Starting phenix.real_space_refine
on Tue Nov 18 05:23:12 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/5n8o_3601/11_2025/5n8o_3601_neut.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/5n8o_3601/11_2025/5n8o_3601.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=3.9
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/cci-nas-00/data/ceres_data/5n8o_3601/11_2025/5n8o_3601.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/5n8o_3601/11_2025/5n8o_3601.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/5n8o_3601/11_2025/5n8o_3601_neut.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/5n8o_3601/11_2025/5n8o_3601_neut.cif"
  }
  resolution = 3.9
  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=   0.012
Set stop_for_unknowns flag
  Set to: True
Assert model is a single copy model
Assert all atoms have isotropic ADPs
Construct map_model_manager
Extract box with map and model
Check model and map are aligned
Set scattering table
  Set to: electron
  Number of scattering types: 5
    Type Number    sf(0)   Gaussians
     P      18      5.49       5
     S      45      5.16       5
     C    6975      2.51       5
     N    2046      2.21       5
     O    2278      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 25 residue(s): 0.01s

  Monomer Library directory:
    "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5881/lib/python3.9/site-packages/chem_data/mon_lib"
  Total number of atoms: 11362
  Number of models: 1
  Model: ""
    Number of chains: 2
    Chain: "A"
      Number of atoms: 11002
      Number of conformers: 2
      Conformer: "A"
        Number of residues, atoms: 1432, 10991
          Classifications: {'peptide': 1432}
          Link IDs: {'CIS': 7, 'PCIS': 1, 'PTRANS': 51, 'TRANS': 1372}
          Chain breaks: 5
      Conformer: "B"
        Number of residues, atoms: 1432, 10991
          Classifications: {'peptide': 1432}
          Link IDs: {'CIS': 7, 'PCIS': 1, 'PTRANS': 51, 'TRANS': 1372}
          Chain breaks: 5
          bond proxies already assigned to first conformer: 11141
    Chain: "C"
      Number of atoms: 360
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 18, 360
          Classifications: {'DNA': 18}
          Link IDs: {'rna3p': 17}
  Time building chain proxies: 4.45, per 1000 atoms: 0.39
  Number of scatterers: 11362
  At special positions: 0
  Unit cell: (113.4, 131.25, 102.9, 90, 90, 90)
  Space group: P 1 (No. 1)
  Number of sites at special positions: 0
  Number of scattering types: 5
    Type Number    sf(0)
     S      45     16.00
     P      18     15.00
     O    2278      8.00
     N    2046      7.00
     C    6975      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: 0.85
  Conformation dependent library (CDL) restraints added in 959.5 milliseconds
  

  2846 Ramachandran restraints generated.
    1423 Oldfield, 0 Emsley, 1423 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  2632

