Starting phenix.real_space_refine
on Thu Aug  6 07:10:53 2026 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/10sm_75437/08_2026/10sm_75437_neut.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/10sm_75437/08_2026/10sm_75437.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=3.5
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    model {
      file = "/net/cci-nas-00/data/ceres_data/10sm_75437/08_2026/10sm_75437_neut.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/10sm_75437/08_2026/10sm_75437_neut.cif"
    real_map_files = "/net/cci-nas-00/data/ceres_data/10sm_75437/08_2026/10sm_75437.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/10sm_75437/08_2026/10sm_75437.map"
  }
  resolution = 3.5
  write_initial_geo_file = False
  refinement {
    macro_cycles = 10
  }


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

Validating inputs
Origin is already at (0, 0, 0), no shifts will be applied
-------------------------------------------------------------------------------
Processing inputs
*****************
Set random seed
  Set to: 0
Set model cs if undefined
Decide on map wrapping
  Map wrapping is set to: False
Normalize map: mean=0, sd=1
  Input map: mean=   0.001 sd=   0.019
Set stop_for_unknowns flag
  Set to: True
Assert model is a single copy model
Assert all atoms have isotropic ADPs
  Anisotropic ADP refinement not supported. Converting 7058 atoms to isotropic.
Construct map_model_manager
Extract box with map and model
Check model and map are aligned
Set scattering table
  Set to: electron
  Number of scattering types: 4
    Type Number    sf(0)   Gaussians
     S      46      5.16       5
     C    5179      2.51       5
     N    1363      2.21       5
     O    1496      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 4 residue(s): 0.01s

  Monomer Library directory:
    "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.2rc3-6140/lib/python3.11/site-packages/chem_data/mon_lib"
  Total number of atoms: 8084
  Number of models: 1
  Model: ""
    Number of chains: 2
    Chain: "A"
      Number of atoms: 814
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 95, 814
          Classifications: {'peptide': 95}
          Link IDs: {'PTRANS': 2, 'TRANS': 92}
    Chain: "D"
      Number of atoms: 7270
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 927, 7270
          Classifications: {'peptide': 927}
          Modifications used: {'COO': 1}
          Incomplete info: {'truncation_to_alanine': 1}
          Link IDs: {'PCIS': 2, 'PTRANS': 40, 'TRANS': 884}
          Chain breaks: 5
          Unresolved non-hydrogen bonds: 4
          Unresolved non-hydrogen angles: 5
          Unresolved non-hydrogen dihedrals: 3
          Planarities with less than four sites: {'GLU:plan': 1}
          Unresolved non-hydrogen planarities: 4
  Time building chain proxies: 1.81, per 1000 atoms: 0.22
  Number of scatterers: 8084
  At special positions: 0
  Unit cell: (90.885, 88.395, 110.805, 90, 90, 90)
  Space group: P 1 (No. 1)
  Number of sites at special positions: 0
  Number of scattering types: 4
    Type Number    sf(0)
     S      46     16.00
     O    1496      8.00
     N    1363      7.00
     C    5179      6.00
    sf(0) = scattering factor at diffraction angle 0.

  Number of disulfides: simple=0, symmetry=0

  Automatic linking
    Parameters for automatic linking
      Linking & cutoffs
        Metal                : Auto  - 3.00
        Amino acid           : True  - 1.90
        Carbohydrate         : True  - 1.99
        Ligands              : True  - 1.99
        Small molecules      : False - 1.98
        Amino acid - RNA/DNA : False
      
  Number of custom bonds: simple=0, symmetry=0
  Time building additional restraints: 0.78
  Conformation dependent library (CDL) restraints added in 291.0 milliseconds
  

  2016 Ramachandran restraints generated.
    1008 Oldfield, 0 Emsley, 1008 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  1958

  Finding SS restraints...
    Secondary structure from input PDB file:
      61 helices and 2 sheets defined
      83.4% alpha, 1.6% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 0.27
  Creating SS restraints...
    Processing helix  chain 'A' and resid 208 through 219
    Processing helix  chain 'A' and resid 220 through 223
    Processing helix  chain 'A' and resid 241 through 254
    Processing helix  chain 'A' and resid 259 through 269
      removed outlier: 4.347A  pdb=" N   TYR A 269 " --> pdb=" O   ARG A 265 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 270 through 272
      No H-bonds generated for 'chain 'A' and resid 270 through 272'
    Processing helix  chain 'D' and resid 24 through 34
    Processing helix  chain 'D' and resid 36 through 52
      removed outlier: 4.164A  pdb=" N   VAL D  52 " --> pdb=" O   LYS D  48 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 53 through 64
      removed outlier: 4.294A  pdb=" N   GLY D  57 " --> pdb=" O   THR D  53 " (cutoff:3.500A)
      removed outlier: 4.024A  pdb=" N   VAL D  58 " --> pdb=" O   GLU D  54 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 70 through 88
    Processing helix  chain 'D' and resid 102 through 113
      removed outlier: 4.318A  pdb=" N   LYS D 106 " --> pdb=" O   THR D 102 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 114 through 119
      removed outlier: 3.642A  pdb=" N   GLU D 119 " --> pdb=" O   ASN D 115 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 121 through 158
      removed outlier: 4.152A  pdb=" N   TRP D 138 " --> pdb=" O   ALA D 134 " (cutoff:3.500A)
      Proline residue:  D 141  - end of helix
      Proline residue:  D 145  - end of helix
    Processing helix  chain 'D' and resid 158 through 174
      removed outlier: 3.609A  pdb=" N   VAL D 163 " --> pdb=" O   ASP D 159 " (cutoff:3.500A)
      removed outlier: 7.245A  pdb=" N   HIS D 164 " --> pdb=" O   LEU D 160 " (cutoff:3.500A)
      removed outlier: 5.479A  pdb=" N   GLY D 165 " --> pdb=" O   ASN D 161 " (cutoff:3.500A)
      removed outlier: 3.797A  pdb=" N   GLU D 172 " --> pdb=" O   ARG D 168 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 181 through 199
      Proline residue:  D 187  - end of helix
      Proline residue:  D 191  - end of helix
    Processing helix  chain 'D' and resid 204 through 224
    Processing helix  chain 'D' and resid 227 through 237
    Processing helix  chain 'D' and resid 237 through 254
      removed outlier: 3.743A  pdb=" N   GLN D 250 " --> pdb=" O   GLU D 246 " (cutoff:3.500A)
      removed outlier: 3.779A  pdb=" N   GLN D 253 " --> pdb=" O   VAL D 249 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 261 through 277
      removed outlier: 3.610A  pdb=" N   LYS D 277 " --> pdb=" O   THR D 273 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 279 through 285
      removed outlier: 3.939A  pdb=" N   SER D 285 " --> pdb=" O   LYS D 281 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 286 through 310
      Proline residue:  D 292  - end of helix
    Processing helix  chain 'D' and resid 328 through 346
    Processing helix  chain 'D' and resid 349 through 368
      removed outlier: 3.613A  pdb=" N   VAL D 353 " --> pdb=" O   PHE D 349 " (cutoff:3.500A)
      Proline residue:  D 358  - end of helix
      removed outlier: 3.814A  pdb=" N   TYR D 362 " --> pdb=" O   PRO D 358 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 371 through 381
    Processing helix  chain 'D' and resid 381 through 390
    Processing helix  chain 'D' and resid 397 through 411
    Processing helix  chain 'D' and resid 413 through 438
    Processing helix  chain 'D' and resid 440 through 442
      No H-bonds generated for 'chain 'D' and resid 440 through 442'
    Processing helix  chain 'D' and resid 443 through 457
      removed outlier: 3.560A  pdb=" N   HIS D 447 " --> pdb=" O   TRP D 443 " (cutoff:3.500A)
      removed outlier: 3.721A  pdb=" N   VAL D 457 " --> pdb=" O   ALA D 453 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 457 through 468
      removed outlier: 3.507A  pdb=" N   ILE D 461 " --> pdb=" O   VAL D 457 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 473 through 481
    Processing helix  chain 'D' and resid 481 through 488
    Processing helix  chain 'D' and resid 491 through 504
    Processing helix  chain 'D' and resid 505 through 509
    Processing helix  chain 'D' and resid 510 through 525
    Processing helix  chain 'D' and resid 530 through 552
    Processing helix  chain 'D' and resid 553 through 559
      Proline residue:  D 559  - end of helix
    Processing helix  chain 'D' and resid 560 through 573
      removed outlier: 3.601A  pdb=" N   ALA D 573 " --> pdb=" O   ILE D 569 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 577 through 592
      removed outlier: 3.770A  pdb=" N   THR D 592 " --> pdb=" O   CYS D 588 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 594 through 616
      removed outlier: 5.134A  pdb=" N   SER D 603 " --> pdb=" O   ALA D 599 " (cutoff:3.500A)
      removed outlier: 5.826A  pdb=" N   LYS D 604 " --> pdb=" O   SER D 600 " (cutoff:3.500A)
      Proline residue:  D 607  - end of helix
    Processing helix  chain 'D' and resid 619 through 635
    Processing helix  chain 'D' and resid 639 through 657
      Proline residue:  D 649  - end of helix
    Processing helix  chain 'D' and resid 658 through 662
      removed outlier: 3.695A  pdb=" N   ILE D 662 " --> pdb=" O   ALA D 659 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 665 through 680
    Processing helix  chain 'D' and resid 686 through 704
      removed outlier: 3.535A  pdb=" N   ILE D 690 " --> pdb=" O   SER D 686 " (cutoff:3.500A)
      removed outlier: 4.373A  pdb=" N   PHE D 694 " --> pdb=" O   ILE D 690 " (cutoff:3.500A)
      Proline residue:  D 695  - end of helix
    Processing helix  chain 'D' and resid 706 through 723
    Processing helix  chain 'D' and resid 724 through 731
      removed outlier: 3.598A  pdb=" N   VAL D 728 " --> pdb=" O   THR D 724 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 738 through 751
    Processing helix  chain 'D' and resid 756 through 761
    Processing helix  chain 'D' and resid 762 through 775
    Processing helix  chain 'D' and resid 778 through 780
      No H-bonds generated for 'chain 'D' and resid 778 through 780'
    Processing helix  chain 'D' and resid 781 through 796
    Processing helix  chain 'D' and resid 798 through 814
      removed outlier: 3.700A  pdb=" N   SER D 804 " --> pdb=" O   SER D 800 " (cutoff:3.500A)
      removed outlier: 3.841A  pdb=" N   VAL D 808 " --> pdb=" O   SER D 804 " (cutoff:3.500A)
      removed outlier: 4.097A  pdb=" N   PHE D 809 " --> pdb=" O   LEU D 805 " (cutoff:3.500A)
      removed outlier: 3.861A  pdb=" N   HIS D 814 " --> pdb=" O   ALA D 810 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 816 through 827
      removed outlier: 3.532A  pdb=" N   LEU D 827 " --> pdb=" O   PHE D 823 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 834 through 848
      removed outlier: 3.788A  pdb=" N   PHE D 838 " --> pdb=" O   PRO D 834 " (cutoff:3.500A)
      removed outlier: 4.721A  pdb=" N   HIS D 848 " --> pdb=" O   THR D 844 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 852 through 874
    Processing helix  chain 'D' and resid 875 through 880
    Processing helix  chain 'D' and resid 913 through 934
    Processing helix  chain 'D' and resid 997 through 1002
    Processing helix  chain 'D' and resid 1003 through 1017
      removed outlier: 3.933A  pdb=" N   GLN D1017 " --> pdb=" O   CYS D1013 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 1020 through 1028
    Processing helix  chain 'D' and resid 1029 through 1040
    Processing sheet with id=AA1, first strand: chain 'A' and resid 227 through 231
      removed outlier: 6.230A  pdb=" N   VAL A 236 " --> pdb=" O   GLU A 230 " (cutoff:3.500A)
    Processing sheet with id=AA2, first strand: chain 'D' and resid 882 through 884

