             0.510
  Set stop_for_unknowns flag:              0.000
  Assert model is a single copy model:     0.000
  Assert all atoms have isotropic ADPs:    0.000
  Construct map_model_manager:             0.010
  Extract box with map and model:          0.220
  Check model and map are aligned:         0.030
  Set scattering table:                    0.030
  Process input model:                     13.820
  Find NCS groups from input model:        0.050
  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:             0.010
  Load rotamer database and sin/cos tables:1.220
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   15.930
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7886
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      :  0.003   0.030  12122  Z= 0.233
  Angle     :  0.518   9.540  16857  Z= 0.367
  Chirality :  0.037   0.135   1941
  Planarity :  0.003   0.028   1735
  Dihedral  : 16.207 150.162   5235
  Min Nonbonded Distance : 1.296

Molprobity Statistics.
  All-atom Clashscore : 4.97
  Ramachandran Plot:
    Outliers :  0.09 %
    Allowed  :  1.95 %
    Favored  : 97.96 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  0.10 %
    Favored  : 99.90 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  1.43 (0.25), residues: 1128
  helix:  1.47 (0.22), residues: 597
  sheet:  0.88 (0.55), residues: 87
  loop :  0.40 (0.30), residues: 444

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARG A 324 
 TYR   0.018   0.001   TYR A 451 
 PHE   0.018   0.001   PHE A 491 
 TRP   0.008   0.001   TRP A1126 
 HIS   0.005   0.001   HIS A 985 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00333 /  0.23 (12122)
  covalent geometry    : angle       0.51786 /  0.37 (16857)
  hydrogen bonds       : bond        0.15571 / 10.38 (  558)
  hydrogen bonds       : angle       5.99214 /  4.18 ( 1540)

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

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

  2256 Ramachandran restraints generated.
    1128 Oldfield, 0 Emsley, 1128 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2256 Ramachandran restraints generated.
    1128 Oldfield, 0 Emsley, 1128 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  266 residues out of total 1014 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 266
  time to evaluate  : 0.382 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   76 LYS cc_start: 0.8079 (tttt) cc_final: 0.7816 (tptt)
REVERT: A   84 GLU cc_start: 0.8097 (tt0) cc_final: 0.7664 (tp30)
REVERT: A  147 ASP cc_start: 0.7878 (m-30) cc_final: 0.7430 (p0)
REVERT: A  183 LYS cc_start: 0.6233 (tttt) cc_final: 0.5908 (mmtm)
REVERT: A  202 ASN cc_start: 0.7897 (t0) cc_final: 0.7586 (p0)
REVERT: A  273 ASP cc_start: 0.8324 (m-30) cc_final: 0.7754 (p0)
REVERT: A  314 LYS cc_start: 0.8387 (mttt) cc_final: 0.7795 (mtmt)
REVERT: A  334 LEU cc_start: 0.8226 (tp) cc_final: 0.7839 (tt)
REVERT: A  516 GLU cc_start: 0.7835 (mt-10) cc_final: 0.7501 (mt-10)
REVERT: A  534 MET cc_start: 0.4246 (mtp) cc_final: 0.3172 (ptm)
REVERT: A  570 LYS cc_start: 0.8821 (tttt) cc_final: 0.8289 (tppt)
REVERT: A  696 LEU cc_start: 0.8493 (mt) cc_final: 0.8107 (mm)
REVERT: A  751 MET cc_start: 0.8551 (mmm) cc_final: 0.8347 (mmm)
REVERT: A  959 LYS cc_start: 0.6670 (mmpt) cc_final: 0.6312 (mttp)
REVERT: A  977 GLU cc_start: 0.7710 (mp0) cc_final: 0.7256 (mp0)
REVERT: A  999 LYS cc_start: 0.8404 (mmtm) cc_final: 0.7415 (ttpp)
REVERT: A 1170 GLU cc_start: 0.8732 (mt-10) cc_final: 0.8485 (mt-10)
REVERT: A 1188 LYS cc_start: 0.8347 (mttt) cc_final: 0.8080 (mmmt)
REVERT: A 1256 GLN cc_start: 0.7232 (mt0) cc_final: 0.6799 (mm110)
REVERT: A 1258 PHE cc_start: 0.7389 (t80) cc_final: 0.6925 (t80)
REVERT: A 1263 LYS cc_start: 0.8379 (tttt) cc_final: 0.7720 (mtmt)
REVERT: A 1264 HIS cc_start: 0.6106 (p-80) cc_final: 0.5881 (p-80)
REVERT: A 1272 GLN cc_start: 0.7071 (mt0) cc_final: 0.6710 (mm-40)
REVERT: A 1307 GLU cc_start: 0.7681 (mt-10) cc_final: 0.7320 (mt-10)
  outliers start: 0
  outliers final: 0
  residues processed: 266
  average time/residue: 0.1442
  time to fit residues: 50.4166
Evaluate side-chains
  134 residues out of total 1014 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 134
  time to evaluate  : 0.376 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 123
   random chunks:
   chunk 108 optimal weight:    4.9990
   chunk 49 optimal weight:    2.9990
   chunk 97 optimal weight:    2.9990
   chunk 113 optimal weight:   40.0000
   chunk 53 optimal weight:   30.0000
   chunk 5 optimal weight:    2.9990
   chunk 33 optimal weight:    5.9990
   chunk 65 optimal weight:    8.9990
   chunk 62 optimal weight:    4.9990
   chunk 51 optimal weight:    8.9990
   chunk 117 optimal weight:   30.0000
   overall best weight:    3.7990

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
A 194 GLN
A 716 GLN
** A 930 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3957 r_free = 0.3957 target = 0.157161 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 56)----------------|
| r_work = 0.3287 r_free = 0.3287 target = 0.104045 restraints weight = 16817.738|
|-----------------------------------------------------------------------------|
r_work (start): 0.3273 rms_B_bonded: 2.52
r_work: 0.3122 rms_B_bonded: 3.54 restraints_weight: 0.5000
r_work (final): 0.3122
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8064
moved from start:          0.1960

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.006   0.044  12122  Z= 0.260
  Angle     :  0.595   6.578  16857  Z= 0.331
  Chirality :  0.042   0.237   1941
  Planarity :  0.005   0.060   1735
  Dihedral  : 18.634 151.543   2843
  Min Nonbonded Distance : 2.454

Molprobity Statistics.
  All-atom Clashscore : 4.84
  Ramachandran Plot:
    Outliers :  0.09 %
    Allowed  :  1.60 %
    Favored  : 98.32 %
  Rotamer:
    Outliers :  1.78 %
    Allowed  :  7.50 %
    Favored  : 90.73 %
  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:  0.89 (0.25), residues: 1128
  helix:  1.15 (0.21), residues: 603
  sheet: -0.07 (0.49), residues: 111
  loop :  0.12 (0.30), residues: 414

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.007   0.001   ARG A1303 
 TYR   0.015   0.002   TYR A1242 
 PHE   0.018   0.002   PHE A 491 
 TRP   0.005   0.001   TRP A1126 
 HIS   0.006   0.001   HIS A 167 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00582 /  0.26 (12122)
  covalent geometry    : angle       0.59549 /  0.33 (16857)
  hydrogen bonds       : bond        0.05355 /  3.58 (  558)
  hydrogen bonds       : angle       4.98880 /  3.50 ( 1540)