  Finding SS restraints...
    Secondary structure from input PDB file:
      50 helices and 18 sheets defined
      36.5% alpha, 8.5% beta
      0 base pairs and 7 stacking pairs defined.
    Time for finding SS restraints: 1.53
  Creating SS restraints...
    Processing helix  chain 'A' and resid 11 through 18
      removed outlier: 4.223A  pdb=" N   THR A  18 " --> pdb=" O   GLY A  14 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 35 through 41
    Processing helix  chain 'A' and resid 48 through 58
    Processing helix  chain 'A' and resid 87 through 96
    Processing helix  chain 'A' and resid 100 through 120
      removed outlier: 4.209A  pdb=" N  AARG A 115 " --> pdb=" O   ASP A 111 " (cutoff:3.500A)
      removed outlier: 4.035A  pdb=" N   GLN A 116 " --> pdb=" O   PHE A 112 " (cutoff:3.500A)
      removed outlier: 3.824A  pdb=" N   VAL A 117 " --> pdb=" O   ALA A 113 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 185 through 192
    Processing helix  chain 'A' and resid 192 through 212
    Processing helix  chain 'A' and resid 269 through 282
      removed outlier: 3.853A  pdb=" N   ARG A 273 " --> pdb=" O   ASP A 269 " (cutoff:3.500A)
      removed outlier: 4.063A  pdb=" N   LYS A 282 " --> pdb=" O   MET A 278 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 287 through 304
      removed outlier: 3.597A  pdb=" N   THR A 299 " --> pdb=" O   ALA A 295 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 316 through 328
    Processing helix  chain 'A' and resid 336 through 347
      removed outlier: 3.739A  pdb=" N   LEU A 340 " --> pdb=" O   TYR A 336 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 353 through 354
      No H-bonds generated for 'chain 'A' and resid 353 through 354'
    Processing helix  chain 'A' and resid 356 through 367
    Processing helix  chain 'A' and resid 383 through 402
      removed outlier: 4.131A  pdb=" N   ARG A 397 " --> pdb=" O   ARG A 393 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 423 through 430
      removed outlier: 3.929A  pdb=" N   ARG A 430 " --> pdb=" O   LEU A 426 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 443 through 460
      removed outlier: 3.600A  pdb=" N   GLN A 459 " --> pdb=" O   MET A 455 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 509 through 513
      removed outlier: 3.520A  pdb=" N   LEU A 513 " --> pdb=" O   GLY A 510 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 515 through 527
      removed outlier: 4.577A  pdb=" N   LEU A 521 " --> pdb=" O   GLU A 517 " (cutoff:3.500A)
      removed outlier: 4.020A  pdb=" N   ARG A 527 " --> pdb=" O   ASP A 523 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 547 through 552
    Processing helix  chain 'A' and resid 576 through 593
    Processing helix  chain 'A' and resid 604 through 621
    Processing helix  chain 'A' and resid 696 through 698
      No H-bonds generated for 'chain 'A' and resid 696 through 698'
    Processing helix  chain 'A' and resid 763 through 767
      removed outlier: 3.653A  pdb=" N   ALA A 767 " --> pdb=" O   PRO A 764 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 835 through 844
      removed outlier: 3.844A  pdb=" N   GLN A 839 " --> pdb=" O   VAL A 835 " (cutoff:3.500A)
      removed outlier: 3.541A  pdb=" N   ALA A 844 " --> pdb=" O   ILE A 840 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 848 through 858
      removed outlier: 3.628A  pdb=" N   ALA A 852 " --> pdb=" O   LEU A 848 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 862 through 877
      Proline residue:  A 873  - end of helix
    Processing helix  chain 'A' and resid 885 through 894
    Processing helix  chain 'A' and resid 901 through 914
      removed outlier: 3.750A  pdb=" N   GLY A 905 " --> pdb=" O   PHE A 901 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 936 through 952
      removed outlier: 3.545A  pdb=" N   GLU A 940 " --> pdb=" O   SER A 936 " (cutoff:3.500A)
      removed outlier: 3.689A  pdb=" N   SER A 942 " --> pdb=" O   GLU A 938 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 973 through 978
      removed outlier: 4.011A  pdb=" N   THR A 977 " --> pdb=" O   GLN A 973 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 999 through 1011
    Processing helix  chain 'A' and resid 1026 through 1036
    Processing helix  chain 'A' and resid 1043 through 1056
      removed outlier: 3.671A  pdb=" N   LEU A1047 " --> pdb=" O   LEU A1043 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 1071 through 1075
      removed outlier: 3.886A  pdb=" N   VAL A1075 " --> pdb=" O   SER A1072 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 1077 through 1086
    Processing helix  chain 'A' and resid 1112 through 1117
    Processing helix  chain 'A' and resid 1133 through 1135
      No H-bonds generated for 'chain 'A' and resid 1133 through 1135'
    Processing helix  chain 'A' and resid 1136 through 1146
    Processing helix  chain 'A' and resid 1147 through 1155
    Processing helix  chain 'A' and resid 1156 through 1158
      No H-bonds generated for 'chain 'A' and resid 1156 through 1158'
    Processing helix  chain 'A' and resid 1183 through 1195
    Processing helix  chain 'A' and resid 1209 through 1217
      removed outlier: 4.124A  pdb=" N   VAL A1213 " --> pdb=" O   TYR A1209 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 1220 through 1224
    Processing helix  chain 'A' and resid 1235 through 1251
    Processing helix  chain 'A' and resid 1271 through 1275
      removed outlier: 4.524A  pdb=" N   LEU A1274 " --> pdb=" O   ASP A1271 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 1276 through 1281
      removed outlier: 3.908A  pdb=" N   TRP A1280 " --> pdb=" O   ARG A1276 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 1388 through 1392
    Processing helix  chain 'A' and resid 1428 through 1436
      removed outlier: 3.835A  pdb=" N   ALA A1432 " --> pdb=" O   GLY A1428 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 1451 through 1459
    Processing helix  chain 'A' and resid 1465 through 1469
    Processing sheet with id=AA1, first strand: chain 'A' and resid 2 through 6
    Processing sheet with id=AA2, first strand: chain 'A' and resid 32 through 34
      removed outlier: 3.561A  pdb=" N   ARG A  32 " --> pdb=" O   LEU A 143 " (cutoff:3.500A)
    Processing sheet with id=AA3, first strand: chain 'A' and resid 69 through 70
    Processing sheet with id=AA4, first strand: chain 'A' and resid 122 through 127
    Processing sheet with id=AA5, first strand: chain 'A' and resid 505 through 506
      removed outlier: 7.096A  pdb=" N   VAL A 505 " --> pdb=" O   LEU A 533 " (cutoff:3.500A)
      removed outlier: 7.744A  pdb=" N   THR A 535 " --> pdb=" O   VAL A 505 " (cutoff:3.500A)
      removed outlier: 5.790A  pdb=" N   ALA A 434 " --> pdb=" O   ILE A 534 " (cutoff:3.500A)
      removed outlier: 6.940A  pdb=" N   ASP A 536 " --> pdb=" O   ALA A 434 " (cutoff:3.500A)
      removed outlier: 6.534A  pdb=" N   VAL A 436 " --> pdb=" O   ASP A 536 " (cutoff:3.500A)
    Processing sheet with id=AA6, first strand: chain 'A' and resid 569 through 570
      removed outlier: 6.207A  pdb=" N   THR A 569 " --> pdb=" O   LEU A 814 " (cutoff:3.500A)
      removed outlier: 6.096A  pdb=" N   VAL A 788 " --> pdb=" O   ARG A 813 " (cutoff:3.500A)
      removed outlier: 8.994A  pdb=" N   GLU A 776 " --> pdb=" O   SER A 597 " (cutoff:3.500A)
      removed outlier: 6.865A  pdb=" N   ALA A 599 " --> pdb=" O   GLU A 776 " (cutoff:3.500A)
    Processing sheet with id=AA7, first strand: chain 'A' and resid 629 through 631
    Processing sheet with id=AA8, first strand: chain 'A' and resid 655 through 660
      removed outlier: 3.772A  pdb=" N   SER A 665 " --> pdb=" O   ASN A 660 " (cutoff:3.500A)
    Processing sheet with id=AA9, first strand: chain 'A' and resid 674 through 675
      removed outlier: 3.502A  pdb=" N   THR A 675 " --> pdb=" O   SER A 680 " (cutoff:3.500A)
    Processing sheet with id=AB1, first strand: chain 'A' and resid 733 through 735
      removed outlier: 3.800A  pdb=" N   ASP A 733 " --> pdb=" O   VAL A 720 " (cutoff:3.500A)
      removed outlier: 3.836A  pdb=" N   VAL A 720 " --> pdb=" O   ASP A 733 " (cutoff:3.500A)
      removed outlier: 3.620A  pdb=" N   LEU A 718 " --> pdb=" O   LEU A 735 " (cutoff:3.500A)
    Processing sheet with id=AB2, first strand: chain 'A' and resid 745 through 746
    Processing sheet with id=AB3, first strand: chain 'A' and resid 987 through 989
      removed outlier: 6.687A  pdb=" N   THR A 988 " --> pdb=" O   ALA A1096 " (cutoff:3.500A)
  No H-bonds generated for sheet with id=AB3
    Processing sheet with id=AB4, first strand: chain 'A' and resid 1040 through 1041
      removed outlier: 6.287A  pdb=" N   GLY A1022 " --> pdb=" O   GLN A1041 " (cutoff:3.500A)
    Processing sheet with id=AB5, first strand: chain 'A' and resid 1399 through 1401
      removed outlier: 7.005A  pdb=" N   ALA A1413 " --> pdb=" O   GLN A1444 " (cutoff:3.500A)
    Processing sheet with id=AB6, first strand: chain 'A' and resid 1260 through 1266
    Processing sheet with id=AB7, first strand: chain 'A' and resid 1296 through 1301
      removed outlier: 6.949A  pdb=" N   THR A1308 " --> pdb=" O   ALA A1298 " (cutoff:3.500A)
      removed outlier: 4.684A  pdb=" N   ILE A1300 " --> pdb=" O   LEU A1306 " (cutoff:3.500A)
      removed outlier: 7.100A  pdb=" N   LEU A1306 " --> pdb=" O   ILE A1300 " (cutoff:3.500A)
    Processing sheet with id=AB8, first strand: chain 'A' and resid 1361 through 1363
    Processing sheet with id=AB9, first strand: chain 'A' and resid 1372 through 1374
      removed outlier: 3.752A  pdb=" N   ARG A1381 " --> pdb=" O   LEU A1374 " (cutoff:3.500A)

    369 hydrogen bonds defined for protein.
    1047 hydrogen bond angles defined for protein.
    Restraints generated for nucleic acids:
      0 hydrogen bonds
      0 hydrogen bond angles
      0 basepair planarities
      0 basepair parallelities
      7 stacking parallelities
  Total time for adding SS restraints: 2.30