    562 hydrogen bonds defined for protein.
    1647 hydrogen bond angles defined for protein.
    Restraints generated for nucleic acids:
      0 hydrogen bonds
      0 hydrogen bond angles
      0 basepair planarities
      0 basepair parallelities
      0 stacking parallelities
  Total time for adding SS restraints: 1.42

  Time building geometry restraints manager: 1.03 seconds

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

  Histogram of bond lengths:
        1.18 -     1.31: 1350
        1.31 -     1.44: 2094
        1.44 -     1.56: 4729
        1.56 -     1.69: 0
        1.69 -     1.81: 76
  Bond restraints: 8249
  Sorted by residual:
  bond pdb=" CG  ASP D 139 "
       pdb=" OD2 ASP D 139 "
    ideal  model  delta    sigma   weight residual
    1.249  1.330 -0.081 1.90e-02 2.77e+03 1.81e+01
  bond pdb=" CG  ASP D 139 "
       pdb=" OD1 ASP D 139 "
    ideal  model  delta    sigma   weight residual
    1.249  1.185  0.064 1.90e-02 2.77e+03 1.14e+01
  bond pdb=" N   GLU D  23 "
       pdb=" CA  GLU D  23 "
    ideal  model  delta    sigma   weight residual
    1.458  1.491 -0.033 1.90e-02 2.77e+03 3.03e+00
  bond pdb=" CA  SER D 577 "
       pdb=" CB  SER D 577 "
    ideal  model  delta    sigma   weight residual
    1.530  1.509  0.021 1.69e-02 3.50e+03 1.56e+00
  bond pdb=" N   SER D 577 "
       pdb=" CA  SER D 577 "
    ideal  model  delta    sigma   weight residual
    1.457  1.472 -0.015 1.29e-02 6.01e+03 1.34e+00
  ... (remaining 8244 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     1.13: 10809
        1.13 -     2.26: 305
        2.26 -     3.39: 48
        3.39 -     4.51: 31
        4.51 -     5.64: 6
  Bond angle restraints: 11199
  Sorted by residual:
  angle pdb=" N   SER D 120 "
        pdb=" CA  SER D 120 "
        pdb=" C   SER D 120 "
      ideal   model   delta    sigma   weight residual
     108.52  112.20   -3.68 1.52e+00 4.33e-01 5.87e+00
  angle pdb=" C   GLN D 181 "
        pdb=" N   MET D 182 "
        pdb=" CA  MET D 182 "
      ideal   model   delta    sigma   weight residual
     120.58  123.71   -3.13 1.32e+00 5.74e-01 5.62e+00
  angle pdb=" C   SER D 577 "
        pdb=" CA  SER D 577 "
        pdb=" CB  SER D 577 "
      ideal   model   delta    sigma   weight residual
     110.42  115.02   -4.60 1.99e+00 2.53e-01 5.34e+00
  angle pdb=" N   SER D 489 "
        pdb=" CA  SER D 489 "
        pdb=" C   SER D 489 "
      ideal   model   delta    sigma   weight residual
     110.06  113.15   -3.09 1.43e+00 4.89e-01 4.68e+00
  angle pdb=" CA  SER D 489 "
        pdb=" C   SER D 489 "
        pdb=" O   SER D 489 "
      ideal   model   delta    sigma   weight residual
     121.78  119.38    2.40 1.12e+00 7.97e-01 4.61e+00
  ... (remaining 11194 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    17.81: 4600
       17.81 -    35.63: 318
       35.63 -    53.44: 48
       53.44 -    71.26: 16
       71.26 -    89.07: 8
  Dihedral angle restraints: 4990
    sinusoidal: 1993
      harmonic: 2997
  Sorted by residual:
  dihedral pdb=" CA  HIS A 208 "
           pdb=" C   HIS A 208 "
           pdb=" N   LEU A 209 "
           pdb=" CA  LEU A 209 "
      ideal   model   delta  harmonic     sigma   weight residual
    -180.00 -160.67  -19.33     0      5.00e+00 4.00e-02 1.49e+01
  dihedral pdb=" CA  GLU D 989 "
           pdb=" C   GLU D 989 "
           pdb=" N   ASP D 990 "
           pdb=" CA  ASP D 990 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00 -162.33  -17.67     0      5.00e+00 4.00e-02 1.25e+01
  dihedral pdb=" CA  ASP D 783 "
           pdb=" CB  ASP D 783 "
           pdb=" CG  ASP D 783 "
           pdb=" OD1 ASP D 783 "
      ideal   model   delta sinusoidal    sigma   weight residual
     -30.00  -84.28   54.28     1      2.00e+01 2.50e-03 9.99e+00
  ... (remaining 4987 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.029: 895
       0.029 -    0.057: 256
       0.057 -    0.086: 109
       0.086 -    0.114: 39
       0.114 -    0.143: 2
  Chirality restraints: 1301
  Sorted by residual:
  chirality pdb=" CA  ILE D 254 "
            pdb=" N   ILE D 254 "
            pdb=" C   ILE D 254 "
            pdb=" CB  ILE D 254 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.43    2.58   -0.14 2.00e-01 2.50e+01 5.10e-01
  chirality pdb=" CA  ASP D  66 "
            pdb=" N   ASP D  66 "
            pdb=" C   ASP D  66 "
            pdb=" CB  ASP D  66 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.38    0.13 2.00e-01 2.50e+01 4.42e-01
  chirality pdb=" CA  VAL A 236 "
            pdb=" N   VAL A 236 "
            pdb=" C   VAL A 236 "
            pdb=" CB  VAL A 236 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.44    2.55   -0.11 2.00e-01 2.50e+01 3.13e-01
  ... (remaining 1298 not shown)

  Planarity restraints: 1426
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CB  ASP D  66 "    0.006 2.00e-02 2.50e+03   1.32e-02 1.73e+00
        pdb=" CG  ASP D  66 "   -0.023 2.00e-02 2.50e+03
        pdb=" OD1 ASP D  66 "    0.008 2.00e-02 2.50e+03
        pdb=" OD2 ASP D  66 "    0.008 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  VAL D 306 "   -0.005 2.00e-02 2.50e+03   1.02e-02 1.05e+00
        pdb=" C   VAL D 306 "    0.018 2.00e-02 2.50e+03
        pdb=" O   VAL D 306 "   -0.007 2.00e-02 2.50e+03
        pdb=" N   ARG D 307 "   -0.006 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   ASP D 991 "    0.015 5.00e-02 4.00e+02   2.31e-02 8.56e-01
        pdb=" N   PRO D 992 "   -0.040 5.00e-02 4.00e+02
        pdb=" CA  PRO D 992 "    0.012 5.00e-02 4.00e+02
        pdb=" CD  PRO D 992 "    0.013 5.00e-02 4.00e+02
  ... (remaining 1423 not shown)

  Histogram of nonbonded interaction distances:
        2.02 -     2.60: 91
        2.60 -     3.17: 7766
        3.17 -     3.75: 13345
        3.75 -     4.32: 17344
        4.32 -     4.90: 29064
  Nonbonded interactions: 67610
  Sorted by model distance:
  nonbonded pdb=" O   ARG D 168 "
            pdb=" OG1 THR D 171 "
     model   vdw
     2.019 3.040
  nonbonded pdb=" OH  TYR A 269 "
            pdb=" OE2 GLU D 585 "
     model   vdw
     2.125 3.040
  nonbonded pdb=" OG  SER D 510 "
            pdb=" OE1 GLU D 512 "
     model   vdw
     2.226 3.040
  nonbonded pdb=" OH  TYR A 270 "
            pdb=" OD2 ASP D 392 "
     model   vdw
     2.232 3.040
  nonbonded pdb=" O   VAL D  79 "
            pdb=" OE1 GLN D  83 "
     model   vdw
     2.255 3.040
  ... (remaining 67605 not shown)

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

  No NCS relation were found !!!