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

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

  2256 Ramachandran restraints generated.
    1128 Oldfield, 0 Emsley, 1128 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2256 Ramachandran restraints generated.
    1128 Oldfield, 0 Emsley, 1128 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  162 residues out of total 1014 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 18
    poor density    : 144
  time to evaluate  : 0.331 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   76 LYS cc_start: 0.8354 (tttt) cc_final: 0.7957 (tptt)
REVERT: A   84 GLU cc_start: 0.8082 (tt0) cc_final: 0.7736 (tp30)
REVERT: A   89 GLU cc_start: 0.7699 (mm-30) cc_final: 0.7082 (tp30)
REVERT: A  147 ASP cc_start: 0.8008 (m-30) cc_final: 0.7600 (p0)
REVERT: A  183 LYS cc_start: 0.5969 (tttt) cc_final: 0.5747 (ttpp)
REVERT: A  202 ASN cc_start: 0.8080 (t0) cc_final: 0.7716 (p0)
REVERT: A  215 ARG cc_start: 0.7276 (mmm160) cc_final: 0.7035 (mmm160)
REVERT: A  234 LYS cc_start: 0.8698 (pttt) cc_final: 0.8362 (ptmm)
REVERT: A  252 PHE cc_start: 0.7525 (m-80) cc_final: 0.7196 (m-80)
REVERT: A  273 ASP cc_start: 0.8199 (m-30) cc_final: 0.7965 (p0)
REVERT: A  314 LYS cc_start: 0.8567 (mttt) cc_final: 0.7988 (mtmt)
REVERT: A  353 ASP cc_start: 0.8298 (t0) cc_final: 0.8033 (t0)
REVERT: A  356 LYS cc_start: 0.8561 (mmtt) cc_final: 0.8263 (mptt)
REVERT: A  534 MET cc_start: 0.4302 (mtp) cc_final: 0.3070 (ptm)
REVERT: A  682 PHE cc_start: 0.7628 (m-10) cc_final: 0.7067 (m-10)
REVERT: A  705 LYS cc_start: 0.7229 (ttmm) cc_final: 0.7000 (ttmm)
REVERT: A  751 MET cc_start: 0.8617 (mmm) cc_final: 0.8297 (mmm)
REVERT: A  926 GLN cc_start: 0.7606 (mp10) cc_final: 0.7240 (mm-40)
REVERT: A  929 LYS cc_start: 0.8298 (mtpt) cc_final: 0.7329 (tptt)
REVERT: A  933 GLN cc_start: 0.8000 (OUTLIER) cc_final: 0.7004 (pm20)
REVERT: A  953 VAL cc_start: 0.8914 (t) cc_final: 0.8656 (t)
REVERT: A  959 LYS cc_start: 0.7047 (mmpt) cc_final: 0.6532 (mttp)
REVERT: A  977 GLU cc_start: 0.7856 (mp0) cc_final: 0.7432 (mp0)
REVERT: A  999 LYS cc_start: 0.8396 (mmtm) cc_final: 0.7407 (ttpp)
REVERT: A 1170 GLU cc_start: 0.8808 (mt-10) cc_final: 0.8596 (mt-10)
REVERT: A 1188 LYS cc_start: 0.8560 (mttt) cc_final: 0.8328 (mmmt)
REVERT: A 1242 TYR cc_start: 0.7520 (t80) cc_final: 0.7135 (t80)
REVERT: A 1258 PHE cc_start: 0.7213 (t80) cc_final: 0.6771 (t80)
REVERT: A 1263 LYS cc_start: 0.8252 (tttt) cc_final: 0.7645 (mtmt)
REVERT: A 1303 ARG cc_start: 0.6556 (mtp-110) cc_final: 0.6217 (mtp-110)
REVERT: A 1307 GLU cc_start: 0.7719 (mt-10) cc_final: 0.7338 (mt-10)
  outliers start: 18
  outliers final: 12
  residues processed: 158
  average time/residue: 0.1450
  time to fit residues: 30.2042
Evaluate side-chains
  136 residues out of total 1014 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 123
  time to evaluate  : 0.415 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   80 CYS
Chi-restraints excluded: chain A residue  189 VAL
Chi-restraints excluded: chain A residue  249 THR
Chi-restraints excluded: chain A residue  272 ASP
Chi-restraints excluded: chain A residue  304 ASP
Chi-restraints excluded: chain A residue  327 GLU
Chi-restraints excluded: chain A residue  492 ILE
Chi-restraints excluded: chain A residue  590 SER
Chi-restraints excluded: chain A residue  649 LYS
Chi-restraints excluded: chain A residue  657 THR
Chi-restraints excluded: chain A residue  933 GLN
Chi-restraints excluded: chain A residue 1160 VAL
Chi-restraints excluded: chain A residue 1280 VAL
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 123
   random chunks:
   chunk 5 optimal weight:    0.9980
   chunk 116 optimal weight:   10.0000
   chunk 22 optimal weight:    5.9990
   chunk 2 optimal weight:    0.9990
   chunk 114 optimal weight:   10.0000
   chunk 4 optimal weight:    0.0980
   chunk 77 optimal weight:    6.9990
   chunk 89 optimal weight:    0.6980
   chunk 17 optimal weight:    2.9990
   chunk 35 optimal weight:    2.9990
   chunk 34 optimal weight:    8.9990
   overall best weight:    1.1584

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
A 194 GLN
** A 930 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3983 r_free = 0.3983 target = 0.159346 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 59)----------------|
| r_work = 0.3325 r_free = 0.3325 target = 0.106410 restraints weight = 16941.626|
|-----------------------------------------------------------------------------|
r_work (start): 0.3307 rms_B_bonded: 2.51
r_work: 0.3161 rms_B_bonded: 3.54 restraints_weight: 0.5000
r_work (final): 0.3161
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8002
moved from start:          0.2212

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.032  12122  Z= 0.127
  Angle     :  0.469   5.753  16857  Z= 0.267
  Chirality :  0.037   0.242   1941
  Planarity :  0.003   0.055   1735
  Dihedral  : 18.711 153.018   2843
  Min Nonbonded Distance : 2.502

Molprobity Statistics.
  All-atom Clashscore : 4.75
  Ramachandran Plot:
    Outliers :  0.09 %
    Allowed  :  1.86 %
    Favored  : 98.05 %
  Rotamer:
    Outliers :  1.87 %
    Allowed  :  9.07 %
    Favored  : 89.05 %
  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:  1.16 (0.25), residues: 1128
  helix:  1.44 (0.22), residues: 603
  sheet:  0.34 (0.52), residues: 94
  loop :  0.04 (0.29), residues: 431

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARG A  63 
 TYR   0.014   0.001   TYR A1242 
 PHE   0.015   0.001   PHE A 569 
 TRP   0.005   0.001   TRP A 476 
 HIS   0.003   0.001   HIS A 328 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00260 /  0.13 (12122)
  covalent geometry    : angle       0.46950 /  0.27 (16857)
  hydrogen bonds       : bond        0.04479 /  2.91 (  558)
  hydrogen bonds       : angle       4.57172 /  3.22 ( 1540)

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

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

  2256 Ramachandran restraints generated.
    1128 Oldfield, 0 Emsley, 1128 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2256 Ramachandran restraints generated.
    1128 Oldfield, 0 Emsley, 1128 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  156 residues out of total 1014 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 19
    poor density    : 137
  time to evaluate  : 0.364 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   76 LYS cc_start: 0.8332 (tttt) cc_final: 0.7883 (tptt)
REVERT: A   84 GLU cc_start: 0.8015 (tt0) cc_final: 0.7672 (tp30)
REVERT: A  147 ASP cc_start: 0.7991 (m-30) cc_final: 0.7617 (p0)
REVERT: A  202 ASN cc_start: 0.8101 (t0) cc_final: 0.7692 (p0)
REVERT: A  273 ASP cc_start: 0.8202 (m-30) cc_final: 0.7922 (p0)
REVERT: A  314 LYS cc_start: 0.8487 (mttt) cc_final: 0.7858 (mtmt)
REVERT: A  339 VAL cc_start: 0.8183 (p) cc_final: 0.7951 (p)
REVERT: A  353 ASP cc_start: 0.8316 (t0) cc_final: 0.7989 (t0)
REVERT: A  518 PHE cc_start: 0.7947 (t80) cc_final: 0.7661 (t80)
REVERT: A  534 MET cc_start: 0.4213 (mtp) cc_final: 0.2940 (ptm)
REVERT: A  628 ASP cc_start: 0.7964 (t0) cc_final: 0.7689 (t0)
REVERT: A  682 PHE cc_start: 0.7632 (m-10) cc_final: 0.7037 (m-10)
REVERT: A  705 LYS cc_start: 0.7524 (OUTLIER) cc_final: 0.7264 (ttmm)
REVERT: A  959 LYS cc_start: 0.7021 (mmpt) cc_final: 0.6420 (mttp)
REVERT: A  977 GLU cc_start: 0.7847 (mp0) cc_final: 0.7482 (mp0)
REVERT: A 1170 GLU cc_start: 0.8776 (mt-10) cc_final: 0.8452 (mt-10)
REVERT: A 1188 LYS cc_start: 0.8535 (mttt) cc_final: 0.8330 (mmmt)
REVERT: A 1213 MET cc_start: 0.8737 (OUTLIER) cc_final: 0.8420 (mtm)
REVERT: A 1242 TYR cc_start: 0.7497 (t80) cc_final: 0.6914 (t80)
REVERT: A 1258 PHE cc_start: 0.7162 (t80) cc_final: 0.6707 (t80)
REVERT: A 1263 LYS cc_start: 0.8137 (tttt) cc_final: 0.7615 (mtmt)
REVERT: A 1301 PRO cc_start: 0.7440 (Cg_exo) cc_final: 0.6964 (Cg_endo)
REVERT: A 1303 ARG cc_start: 0.6323 (mtp-110) cc_final: 0.5926 (mtp-110)
REVERT: A 1307 GLU cc_start: 0.7581 (mt-10) cc_final: 0.7167 (mt-10)
  outliers start: 19
  outliers final: 10
  residues processed: 151
  average time/residue: 0.1377
  time to fit residues: 27.6643
Evaluate side-chains
  138 residues out of total 1014 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 126
  time to evaluate  : 0.380 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  189 VAL
Chi-restraints excluded: chain A residue  249 THR
Chi-restraints excluded: chain A residue  272 ASP
Chi-restraints excluded: chain A residue  304 ASP
Chi-restraints excluded: chain A residue  480 GLU
Chi-restraints excluded: chain A residue  492 ILE
Chi-restraints excluded: chain A residue  590 SER
Chi-restraints excluded: chain A residue  705 LYS
Chi-restraints excluded: chain A residue  740 THR
Chi-restraints excluded: chain A residue  936 ASP
Chi-restraints excluded: chain A residue 1160 VAL
Chi-restraints excluded: chain A residue 1213 MET
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 123
   random chunks:
   chunk 113 optimal weight:   40.0000
   chunk 84 optimal weight:   10.0000
   chunk 57 optimal weight:    0.2980
   chunk 118 optimal weight:   10.0000
   chunk 78 optimal weight:   20.0000
   chunk 44 optimal weight:    0.0270
   chunk 52 optimal weight:    9.9990
   chunk 41 optimal weight:    5.9990
   chunk 104 optimal weight:    0.9980
   chunk 10 optimal weight:    5.9990
   chunk 88 optimal weight:    0.0870
   overall best weight:    1.4818