  Time building geometry restraints manager: 1.21 seconds

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

  Histogram of bond lengths:
        1.20 -     1.32: 2304
        1.32 -     1.44: 2620
        1.44 -     1.57: 6509
        1.57 -     1.69: 37
        1.69 -     1.81: 90
  Bond restraints: 11560
  Sorted by residual:
  bond pdb=" C   GLU A1471 "
       pdb=" N   PRO A1472 "
    ideal  model  delta    sigma   weight residual
    1.334  1.386 -0.052 2.34e-02 1.83e+03 4.96e+00
  bond pdb=" C   VAL A 413 "
       pdb=" N   PRO A 414 "
    ideal  model  delta    sigma   weight residual
    1.334  1.384 -0.050 2.34e-02 1.83e+03 4.64e+00
  bond pdb=" CB  THR A 541 "
       pdb=" CG2 THR A 541 "
    ideal  model  delta    sigma   weight residual
    1.521  1.456  0.065 3.30e-02 9.18e+02 3.83e+00
  bond pdb=" CG  LEU A1416 "
       pdb=" CD2 LEU A1416 "
    ideal  model  delta    sigma   weight residual
    1.521  1.459  0.062 3.30e-02 9.18e+02 3.54e+00
  bond pdb=" C   LEU A 872 "
       pdb=" N   PRO A 873 "
    ideal  model  delta    sigma   weight residual
    1.334  1.378 -0.044 2.34e-02 1.83e+03 3.54e+00
  ... (remaining 11555 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     3.84: 15409
        3.84 -     7.68: 258
        7.68 -    11.52: 32
       11.52 -    15.36: 7
       15.36 -    19.20: 2
  Bond angle restraints: 15708
  Sorted by residual:
  angle pdb=" CA  LEU A 818 "
        pdb=" CB  LEU A 818 "
        pdb=" CG  LEU A 818 "
      ideal   model   delta    sigma   weight residual
     116.30  135.50  -19.20 3.50e+00 8.16e-02 3.01e+01
  angle pdb=" C   VAL A 782 "
        pdb=" N   SER A 783 "
        pdb=" CA  SER A 783 "
      ideal   model   delta    sigma   weight residual
     121.54  111.24   10.30 1.91e+00 2.74e-01 2.91e+01
  angle pdb=" N   GLU A1471 "
        pdb=" CA  GLU A1471 "
        pdb=" C   GLU A1471 "
      ideal   model   delta    sigma   weight residual
     109.81  121.55  -11.74 2.21e+00 2.05e-01 2.82e+01
  angle pdb=" C   ASP A1291 "
        pdb=" N   ASN A1292 "
        pdb=" CA  ASN A1292 "
      ideal   model   delta    sigma   weight residual
     121.70  131.16   -9.46 1.80e+00 3.09e-01 2.76e+01
  angle pdb=" C   PHE A 380 "
        pdb=" N   THR A 381 "
        pdb=" CA  THR A 381 "
      ideal   model   delta    sigma   weight residual
     121.54  131.04   -9.50 1.91e+00 2.74e-01 2.47e+01
  ... (remaining 15703 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    17.32: 6619
       17.32 -    34.64: 284
       34.64 -    51.96: 67
       51.96 -    69.28: 21
       69.28 -    86.59: 14
  Dihedral angle restraints: 7005
    sinusoidal: 2914
      harmonic: 4091
  Sorted by residual:
  dihedral pdb=" CA  GLU A 376 "
           pdb=" C   GLU A 376 "
           pdb=" N   LYS A 377 "
           pdb=" CA  LYS A 377 "
      ideal   model   delta  harmonic     sigma   weight residual
    -180.00 -150.93  -29.07     0      5.00e+00 4.00e-02 3.38e+01
  dihedral pdb=" CA  ILE A 571 "
           pdb=" C   ILE A 571 "
           pdb=" N   SER A 572 "
           pdb=" CA  SER A 572 "
      ideal   model   delta  harmonic     sigma   weight residual
    -180.00 -151.05  -28.95     0      5.00e+00 4.00e-02 3.35e+01
  dihedral pdb=" CA  ASP A 819 "
           pdb=" C   ASP A 819 "
           pdb=" N   GLU A 820 "
           pdb=" CA  GLU A 820 "
      ideal   model   delta  harmonic     sigma   weight residual
    -180.00 -151.93  -28.07     0      5.00e+00 4.00e-02 3.15e+01
  ... (remaining 7002 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.065: 1286
       0.065 -    0.129: 410
       0.129 -    0.194: 76
       0.194 -    0.258: 14
       0.258 -    0.322: 4
  Chirality restraints: 1790
  Sorted by residual:
  chirality pdb=" CB  ILE A 487 "
            pdb=" CA  ILE A 487 "
            pdb=" CG1 ILE A 487 "
            pdb=" CG2 ILE A 487 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.64    2.32    0.32 2.00e-01 2.50e+01 2.60e+00
  chirality pdb=" CB  THR A1308 "
            pdb=" CA  THR A1308 "
            pdb=" OG1 THR A1308 "
            pdb=" CG2 THR A1308 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.55    2.25    0.30 2.00e-01 2.50e+01 2.30e+00
  chirality pdb=" CG  LEU A1287 "
            pdb=" CB  LEU A1287 "
            pdb=" CD1 LEU A1287 "
            pdb=" CD2 LEU A1287 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.59   -2.86    0.27 2.00e-01 2.50e+01 1.82e+00
  ... (remaining 1787 not shown)

  Planarity restraints: 2015
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   ASN A1283 "    0.044 5.00e-02 4.00e+02   6.82e-02 7.43e+00
        pdb=" N   PRO A1284 "   -0.118 5.00e-02 4.00e+02
        pdb=" CA  PRO A1284 "    0.035 5.00e-02 4.00e+02
        pdb=" CD  PRO A1284 "    0.039 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  ARG A 576 "    0.012 2.00e-02 2.50e+03   2.34e-02 5.49e+00
        pdb=" C   ARG A 576 "   -0.041 2.00e-02 2.50e+03
        pdb=" O   ARG A 576 "    0.015 2.00e-02 2.50e+03
        pdb=" N   ASN A 577 "    0.014 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  THR A 335 "   -0.011 2.00e-02 2.50e+03   2.25e-02 5.04e+00
        pdb=" C   THR A 335 "    0.039 2.00e-02 2.50e+03
        pdb=" O   THR A 335 "   -0.015 2.00e-02 2.50e+03
        pdb=" N   TYR A 336 "   -0.013 2.00e-02 2.50e+03
  ... (remaining 2012 not shown)