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

Found NCS groups:
  found none.
Set up NCS constraints
  No NCS constraints will be used in refinement.
Set refine NCS operators
Adjust number of macro_cycles
  Number of macro_cycles: 10
Reset NCS operators
Extract rigid body selections
Check and reset occupancies
  Occupancies: min=1.00 max=1.00 mean=1.00
Load rotamer database and sin/cos tables
Set ADP refinement strategy
  ADPs will be refined as group one per residue
Make a string to write initial .geo file
Internal consistency checks
Time:
  Set random seed:                         0.000
  Set model cs if undefined:               0.000
  Decide on map wrapping:                  0.000
  Normalize map: mean=0, sd=1:             0.950
  Set stop_for_unknowns flag:              0.000
  Assert model is a single copy model:     0.000
  Assert all atoms have isotropic ADPs:    0.040
  Construct map_model_manager:             0.000
  Extract box with map and model:          0.130
  Check model and map are aligned:         0.020
  Set scattering table:                    0.020
  Process input model:                     8.960
  Find NCS groups from input model:        0.040
  Set up NCS constraints:                  0.020
  Set refine NCS operators:                0.000
  Adjust number of macro_cycles:           0.000
  Reset NCS operators:                     0.000
  Extract rigid body selections:           0.000
  Check and reset occupancies:             0.000
  Load rotamer database and sin/cos tables:1.320
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   11.500
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6656
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   0.081   8249  Z= 0.137
  Angle     :  0.511   5.642  11199  Z= 0.292
  Chirality :  0.034   0.143   1301
  Planarity :  0.003   0.023   1426
  Dihedral  : 13.070  89.070   3032
  Min Nonbonded Distance : 2.019

Molprobity Statistics.
  All-atom Clashscore : 5.42
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.79 %
    Favored  : 98.21 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  0.00 %
    Favored  : 100.00 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 4.55 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  2.68 (0.27), residues: 1008
  helix:  2.11 (0.19), residues: 745
  sheet: -0.70 (1.45), residues: 17
  loop :  1.12 (0.44), residues: 246

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG D 718 
 TYR   0.009   0.001   TYR D 363 
 PHE   0.007   0.001   PHE D 329 
 TRP   0.006   0.001   TRP D 140 
 HIS   0.006   0.001   HIS A 208 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00271 /  0.14 ( 8249)
  covalent geometry    : angle       0.51140 /  0.29 (11199)
  hydrogen bonds       : bond        0.14520 /  9.71 (  562)
  hydrogen bonds       : angle       5.70039 /  4.04 ( 1647)

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

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

  2016 Ramachandran restraints generated.
    1008 Oldfield, 0 Emsley, 1008 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2016 Ramachandran restraints generated.
    1008 Oldfield, 0 Emsley, 1008 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  214 residues out of total 887 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 214
  time to evaluate  : 0.242 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  228 LYS cc_start: 0.7694 (pptt) cc_final: 0.7348 (ptmt)
REVERT: A  229 TRP cc_start: 0.8195 (m100) cc_final: 0.7429 (m100)
REVERT: A  291 ASN cc_start: 0.6449 (m-40) cc_final: 0.6117 (m110)
REVERT: D   60 LEU cc_start: 0.8435 (mt) cc_final: 0.8135 (tt)
REVERT: D  152 MET cc_start: 0.8193 (tmm) cc_final: 0.7931 (tmm)
REVERT: D  167 MET cc_start: 0.7778 (mtp) cc_final: 0.7157 (mtp)
REVERT: D  182 MET cc_start: 0.6739 (tmm) cc_final: 0.6133 (tmm)
REVERT: D  192 GLU cc_start: 0.8296 (mm-30) cc_final: 0.7970 (pm20)
REVERT: D  195 LYS cc_start: 0.8209 (ttpt) cc_final: 0.7988 (ttpt)
REVERT: D  202 VAL cc_start: 0.9180 (t) cc_final: 0.8771 (t)
REVERT: D  221 MET cc_start: 0.6516 (tpt) cc_final: 0.6014 (tpt)
REVERT: D  266 MET cc_start: 0.7256 (tmm) cc_final: 0.6908 (tmm)
REVERT: D  270 LYS cc_start: 0.6781 (mtpt) cc_final: 0.6488 (ttmm)
REVERT: D  276 VAL cc_start: 0.7712 (p) cc_final: 0.7384 (t)
REVERT: D  287 MET cc_start: 0.7526 (mmm) cc_final: 0.7197 (mmt)
REVERT: D  291 LEU cc_start: 0.6479 (mt) cc_final: 0.6258 (mm)
REVERT: D  301 SER cc_start: 0.7609 (m) cc_final: 0.7204 (m)
REVERT: D  349 PHE cc_start: 0.7452 (m-80) cc_final: 0.7158 (m-80)
REVERT: D  433 GLU cc_start: 0.7383 (tp30) cc_final: 0.7129 (tp30)
REVERT: D  442 HIS cc_start: 0.6877 (m90) cc_final: 0.6631 (m90)
REVERT: D  450 CYS cc_start: 0.5527 (m) cc_final: 0.5138 (m)
REVERT: D  458 LYS cc_start: 0.6692 (pttm) cc_final: 0.6155 (ptpt)
REVERT: D  553 SER cc_start: 0.7629 (m) cc_final: 0.6807 (p)
REVERT: D  602 GLU cc_start: 0.7310 (tm-30) cc_final: 0.6990 (tm-30)
REVERT: D  682 LYS cc_start: 0.8005 (mtpp) cc_final: 0.7684 (mtpp)
REVERT: D  704 THR cc_start: 0.7866 (t) cc_final: 0.7566 (t)
REVERT: D  706 ASP cc_start: 0.6641 (t0) cc_final: 0.6306 (t0)
REVERT: D  732 HIS cc_start: 0.7140 (m90) cc_final: 0.6892 (m90)
REVERT: D  757 GLU cc_start: 0.7169 (pt0) cc_final: 0.6656 (pt0)
REVERT: D  758 PHE cc_start: 0.7645 (m-10) cc_final: 0.7341 (m-10)
REVERT: D  780 GLU cc_start: 0.6908 (pm20) cc_final: 0.6530 (tm-30)
REVERT: D  855 GLU cc_start: 0.7452 (mt-10) cc_final: 0.6727 (mm-30)
REVERT: D  865 LYS cc_start: 0.7425 (mmtt) cc_final: 0.7220 (mmtm)
REVERT: D  876 LYS cc_start: 0.8123 (mmmt) cc_final: 0.7783 (mmmt)
REVERT: D  920 LEU cc_start: 0.6681 (mt) cc_final: 0.6431 (mt)
REVERT: D  927 ASN cc_start: 0.7202 (t0) cc_final: 0.6965 (t0)
REVERT: D  929 MET cc_start: 0.6852 (mmm) cc_final: 0.5985 (tpp)
  outliers start: 0
  outliers final: 0
  residues processed: 214
  average time/residue: 0.1054
  time to fit residues: 29.7850
Evaluate side-chains
  181 residues out of total 887 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 181
  time to evaluate  : 0.295 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 101
   random chunks:
   chunk 49 optimal weight:    0.8980
   chunk 97 optimal weight:    0.6980
   chunk 53 optimal weight:    0.8980
   chunk 5 optimal weight:    2.9990
   chunk 33 optimal weight:    1.9990
   chunk 65 optimal weight:    0.9990
   chunk 62 optimal weight:    0.9980
   chunk 51 optimal weight:    2.9990
   chunk 100 optimal weight:    2.9990
   chunk 38 optimal weight:    0.0870
   chunk 61 optimal weight:    0.0770
   overall best weight:    0.5316

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
A 208 HIS
D 289 GLN
D 707 ASN
D1017 GLN
D1018 GLN

Total number of N/Q/H flips: 5

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3996 r_free = 0.3996 target = 0.158192 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 40)----------------|
| r_work = 0.3622 r_free = 0.3622 target = 0.129963 restraints weight = 12489.789|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 38)----------------|
| r_work = 0.3678 r_free = 0.3678 target = 0.133821 restraints weight = 6114.321|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 34)----------------|
| r_work = 0.3712 r_free = 0.3712 target = 0.136344 restraints weight = 3686.307|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 38)----------------|
| r_work = 0.3734 r_free = 0.3734 target = 0.137954 restraints weight = 2552.604|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 41)----------------|
| r_work = 0.3749 r_free = 0.3749 target = 0.139039 restraints weight = 1967.382|
|-----------------------------------------------------------------------------|
r_work (final): 0.3742
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7281
moved from start:          0.2128

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.042   8249  Z= 0.156
  Angle     :  0.583  14.621  11199  Z= 0.298
  Chirality :  0.040   0.158   1301
  Planarity :  0.004   0.033   1426
  Dihedral  :  4.060  22.300   1085
  Min Nonbonded Distance : 2.552

Molprobity Statistics.
  All-atom Clashscore : 6.22
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.98 %
    Favored  : 98.02 %
  Rotamer:
    Outliers :  1.02 %
    Allowed  :  6.21 %
    Favored  : 92.78 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 4.55 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  2.56 (0.27), residues: 1008
  helix:  2.00 (0.19), residues: 745
  sheet: -0.60 (1.46), residues: 17
  loop :  1.16 (0.44), residues: 246

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARG A 265 
 TYR   0.014   0.001   TYR D 362 
 PHE   0.016   0.002   PHE D 238 
 TRP   0.013   0.001   TRP D 542 
 HIS   0.006   0.001   HIS D 869 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00356 /  0.16 ( 8249)
  covalent geometry    : angle       0.58273 /  0.30 (11199)
  hydrogen bonds       : bond        0.04058 /  2.69 (  562)
  hydrogen bonds       : angle       4.49130 /  3.16 ( 1647)