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
A 116 HIS
A 194 GLN
A 369 GLN
** A 930 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
A1254 GLN
A1256 GLN

Total number of N/Q/H flips: 5

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3978 r_free = 0.3978 target = 0.158785 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 30)----------------|
| r_work = 0.3437 r_free = 0.3437 target = 0.113013 restraints weight = 16936.985|
|-----------------------------------------------------------------------------|
r_work (start): 0.3407 rms_B_bonded: 2.91
r_work: 0.3106 rms_B_bonded: 4.12 restraints_weight: 0.5000
r_work (final): 0.3106
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8085
moved from start:          0.2448

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.029  12122  Z= 0.132
  Angle     :  0.456   5.616  16857  Z= 0.258
  Chirality :  0.037   0.242   1941
  Planarity :  0.004   0.059   1735
  Dihedral  : 18.707 153.400   2843
  Min Nonbonded Distance : 2.517

Molprobity Statistics.
  All-atom Clashscore : 4.52
  Ramachandran Plot:
    Outliers :  0.09 %
    Allowed  :  2.30 %
    Favored  : 97.61 %
  Rotamer:
    Outliers :  1.87 %
    Allowed  : 10.45 %
    Favored  : 87.67 %
  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:  1.20 (0.25), residues: 1128
  helix:  1.51 (0.22), residues: 604
  sheet:  0.32 (0.52), residues: 94
  loop : -0.01 (0.29), residues: 430

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.000   ARG A 691 
 TYR   0.013   0.001   TYR A 450 
 PHE   0.016   0.001   PHE A1327 
 TRP   0.005   0.001   TRP A 476 
 HIS   0.004   0.001   HIS A 698 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00281 /  0.13 (12122)
  covalent geometry    : angle       0.45557 /  0.26 (16857)
  hydrogen bonds       : bond        0.04113 /  2.70 (  558)
  hydrogen bonds       : angle       4.45895 /  3.15 ( 1540)

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

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

  2256 Ramachandran restraints generated.
    1128 Oldfield, 0 Emsley, 1128 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2256 Ramachandran restraints generated.
    1128 Oldfield, 0 Emsley, 1128 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  151 residues out of total 1014 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 19
    poor density    : 132
  time to evaluate  : 0.368 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   76 LYS cc_start: 0.8344 (tttt) cc_final: 0.7956 (tptt)
REVERT: A   84 GLU cc_start: 0.8109 (tt0) cc_final: 0.7754 (tp30)
REVERT: A   89 GLU cc_start: 0.7560 (mm-30) cc_final: 0.7167 (tp30)
REVERT: A   90 MET cc_start: 0.8274 (mmm) cc_final: 0.7956 (tmm)
REVERT: A  147 ASP cc_start: 0.8012 (m-30) cc_final: 0.7647 (p0)
REVERT: A  202 ASN cc_start: 0.8054 (t0) cc_final: 0.7629 (p0)
REVERT: A  273 ASP cc_start: 0.8210 (m-30) cc_final: 0.7893 (p0)
REVERT: A  314 LYS cc_start: 0.8484 (mttt) cc_final: 0.7866 (mtmt)
REVERT: A  339 VAL cc_start: 0.8163 (p) cc_final: 0.7942 (p)
REVERT: A  353 ASP cc_start: 0.8401 (t0) cc_final: 0.8109 (t0)
REVERT: A  356 LYS cc_start: 0.8516 (mmtt) cc_final: 0.8263 (mptt)
REVERT: A  495 MET cc_start: 0.8328 (ppp) cc_final: 0.7890 (ppp)
REVERT: A  518 PHE cc_start: 0.7994 (t80) cc_final: 0.7681 (t80)
REVERT: A  534 MET cc_start: 0.4476 (mtp) cc_final: 0.3311 (ptm)
REVERT: A  610 GLU cc_start: 0.8169 (mt-10) cc_final: 0.7722 (mt-10)
REVERT: A  628 ASP cc_start: 0.8074 (t0) cc_final: 0.7814 (t0)
REVERT: A  682 PHE cc_start: 0.7610 (m-80) cc_final: 0.7018 (m-10)
REVERT: A  705 LYS cc_start: 0.7481 (OUTLIER) cc_final: 0.7240 (ttmm)
REVERT: A  926 GLN cc_start: 0.7550 (mp10) cc_final: 0.7142 (mm-40)
REVERT: A  959 LYS cc_start: 0.7044 (mmpt) cc_final: 0.6452 (mttp)
REVERT: A  977 GLU cc_start: 0.7934 (mp0) cc_final: 0.7614 (mp0)
REVERT: A  988 TYR cc_start: 0.7818 (t80) cc_final: 0.7561 (t80)
REVERT: A 1170 GLU cc_start: 0.8878 (mt-10) cc_final: 0.8569 (mt-10)
REVERT: A 1188 LYS cc_start: 0.8515 (mttt) cc_final: 0.8287 (mmmt)
REVERT: A 1256 GLN cc_start: 0.6820 (mt0) cc_final: 0.6353 (mm110)
REVERT: A 1258 PHE cc_start: 0.7166 (t80) cc_final: 0.6697 (t80)
REVERT: A 1263 LYS cc_start: 0.8162 (tttt) cc_final: 0.7653 (mtmt)
REVERT: A 1303 ARG cc_start: 0.6292 (mtp-110) cc_final: 0.5839 (mtp-110)
REVERT: A 1307 GLU cc_start: 0.7563 (mt-10) cc_final: 0.7220 (mt-10)
REVERT: A 1332 ASP cc_start: 0.8308 (m-30) cc_final: 0.7859 (t0)
  outliers start: 19
  outliers final: 12
  residues processed: 144
  average time/residue: 0.1298
  time to fit residues: 25.2033
Evaluate side-chains
  128 residues out of total 1014 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 115
  time to evaluate  : 0.399 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  189 VAL
Chi-restraints excluded: chain A residue  249 THR
Chi-restraints excluded: chain A residue  278 LEU
Chi-restraints excluded: chain A residue  480 GLU
Chi-restraints excluded: chain A residue  492 ILE
Chi-restraints excluded: chain A residue  590 SER
Chi-restraints excluded: chain A residue  630 GLU
Chi-restraints excluded: chain A residue  657 THR
Chi-restraints excluded: chain A residue  705 LYS
Chi-restraints excluded: chain A residue  740 THR
Chi-restraints excluded: chain A residue  933 GLN
Chi-restraints excluded: chain A residue  936 ASP
Chi-restraints excluded: chain A residue 1160 VAL
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 123
   random chunks:
   chunk 118 optimal weight:   10.0000
   chunk 51 optimal weight:    8.9990
   chunk 82 optimal weight:    5.9990
   chunk 40 optimal weight:    0.9990
   chunk 48 optimal weight:    5.9990
   chunk 122 optimal weight:   20.0000
   chunk 97 optimal weight:    2.9990
   chunk 105 optimal weight:   10.0000
   chunk 17 optimal weight:    4.9990
   chunk 15 optimal weight:    3.9990
   chunk 61 optimal weight:    2.9990
   overall best weight:    3.1990