  Histogram of nonbonded interaction distances:
        1.88 -     2.48: 71
        2.48 -     3.09: 7690
        3.09 -     3.69: 16792
        3.69 -     4.30: 23982
        4.30 -     4.90: 38556
  Nonbonded interactions: 87091
  Sorted by model distance:
  nonbonded pdb=" OG  SER A1350 "
            pdb=" O   TYR A1356 "
     model   vdw
     1.878 3.040
  nonbonded pdb=" O   GLY A1355 "
            pdb=" NH2 ARG A1381 "
     model   vdw
     2.033 3.120
  nonbonded pdb=" OD2 ASP A1215 "
            pdb=" OH  TYR A1446 "
     model   vdw
     2.093 3.040
  nonbonded pdb=" ND2 ASN A1265 "
            pdb=" OD2 ASP A1335 "
     model   vdw
     2.119 3.120
  nonbonded pdb=" OE2 GLU A 376 "
            pdb=" ND1 HIS A 869 "
     model   vdw
     2.123 3.120
  ... (remaining 87086 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=0.50 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:             0.470
  Set stop_for_unknowns flag:              0.000
  Assert model is a single copy model:     0.000
  Assert all atoms have isotropic ADPs:    0.000
  Construct map_model_manager:             0.010
  Extract box with map and model:          0.160
  Check model and map are aligned:         0.030
  Set scattering table:                    0.040
  Process input model:                     15.340
  Find NCS groups from input model:        0.050
  Set up NCS constraints:                  0.040
  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:1.310
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   17.450
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7597
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      :  0.008   0.068  11560  Z= 0.337
  Angle     :  1.259  19.196  15708  Z= 0.660
  Chirality :  0.065   0.322   1790
  Planarity :  0.007   0.068   2015
  Dihedral  : 11.993  86.593   4373
  Min Nonbonded Distance : 1.878

Molprobity Statistics.
  All-atom Clashscore : 9.72
  Ramachandran Plot:
    Outliers :  0.21 %
    Allowed  : 15.00 %
    Favored  : 84.79 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  1.71 %
    Favored  : 98.29 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 1.92 %
    Cis-general     : 0.51 %
    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: -5.69 (0.16), residues: 1423
  helix: -3.62 (0.13), residues: 506
  sheet: -3.26 (0.30), residues: 213
  loop : -4.11 (0.18), residues: 704

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.017   0.001   ARG A 934 
 TYR   0.021   0.003   TYR A 190 
 PHE   0.037   0.005   PHE A1412 
 TRP   0.028   0.004   TRP A1280 
 HIS   0.012   0.002   HIS A 528 

Details of bonding type rmsd
  covalent geometry    : bond        0.00761 (11560)
  covalent geometry    : angle       1.25871 (15708)
  hydrogen bonds       : bond        0.17517 (  369)
  hydrogen bonds       : angle      10.72234 ( 1047)

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

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

  2846 Ramachandran restraints generated.
    1423 Oldfield, 0 Emsley, 1423 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2846 Ramachandran restraints generated.
    1423 Oldfield, 0 Emsley, 1423 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  299 residues out of total 1167 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 299
  time to evaluate  : 0.331 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   59 ARG cc_start: 0.8587 (mtt90) cc_final: 0.8027 (ttm-80)
REVERT: A  104 ASP cc_start: 0.8900 (m-30) cc_final: 0.8646 (m-30)
REVERT: A  118 GLU cc_start: 0.8552 (tt0) cc_final: 0.7918 (tm-30)
REVERT: A  141 MET cc_start: 0.7229 (mtm) cc_final: 0.7019 (ttm)
REVERT: A  183 THR cc_start: 0.5402 (p) cc_final: 0.4842 (p)
REVERT: A  202 GLU cc_start: 0.8612 (tp30) cc_final: 0.8234 (mm-30)
REVERT: A  398 ASP cc_start: 0.7994 (m-30) cc_final: 0.7736 (t0)
REVERT: A  402 GLN cc_start: 0.8519 (mp-120) cc_final: 0.8028 (mp10)
REVERT: A  486 LEU cc_start: 0.6250 (pp) cc_final: 0.5753 (tp)
REVERT: A  536 ASP cc_start: 0.7444 (t70) cc_final: 0.7233 (t0)
REVERT: A  631 MET cc_start: 0.8343 (ttp) cc_final: 0.8078 (ttt)
REVERT: A  667 ASP cc_start: 0.8105 (m-30) cc_final: 0.7881 (p0)
REVERT: A  795 MET cc_start: 0.7755 (mtp) cc_final: 0.7420 (mtp)
REVERT: A  819 ASP cc_start: 0.7300 (m-30) cc_final: 0.6964 (p0)
REVERT: A  937 TYR cc_start: 0.7954 (t80) cc_final: 0.7719 (t80)
REVERT: A  974 ARG cc_start: 0.7639 (ptm160) cc_final: 0.7232 (ptm160)
REVERT: A 1011 MET cc_start: 0.8917 (ttt) cc_final: 0.8443 (tmm)
REVERT: A 1032 GLU cc_start: 0.8418 (tt0) cc_final: 0.7841 (tm-30)
REVERT: A 1070 ASP cc_start: 0.8284 (p0) cc_final: 0.6705 (p0)
REVERT: A 1195 MET cc_start: 0.8017 (mmm) cc_final: 0.7475 (mmt)
REVERT: A 1226 GLN cc_start: 0.6255 (tp-100) cc_final: 0.5699 (tt0)
REVERT: A 1273 GLU cc_start: 0.8101 (tt0) cc_final: 0.7778 (tt0)
REVERT: A 1400 ILE cc_start: 0.8072 (mp) cc_final: 0.7814 (mm)
REVERT: A 1425 LEU cc_start: 0.7944 (pp) cc_final: 0.7643 (mt)
  outliers start: 0
  outliers final: 0
  residues processed: 299
  average time/residue: 0.1529
  time to fit residues: 59.6294
Evaluate side-chains
  172 residues out of total 1167 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 172
  time to evaluate  : 0.443 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 144
   random chunks:
   chunk 98 optimal weight:    0.5980
   chunk 107 optimal weight:    5.9990
   chunk 10 optimal weight:    5.9990
   chunk 66 optimal weight:    7.9990
   chunk 130 optimal weight:    0.9990
   chunk 124 optimal weight:    3.9990
   chunk 103 optimal weight:    0.6980
   chunk 77 optimal weight:    5.9990
   chunk 122 optimal weight:    6.9990
   chunk 91 optimal weight:    0.0020
   chunk 55 optimal weight:    0.0970
   overall best weight:    0.4788

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

Flipped N/Q/H residues before XYZ refinement:
A  76 HIS
** A 106 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 107 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 152 GLN
A 351 ASN
A 445 GLN
** A 946 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 991 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
A1048 HIS
A1102 GLN
** A1116 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
A1191 GLN
** A1295 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** A1403 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 7

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3773 r_free = 0.3773 target = 0.116604 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 32)----------------|
| r_work = 0.3428 r_free = 0.3428 target = 0.095524 restraints weight = 69769.015|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 29)----------------|
| r_work = 0.3513 r_free = 0.3513 target = 0.100853 restraints weight = 28751.234|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 32)----------------|
| r_work = 0.3555 r_free = 0.3555 target = 0.103401 restraints weight = 13429.004|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 28)----------------|
| r_work = 0.3570 r_free = 0.3570 target = 0.104210 restraints weight = 8852.746|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 24)----------------|
| r_work = 0.3576 r_free = 0.3576 target = 0.104570 restraints weight = 8407.850|
|-----------------------------------------------------------------------------|
r_work (final): 0.3578
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3577
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3577 r_free = 0.3577    target_work(ls_wunit_k1) = 0.104         |
| occupancies: max = 1.00  min = 0.50   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3573 r_free = 0.3573    target_work(ls_wunit_k1) = 0.104         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:       12 |
|-----------------------------------------------------------------------------|
r_final: 0.3573
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7612
moved from start:          0.2967