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

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

  2016 Ramachandran restraints generated.
    1008 Oldfield, 0 Emsley, 1008 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2016 Ramachandran restraints generated.
    1008 Oldfield, 0 Emsley, 1008 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  181 residues out of total 887 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 9
    poor density    : 172
  time to evaluate  : 0.337 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  267 MET cc_start: 0.7783 (mtp) cc_final: 0.7394 (mtp)
REVERT: A  275 ILE cc_start: 0.8261 (mm) cc_final: 0.8040 (mm)
REVERT: A  291 ASN cc_start: 0.7203 (m-40) cc_final: 0.6972 (m110)
REVERT: D  167 MET cc_start: 0.7231 (mtp) cc_final: 0.6898 (mtp)
REVERT: D  199 MET cc_start: 0.5959 (tpp) cc_final: 0.5277 (tpp)
REVERT: D  202 VAL cc_start: 0.8817 (t) cc_final: 0.8281 (m)
REVERT: D  221 MET cc_start: 0.5696 (tpt) cc_final: 0.5140 (tpt)
REVERT: D  266 MET cc_start: 0.7676 (tmm) cc_final: 0.7097 (tmm)
REVERT: D  276 VAL cc_start: 0.8022 (p) cc_final: 0.7710 (t)
REVERT: D  287 MET cc_start: 0.7869 (mmm) cc_final: 0.7506 (mmt)
REVERT: D  301 SER cc_start: 0.8320 (m) cc_final: 0.8023 (m)
REVERT: D  368 MET cc_start: 0.8778 (mtm) cc_final: 0.8547 (mtm)
REVERT: D  430 GLN cc_start: 0.7057 (OUTLIER) cc_final: 0.6822 (mp10)
REVERT: D  479 THR cc_start: 0.8075 (m) cc_final: 0.7808 (p)
REVERT: D  542 TRP cc_start: 0.7737 (t60) cc_final: 0.7454 (t60)
REVERT: D  553 SER cc_start: 0.8477 (m) cc_final: 0.7521 (p)
REVERT: D  706 ASP cc_start: 0.6904 (t0) cc_final: 0.6691 (t0)
REVERT: D  744 MET cc_start: 0.7366 (mmm) cc_final: 0.6919 (mmt)
REVERT: D  865 LYS cc_start: 0.8164 (mmtt) cc_final: 0.7889 (mmtm)
REVERT: D  920 LEU cc_start: 0.7618 (mt) cc_final: 0.7381 (mt)
REVERT: D  927 ASN cc_start: 0.7476 (t0) cc_final: 0.7054 (t0)
REVERT: D 1035 VAL cc_start: 0.8427 (t) cc_final: 0.8210 (t)
  outliers start: 9
  outliers final: 5
  residues processed: 177
  average time/residue: 0.0969
  time to fit residues: 23.2716
Evaluate side-chains
  167 residues out of total 887 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 6
    poor density    : 161
  time to evaluate  : 0.299 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain D residue  241 VAL
Chi-restraints excluded: chain D residue  290 ILE
Chi-restraints excluded: chain D residue  397 THR
Chi-restraints excluded: chain D residue  407 LEU
Chi-restraints excluded: chain D residue  430 GLN
Chi-restraints excluded: chain D residue  752 ASP
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 101
   random chunks:
   chunk 54 optimal weight:    0.9990
   chunk 83 optimal weight:    0.6980
   chunk 41 optimal weight:    0.9990
   chunk 64 optimal weight:    0.8980
   chunk 12 optimal weight:    9.9990
   chunk 11 optimal weight:    4.9990
   chunk 61 optimal weight:    0.0970
   chunk 37 optimal weight:    0.5980
   chunk 92 optimal weight:    0.2980
   chunk 63 optimal weight:    0.5980
   chunk 59 optimal weight:    0.5980
   overall best weight:    0.4378

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
** D  88 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
D 289 GLN
D 442 HIS
D 526 HIS
D 816 GLN
D 853 GLN
** D1005 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 5

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3993 r_free = 0.3993 target = 0.156792 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 53)----------------|
| r_work = 0.3622 r_free = 0.3622 target = 0.128928 restraints weight = 12318.398|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 28)----------------|
| r_work = 0.3672 r_free = 0.3672 target = 0.132531 restraints weight = 6017.275|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 40)----------------|
| r_work = 0.3712 r_free = 0.3712 target = 0.135118 restraints weight = 3684.494|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 35)----------------|
| r_work = 0.3732 r_free = 0.3732 target = 0.136614 restraints weight = 2544.473|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 36)----------------|
| r_work = 0.3747 r_free = 0.3747 target = 0.137707 restraints weight = 1979.049|
|-----------------------------------------------------------------------------|
r_work (final): 0.3743
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7288
moved from start:          0.2786

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.033   8249  Z= 0.139
  Angle     :  0.562  12.340  11199  Z= 0.287
  Chirality :  0.039   0.151   1301
  Planarity :  0.004   0.035   1426
  Dihedral  :  4.048  24.407   1085
  Min Nonbonded Distance : 2.533

Molprobity Statistics.
  All-atom Clashscore : 7.03
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.28 %
    Favored  : 97.72 %
  Rotamer:
    Outliers :  1.02 %
    Allowed  : 10.72 %
    Favored  : 88.26 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 4.55 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  2.44 (0.27), residues: 1008
  helix:  1.97 (0.19), residues: 750
  sheet: -0.28 (1.50), residues: 17
  loop :  0.83 (0.43), residues: 241

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.000   ARG D 118 
 TYR   0.012   0.001   TYR D 362 
 PHE   0.018   0.002   PHE D 238 
 TRP   0.011   0.001   TRP A 210 
 HIS   0.008   0.001   HIS D 282 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00316 /  0.14 ( 8249)
  covalent geometry    : angle       0.56206 /  0.29 (11199)
  hydrogen bonds       : bond        0.03695 /  2.44 (  562)
  hydrogen bonds       : angle       4.32521 /  3.02 ( 1647)

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

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

  2016 Ramachandran restraints generated.
    1008 Oldfield, 0 Emsley, 1008 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2016 Ramachandran restraints generated.
    1008 Oldfield, 0 Emsley, 1008 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  181 residues out of total 887 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 9
    poor density    : 172
  time to evaluate  : 0.313 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  238 ARG cc_start: 0.6828 (ttm-80) cc_final: 0.6575 (mtp-110)
REVERT: A  267 MET cc_start: 0.7842 (mtp) cc_final: 0.7431 (mtp)
REVERT: A  273 ARG cc_start: 0.7921 (ptp90) cc_final: 0.7520 (ptt180)
REVERT: A  275 ILE cc_start: 0.8366 (mm) cc_final: 0.8163 (mm)
REVERT: A  283 ARG cc_start: 0.6380 (ptm-80) cc_final: 0.6052 (ptm-80)
REVERT: A  291 ASN cc_start: 0.7361 (m-40) cc_final: 0.7148 (m110)
REVERT: D  154 MET cc_start: 0.6486 (tpt) cc_final: 0.6251 (tpt)
REVERT: D  167 MET cc_start: 0.7113 (mtp) cc_final: 0.6907 (mtp)
REVERT: D  193 MET cc_start: 0.6477 (mmm) cc_final: 0.5904 (mmm)
REVERT: D  201 GLU cc_start: 0.7581 (pm20) cc_final: 0.7198 (pm20)
REVERT: D  203 TYR cc_start: 0.7619 (m-80) cc_final: 0.6964 (m-80)
REVERT: D  221 MET cc_start: 0.5574 (tpt) cc_final: 0.4947 (tpt)
REVERT: D  266 MET cc_start: 0.7622 (tmm) cc_final: 0.7217 (tmm)
REVERT: D  276 VAL cc_start: 0.7996 (p) cc_final: 0.7694 (t)
REVERT: D  301 SER cc_start: 0.8269 (m) cc_final: 0.7980 (m)
REVERT: D  430 GLN cc_start: 0.7058 (OUTLIER) cc_final: 0.6815 (mp10)
REVERT: D  500 TRP cc_start: 0.6966 (t60) cc_final: 0.6585 (t60)
REVERT: D  542 TRP cc_start: 0.7733 (t60) cc_final: 0.7451 (t60)
REVERT: D  553 SER cc_start: 0.8448 (m) cc_final: 0.7271 (t)
REVERT: D  744 MET cc_start: 0.7289 (mmm) cc_final: 0.6978 (mmm)
REVERT: D  745 GLN cc_start: 0.7262 (mp10) cc_final: 0.7053 (mp10)
REVERT: D  773 LYS cc_start: 0.8203 (mmmt) cc_final: 0.7922 (mmtt)
REVERT: D  791 SER cc_start: 0.7788 (m) cc_final: 0.7507 (t)
REVERT: D  865 LYS cc_start: 0.8360 (mmtt) cc_final: 0.7987 (mmtm)
REVERT: D  868 GLN cc_start: 0.7415 (tm-30) cc_final: 0.7188 (tm-30)
REVERT: D  927 ASN cc_start: 0.7445 (t0) cc_final: 0.6928 (t0)
REVERT: D 1018 GLN cc_start: 0.7732 (tm-30) cc_final: 0.7517 (tm-30)
  outliers start: 9
  outliers final: 4
  residues processed: 176
  average time/residue: 0.1136
  time to fit residues: 26.1384
Evaluate side-chains
  169 residues out of total 887 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 5
    poor density    : 164
  time to evaluate  : 0.323 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain D residue  241 VAL
Chi-restraints excluded: chain D residue  397 THR
Chi-restraints excluded: chain D residue  430 GLN
Chi-restraints excluded: chain D residue  486 LEU
Chi-restraints excluded: chain D residue  752 ASP
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 101
   random chunks:
   chunk 14 optimal weight:    2.9990
   chunk 71 optimal weight:    0.7980
   chunk 59 optimal weight:    0.9980
   chunk 35 optimal weight:    0.4980
   chunk 94 optimal weight:    0.5980
   chunk 80 optimal weight:    0.9980
   chunk 68 optimal weight:    0.9980
   chunk 83 optimal weight:    0.5980
   chunk 41 optimal weight:    0.0980
   chunk 32 optimal weight:    0.6980
   chunk 72 optimal weight:    0.5980
   overall best weight:    0.4780

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
** D  88 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
D 442 HIS
D 526 HIS
D 547 GLN
D 816 GLN
D 853 GLN

Total number of N/Q/H flips: 5

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3985 r_free = 0.3985 target = 0.156344 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 43)----------------|
| r_work = 0.3603 r_free = 0.3603 target = 0.128049 restraints weight = 12511.236|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 36)----------------|
| r_work = 0.3659 r_free = 0.3659 target = 0.131934 restraints weight = 6075.209|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 40)----------------|
| r_work = 0.3695 r_free = 0.3695 target = 0.134478 restraints weight = 3656.374|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 37)----------------|
| r_work = 0.3717 r_free = 0.3717 target = 0.136066 restraints weight = 2528.223|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 28)----------------|
| r_work = 0.3727 r_free = 0.3727 target = 0.136801 restraints weight = 1947.640|
|-----------------------------------------------------------------------------|
r_work (final): 0.3722
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7309
moved from start:          0.3238