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
A 194 GLN
** A 930 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3943 r_free = 0.3943 target = 0.155695 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 61)----------------|
| r_work = 0.3276 r_free = 0.3276 target = 0.102865 restraints weight = 16889.558|
|-----------------------------------------------------------------------------|
r_work (start): 0.3257 rms_B_bonded: 2.48
r_work: 0.3107 rms_B_bonded: 3.51 restraints_weight: 0.5000
r_work (final): 0.3107
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8067
moved from start:          0.2689

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.070  12122  Z= 0.223
  Angle     :  0.543  15.515  16857  Z= 0.295
  Chirality :  0.040   0.248   1941
  Planarity :  0.004   0.063   1735
  Dihedral  : 18.703 152.361   2843
  Min Nonbonded Distance : 2.510

Molprobity Statistics.
  All-atom Clashscore : 4.43
  Ramachandran Plot:
    Outliers :  0.09 %
    Allowed  :  2.57 %
    Favored  : 97.34 %
  Rotamer:
    Outliers :  1.68 %
    Allowed  : 11.05 %
    Favored  : 87.28 %
  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:  0.95 (0.25), residues: 1128
  helix:  1.40 (0.22), residues: 602
  sheet: -0.31 (0.48), residues: 111
  loop : -0.12 (0.29), residues: 415

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.007   0.001   ARG A 395 
 TYR   0.019   0.002   TYR A 286 
 PHE   0.043   0.002   PHE A1327 
 TRP   0.006   0.001   TRP A 464 
 HIS   0.006   0.001   HIS A 167 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00502 /  0.22 (12122)
  covalent geometry    : angle       0.54300 /  0.30 (16857)
  hydrogen bonds       : bond        0.04706 /  3.14 (  558)
  hydrogen bonds       : angle       4.55717 /  3.24 ( 1540)

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

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

  2256 Ramachandran restraints generated.
    1128 Oldfield, 0 Emsley, 1128 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2256 Ramachandran restraints generated.
    1128 Oldfield, 0 Emsley, 1128 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  138 residues out of total 1014 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 17
    poor density    : 121
  time to evaluate  : 0.354 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   76 LYS cc_start: 0.8343 (tttt) cc_final: 0.7943 (tptt)
REVERT: A   84 GLU cc_start: 0.8063 (tt0) cc_final: 0.7688 (tp30)
REVERT: A  147 ASP cc_start: 0.8074 (m-30) cc_final: 0.7730 (p0)
REVERT: A  196 PHE cc_start: 0.7657 (m-80) cc_final: 0.7172 (m-80)
REVERT: A  202 ASN cc_start: 0.8052 (t0) cc_final: 0.7669 (p0)
REVERT: A  273 ASP cc_start: 0.8110 (m-30) cc_final: 0.7878 (p0)
REVERT: A  286 TYR cc_start: 0.6660 (m-10) cc_final: 0.6426 (m-10)
REVERT: A  314 LYS cc_start: 0.8529 (mttt) cc_final: 0.7927 (mtmt)
REVERT: A  353 ASP cc_start: 0.8366 (t0) cc_final: 0.8075 (t0)
REVERT: A  356 LYS cc_start: 0.8536 (mmtt) cc_final: 0.8267 (mptt)
REVERT: A  534 MET cc_start: 0.4324 (mtp) cc_final: 0.3219 (ptm)
REVERT: A  610 GLU cc_start: 0.8199 (mt-10) cc_final: 0.7745 (mt-10)
REVERT: A  661 ARG cc_start: 0.7333 (mtp85) cc_final: 0.7013 (mtp85)
REVERT: A  682 PHE cc_start: 0.7572 (m-10) cc_final: 0.6945 (m-10)
REVERT: A  705 LYS cc_start: 0.7572 (OUTLIER) cc_final: 0.7303 (ttmm)
REVERT: A  926 GLN cc_start: 0.7518 (mp10) cc_final: 0.7089 (mm-40)
REVERT: A  959 LYS cc_start: 0.6996 (mmpt) cc_final: 0.6469 (mttp)
REVERT: A  977 GLU cc_start: 0.7958 (mp0) cc_final: 0.7625 (mp0)
REVERT: A  988 TYR cc_start: 0.7938 (t80) cc_final: 0.7656 (t80)
REVERT: A 1170 GLU cc_start: 0.8862 (mt-10) cc_final: 0.8524 (mt-10)
REVERT: A 1188 LYS cc_start: 0.8544 (mttt) cc_final: 0.8302 (mmmt)
REVERT: A 1263 LYS cc_start: 0.8190 (tttt) cc_final: 0.7613 (mtmt)
REVERT: A 1294 TYR cc_start: 0.8288 (t80) cc_final: 0.7241 (t80)
REVERT: A 1303 ARG cc_start: 0.6282 (mtp-110) cc_final: 0.5936 (mtp-110)
REVERT: A 1307 GLU cc_start: 0.7521 (mt-10) cc_final: 0.7161 (mt-10)
REVERT: A 1327 PHE cc_start: 0.7570 (m-10) cc_final: 0.7307 (m-80)
REVERT: A 1332 ASP cc_start: 0.8250 (m-30) cc_final: 0.7810 (t0)
  outliers start: 17
  outliers final: 13
  residues processed: 133
  average time/residue: 0.1305
  time to fit residues: 23.1662
Evaluate side-chains
  125 residues out of total 1014 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 111
  time to evaluate  : 0.381 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  189 VAL
Chi-restraints excluded: chain A residue  249 THR
Chi-restraints excluded: chain A residue  278 LEU
Chi-restraints excluded: chain A residue  480 GLU
Chi-restraints excluded: chain A residue  590 SER
Chi-restraints excluded: chain A residue  630 GLU
Chi-restraints excluded: chain A residue  657 THR
Chi-restraints excluded: chain A residue  705 LYS
Chi-restraints excluded: chain A residue  740 THR
Chi-restraints excluded: chain A residue  933 GLN
Chi-restraints excluded: chain A residue  936 ASP
Chi-restraints excluded: chain A residue 1160 VAL
Chi-restraints excluded: chain A residue 1280 VAL
Chi-restraints excluded: chain A residue 1352 ILE
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 123
   random chunks:
   chunk 54 optimal weight:    0.9980
   chunk 120 optimal weight:   10.0000
   chunk 111 optimal weight:    0.9990
   chunk 73 optimal weight:    0.0870
   chunk 85 optimal weight:    0.8980
   chunk 106 optimal weight:    9.9990
   chunk 71 optimal weight:   20.0000
   chunk 76 optimal weight:    9.9990
   chunk 29 optimal weight:    8.9990
   chunk 65 optimal weight:    0.9980
   chunk 45 optimal weight:    1.9990
   overall best weight:    0.7960

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
A  77 ASN
A 194 GLN
** A 930 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3975 r_free = 0.3975 target = 0.158657 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 53)----------------|
| r_work = 0.3327 r_free = 0.3327 target = 0.106222 restraints weight = 16868.094|
|-----------------------------------------------------------------------------|
r_work (start): 0.3312 rms_B_bonded: 2.49
r_work: 0.3164 rms_B_bonded: 3.52 restraints_weight: 0.5000
r_work (final): 0.3164
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8019
moved from start:          0.2794

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.059  12122  Z= 0.107
  Angle     :  0.450  10.759  16857  Z= 0.251
  Chirality :  0.036   0.246   1941
  Planarity :  0.003   0.051   1735
  Dihedral  : 18.744 155.460   2843
  Min Nonbonded Distance : 2.528

Molprobity Statistics.
  All-atom Clashscore : 4.34
  Ramachandran Plot:
    Outliers :  0.09 %
    Allowed  :  2.57 %
    Favored  : 97.34 %
  Rotamer:
    Outliers :  1.58 %
    Allowed  : 11.54 %
    Favored  : 86.88 %
  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:  1.20 (0.25), residues: 1128
  helix:  1.58 (0.22), residues: 603
  sheet:  0.30 (0.52), residues: 93
  loop : -0.13 (0.29), residues: 432