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.053  11560  Z= 0.146
  Angle     :  0.843  18.235  15708  Z= 0.429
  Chirality :  0.047   0.312   1790
  Planarity :  0.006   0.068   2015
  Dihedral  : 12.948  89.707   1749
  Min Nonbonded Distance : 2.427

Molprobity Statistics.
  All-atom Clashscore : 10.53
  Ramachandran Plot:
    Outliers :  0.14 %
    Allowed  : 12.75 %
    Favored  : 87.11 %
  Rotamer:
    Outliers :  1.80 %
    Allowed  :  9.41 %
    Favored  : 88.79 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 1.92 %
    Cis-general     : 0.51 %
    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: -4.24 (0.19), residues: 1423
  helix: -1.67 (0.20), residues: 504
  sheet: -2.94 (0.29), residues: 233
  loop : -3.73 (0.20), residues: 686

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.010   0.001   ARG A1093 
 TYR   0.027   0.002   TYR A1141 
 PHE   0.025   0.002   PHE A 380 
 TRP   0.024   0.002   TRP A 560 
 HIS   0.009   0.001   HIS A  76 

Details of bonding type rmsd
  covalent geometry    : bond        0.00315 (11560)
  covalent geometry    : angle       0.84324 (15708)
  hydrogen bonds       : bond        0.03829 (  369)
  hydrogen bonds       : angle       6.42984 ( 1047)

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

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

  2846 Ramachandran restraints generated.
    1423 Oldfield, 0 Emsley, 1423 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2846 Ramachandran restraints generated.
    1423 Oldfield, 0 Emsley, 1423 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  242 residues out of total 1167 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 21
    poor density    : 221
  time to evaluate  : 0.431 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   59 ARG cc_start: 0.8356 (mtt90) cc_final: 0.7821 (ttm-80)
REVERT: A   69 MET cc_start: 0.6099 (mmm) cc_final: 0.5874 (tmm)
REVERT: A   92 MET cc_start: 0.8739 (ttp) cc_final: 0.8229 (tmm)
REVERT: A  100 LYS cc_start: 0.8797 (mttt) cc_final: 0.8182 (tmmt)
REVERT: A  104 ASP cc_start: 0.8619 (m-30) cc_final: 0.8242 (m-30)
REVERT: A  118 GLU cc_start: 0.8110 (tt0) cc_final: 0.7654 (mm-30)
REVERT: A  164 ASN cc_start: 0.7237 (t0) cc_final: 0.7014 (t0)
REVERT: A  183 THR cc_start: 0.5490 (p) cc_final: 0.5278 (p)
REVERT: A  202 GLU cc_start: 0.8388 (tp30) cc_final: 0.8130 (mm-30)
REVERT: A  402 GLN cc_start: 0.8386 (mp-120) cc_final: 0.7891 (mp10)
REVERT: A  772 ASN cc_start: 0.7082 (t0) cc_final: 0.6562 (t0)
REVERT: A  795 MET cc_start: 0.7451 (mtp) cc_final: 0.7216 (mtp)
REVERT: A  838 GLU cc_start: 0.8148 (tp30) cc_final: 0.7910 (tp30)
REVERT: A  884 MET cc_start: 0.6402 (mmm) cc_final: 0.5611 (mmm)
REVERT: A 1011 MET cc_start: 0.8840 (ttt) cc_final: 0.8352 (tmm)
REVERT: A 1033 MET cc_start: 0.7511 (OUTLIER) cc_final: 0.7306 (mtt)
REVERT: A 1070 ASP cc_start: 0.7950 (p0) cc_final: 0.7390 (p0)
REVERT: A 1195 MET cc_start: 0.7600 (mmm) cc_final: 0.7227 (mmt)
REVERT: A 1226 GLN cc_start: 0.6188 (tp-100) cc_final: 0.5710 (tt0)
REVERT: A 1273 GLU cc_start: 0.7989 (tt0) cc_final: 0.7657 (tt0)
REVERT: A 1459 ASN cc_start: 0.8411 (m110) cc_final: 0.8098 (m-40)
  outliers start: 21
  outliers final: 7
  residues processed: 231
  average time/residue: 0.1195
  time to fit residues: 38.3713
Evaluate side-chains
  154 residues out of total 1167 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 8
    poor density    : 146
  time to evaluate  : 0.429 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  145 ASN
Chi-restraints excluded: chain A residue  449 VAL
Chi-restraints excluded: chain A residue  503 SER
Chi-restraints excluded: chain A residue  932 VAL
Chi-restraints excluded: chain A residue 1033 MET
Chi-restraints excluded: chain A residue 1114 LEU
Chi-restraints excluded: chain A residue 1429 PHE
Chi-restraints excluded: chain A residue 1445 VAL
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 144
   random chunks:
   chunk 127 optimal weight:    1.9990
   chunk 86 optimal weight:    0.9980
   chunk 21 optimal weight:    4.9990
   chunk 59 optimal weight:   10.0000
   chunk 75 optimal weight:    7.9990
   chunk 41 optimal weight:   10.0000
   chunk 10 optimal weight:    4.9990
   chunk 70 optimal weight:   20.0000
   chunk 3 optimal weight:    6.9990
   chunk 6 optimal weight:   20.0000
   chunk 20 optimal weight:    0.9990
   overall best weight:    2.7988

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

Flipped N/Q/H residues before XYZ refinement:
** A 106 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 107 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 145 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 780 HIS
** A 991 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A1116 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
A1283 ASN
** A1292 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A1295 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** A1403 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3686 r_free = 0.3686 target = 0.110734 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 41)----------------|
| r_work = 0.3339 r_free = 0.3339 target = 0.090387 restraints weight = 50960.895|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 39)----------------|
| r_work = 0.3399 r_free = 0.3399 target = 0.093716 restraints weight = 24762.594|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 38)----------------|
| r_work = 0.3439 r_free = 0.3439 target = 0.096001 restraints weight = 15009.327|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 33)----------------|
| r_work = 0.3466 r_free = 0.3466 target = 0.097582 restraints weight = 10510.079|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 40)----------------|
| r_work = 0.3485 r_free = 0.3485 target = 0.098660 restraints weight = 8134.890|
|-----------------------------------------------------------------------------|
r_work (final): 0.3484
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3485
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3485 r_free = 0.3485    target_work(ls_wunit_k1) = 0.098         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:       12 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3485 r_free = 0.3485    target_work(ls_wunit_k1) = 0.098         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:       12 |
|-----------------------------------------------------------------------------|
r_final: 0.3485
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7740
moved from start:          0.3554