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.029   8249  Z= 0.141
  Angle     :  0.552   9.545  11199  Z= 0.283
  Chirality :  0.039   0.148   1301
  Planarity :  0.004   0.035   1426
  Dihedral  :  4.121  23.765   1085
  Min Nonbonded Distance : 2.560

Molprobity Statistics.
  All-atom Clashscore : 7.27
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.18 %
    Favored  : 97.82 %
  Rotamer:
    Outliers :  1.58 %
    Allowed  : 12.19 %
    Favored  : 86.23 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 4.55 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  2.34 (0.26), residues: 1008
  helix:  1.96 (0.19), residues: 751
  sheet: -0.03 (1.54), residues: 17
  loop :  0.49 (0.42), residues: 240

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARG A 214 
 TYR   0.011   0.001   TYR D 362 
 PHE   0.021   0.002   PHE D 413 
 TRP   0.011   0.001   TRP A 210 
 HIS   0.013   0.001   HIS D 282 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00326 /  0.14 ( 8249)
  covalent geometry    : angle       0.55199 /  0.28 (11199)
  hydrogen bonds       : bond        0.03577 /  2.37 (  562)
  hydrogen bonds       : angle       4.25687 /  2.97 ( 1647)

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

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

  2016 Ramachandran restraints generated.
    1008 Oldfield, 0 Emsley, 1008 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2016 Ramachandran restraints generated.
    1008 Oldfield, 0 Emsley, 1008 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  188 residues out of total 887 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 174
  time to evaluate  : 0.305 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  238 ARG cc_start: 0.6706 (ttm-80) cc_final: 0.6446 (mtp-110)
REVERT: A  267 MET cc_start: 0.7861 (mtp) cc_final: 0.7404 (mtp)
REVERT: A  283 ARG cc_start: 0.6517 (ptm-80) cc_final: 0.6287 (ptm-80)
REVERT: A  285 VAL cc_start: 0.7706 (t) cc_final: 0.7503 (t)
REVERT: A  291 ASN cc_start: 0.7527 (m-40) cc_final: 0.7301 (m110)
REVERT: D  167 MET cc_start: 0.7225 (mtp) cc_final: 0.6963 (mtp)
REVERT: D  193 MET cc_start: 0.6632 (mmm) cc_final: 0.6362 (mmm)
REVERT: D  266 MET cc_start: 0.7520 (tmm) cc_final: 0.7261 (tmm)
REVERT: D  276 VAL cc_start: 0.8067 (p) cc_final: 0.7747 (t)
REVERT: D  301 SER cc_start: 0.8097 (m) cc_final: 0.7835 (m)
REVERT: D  362 TYR cc_start: 0.7221 (t80) cc_final: 0.6709 (t80)
REVERT: D  430 GLN cc_start: 0.7036 (OUTLIER) cc_final: 0.6754 (mp10)
REVERT: D  490 VAL cc_start: 0.8120 (p) cc_final: 0.7741 (t)
REVERT: D  542 TRP cc_start: 0.7727 (t60) cc_final: 0.7417 (t60)
REVERT: D  553 SER cc_start: 0.8434 (m) cc_final: 0.7275 (t)
REVERT: D  744 MET cc_start: 0.7150 (mmm) cc_final: 0.6932 (mmm)
REVERT: D  745 GLN cc_start: 0.7238 (mp10) cc_final: 0.6939 (mp10)
REVERT: D  773 LYS cc_start: 0.8137 (mmmt) cc_final: 0.7868 (mmtt)
REVERT: D  791 SER cc_start: 0.7831 (m) cc_final: 0.7515 (t)
REVERT: D  865 LYS cc_start: 0.8300 (mmtt) cc_final: 0.7824 (mmtm)
REVERT: D  927 ASN cc_start: 0.7382 (t0) cc_final: 0.6969 (t0)
  outliers start: 14
  outliers final: 5
  residues processed: 181
  average time/residue: 0.1191
  time to fit residues: 28.0789
Evaluate side-chains
  169 residues out of total 887 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 6
    poor density    : 163
  time to evaluate  : 0.236 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain D residue  282 HIS
Chi-restraints excluded: chain D residue  397 THR
Chi-restraints excluded: chain D residue  430 GLN
Chi-restraints excluded: chain D residue  486 LEU
Chi-restraints excluded: chain D residue  752 ASP
Chi-restraints excluded: chain D residue  999 LEU
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 101
   random chunks:
   chunk 21 optimal weight:    0.9980
   chunk 46 optimal weight:    0.6980
   chunk 70 optimal weight:    1.9990
   chunk 27 optimal weight:    4.9990
   chunk 62 optimal weight:    0.9990
   chunk 29 optimal weight:    0.7980
   chunk 19 optimal weight:    1.9990
   chunk 10 optimal weight:    9.9990
   chunk 87 optimal weight:    0.6980
   chunk 89 optimal weight:    0.5980
   chunk 44 optimal weight:    0.8980
   overall best weight:    0.7380

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
** D  88 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
D 442 HIS
D 526 HIS
D 816 GLN
D 853 GLN
D 879 GLN

Total number of N/Q/H flips: 5

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3957 r_free = 0.3957 target = 0.153797 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.3569 r_free = 0.3569 target = 0.125484 restraints weight = 12392.648|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 36)----------------|
| r_work = 0.3627 r_free = 0.3627 target = 0.129428 restraints weight = 6028.505|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 38)----------------|
| r_work = 0.3664 r_free = 0.3664 target = 0.131993 restraints weight = 3603.886|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 40)----------------|
| r_work = 0.3685 r_free = 0.3685 target = 0.133514 restraints weight = 2466.762|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 40)----------------|
| r_work = 0.3701 r_free = 0.3701 target = 0.134586 restraints weight = 1909.801|
|-----------------------------------------------------------------------------|
r_work (final): 0.3691
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7342
moved from start:          0.3664

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.036   8249  Z= 0.182
  Angle     :  0.593   8.361  11199  Z= 0.303
  Chirality :  0.041   0.147   1301
  Planarity :  0.004   0.050   1426
  Dihedral  :  4.241  24.142   1085
  Min Nonbonded Distance : 2.511

Molprobity Statistics.
  All-atom Clashscore : 7.77
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.38 %
    Favored  : 97.62 %
  Rotamer:
    Outliers :  1.35 %
    Allowed  : 14.00 %
    Favored  : 84.65 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 4.55 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  2.16 (0.26), residues: 1008
  helix:  1.86 (0.19), residues: 757
  sheet: -0.32 (1.53), residues: 17
  loop :  0.28 (0.42), residues: 234

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARG A 282 
 TYR   0.013   0.002   TYR D 742 
 PHE   0.019   0.002   PHE D 413 
 TRP   0.011   0.001   TRP A 210 
 HIS   0.007   0.001   HIS D 282 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00429 /  0.18 ( 8249)
  covalent geometry    : angle       0.59268 /  0.30 (11199)
  hydrogen bonds       : bond        0.04018 /  2.63 (  562)
  hydrogen bonds       : angle       4.30866 /  3.02 ( 1647)

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

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

  2016 Ramachandran restraints generated.
    1008 Oldfield, 0 Emsley, 1008 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2016 Ramachandran restraints generated.
    1008 Oldfield, 0 Emsley, 1008 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  181 residues out of total 887 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 169
  time to evaluate  : 0.297 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  238 ARG cc_start: 0.6781 (ttm-80) cc_final: 0.6444 (mtp-110)
REVERT: A  267 MET cc_start: 0.7929 (mtp) cc_final: 0.7480 (mtp)
REVERT: A  268 ARG cc_start: 0.7145 (mtm-85) cc_final: 0.6718 (mtm180)
REVERT: A  283 ARG cc_start: 0.6571 (ptm-80) cc_final: 0.6287 (ptm-80)
REVERT: A  291 ASN cc_start: 0.7762 (m-40) cc_final: 0.7534 (m110)
REVERT: D  266 MET cc_start: 0.7386 (tmm) cc_final: 0.7008 (tmm)
REVERT: D  276 VAL cc_start: 0.8164 (p) cc_final: 0.7794 (t)
REVERT: D  301 SER cc_start: 0.8103 (m) cc_final: 0.7784 (m)
REVERT: D  362 TYR cc_start: 0.7131 (t80) cc_final: 0.6451 (t80)
REVERT: D  430 GLN cc_start: 0.7111 (OUTLIER) cc_final: 0.6825 (mp10)
REVERT: D  506 THR cc_start: 0.7922 (m) cc_final: 0.7716 (p)
REVERT: D  553 SER cc_start: 0.8481 (m) cc_final: 0.7557 (p)
REVERT: D  601 MET cc_start: 0.7235 (mmt) cc_final: 0.6974 (mmm)
REVERT: D  616 TYR cc_start: 0.8427 (m-80) cc_final: 0.8112 (m-80)
REVERT: D  745 GLN cc_start: 0.7092 (mp10) cc_final: 0.6815 (mp10)
REVERT: D  762 PHE cc_start: 0.8180 (m-10) cc_final: 0.7954 (m-80)
REVERT: D  773 LYS cc_start: 0.8198 (mmmt) cc_final: 0.7887 (mmtt)
REVERT: D  791 SER cc_start: 0.7785 (m) cc_final: 0.7567 (t)
REVERT: D  821 LEU cc_start: 0.8009 (mt) cc_final: 0.7804 (mt)
REVERT: D  865 LYS cc_start: 0.8370 (mmtt) cc_final: 0.7992 (mmtm)
REVERT: D  868 GLN cc_start: 0.7508 (tm-30) cc_final: 0.7154 (tm-30)
REVERT: D  914 LEU cc_start: 0.7996 (mm) cc_final: 0.7710 (mp)
REVERT: D  927 ASN cc_start: 0.7412 (t0) cc_final: 0.6970 (t0)
  outliers start: 12
  outliers final: 10
  residues processed: 176
  average time/residue: 0.1190
  time to fit residues: 27.1349
Evaluate side-chains
  171 residues out of total 887 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 160
  time to evaluate  : 0.297 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain D residue   36 VAL
Chi-restraints excluded: chain D residue  291 LEU
Chi-restraints excluded: chain D residue  349 PHE
Chi-restraints excluded: chain D residue  361 ILE
Chi-restraints excluded: chain D residue  397 THR
Chi-restraints excluded: chain D residue  407 LEU
Chi-restraints excluded: chain D residue  430 GLN
Chi-restraints excluded: chain D residue  486 LEU
Chi-restraints excluded: chain D residue  752 ASP
Chi-restraints excluded: chain D residue  827 LEU
Chi-restraints excluded: chain D residue 1023 MET
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 101
   random chunks:
   chunk 98 optimal weight:    0.6980
   chunk 78 optimal weight:    0.4980
   chunk 87 optimal weight:    4.9990
   chunk 96 optimal weight:    0.0870
   chunk 45 optimal weight:    0.9980
   chunk 2 optimal weight:    0.9990
   chunk 23 optimal weight:    4.9990
   chunk 30 optimal weight:    0.9980
   chunk 76 optimal weight:    0.1980
   chunk 10 optimal weight:   10.0000
   chunk 47 optimal weight:    1.9990
   overall best weight:    0.4958