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.010   0.000   ARG A 671 
 TYR   0.015   0.001   TYR A 450 
 PHE   0.023   0.001   PHE A1327 
 TRP   0.005   0.001   TRP A 476 
 HIS   0.003   0.001   HIS A 328 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00228 /  0.11 (12122)
  covalent geometry    : angle       0.44984 /  0.25 (16857)
  hydrogen bonds       : bond        0.03946 /  2.53 (  558)
  hydrogen bonds       : angle       4.34946 /  3.08 ( 1540)

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

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

  2256 Ramachandran restraints generated.
    1128 Oldfield, 0 Emsley, 1128 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2256 Ramachandran restraints generated.
    1128 Oldfield, 0 Emsley, 1128 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  137 residues out of total 1014 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 121
  time to evaluate  : 0.377 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   76 LYS cc_start: 0.8259 (tttt) cc_final: 0.7849 (tptt)
REVERT: A   84 GLU cc_start: 0.7998 (tt0) cc_final: 0.7671 (tp30)
REVERT: A   89 GLU cc_start: 0.7485 (mm-30) cc_final: 0.7172 (tp30)
REVERT: A  147 ASP cc_start: 0.7984 (m-30) cc_final: 0.7675 (p0)
REVERT: A  183 LYS cc_start: 0.4743 (ttpp) cc_final: 0.4396 (mmtm)
REVERT: A  196 PHE cc_start: 0.7541 (m-80) cc_final: 0.7163 (m-80)
REVERT: A  202 ASN cc_start: 0.8054 (t0) cc_final: 0.7663 (p0)
REVERT: A  215 ARG cc_start: 0.6955 (mmm160) cc_final: 0.6596 (mmm160)
REVERT: A  314 LYS cc_start: 0.8452 (mttt) cc_final: 0.7819 (mtmt)
REVERT: A  339 VAL cc_start: 0.8047 (p) cc_final: 0.7835 (p)
REVERT: A  353 ASP cc_start: 0.8381 (t0) cc_final: 0.8066 (t0)
REVERT: A  356 LYS cc_start: 0.8500 (mmtt) cc_final: 0.8262 (mptt)
REVERT: A  495 MET cc_start: 0.8162 (ppp) cc_final: 0.7715 (ppp)
REVERT: A  610 GLU cc_start: 0.8128 (mt-10) cc_final: 0.7701 (mt-10)
REVERT: A  628 ASP cc_start: 0.8006 (t0) cc_final: 0.7788 (t0)
REVERT: A  661 ARG cc_start: 0.7323 (mtp85) cc_final: 0.7012 (mtp85)
REVERT: A  682 PHE cc_start: 0.7492 (m-10) cc_final: 0.6832 (m-10)
REVERT: A  705 LYS cc_start: 0.7549 (OUTLIER) cc_final: 0.7284 (ttmm)
REVERT: A  926 GLN cc_start: 0.7555 (mp10) cc_final: 0.7076 (mm-40)
REVERT: A  959 LYS cc_start: 0.6995 (mmpt) cc_final: 0.6376 (mttp)
REVERT: A  977 GLU cc_start: 0.7922 (mp0) cc_final: 0.7600 (mp0)
REVERT: A  988 TYR cc_start: 0.7703 (t80) cc_final: 0.7459 (t80)
REVERT: A 1129 LYS cc_start: 0.9141 (mttt) cc_final: 0.8713 (mmmt)
REVERT: A 1170 GLU cc_start: 0.8793 (mt-10) cc_final: 0.8469 (mt-10)
REVERT: A 1188 LYS cc_start: 0.8445 (mttt) cc_final: 0.8186 (mmmt)
REVERT: A 1256 GLN cc_start: 0.7214 (mt0) cc_final: 0.6575 (mm110)
REVERT: A 1263 LYS cc_start: 0.8130 (tttt) cc_final: 0.7585 (mtmt)
REVERT: A 1307 GLU cc_start: 0.7574 (mt-10) cc_final: 0.7230 (mt-10)
REVERT: A 1327 PHE cc_start: 0.7494 (m-80) cc_final: 0.7254 (m-10)
REVERT: A 1332 ASP cc_start: 0.8249 (m-30) cc_final: 0.7806 (t0)
  outliers start: 16
  outliers final: 11
  residues processed: 132
  average time/residue: 0.1254
  time to fit residues: 22.3572
Evaluate side-chains
  124 residues out of total 1014 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 112
  time to evaluate  : 0.368 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  189 VAL
Chi-restraints excluded: chain A residue  249 THR
Chi-restraints excluded: chain A residue  278 LEU
Chi-restraints excluded: chain A residue  480 GLU
Chi-restraints excluded: chain A residue  590 SER
Chi-restraints excluded: chain A residue  630 GLU
Chi-restraints excluded: chain A residue  657 THR
Chi-restraints excluded: chain A residue  705 LYS
Chi-restraints excluded: chain A residue  740 THR
Chi-restraints excluded: chain A residue  933 GLN
Chi-restraints excluded: chain A residue  936 ASP
Chi-restraints excluded: chain A residue 1160 VAL
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 123
   random chunks:
   chunk 18 optimal weight:    9.9990
   chunk 64 optimal weight:    9.9990
   chunk 27 optimal weight:    6.9990
   chunk 108 optimal weight:    6.9990
   chunk 20 optimal weight:   10.0000
   chunk 13 optimal weight:    5.9990
   chunk 65 optimal weight:    1.9990
   chunk 1 optimal weight:    3.9990
   chunk 2 optimal weight:    0.0060
   chunk 0 optimal weight:    4.9990
   chunk 33 optimal weight:    2.9990
   overall best weight:    2.8004

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
A  77 ASN
A 194 GLN
** A 726 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 930 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3947 r_free = 0.3947 target = 0.156236 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 64)----------------|
| r_work = 0.3287 r_free = 0.3287 target = 0.103509 restraints weight = 16847.143|
|-----------------------------------------------------------------------------|
r_work (start): 0.3267 rms_B_bonded: 2.48
r_work: 0.3119 rms_B_bonded: 3.51 restraints_weight: 0.5000
r_work (final): 0.3119
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8060
moved from start:          0.2899

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.070  12122  Z= 0.190
  Angle     :  0.493   8.997  16857  Z= 0.272
  Chirality :  0.038   0.246   1941
  Planarity :  0.004   0.050   1735
  Dihedral  : 18.697 154.247   2843
  Min Nonbonded Distance : 2.460

Molprobity Statistics.
  All-atom Clashscore : 4.79
  Ramachandran Plot:
    Outliers :  0.09 %
    Allowed  :  2.66 %
    Favored  : 97.25 %
  Rotamer:
    Outliers :  1.68 %
    Allowed  : 11.93 %
    Favored  : 86.39 %
  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:  1.08 (0.25), residues: 1128
  helix:  1.54 (0.22), residues: 603
  sheet: -0.20 (0.48), residues: 110
  loop : -0.14 (0.29), residues: 415

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.008   0.001   ARG A 671 
 TYR   0.015   0.002   TYR A 286 
 PHE   0.019   0.002   PHE A 518 
 TRP   0.005   0.001   TRP A 476 
 HIS   0.006   0.001   HIS A 167 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00425 /  0.19 (12122)
  covalent geometry    : angle       0.49270 /  0.27 (16857)
  hydrogen bonds       : bond        0.04344 /  2.89 (  558)
  hydrogen bonds       : angle       4.42234 /  3.14 ( 1540)