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.063  11560  Z= 0.192
  Angle     :  0.855  17.727  15708  Z= 0.434
  Chirality :  0.048   0.227   1790
  Planarity :  0.006   0.064   2015
  Dihedral  : 12.796  89.263   1749
  Min Nonbonded Distance : 2.337

Molprobity Statistics.
  All-atom Clashscore : 12.57
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  : 13.59 %
    Favored  : 86.41 %
  Rotamer:
    Outliers :  3.25 %
    Allowed  : 11.89 %
    Favored  : 84.86 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 1.92 %
    Cis-general     : 0.51 %
    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: -3.67 (0.20), residues: 1423
  helix: -0.99 (0.21), residues: 529
  sheet: -2.67 (0.31), residues: 214
  loop : -3.63 (0.20), residues: 680

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.008   0.001   ARG A1093 
 TYR   0.015   0.002   TYR A1398 
 PHE   0.029   0.002   PHE A 894 
 TRP   0.021   0.002   TRP A 702 
 HIS   0.008   0.001   HIS A 528 

Details of bonding type rmsd
  covalent geometry    : bond        0.00430 (11560)
  covalent geometry    : angle       0.85549 (15708)
  hydrogen bonds       : bond        0.03782 (  369)
  hydrogen bonds       : angle       5.86464 ( 1047)

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

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

  2846 Ramachandran restraints generated.
    1423 Oldfield, 0 Emsley, 1423 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2846 Ramachandran restraints generated.
    1423 Oldfield, 0 Emsley, 1423 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  202 residues out of total 1167 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 38
    poor density    : 164
  time to evaluate  : 0.417 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   59 ARG cc_start: 0.8164 (mtt90) cc_final: 0.7901 (ttm-80)
REVERT: A  100 LYS cc_start: 0.8705 (mttt) cc_final: 0.8167 (tmmt)
REVERT: A  104 ASP cc_start: 0.8600 (m-30) cc_final: 0.8136 (m-30)
REVERT: A  118 GLU cc_start: 0.8205 (tt0) cc_final: 0.7937 (mm-30)
REVERT: A  183 THR cc_start: 0.5877 (p) cc_final: 0.5640 (p)
REVERT: A  486 LEU cc_start: 0.6136 (pp) cc_final: 0.5352 (tp)
REVERT: A  772 ASN cc_start: 0.7496 (t0) cc_final: 0.7063 (t0)
REVERT: A  795 MET cc_start: 0.7436 (mtp) cc_final: 0.7201 (mtp)
REVERT: A  884 MET cc_start: 0.6134 (mmm) cc_final: 0.5884 (mmm)
REVERT: A 1011 MET cc_start: 0.8720 (ttt) cc_final: 0.8390 (tmm)
REVERT: A 1099 ASP cc_start: 0.6398 (t70) cc_final: 0.5681 (t0)
REVERT: A 1226 GLN cc_start: 0.6447 (tp-100) cc_final: 0.6161 (tt0)
REVERT: A 1260 MET cc_start: 0.7789 (mmm) cc_final: 0.7565 (mmp)
REVERT: A 1392 GLN cc_start: 0.8495 (mm-40) cc_final: 0.7781 (mp10)
REVERT: A 1459 ASN cc_start: 0.8371 (m110) cc_final: 0.8109 (m-40)
  outliers start: 38
  outliers final: 20
  residues processed: 188
  average time/residue: 0.1209
  time to fit residues: 31.8661
Evaluate side-chains
  162 residues out of total 1167 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 20
    poor density    : 142
  time to evaluate  : 0.417 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  445 GLN
Chi-restraints excluded: chain A residue  449 VAL
Chi-restraints excluded: chain A residue  503 SER
Chi-restraints excluded: chain A residue  517 GLU
Chi-restraints excluded: chain A residue  532 VAL
Chi-restraints excluded: chain A residue  571 ILE
Chi-restraints excluded: chain A residue  616 SER
Chi-restraints excluded: chain A residue  698 LEU
Chi-restraints excluded: chain A residue  788 VAL
Chi-restraints excluded: chain A residue  791 SER
Chi-restraints excluded: chain A residue  812 VAL
Chi-restraints excluded: chain A residue  874 VAL
Chi-restraints excluded: chain A residue  988 THR
Chi-restraints excluded: chain A residue 1009 VAL
Chi-restraints excluded: chain A residue 1065 THR
Chi-restraints excluded: chain A residue 1123 VAL
Chi-restraints excluded: chain A residue 1244 ILE
Chi-restraints excluded: chain A residue 1333 THR
Chi-restraints excluded: chain A residue 1396 LEU
Chi-restraints excluded: chain A residue 1445 VAL
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 144
   random chunks:
   chunk 20 optimal weight:    2.9990
   chunk 102 optimal weight:   10.0000
   chunk 94 optimal weight:    3.9990
   chunk 44 optimal weight:    2.9990
   chunk 57 optimal weight:    0.9990
   chunk 116 optimal weight:    2.9990
   chunk 53 optimal weight:    4.9990
   chunk 2 optimal weight:    8.9990
   chunk 43 optimal weight:    0.7980
   chunk 138 optimal weight:    8.9990
   chunk 51 optimal weight:    0.1980
   overall best weight:    1.5986

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

Flipped N/Q/H residues before XYZ refinement:
** A 106 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 107 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 529 ASN
** A 794 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 991 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A1116 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A1241 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A1292 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A1295 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** A1403 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3712 r_free = 0.3712 target = 0.112375 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 31)----------------|
| r_work = 0.3358 r_free = 0.3358 target = 0.091536 restraints weight = 68744.601|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 31)----------------|
| r_work = 0.3445 r_free = 0.3445 target = 0.096564 restraints weight = 28597.065|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 32)----------------|
| r_work = 0.3477 r_free = 0.3477 target = 0.098504 restraints weight = 14176.124|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 29)----------------|
| r_work = 0.3500 r_free = 0.3500 target = 0.099685 restraints weight = 9611.980|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 27)----------------|
| r_work = 0.3503 r_free = 0.3503 target = 0.099928 restraints weight = 8556.265|
|-----------------------------------------------------------------------------|
r_work (final): 0.3504
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3505
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3505 r_free = 0.3505    target_work(ls_wunit_k1) = 0.100         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:       12 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3504 r_free = 0.3504    target_work(ls_wunit_k1) = 0.100         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:       12 |
|-----------------------------------------------------------------------------|
r_final: 0.3504
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7714
moved from start:          0.3911

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.041  11560  Z= 0.149
  Angle     :  0.812  16.488  15708  Z= 0.407
  Chirality :  0.046   0.213   1790
  Planarity :  0.005   0.065   2015
  Dihedral  : 12.640  89.769   1749
  Min Nonbonded Distance : 2.444