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
** D  88 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
D 442 HIS
D 816 GLN
D 853 GLN
D 879 GLN

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3972 r_free = 0.3972 target = 0.155226 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 40)----------------|
| r_work = 0.3588 r_free = 0.3588 target = 0.126889 restraints weight = 12214.036|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 27)----------------|
| r_work = 0.3645 r_free = 0.3645 target = 0.130812 restraints weight = 5990.276|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 40)----------------|
| r_work = 0.3681 r_free = 0.3681 target = 0.133363 restraints weight = 3614.877|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 39)----------------|
| r_work = 0.3704 r_free = 0.3704 target = 0.134954 restraints weight = 2504.488|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 35)----------------|
| r_work = 0.3719 r_free = 0.3719 target = 0.136007 restraints weight = 1927.496|
|-----------------------------------------------------------------------------|
r_work (final): 0.3717
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7320
moved from start:          0.3860

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.031   8249  Z= 0.143
  Angle     :  0.572  12.695  11199  Z= 0.289
  Chirality :  0.039   0.149   1301
  Planarity :  0.004   0.039   1426
  Dihedral  :  4.143  25.689   1085
  Min Nonbonded Distance : 2.535

Molprobity Statistics.
  All-atom Clashscore : 7.64
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.28 %
    Favored  : 97.72 %
  Rotamer:
    Outliers :  1.81 %
    Allowed  : 14.22 %
    Favored  : 83.97 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 4.55 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  2.13 (0.27), residues: 1008
  helix:  1.87 (0.19), residues: 755
  sheet: -0.64 (1.44), residues: 17
  loop :  0.21 (0.42), residues: 236

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.009   0.001   ARG A 214 
 TYR   0.011   0.001   TYR D1007 
 PHE   0.019   0.002   PHE D 413 
 TRP   0.011   0.001   TRP A 210 
 HIS   0.004   0.001   HIS D 869 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00333 /  0.14 ( 8249)
  covalent geometry    : angle       0.57193 /  0.29 (11199)
  hydrogen bonds       : bond        0.03562 /  2.35 (  562)
  hydrogen bonds       : angle       4.20982 /  2.97 ( 1647)

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

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

  2016 Ramachandran restraints generated.
    1008 Oldfield, 0 Emsley, 1008 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2016 Ramachandran restraints generated.
    1008 Oldfield, 0 Emsley, 1008 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  180 residues out of total 887 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 164
  time to evaluate  : 0.303 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  291 ASN cc_start: 0.7755 (m-40) cc_final: 0.7541 (m110)
REVERT: D  113 LEU cc_start: 0.8491 (tp) cc_final: 0.8198 (tp)
REVERT: D  266 MET cc_start: 0.7351 (tmm) cc_final: 0.6253 (tmm)
REVERT: D  270 LYS cc_start: 0.7452 (ttmm) cc_final: 0.7131 (mtmm)
REVERT: D  276 VAL cc_start: 0.8112 (p) cc_final: 0.7814 (t)
REVERT: D  301 SER cc_start: 0.8026 (m) cc_final: 0.7745 (m)
REVERT: D  430 GLN cc_start: 0.7085 (OUTLIER) cc_final: 0.6766 (mp10)
REVERT: D  542 TRP cc_start: 0.7698 (t60) cc_final: 0.7462 (t60)
REVERT: D  553 SER cc_start: 0.8502 (m) cc_final: 0.7646 (p)
REVERT: D  601 MET cc_start: 0.7268 (mmt) cc_final: 0.6952 (mmm)
REVERT: D  745 GLN cc_start: 0.7353 (OUTLIER) cc_final: 0.7039 (mp10)
REVERT: D  791 SER cc_start: 0.7811 (m) cc_final: 0.7562 (t)
REVERT: D  865 LYS cc_start: 0.8224 (mmtt) cc_final: 0.7855 (mmtm)
REVERT: D  868 GLN cc_start: 0.7450 (tm-30) cc_final: 0.7088 (tm-30)
REVERT: D  914 LEU cc_start: 0.7994 (mm) cc_final: 0.7698 (mp)
REVERT: D  927 ASN cc_start: 0.7417 (t0) cc_final: 0.6967 (t0)
  outliers start: 16
  outliers final: 13
  residues processed: 173
  average time/residue: 0.0921
  time to fit residues: 21.9121
Evaluate side-chains
  169 residues out of total 887 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 15
    poor density    : 154
  time to evaluate  : 0.297 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain D residue   36 VAL
Chi-restraints excluded: chain D residue  265 LYS
Chi-restraints excluded: chain D residue  291 LEU
Chi-restraints excluded: chain D residue  349 PHE
Chi-restraints excluded: chain D residue  397 THR
Chi-restraints excluded: chain D residue  430 GLN
Chi-restraints excluded: chain D residue  486 LEU
Chi-restraints excluded: chain D residue  503 SER
Chi-restraints excluded: chain D residue  645 MET
Chi-restraints excluded: chain D residue  687 GLN
Chi-restraints excluded: chain D residue  745 GLN
Chi-restraints excluded: chain D residue  752 ASP
Chi-restraints excluded: chain D residue  756 SER
Chi-restraints excluded: chain D residue  827 LEU
Chi-restraints excluded: chain D residue 1023 MET
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 101
   random chunks:
   chunk 80 optimal weight:    0.8980
   chunk 88 optimal weight:    0.3980
   chunk 74 optimal weight:    0.0970
   chunk 78 optimal weight:    0.7980
   chunk 94 optimal weight:    0.9980
   chunk 70 optimal weight:    1.9990
   chunk 0 optimal weight:    2.9990
   chunk 86 optimal weight:    0.9990
   chunk 82 optimal weight:    0.0000
   chunk 98 optimal weight:    0.8980
   chunk 44 optimal weight:    0.8980
   overall best weight:    0.4382

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
** D  88 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** D 282 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
D 442 HIS
D 816 GLN
D 853 GLN
D 879 GLN

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4008 r_free = 0.4008 target = 0.158178 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.3636 r_free = 0.3636 target = 0.130612 restraints weight = 12321.297|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 39)----------------|
| r_work = 0.3692 r_free = 0.3692 target = 0.134461 restraints weight = 5915.464|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 31)----------------|
| r_work = 0.3722 r_free = 0.3722 target = 0.136727 restraints weight = 3517.412|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 39)----------------|
| r_work = 0.3746 r_free = 0.3746 target = 0.138390 restraints weight = 2462.838|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 33)----------------|
| r_work = 0.3758 r_free = 0.3758 target = 0.139304 restraints weight = 1886.880|
|-----------------------------------------------------------------------------|
r_work (final): 0.3751
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7317
moved from start:          0.4031

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.036   8249  Z= 0.138
  Angle     :  0.570  11.117  11199  Z= 0.289
  Chirality :  0.039   0.148   1301
  Planarity :  0.004   0.039   1426
  Dihedral  :  4.110  25.526   1085
  Min Nonbonded Distance : 2.536

Molprobity Statistics.
  All-atom Clashscore : 8.51
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.38 %
    Favored  : 97.62 %
  Rotamer:
    Outliers :  1.81 %
    Allowed  : 15.01 %
    Favored  : 83.18 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 4.55 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  2.15 (0.27), residues: 1008
  helix:  1.84 (0.19), residues: 766
  sheet: -0.66 (1.43), residues: 17
  loop :  0.29 (0.43), residues: 225

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.007   0.000   ARG A 214 
 TYR   0.020   0.001   TYR D1007 
 PHE   0.018   0.002   PHE D 413 
 TRP   0.009   0.001   TRP A 210 
 HIS   0.004   0.001   HIS D 428 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00323 /  0.14 ( 8249)
  covalent geometry    : angle       0.57011 /  0.29 (11199)
  hydrogen bonds       : bond        0.03483 /  2.31 (  562)
  hydrogen bonds       : angle       4.17069 /  2.94 ( 1647)