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

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

  2256 Ramachandran restraints generated.
    1128 Oldfield, 0 Emsley, 1128 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2256 Ramachandran restraints generated.
    1128 Oldfield, 0 Emsley, 1128 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  137 residues out of total 1014 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 17
    poor density    : 120
  time to evaluate  : 0.364 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   76 LYS cc_start: 0.8306 (tttt) cc_final: 0.7919 (tptt)
REVERT: A   84 GLU cc_start: 0.8078 (tt0) cc_final: 0.7704 (tp30)
REVERT: A  147 ASP cc_start: 0.8013 (m-30) cc_final: 0.7732 (p0)
REVERT: A  196 PHE cc_start: 0.7738 (m-80) cc_final: 0.7306 (m-80)
REVERT: A  202 ASN cc_start: 0.8092 (t0) cc_final: 0.7740 (p0)
REVERT: A  314 LYS cc_start: 0.8485 (mttt) cc_final: 0.7882 (mtmt)
REVERT: A  339 VAL cc_start: 0.8091 (p) cc_final: 0.7862 (p)
REVERT: A  353 ASP cc_start: 0.8374 (t0) cc_final: 0.8064 (t0)
REVERT: A  356 LYS cc_start: 0.8540 (mmtt) cc_final: 0.8272 (mptt)
REVERT: A  534 MET cc_start: 0.3501 (mtm) cc_final: 0.3034 (ptm)
REVERT: A  610 GLU cc_start: 0.8171 (mt-10) cc_final: 0.7723 (mt-10)
REVERT: A  628 ASP cc_start: 0.8127 (t0) cc_final: 0.7861 (t0)
REVERT: A  661 ARG cc_start: 0.7373 (mtp85) cc_final: 0.7073 (mtp85)
REVERT: A  682 PHE cc_start: 0.7562 (m-10) cc_final: 0.6912 (m-10)
REVERT: A  705 LYS cc_start: 0.7555 (OUTLIER) cc_final: 0.7304 (ttmm)
REVERT: A  926 GLN cc_start: 0.7671 (mp10) cc_final: 0.7204 (mm-40)
REVERT: A  959 LYS cc_start: 0.6980 (mmpt) cc_final: 0.6476 (mttp)
REVERT: A  977 GLU cc_start: 0.7985 (mp0) cc_final: 0.7679 (mp0)
REVERT: A  988 TYR cc_start: 0.7873 (t80) cc_final: 0.7618 (t80)
REVERT: A 1129 LYS cc_start: 0.9141 (mttt) cc_final: 0.8699 (mmmt)
REVERT: A 1170 GLU cc_start: 0.8830 (mt-10) cc_final: 0.8501 (mt-10)
REVERT: A 1188 LYS cc_start: 0.8493 (mttt) cc_final: 0.8223 (mmmt)
REVERT: A 1256 GLN cc_start: 0.7239 (mt0) cc_final: 0.6597 (mm110)
REVERT: A 1263 LYS cc_start: 0.8201 (tttt) cc_final: 0.7601 (mtmt)
REVERT: A 1307 GLU cc_start: 0.7600 (mt-10) cc_final: 0.7244 (mt-10)
REVERT: A 1327 PHE cc_start: 0.7574 (m-80) cc_final: 0.7339 (m-80)
REVERT: A 1332 ASP cc_start: 0.8257 (m-30) cc_final: 0.7815 (t0)
  outliers start: 17
  outliers final: 11
  residues processed: 131
  average time/residue: 0.1349
  time to fit residues: 23.5264
Evaluate side-chains
  125 residues out of total 1014 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 113
  time to evaluate  : 0.392 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   80 CYS
Chi-restraints excluded: chain A residue  189 VAL
Chi-restraints excluded: chain A residue  249 THR
Chi-restraints excluded: chain A residue  272 ASP
Chi-restraints excluded: chain A residue  480 GLU
Chi-restraints excluded: chain A residue  590 SER
Chi-restraints excluded: chain A residue  630 GLU
Chi-restraints excluded: chain A residue  657 THR
Chi-restraints excluded: chain A residue  705 LYS
Chi-restraints excluded: chain A residue  740 THR
Chi-restraints excluded: chain A residue  933 GLN
Chi-restraints excluded: chain A residue  936 ASP
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 123
   random chunks:
   chunk 44 optimal weight:    1.9990
   chunk 101 optimal weight:    0.8980
   chunk 91 optimal weight:    0.2980
   chunk 37 optimal weight:    0.7980
   chunk 79 optimal weight:    3.9990
   chunk 67 optimal weight:   10.0000
   chunk 65 optimal weight:    8.9990
   chunk 19 optimal weight:   10.0000
   chunk 97 optimal weight:    3.9990
   chunk 71 optimal weight:    0.0670
   chunk 54 optimal weight:    2.9990
   overall best weight:    0.8120

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
A  77 ASN
A 194 GLN
A 726 ASN
** A 930 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3975 r_free = 0.3975 target = 0.158679 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 56)----------------|
| r_work = 0.3325 r_free = 0.3325 target = 0.106110 restraints weight = 16801.507|
|-----------------------------------------------------------------------------|
r_work (start): 0.3307 rms_B_bonded: 2.49
r_work: 0.3161 rms_B_bonded: 3.50 restraints_weight: 0.5000
r_work (final): 0.3161
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8020
moved from start:          0.2998

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.052  12122  Z= 0.105
  Angle     :  0.454   7.675  16857  Z= 0.253
  Chirality :  0.037   0.247   1941
  Planarity :  0.003   0.050   1735
  Dihedral  : 18.727 155.488   2843
  Min Nonbonded Distance : 2.499

Molprobity Statistics.
  All-atom Clashscore : 5.06
  Ramachandran Plot:
    Outliers :  0.09 %
    Allowed  :  2.57 %
    Favored  : 97.34 %
  Rotamer:
    Outliers :  1.28 %
    Allowed  : 12.43 %
    Favored  : 86.29 %
  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:  1.23 (0.25), residues: 1128
  helix:  1.66 (0.22), residues: 603
  sheet:  0.11 (0.51), residues: 102
  loop : -0.15 (0.29), residues: 423

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.009   0.000   ARG A 671 
 TYR   0.013   0.001   TYR A1242 
 PHE   0.018   0.001   PHE A 518 
 TRP   0.005   0.001   TRP A 476 
 HIS   0.003   0.001   HIS A 328 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00220 /  0.11 (12122)
  covalent geometry    : angle       0.45432 /  0.25 (16857)
  hydrogen bonds       : bond        0.03828 /  2.45 (  558)
  hydrogen bonds       : angle       4.30519 /  3.05 ( 1540)

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

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

  2256 Ramachandran restraints generated.
    1128 Oldfield, 0 Emsley, 1128 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2256 Ramachandran restraints generated.
    1128 Oldfield, 0 Emsley, 1128 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  135 residues out of total 1014 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 122
  time to evaluate  : 0.240 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   76 LYS cc_start: 0.8236 (tttt) cc_final: 0.7848 (tptt)
REVERT: A   84 GLU cc_start: 0.8052 (tt0) cc_final: 0.7709 (tp30)
REVERT: A  147 ASP cc_start: 0.8036 (m-30) cc_final: 0.7775 (p0)
REVERT: A  183 LYS cc_start: 0.5205 (ttmt) cc_final: 0.4489 (mmtp)
REVERT: A  196 PHE cc_start: 0.7546 (m-80) cc_final: 0.7093 (m-80)
REVERT: A  202 ASN cc_start: 0.8093 (t0) cc_final: 0.7736 (p0)
REVERT: A  314 LYS cc_start: 0.8410 (mttt) cc_final: 0.7797 (mtmt)
REVERT: A  353 ASP cc_start: 0.8349 (t0) cc_final: 0.7995 (t0)
REVERT: A  495 MET cc_start: 0.8217 (ppp) cc_final: 0.7895 (ppp)
REVERT: A  534 MET cc_start: 0.3595 (mtm) cc_final: 0.3057 (ptm)
REVERT: A  610 GLU cc_start: 0.8084 (mt-10) cc_final: 0.7664 (mt-10)
REVERT: A  628 ASP cc_start: 0.8045 (t0) cc_final: 0.7798 (t0)
REVERT: A  661 ARG cc_start: 0.7247 (mtp85) cc_final: 0.6953 (mtp85)
REVERT: A  682 PHE cc_start: 0.7584 (m-80) cc_final: 0.6890 (m-10)
REVERT: A  705 LYS cc_start: 0.7525 (OUTLIER) cc_final: 0.7307 (ttmm)
REVERT: A  926 GLN cc_start: 0.7618 (mp10) cc_final: 0.7136 (mm-40)
REVERT: A  959 LYS cc_start: 0.7002 (mmpt) cc_final: 0.6356 (mttp)
REVERT: A  977 GLU cc_start: 0.7939 (mp0) cc_final: 0.7633 (mp0)
REVERT: A  988 TYR cc_start: 0.7683 (t80) cc_final: 0.7458 (t80)
REVERT: A 1170 GLU cc_start: 0.8786 (mt-10) cc_final: 0.8457 (mt-10)
REVERT: A 1188 LYS cc_start: 0.8470 (mttt) cc_final: 0.8220 (mmmt)
REVERT: A 1263 LYS cc_start: 0.8147 (tttt) cc_final: 0.7564 (mtmt)
REVERT: A 1303 ARG cc_start: 0.6297 (mtp-110) cc_final: 0.6013 (mtp-110)
REVERT: A 1307 GLU cc_start: 0.7545 (mt-10) cc_final: 0.7130 (mt-10)
REVERT: A 1327 PHE cc_start: 0.7562 (m-80) cc_final: 0.7342 (m-80)
REVERT: A 1332 ASP cc_start: 0.8259 (m-30) cc_final: 0.7816 (t0)
  outliers start: 13
  outliers final: 11
  residues processed: 129
  average time/residue: 0.1217
  time to fit residues: 21.4667
Evaluate side-chains
  124 residues out of total 1014 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 112
  time to evaluate  : 0.380 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  156 LEU
Chi-restraints excluded: chain A residue  189 VAL
Chi-restraints excluded: chain A residue  249 THR
Chi-restraints excluded: chain A residue  278 LEU
Chi-restraints excluded: chain A residue  480 GLU
Chi-restraints excluded: chain A residue  590 SER
Chi-restraints excluded: chain A residue  630 GLU
Chi-restraints excluded: chain A residue  657 THR
Chi-restraints excluded: chain A residue  705 LYS
Chi-restraints excluded: chain A residue  740 THR
Chi-restraints excluded: chain A residue  933 GLN
Chi-restraints excluded: chain A residue  936 ASP
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 123
   random chunks:
   chunk 53 optimal weight:    7.9990
   chunk 35 optimal weight:    7.9990
   chunk 78 optimal weight:    8.9990
   chunk 84 optimal weight:   10.0000
   chunk 94 optimal weight:    0.0470
   chunk 72 optimal weight:    0.9990
   chunk 71 optimal weight:    0.0870
   chunk 85 optimal weight:    2.9990
   chunk 14 optimal weight:    5.9990
   chunk 76 optimal weight:    4.9990
   chunk 51 optimal weight:    7.9990
   overall best weight:    1.8262