Molprobity Statistics.
  All-atom Clashscore : 11.99
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  : 12.54 %
    Favored  : 87.46 %
  Rotamer:
    Outliers :  1.97 %
    Allowed  : 13.26 %
    Favored  : 84.77 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 1.92 %
    Cis-general     : 0.51 %
    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: -3.30 (0.21), residues: 1423
  helix: -0.53 (0.23), residues: 523
  sheet: -2.36 (0.33), residues: 209
  loop : -3.60 (0.20), residues: 691

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.010   0.001   ARG A1146 
 TYR   0.011   0.002   TYR A1209 
 PHE   0.019   0.002   PHE A 894 
 TRP   0.023   0.002   TRP A1453 
 HIS   0.007   0.001   HIS A 528 

Details of bonding type rmsd
  covalent geometry    : bond        0.00334 (11560)
  covalent geometry    : angle       0.81210 (15708)
  hydrogen bonds       : bond        0.03371 (  369)
  hydrogen bonds       : angle       5.51427 ( 1047)

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

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

  2846 Ramachandran restraints generated.
    1423 Oldfield, 0 Emsley, 1423 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2846 Ramachandran restraints generated.
    1423 Oldfield, 0 Emsley, 1423 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  185 residues out of total 1167 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 23
    poor density    : 162
  time to evaluate  : 0.438 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   59 ARG cc_start: 0.8396 (mtt90) cc_final: 0.7896 (ttm-80)
REVERT: A   92 MET cc_start: 0.8781 (ttp) cc_final: 0.8394 (tmm)
REVERT: A  100 LYS cc_start: 0.8705 (mttt) cc_final: 0.8109 (tmmt)
REVERT: A  104 ASP cc_start: 0.8734 (m-30) cc_final: 0.8216 (m-30)
REVERT: A  118 GLU cc_start: 0.8224 (tt0) cc_final: 0.7885 (mm-30)
REVERT: A  183 THR cc_start: 0.5762 (p) cc_final: 0.5531 (p)
REVERT: A  486 LEU cc_start: 0.6127 (pp) cc_final: 0.5401 (tp)
REVERT: A  772 ASN cc_start: 0.7362 (t0) cc_final: 0.6859 (t0)
REVERT: A  795 MET cc_start: 0.7509 (mtp) cc_final: 0.7252 (mtp)
REVERT: A  985 ASP cc_start: 0.8001 (t70) cc_final: 0.7288 (m-30)
REVERT: A 1011 MET cc_start: 0.8789 (ttt) cc_final: 0.8390 (ppp)
REVERT: A 1033 MET cc_start: 0.7657 (mtp) cc_final: 0.7267 (mtt)
REVERT: A 1099 ASP cc_start: 0.5924 (t70) cc_final: 0.5555 (t0)
REVERT: A 1210 GLU cc_start: 0.8253 (mp0) cc_final: 0.7669 (tp30)
REVERT: A 1392 GLN cc_start: 0.8506 (mm-40) cc_final: 0.7709 (mp10)
REVERT: A 1453 TRP cc_start: 0.8180 (t60) cc_final: 0.7799 (t60)
REVERT: A 1459 ASN cc_start: 0.8447 (m110) cc_final: 0.8197 (m-40)
  outliers start: 23
  outliers final: 14
  residues processed: 180
  average time/residue: 0.1155
  time to fit residues: 29.3842
Evaluate side-chains
  160 residues out of total 1167 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 146
  time to evaluate  : 0.399 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  449 VAL
Chi-restraints excluded: chain A residue  503 SER
Chi-restraints excluded: chain A residue  532 VAL
Chi-restraints excluded: chain A residue  571 ILE
Chi-restraints excluded: chain A residue  616 SER
Chi-restraints excluded: chain A residue  791 SER
Chi-restraints excluded: chain A residue  812 VAL
Chi-restraints excluded: chain A residue 1065 THR
Chi-restraints excluded: chain A residue 1123 VAL
Chi-restraints excluded: chain A residue 1182 SER
Chi-restraints excluded: chain A residue 1244 ILE
Chi-restraints excluded: chain A residue 1318 LEU
Chi-restraints excluded: chain A residue 1396 LEU
Chi-restraints excluded: chain A residue 1447 THR
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 144
   random chunks:
   chunk 107 optimal weight:    1.9990
   chunk 87 optimal weight:    6.9990
   chunk 64 optimal weight:   20.0000
   chunk 100 optimal weight:    3.9990
   chunk 106 optimal weight:    1.9990
   chunk 74 optimal weight:    9.9990
   chunk 91 optimal weight:    6.9990
   chunk 132 optimal weight:   10.0000
   chunk 103 optimal weight:    1.9990
   chunk 113 optimal weight:    3.9990
   chunk 78 optimal weight:    1.9990
   overall best weight:    2.3990

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

Flipped N/Q/H residues before XYZ refinement:
** A 106 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 107 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 155 GLN
** A 317 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 529 ASN
** A 794 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 856 GLN
A 909 ASN
** A 991 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A1116 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
A1226 GLN
** A1241 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A1292 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A1295 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
A1403 HIS

Total number of N/Q/H flips: 6

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3690 r_free = 0.3690 target = 0.110920 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 43)----------------|
| r_work = 0.3332 r_free = 0.3332 target = 0.089893 restraints weight = 60362.374|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 36)----------------|
| r_work = 0.3397 r_free = 0.3397 target = 0.093493 restraints weight = 27588.099|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 44)----------------|
| r_work = 0.3441 r_free = 0.3441 target = 0.095986 restraints weight = 16102.631|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 45)----------------|
| r_work = 0.3471 r_free = 0.3471 target = 0.097687 restraints weight = 10952.544|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 43)----------------|
| r_work = 0.3491 r_free = 0.3491 target = 0.098861 restraints weight = 8324.288|
|-----------------------------------------------------------------------------|
r_work (final): 0.3492
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3492
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3492 r_free = 0.3492    target_work(ls_wunit_k1) = 0.099         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:       12 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3492 r_free = 0.3492    target_work(ls_wunit_k1) = 0.099         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:       12 |
|-----------------------------------------------------------------------------|
r_final: 0.3492
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7731
moved from start:          0.4137

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.060  11560  Z= 0.172
  Angle     :  0.820  15.094  15708  Z= 0.412
  Chirality :  0.046   0.181   1790
  Planarity :  0.005   0.065   2015
  Dihedral  : 12.592  89.634   1749
  Min Nonbonded Distance : 2.431

Molprobity Statistics.
  All-atom Clashscore : 12.26
  Ramachandran Plot:
    Outliers :  0.07 %
    Allowed  : 13.38 %
    Favored  : 86.55 %
  Rotamer:
    Outliers :  2.57 %
    Allowed  : 13.09 %
    Favored  : 84.35 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 1.92 %
    Cis-general     : 0.51 %
    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: -3.11 (0.21), residues: 1423
  helix: -0.39 (0.23), residues: 532
  sheet: -2.23 (0.33), residues: 209
  loop : -3.50 (0.21), residues: 682