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

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

  2016 Ramachandran restraints generated.
    1008 Oldfield, 0 Emsley, 1008 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2016 Ramachandran restraints generated.
    1008 Oldfield, 0 Emsley, 1008 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  172 residues out of total 887 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 156
  time to evaluate  : 0.285 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: D  113 LEU cc_start: 0.8547 (tp) cc_final: 0.8335 (tp)
REVERT: D  195 LYS cc_start: 0.7721 (ttpt) cc_final: 0.7505 (ttpt)
REVERT: D  266 MET cc_start: 0.7255 (tmm) cc_final: 0.6929 (tmm)
REVERT: D  276 VAL cc_start: 0.8197 (p) cc_final: 0.7895 (t)
REVERT: D  411 THR cc_start: 0.8126 (t) cc_final: 0.7902 (t)
REVERT: D  430 GLN cc_start: 0.7060 (OUTLIER) cc_final: 0.6766 (mp10)
REVERT: D  553 SER cc_start: 0.8505 (m) cc_final: 0.7644 (p)
REVERT: D  601 MET cc_start: 0.7259 (mmt) cc_final: 0.6929 (mmm)
REVERT: D  745 GLN cc_start: 0.7310 (mp10) cc_final: 0.6916 (mp10)
REVERT: D  791 SER cc_start: 0.7814 (m) cc_final: 0.7575 (t)
REVERT: D  865 LYS cc_start: 0.8229 (mmtt) cc_final: 0.7855 (mmtm)
REVERT: D  868 GLN cc_start: 0.7494 (tm-30) cc_final: 0.7108 (tm-30)
REVERT: D  914 LEU cc_start: 0.8008 (mm) cc_final: 0.7782 (mp)
REVERT: D  927 ASN cc_start: 0.7419 (t0) cc_final: 0.6972 (t0)
  outliers start: 16
  outliers final: 9
  residues processed: 164
  average time/residue: 0.0916
  time to fit residues: 20.7271
Evaluate side-chains
  164 residues out of total 887 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 154
  time to evaluate  : 0.300 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain D residue   36 VAL
Chi-restraints excluded: chain D residue  291 LEU
Chi-restraints excluded: chain D residue  349 PHE
Chi-restraints excluded: chain D residue  397 THR
Chi-restraints excluded: chain D residue  407 LEU
Chi-restraints excluded: chain D residue  430 GLN
Chi-restraints excluded: chain D residue  503 SER
Chi-restraints excluded: chain D residue  645 MET
Chi-restraints excluded: chain D residue  756 SER
Chi-restraints excluded: chain D residue 1023 MET
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 101
   random chunks:
   chunk 63 optimal weight:    0.6980
   chunk 85 optimal weight:    0.9990
   chunk 6 optimal weight:    0.6980
   chunk 41 optimal weight:    0.6980
   chunk 76 optimal weight:    0.3980
   chunk 57 optimal weight:    0.4980
   chunk 33 optimal weight:    1.9990
   chunk 78 optimal weight:    0.4980
   chunk 54 optimal weight:    1.9990
   chunk 20 optimal weight:    0.9990
   chunk 92 optimal weight:    0.6980
   overall best weight:    0.5580

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
A 208 HIS
A 291 ASN
** D  88 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** D 282 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
D 442 HIS
D 853 GLN
D 879 GLN

Total number of N/Q/H flips: 5

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3997 r_free = 0.3997 target = 0.157280 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 49)----------------|
| r_work = 0.3628 r_free = 0.3628 target = 0.129911 restraints weight = 12212.612|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 35)----------------|
| r_work = 0.3681 r_free = 0.3681 target = 0.133657 restraints weight = 5870.444|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 36)----------------|
| r_work = 0.3716 r_free = 0.3716 target = 0.136121 restraints weight = 3492.456|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 32)----------------|
| r_work = 0.3736 r_free = 0.3736 target = 0.137591 restraints weight = 2403.166|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 33)----------------|
| r_work = 0.3750 r_free = 0.3750 target = 0.138617 restraints weight = 1858.188|
|-----------------------------------------------------------------------------|
r_work (final): 0.3745
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7329
moved from start:          0.4155

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.048   8249  Z= 0.155
  Angle     :  0.603  10.488  11199  Z= 0.300
  Chirality :  0.040   0.146   1301
  Planarity :  0.004   0.040   1426
  Dihedral  :  4.149  25.643   1085
  Min Nonbonded Distance : 2.529

Molprobity Statistics.
  All-atom Clashscore : 9.12
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.58 %
    Favored  : 97.42 %
  Rotamer:
    Outliers :  1.58 %
    Allowed  : 15.35 %
    Favored  : 83.07 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 4.55 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  2.06 (0.27), residues: 1008
  helix:  1.80 (0.19), residues: 761
  sheet: -0.90 (1.41), residues: 17
  loop :  0.23 (0.43), residues: 230

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.008   0.000   ARG A 214 
 TYR   0.020   0.002   TYR D1007 
 PHE   0.017   0.002   PHE D 413 
 TRP   0.011   0.001   TRP A 210 
 HIS   0.007   0.001   HIS D 282 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00369 /  0.16 ( 8249)
  covalent geometry    : angle       0.60281 /  0.30 (11199)
  hydrogen bonds       : bond        0.03686 /  2.43 (  562)
  hydrogen bonds       : angle       4.20400 /  2.97 ( 1647)

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

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

  2016 Ramachandran restraints generated.
    1008 Oldfield, 0 Emsley, 1008 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2016 Ramachandran restraints generated.
    1008 Oldfield, 0 Emsley, 1008 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  176 residues out of total 887 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 162
  time to evaluate  : 0.310 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: D  266 MET cc_start: 0.7220 (tmm) cc_final: 0.6166 (tmm)
REVERT: D  270 LYS cc_start: 0.7424 (ttmm) cc_final: 0.7131 (mtmm)
REVERT: D  276 VAL cc_start: 0.8194 (p) cc_final: 0.7921 (t)
REVERT: D  411 THR cc_start: 0.8140 (t) cc_final: 0.7910 (t)
REVERT: D  430 GLN cc_start: 0.7093 (OUTLIER) cc_final: 0.6825 (mp10)
REVERT: D  542 TRP cc_start: 0.7677 (t60) cc_final: 0.7388 (t60)
REVERT: D  553 SER cc_start: 0.8518 (m) cc_final: 0.7671 (p)
REVERT: D  745 GLN cc_start: 0.7373 (OUTLIER) cc_final: 0.7016 (mp10)
REVERT: D  865 LYS cc_start: 0.8281 (mmtt) cc_final: 0.7893 (mmtm)
REVERT: D  868 GLN cc_start: 0.7451 (tm-30) cc_final: 0.7037 (tm-30)
REVERT: D  871 ILE cc_start: 0.7885 (OUTLIER) cc_final: 0.7593 (mm)
REVERT: D  914 LEU cc_start: 0.7999 (mm) cc_final: 0.7755 (mp)
REVERT: D  927 ASN cc_start: 0.7429 (t0) cc_final: 0.6983 (t0)
  outliers start: 14
  outliers final: 11
  residues processed: 170
  average time/residue: 0.0985
  time to fit residues: 22.6733
Evaluate side-chains
  176 residues out of total 887 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 162
  time to evaluate  : 0.332 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  208 HIS
Chi-restraints excluded: chain D residue   36 VAL
Chi-restraints excluded: chain D residue  291 LEU
Chi-restraints excluded: chain D residue  349 PHE
Chi-restraints excluded: chain D residue  397 THR
Chi-restraints excluded: chain D residue  430 GLN
Chi-restraints excluded: chain D residue  486 LEU
Chi-restraints excluded: chain D residue  503 SER
Chi-restraints excluded: chain D residue  645 MET
Chi-restraints excluded: chain D residue  745 GLN
Chi-restraints excluded: chain D residue  752 ASP
Chi-restraints excluded: chain D residue  756 SER
Chi-restraints excluded: chain D residue  871 ILE
Chi-restraints excluded: chain D residue 1023 MET
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 101
   random chunks:
   chunk 59 optimal weight:    0.5980
   chunk 86 optimal weight:    0.4980
   chunk 53 optimal weight:    0.0770
   chunk 14 optimal weight:    2.9990
   chunk 39 optimal weight:    0.9980
   chunk 33 optimal weight:    0.6980
   chunk 84 optimal weight:    1.9990
   chunk 65 optimal weight:    0.9980
   chunk 61 optimal weight:    0.9990
   chunk 83 optimal weight:    0.4980
   chunk 12 optimal weight:   10.0000
   overall best weight:    0.4738

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
A 208 HIS
A 291 ASN
** D  88 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
D 282 HIS
D 442 HIS
D 853 GLN

Total number of N/Q/H flips: 5

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4002 r_free = 0.4002 target = 0.157969 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 37)----------------|
| r_work = 0.3635 r_free = 0.3635 target = 0.130735 restraints weight = 12273.372|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 43)----------------|
| r_work = 0.3690 r_free = 0.3690 target = 0.134597 restraints weight = 5884.797|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 30)----------------|
| r_work = 0.3720 r_free = 0.3720 target = 0.136832 restraints weight = 3462.405|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 37)----------------|
| r_work = 0.3744 r_free = 0.3744 target = 0.138592 restraints weight = 2406.920|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 37)----------------|
| r_work = 0.3757 r_free = 0.3757 target = 0.139510 restraints weight = 1820.059|
|-----------------------------------------------------------------------------|
r_work (final): 0.3755
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7318
moved from start:          0.4265

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.039   8249  Z= 0.146
  Angle     :  0.614  10.182  11199  Z= 0.306
  Chirality :  0.039   0.153   1301
  Planarity :  0.004   0.040   1426
  Dihedral  :  4.120  26.159   1085
  Min Nonbonded Distance : 2.526

Molprobity Statistics.
  All-atom Clashscore : 9.00
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.38 %
    Favored  : 97.62 %
  Rotamer:
    Outliers :  1.47 %
    Allowed  : 15.91 %
    Favored  : 82.62 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 4.55 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  2.09 (0.27), residues: 1008
  helix:  1.83 (0.19), residues: 760
  sheet: -0.88 (1.43), residues: 17
  loop :  0.23 (0.43), residues: 231

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.007   0.001   ARG A 214 
 TYR   0.019   0.001   TYR D1007 
 PHE   0.017   0.002   PHE D 413 
 TRP   0.013   0.001   TRP A 210 
 HIS   0.004   0.001   HIS D 428 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00345 /  0.15 ( 8249)
  covalent geometry    : angle       0.61384 /  0.31 (11199)
  hydrogen bonds       : bond        0.03549 /  2.35 (  562)
  hydrogen bonds       : angle       4.19866 /  2.97 ( 1647)