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
A 194 GLN
A 674 GLN
** A 930 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3958 r_free = 0.3958 target = 0.157120 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 50)----------------|
| r_work = 0.3306 r_free = 0.3306 target = 0.104659 restraints weight = 16726.716|
|-----------------------------------------------------------------------------|
r_work (start): 0.3286 rms_B_bonded: 2.47
r_work: 0.3137 rms_B_bonded: 3.49 restraints_weight: 0.5000
r_work (final): 0.3137
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8039
moved from start:          0.3077

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.056  12122  Z= 0.148
  Angle     :  0.483   7.179  16857  Z= 0.266
  Chirality :  0.037   0.245   1941
  Planarity :  0.004   0.049   1735
  Dihedral  : 18.681 154.863   2843
  Min Nonbonded Distance : 2.472

Molprobity Statistics.
  All-atom Clashscore : 5.37
  Ramachandran Plot:
    Outliers :  0.09 %
    Allowed  :  2.66 %
    Favored  : 97.25 %
  Rotamer:
    Outliers :  1.18 %
    Allowed  : 12.92 %
    Favored  : 85.90 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  1.18 (0.25), residues: 1128
  helix:  1.67 (0.22), residues: 604
  sheet: -0.08 (0.50), residues: 106
  loop : -0.21 (0.29), residues: 418

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.011   0.001   ARG A 671 
 TYR   0.014   0.001   TYR A 450 
 PHE   0.025   0.002   PHE A1258 
 TRP   0.004   0.001   TRP A 476 
 HIS   0.005   0.001   HIS A 167 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00331 /  0.15 (12122)
  covalent geometry    : angle       0.48326 /  0.27 (16857)
  hydrogen bonds       : bond        0.03992 /  2.62 (  558)
  hydrogen bonds       : angle       4.28931 /  3.05 ( 1540)

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

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

  2256 Ramachandran restraints generated.
    1128 Oldfield, 0 Emsley, 1128 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2256 Ramachandran restraints generated.
    1128 Oldfield, 0 Emsley, 1128 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  136 residues out of total 1014 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 124
  time to evaluate  : 0.390 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   76 LYS cc_start: 0.8264 (tttt) cc_final: 0.7921 (tptt)
REVERT: A   84 GLU cc_start: 0.8075 (tt0) cc_final: 0.7712 (tp30)
REVERT: A   89 GLU cc_start: 0.7639 (mm-30) cc_final: 0.7379 (mm-30)
REVERT: A  147 ASP cc_start: 0.8047 (m-30) cc_final: 0.7774 (p0)
REVERT: A  196 PHE cc_start: 0.7764 (m-80) cc_final: 0.7314 (m-80)
REVERT: A  202 ASN cc_start: 0.8062 (t0) cc_final: 0.7732 (p0)
REVERT: A  314 LYS cc_start: 0.8458 (mttt) cc_final: 0.7860 (mtmt)
REVERT: A  353 ASP cc_start: 0.8335 (t0) cc_final: 0.8013 (t0)
REVERT: A  356 LYS cc_start: 0.8530 (mmtt) cc_final: 0.8269 (mptt)
REVERT: A  495 MET cc_start: 0.8247 (ppp) cc_final: 0.7653 (ppp)
REVERT: A  534 MET cc_start: 0.3621 (mtm) cc_final: 0.3135 (ptm)
REVERT: A  610 GLU cc_start: 0.8237 (mt-10) cc_final: 0.7795 (mt-10)
REVERT: A  628 ASP cc_start: 0.8094 (t0) cc_final: 0.7840 (t0)
REVERT: A  661 ARG cc_start: 0.7262 (mtp85) cc_final: 0.6981 (mtp85)
REVERT: A  682 PHE cc_start: 0.7537 (m-80) cc_final: 0.6836 (m-10)
REVERT: A  926 GLN cc_start: 0.7647 (mp10) cc_final: 0.7176 (mm-40)
REVERT: A  959 LYS cc_start: 0.7011 (mmpt) cc_final: 0.6366 (mttp)
REVERT: A  977 GLU cc_start: 0.7964 (mp0) cc_final: 0.7675 (mp0)
REVERT: A  988 TYR cc_start: 0.7818 (t80) cc_final: 0.7552 (t80)
REVERT: A 1129 LYS cc_start: 0.9098 (mttt) cc_final: 0.8700 (mmmt)
REVERT: A 1170 GLU cc_start: 0.8803 (mt-10) cc_final: 0.8470 (mt-10)
REVERT: A 1188 LYS cc_start: 0.8471 (mttt) cc_final: 0.8208 (mmmt)
REVERT: A 1256 GLN cc_start: 0.7264 (mt0) cc_final: 0.6712 (mm110)
REVERT: A 1263 LYS cc_start: 0.8190 (tttt) cc_final: 0.7601 (mtmt)
REVERT: A 1303 ARG cc_start: 0.6438 (mtp-110) cc_final: 0.6221 (mtp-110)
REVERT: A 1307 GLU cc_start: 0.7443 (mt-10) cc_final: 0.7023 (mt-10)
REVERT: A 1327 PHE cc_start: 0.7551 (m-80) cc_final: 0.7332 (m-80)
REVERT: A 1332 ASP cc_start: 0.8289 (m-30) cc_final: 0.7839 (t0)
  outliers start: 12
  outliers final: 11
  residues processed: 131
  average time/residue: 0.1284
  time to fit residues: 22.7184
Evaluate side-chains
  126 residues out of total 1014 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 115
  time to evaluate  : 0.381 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  156 LEU
Chi-restraints excluded: chain A residue  189 VAL
Chi-restraints excluded: chain A residue  249 THR
Chi-restraints excluded: chain A residue  278 LEU
Chi-restraints excluded: chain A residue  480 GLU
Chi-restraints excluded: chain A residue  590 SER
Chi-restraints excluded: chain A residue  630 GLU
Chi-restraints excluded: chain A residue  657 THR
Chi-restraints excluded: chain A residue  740 THR
Chi-restraints excluded: chain A residue  933 GLN
Chi-restraints excluded: chain A residue  936 ASP
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 123
   random chunks:
   chunk 121 optimal weight:   30.0000
   chunk 22 optimal weight:    4.9990
   chunk 50 optimal weight:    3.9990
   chunk 116 optimal weight:   10.0000
   chunk 96 optimal weight:    3.9990
   chunk 13 optimal weight:    5.9990
   chunk 7 optimal weight:    3.9990
   chunk 113 optimal weight:   40.0000
   chunk 0 optimal weight:    6.9990
   chunk 87 optimal weight:    2.9990
   chunk 66 optimal weight:    2.9990
   overall best weight:    3.5990

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
A  77 ASN
A 194 GLN
** A 930 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3933 r_free = 0.3933 target = 0.154825 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 67)----------------|
| r_work = 0.3264 r_free = 0.3264 target = 0.101925 restraints weight = 16824.287|
|-----------------------------------------------------------------------------|
r_work (start): 0.3247 rms_B_bonded: 2.47
r_work: 0.3096 rms_B_bonded: 3.49 restraints_weight: 0.5000
r_work (final): 0.3096
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8098
moved from start:          0.3203

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.072  12122  Z= 0.240
  Angle     :  0.557  11.354  16857  Z= 0.302
  Chirality :  0.041   0.248   1941
  Planarity :  0.004   0.067   1735
  Dihedral  : 18.692 153.764   2843
  Min Nonbonded Distance : 2.453

Molprobity Statistics.
  All-atom Clashscore : 5.78
  Ramachandran Plot:
    Outliers :  0.09 %
    Allowed  :  2.75 %
    Favored  : 97.16 %
  Rotamer:
    Outliers :  1.68 %
    Allowed  : 12.43 %
    Favored  : 85.90 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  0.93 (0.25), residues: 1128
  helix:  1.46 (0.22), residues: 605
  sheet: -0.39 (0.48), residues: 110
  loop : -0.26 (0.29), residues: 413

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.012   0.001   ARG A 671 
 TYR   0.015   0.002   TYR A 155 
 PHE   0.020   0.002   PHE A 518 
 TRP   0.006   0.002   TRP A  18 
 HIS   0.008   0.001   HIS A 167 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00549 /  0.24 (12122)
  covalent geometry    : angle       0.55675 /  0.30 (16857)
  hydrogen bonds       : bond        0.04661 /  3.11 (  558)
  hydrogen bonds       : angle       4.45865 /  3.16 ( 1540)

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

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

  2256 Ramachandran restraints generated.
    1128 Oldfield, 0 Emsley, 1128 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2256 Ramachandran restraints generated.
    1128 Oldfield, 0 Emsley, 1128 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  137 residues out of total 1014 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 17
    poor density    : 120
  time to evaluate  : 0.393 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   76 LYS cc_start: 0.8344 (tttt) cc_final: 0.7995 (tptt)
REVERT: A   84 GLU cc_start: 0.8090 (tt0) cc_final: 0.7711 (tp30)
REVERT: A   89 GLU cc_start: 0.7678 (mm-30) cc_final: 0.7351 (mm-30)
REVERT: A  147 ASP cc_start: 0.8063 (m-30) cc_final: 0.7781 (p0)
REVERT: A  183 LYS cc_start: 0.4958 (ptmt) cc_final: 0.4750 (ptmt)
REVERT: A  202 ASN cc_start: 0.8081 (t0) cc_final: 0.7788 (p0)
REVERT: A  225 LEU cc_start: 0.7315 (tp) cc_final: 0.6832 (tt)
REVERT: A  314 LYS cc_start: 0.8566 (mttt) cc_final: 0.7973 (mtmt)
REVERT: A  353 ASP cc_start: 0.8363 (t0) cc_final: 0.8012 (t0)
REVERT: A  356 LYS cc_start: 0.8566 (mmtt) cc_final: 0.8329 (mptt)
REVERT: A  495 MET cc_start: 0.8320 (ppp) cc_final: 0.7676 (ppp)
REVERT: A  534 MET cc_start: 0.3677 (mtm) cc_final: 0.3092 (ptm)
REVERT: A  610 GLU cc_start: 0.8289 (mt-10) cc_final: 0.7847 (mt-10)
REVERT: A  628 ASP cc_start: 0.8190 (t0) cc_final: 0.7910 (t0)
REVERT: A  661 ARG cc_start: 0.7303 (mtp85) cc_final: 0.7045 (mtp85)
REVERT: A  682 PHE cc_start: 0.7717 (m-80) cc_final: 0.7004 (m-10)
REVERT: A  926 GLN cc_start: 0.7789 (mp10) cc_final: 0.7360 (mm-40)
REVERT: A  959 LYS cc_start: 0.6973 (mmpt) cc_final: 0.6471 (mttp)
REVERT: A  977 GLU cc_start: 0.8057 (mp0) cc_final: 0.7764 (mp0)
REVERT: A  988 TYR cc_start: 0.7994 (t80) cc_final: 0.7692 (t80)
REVERT: A 1129 LYS cc_start: 0.9104 (mttt) cc_final: 0.8706 (mmmt)
REVERT: A 1188 LYS cc_start: 0.8520 (mttt) cc_final: 0.8246 (mmmt)
REVERT: A 1256 GLN cc_start: 0.7353 (mt0) cc_final: 0.6775 (mm110)
REVERT: A 1263 LYS cc_start: 0.8250 (tttt) cc_final: 0.7645 (mtmt)
REVERT: A 1307 GLU cc_start: 0.7416 (mt-10) cc_final: 0.7037 (mt-10)
REVERT: A 1327 PHE cc_start: 0.7622 (m-80) cc_final: 0.7419 (m-80)
REVERT: A 1332 ASP cc_start: 0.8271 (m-30) cc_final: 0.7831 (t0)
  outliers start: 17
  outliers final: 11
  residues processed: 131
  average time/residue: 0.1331
  time to fit residues: 23.4814
Evaluate side-chains
  126 residues out of total 1014 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 115
  time to evaluate  : 0.367 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   80 CYS
Chi-restraints excluded: chain A residue  189 VAL
Chi-restraints excluded: chain A residue  249 THR
Chi-restraints excluded: chain A residue  480 GLU
Chi-restraints excluded: chain A residue  590 SER
Chi-restraints excluded: chain A residue  630 GLU
Chi-restraints excluded: chain A residue  657 THR
Chi-restraints excluded: chain A residue  740 THR
Chi-restraints excluded: chain A residue  933 GLN
Chi-restraints excluded: chain A residue  936 ASP
Chi-restraints excluded: chain A residue 1270 ILE
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 123
   random chunks:
   chunk 8 optimal weight:    3.9990
   chunk 80 optimal weight:    6.9990
   chunk 93 optimal weight:    3.9990
   chunk 73 optimal weight:    1.9990
   chunk 31 optimal weight:    0.9980
   chunk 122 optimal weight:   20.0000
   chunk 102 optimal weight:    8.9990
   chunk 119 optimal weight:   10.0000
   chunk 88 optimal weight:    0.0170
   chunk 44 optimal weight:    0.5980
   chunk 121 optimal weight:   30.0000
   overall best weight:    1.5222

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
A 194 GLN
A 698 HIS
** A 930 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3963 r_free = 0.3963 target = 0.157541 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 48)----------------|
| r_work = 0.3297 r_free = 0.3297 target = 0.104216 restraints weight = 16972.261|
|-----------------------------------------------------------------------------|
r_work (start): 0.3279 rms_B_bonded: 2.52
r_work: 0.3132 rms_B_bonded: 3.52 restraints_weight: 0.5000
r_work (final): 0.3132
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8057
moved from start:          0.3263

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.052  12122  Z= 0.130
  Angle     :  0.492  10.964  16857  Z= 0.271
  Chirality :  0.038   0.249   1941
  Planarity :  0.004   0.059   1735
  Dihedral  : 18.715 154.753   2843
  Min Nonbonded Distance : 2.485

Molprobity Statistics.
  All-atom Clashscore : 5.87
  Ramachandran Plot:
    Outliers :  0.09 %
    Allowed  :  2.75 %
    Favored  : 97.16 %
  Rotamer:
    Outliers :  0.89 %
    Allowed  : 13.51 %
    Favored  : 85.60 %
  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:  1.07 (0.25), residues: 1128
  helix:  1.59 (0.22), residues: 603
  sheet: -0.23 (0.49), residues: 106
  loop : -0.23 (0.29), residues: 419

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.007   0.000   ARG A 671 
 TYR   0.012   0.001   TYR A 155 
 PHE   0.017   0.001   PHE A 518 
 TRP   0.007   0.001   TRP A 476 
 HIS   0.004   0.001   HIS A 328 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00281 /  0.13 (12122)
  covalent geometry    : angle       0.49210 /  0.27 (16857)
  hydrogen bonds       : bond        0.04068 /  2.64 (  558)
  hydrogen bonds       : angle       4.33873 /  3.08 ( 1540)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 2611.71 seconds
wall clock time: 45 minutes 35.83 seconds (2735.83 seconds total)