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

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

  2016 Ramachandran restraints generated.
    1008 Oldfield, 0 Emsley, 1008 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2016 Ramachandran restraints generated.
    1008 Oldfield, 0 Emsley, 1008 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  175 residues out of total 887 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 162
  time to evaluate  : 0.298 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: D  221 MET cc_start: 0.5612 (tpt) cc_final: 0.5125 (tpt)
REVERT: D  266 MET cc_start: 0.7222 (tmm) cc_final: 0.6330 (tmm)
REVERT: D  270 LYS cc_start: 0.7420 (ttmm) cc_final: 0.7041 (mtmm)
REVERT: D  276 VAL cc_start: 0.8225 (p) cc_final: 0.7928 (t)
REVERT: D  411 THR cc_start: 0.8132 (t) cc_final: 0.7901 (t)
REVERT: D  430 GLN cc_start: 0.7112 (OUTLIER) cc_final: 0.6844 (mp10)
REVERT: D  542 TRP cc_start: 0.7681 (t60) cc_final: 0.7430 (t60)
REVERT: D  553 SER cc_start: 0.8421 (m) cc_final: 0.7349 (t)
REVERT: D  745 GLN cc_start: 0.7327 (mp10) cc_final: 0.7013 (mp10)
REVERT: D  807 MET cc_start: 0.7444 (mmp) cc_final: 0.7175 (mmp)
REVERT: D  865 LYS cc_start: 0.8229 (mmtt) cc_final: 0.7843 (mmtm)
REVERT: D  868 GLN cc_start: 0.7457 (tm-30) cc_final: 0.6966 (tm-30)
REVERT: D  871 ILE cc_start: 0.7940 (mm) cc_final: 0.7678 (tp)
REVERT: D  914 LEU cc_start: 0.8002 (mm) cc_final: 0.7748 (mp)
REVERT: D  927 ASN cc_start: 0.7424 (t0) cc_final: 0.6994 (t0)
  outliers start: 13
  outliers final: 12
  residues processed: 170
  average time/residue: 0.0968
  time to fit residues: 22.4638
Evaluate side-chains
  171 residues out of total 887 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 158
  time to evaluate  : 0.304 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  208 HIS
Chi-restraints excluded: chain D residue   36 VAL
Chi-restraints excluded: chain D residue  291 LEU
Chi-restraints excluded: chain D residue  349 PHE
Chi-restraints excluded: chain D residue  397 THR
Chi-restraints excluded: chain D residue  430 GLN
Chi-restraints excluded: chain D residue  486 LEU
Chi-restraints excluded: chain D residue  503 SER
Chi-restraints excluded: chain D residue  645 MET
Chi-restraints excluded: chain D residue  752 ASP
Chi-restraints excluded: chain D residue  756 SER
Chi-restraints excluded: chain D residue  827 LEU
Chi-restraints excluded: chain D residue 1023 MET
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 101
   random chunks:
   chunk 61 optimal weight:    0.8980
   chunk 29 optimal weight:    0.9980
   chunk 97 optimal weight:    0.5980
   chunk 84 optimal weight:    2.9990
   chunk 23 optimal weight:    5.9990
   chunk 63 optimal weight:    0.9980
   chunk 32 optimal weight:    0.9990
   chunk 34 optimal weight:    0.6980
   chunk 93 optimal weight:    0.1980
   chunk 74 optimal weight:    0.1980
   chunk 54 optimal weight:    0.5980
   overall best weight:    0.4580

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
** D  88 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
D 282 HIS
D 442 HIS

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4001 r_free = 0.4001 target = 0.157764 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 44)----------------|
| r_work = 0.3635 r_free = 0.3635 target = 0.130597 restraints weight = 12148.820|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 26)----------------|
| r_work = 0.3688 r_free = 0.3688 target = 0.134410 restraints weight = 5841.015|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 39)----------------|
| r_work = 0.3722 r_free = 0.3722 target = 0.136898 restraints weight = 3472.003|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 38)----------------|
| r_work = 0.3744 r_free = 0.3744 target = 0.138496 restraints weight = 2363.556|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 28)----------------|
| r_work = 0.3755 r_free = 0.3755 target = 0.139305 restraints weight = 1804.076|
|-----------------------------------------------------------------------------|
r_work (final): 0.3752
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7321
moved from start:          0.4341

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.041   8249  Z= 0.145
  Angle     :  0.611  10.078  11199  Z= 0.307
  Chirality :  0.039   0.164   1301
  Planarity :  0.004   0.040   1426
  Dihedral  :  4.091  25.539   1085
  Min Nonbonded Distance : 2.519

Molprobity Statistics.
  All-atom Clashscore : 9.43
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.48 %
    Favored  : 97.52 %
  Rotamer:
    Outliers :  1.35 %
    Allowed  : 16.48 %
    Favored  : 82.17 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 4.55 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  2.08 (0.27), residues: 1008
  helix:  1.82 (0.19), residues: 762
  sheet: -0.80 (1.43), residues: 17
  loop :  0.18 (0.43), residues: 229

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.000   ARG A 268 
 TYR   0.018   0.001   TYR D1007 
 PHE   0.017   0.002   PHE D 413 
 TRP   0.015   0.001   TRP A 210 
 HIS   0.010   0.001   HIS A 208 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00343 /  0.14 ( 8249)
  covalent geometry    : angle       0.61073 /  0.31 (11199)
  hydrogen bonds       : bond        0.03497 /  2.31 (  562)
  hydrogen bonds       : angle       4.17433 /  2.95 ( 1647)

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

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

  2016 Ramachandran restraints generated.
    1008 Oldfield, 0 Emsley, 1008 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2016 Ramachandran restraints generated.
    1008 Oldfield, 0 Emsley, 1008 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  170 residues out of total 887 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 158
  time to evaluate  : 0.227 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: D  221 MET cc_start: 0.5729 (tpt) cc_final: 0.5219 (tpt)
REVERT: D  266 MET cc_start: 0.7205 (tmm) cc_final: 0.6325 (tmm)
REVERT: D  270 LYS cc_start: 0.7425 (ttmm) cc_final: 0.7049 (mtmm)
REVERT: D  276 VAL cc_start: 0.8218 (p) cc_final: 0.7923 (t)
REVERT: D  411 THR cc_start: 0.8132 (t) cc_final: 0.7906 (t)
REVERT: D  430 GLN cc_start: 0.7096 (OUTLIER) cc_final: 0.6827 (mp10)
REVERT: D  542 TRP cc_start: 0.7672 (t60) cc_final: 0.7425 (t60)
REVERT: D  553 SER cc_start: 0.8412 (m) cc_final: 0.7650 (p)
REVERT: D  745 GLN cc_start: 0.7330 (mp10) cc_final: 0.6914 (mp10)
REVERT: D  807 MET cc_start: 0.7504 (mmp) cc_final: 0.7224 (mmp)
REVERT: D  865 LYS cc_start: 0.8226 (mmtt) cc_final: 0.7857 (mmtm)
REVERT: D  868 GLN cc_start: 0.7466 (tm-30) cc_final: 0.7003 (tm-30)
REVERT: D  914 LEU cc_start: 0.7993 (mm) cc_final: 0.7731 (mp)
REVERT: D  927 ASN cc_start: 0.7417 (t0) cc_final: 0.6963 (t0)
  outliers start: 12
  outliers final: 11
  residues processed: 165
  average time/residue: 0.0860
  time to fit residues: 19.2808
Evaluate side-chains
  170 residues out of total 887 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 158
  time to evaluate  : 0.296 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain D residue   36 VAL
Chi-restraints excluded: chain D residue  291 LEU
Chi-restraints excluded: chain D residue  349 PHE
Chi-restraints excluded: chain D residue  397 THR
Chi-restraints excluded: chain D residue  430 GLN
Chi-restraints excluded: chain D residue  486 LEU
Chi-restraints excluded: chain D residue  503 SER
Chi-restraints excluded: chain D residue  645 MET
Chi-restraints excluded: chain D residue  752 ASP
Chi-restraints excluded: chain D residue  756 SER
Chi-restraints excluded: chain D residue  827 LEU
Chi-restraints excluded: chain D residue 1023 MET
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 101
   random chunks:
   chunk 35 optimal weight:    0.9990
   chunk 24 optimal weight:    2.9990
   chunk 79 optimal weight:    0.3980
   chunk 6 optimal weight:    0.5980
   chunk 51 optimal weight:    0.6980
   chunk 3 optimal weight:    1.9990
   chunk 33 optimal weight:    0.4980
   chunk 25 optimal weight:    0.7980
   chunk 28 optimal weight:    8.9990
   chunk 92 optimal weight:    1.9990
   chunk 76 optimal weight:    0.4980
   overall best weight:    0.5380

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
A 291 ASN
** D  88 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** D 282 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
D 442 HIS
** D 547 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
D 853 GLN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3995 r_free = 0.3995 target = 0.156959 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 43)----------------|
| r_work = 0.3625 r_free = 0.3625 target = 0.129740 restraints weight = 12197.101|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 31)----------------|
| r_work = 0.3677 r_free = 0.3677 target = 0.133532 restraints weight = 5854.354|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 41)----------------|
| r_work = 0.3713 r_free = 0.3713 target = 0.136095 restraints weight = 3475.311|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 34)----------------|
| r_work = 0.3735 r_free = 0.3735 target = 0.137729 restraints weight = 2374.020|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 31)----------------|
| r_work = 0.3746 r_free = 0.3746 target = 0.138534 restraints weight = 1795.520|
|-----------------------------------------------------------------------------|
r_work (final): 0.3743
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7328
moved from start:          0.4444

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.041   8249  Z= 0.155
  Angle     :  0.638  14.635  11199  Z= 0.316
  Chirality :  0.040   0.168   1301
  Planarity :  0.004   0.042   1426
  Dihedral  :  4.115  24.903   1085
  Min Nonbonded Distance : 2.519

Molprobity Statistics.
  All-atom Clashscore : 9.43
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.48 %
    Favored  : 97.52 %
  Rotamer:
    Outliers :  1.35 %
    Allowed  : 16.70 %
    Favored  : 81.94 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 4.55 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  2.01 (0.27), residues: 1008
  helix:  1.80 (0.19), residues: 756
  sheet: -0.85 (1.43), residues: 17
  loop :  0.10 (0.42), residues: 235

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.007   0.001   ARG D 776 
 TYR   0.017   0.001   TYR D1007 
 PHE   0.017   0.002   PHE D 413 
 TRP   0.011   0.001   TRP A 210 
 HIS   0.004   0.001   HIS D 869 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00369 /  0.16 ( 8249)
  covalent geometry    : angle       0.63759 /  0.32 (11199)
  hydrogen bonds       : bond        0.03626 /  2.39 (  562)
  hydrogen bonds       : angle       4.21457 /  2.98 ( 1647)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 1491.19 seconds
wall clock time: 26 minutes 28.65 seconds (1588.65 seconds total)