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.008   0.001   ARG A 934 
 TYR   0.020   0.002   TYR A1209 
 PHE   0.024   0.002   PHE A 894 
 TRP   0.036   0.002   TRP A1170 
 HIS   0.007   0.001   HIS A 528 

Details of bonding type rmsd
  covalent geometry    : bond        0.00391 (11560)
  covalent geometry    : angle       0.81957 (15708)
  hydrogen bonds       : bond        0.03438 (  369)
  hydrogen bonds       : angle       5.40407 ( 1047)

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

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

  2846 Ramachandran restraints generated.
    1423 Oldfield, 0 Emsley, 1423 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2846 Ramachandran restraints generated.
    1423 Oldfield, 0 Emsley, 1423 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  177 residues out of total 1167 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 30
    poor density    : 147
  time to evaluate  : 0.427 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   59 ARG cc_start: 0.8351 (mtt90) cc_final: 0.7921 (ttm-80)
REVERT: A   92 MET cc_start: 0.8753 (ttp) cc_final: 0.8435 (tmm)
REVERT: A  100 LYS cc_start: 0.8707 (mttt) cc_final: 0.8107 (tmmt)
REVERT: A  104 ASP cc_start: 0.8737 (m-30) cc_final: 0.8235 (m-30)
REVERT: A  118 GLU cc_start: 0.8281 (tt0) cc_final: 0.7915 (mm-30)
REVERT: A  183 THR cc_start: 0.5800 (p) cc_final: 0.5564 (p)
REVERT: A  486 LEU cc_start: 0.6106 (pp) cc_final: 0.5384 (tp)
REVERT: A  517 GLU cc_start: 0.8123 (OUTLIER) cc_final: 0.7920 (mm-30)
REVERT: A  772 ASN cc_start: 0.7413 (t0) cc_final: 0.6909 (t0)
REVERT: A  795 MET cc_start: 0.7451 (mtp) cc_final: 0.7222 (mtp)
REVERT: A  856 GLN cc_start: 0.7909 (OUTLIER) cc_final: 0.7630 (mm-40)
REVERT: A  985 ASP cc_start: 0.7944 (t70) cc_final: 0.7223 (m-30)
REVERT: A 1011 MET cc_start: 0.8691 (ttt) cc_final: 0.8398 (ppp)
REVERT: A 1099 ASP cc_start: 0.5908 (t70) cc_final: 0.5624 (t0)
REVERT: A 1210 GLU cc_start: 0.8287 (mp0) cc_final: 0.7826 (mp0)
REVERT: A 1392 GLN cc_start: 0.8516 (mm-40) cc_final: 0.7753 (mp10)
REVERT: A 1453 TRP cc_start: 0.8315 (t60) cc_final: 0.7817 (t60)
  outliers start: 30
  outliers final: 17
  residues processed: 167
  average time/residue: 0.1085
  time to fit residues: 26.1856
Evaluate side-chains
  159 residues out of total 1167 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 19
    poor density    : 140
  time to evaluate  : 0.411 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  449 VAL
Chi-restraints excluded: chain A residue  503 SER
Chi-restraints excluded: chain A residue  517 GLU
Chi-restraints excluded: chain A residue  532 VAL
Chi-restraints excluded: chain A residue  571 ILE
Chi-restraints excluded: chain A residue  716 GLU
Chi-restraints excluded: chain A residue  791 SER
Chi-restraints excluded: chain A residue  812 VAL
Chi-restraints excluded: chain A residue  856 GLN
Chi-restraints excluded: chain A residue  930 LEU
Chi-restraints excluded: chain A residue 1065 THR
Chi-restraints excluded: chain A residue 1103 LEU
Chi-restraints excluded: chain A residue 1123 VAL
Chi-restraints excluded: chain A residue 1182 SER
Chi-restraints excluded: chain A residue 1244 ILE
Chi-restraints excluded: chain A residue 1318 LEU
Chi-restraints excluded: chain A residue 1396 LEU
Chi-restraints excluded: chain A residue 1429 PHE
Chi-restraints excluded: chain A residue 1465 THR
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 144
   random chunks:
   chunk 130 optimal weight:    0.8980
   chunk 14 optimal weight:   10.0000
   chunk 0 optimal weight:   10.0000
   chunk 61 optimal weight:    4.9990
   chunk 72 optimal weight:   10.0000
   chunk 47 optimal weight:    5.9990
   chunk 81 optimal weight:    2.9990
   chunk 9 optimal weight:    3.9990
   chunk 119 optimal weight:    0.7980
   chunk 139 optimal weight:    0.9990
   chunk 60 optimal weight:    0.9990
   overall best weight:    1.3386

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

Flipped N/Q/H residues before XYZ refinement:
** A 106 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 107 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 794 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 991 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A1241 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A1292 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A1295 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3726 r_free = 0.3726 target = 0.113124 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 38)----------------|
| r_work = 0.3361 r_free = 0.3361 target = 0.091657 restraints weight = 71081.495|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 38)----------------|
| r_work = 0.3441 r_free = 0.3441 target = 0.096019 restraints weight = 29721.098|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 26)----------------|
| r_work = 0.3474 r_free = 0.3474 target = 0.098002 restraints weight = 17007.118|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 32)----------------|
| r_work = 0.3520 r_free = 0.3520 target = 0.100723 restraints weight = 11841.444|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 31)----------------|
| r_work = 0.3540 r_free = 0.3540 target = 0.101886 restraints weight = 7389.652|
|-----------------------------------------------------------------------------|
r_work (final): 0.3540
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3540
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3540 r_free = 0.3540    target_work(ls_wunit_k1) = 0.102         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:       12 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3540 r_free = 0.3540    target_work(ls_wunit_k1) = 0.102         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:       12 |
|-----------------------------------------------------------------------------|
r_final: 0.3540
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7673
moved from start:          0.4401

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.060  11560  Z= 0.138
  Angle     :  0.800  16.132  15708  Z= 0.399
  Chirality :  0.045   0.179   1790
  Planarity :  0.005   0.059   2015
  Dihedral  : 12.442  89.118   1749
  Min Nonbonded Distance : 2.458

Molprobity Statistics.
  All-atom Clashscore : 10.79
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  : 12.18 %
    Favored  : 87.82 %
  Rotamer:
    Outliers :  1.97 %
    Allowed  : 13.43 %
    Favored  : 84.60 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 1.92 %
    Cis-general     : 0.51 %
    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: -2.90 (0.21), residues: 1423
  helix: -0.20 (0.23), residues: 531
  sheet: -2.09 (0.33), residues: 219
  loop : -3.41 (0.21), residues: 673

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.008   0.001   ARG A 934 
 TYR   0.015   0.002   TYR A1294 
 PHE   0.019   0.002   PHE A1412 
 TRP   0.028   0.002   TRP A1170 
 HIS   0.006   0.001   HIS A 528 

Details of bonding type rmsd
  covalent geometry    : bond        0.00311 (11560)
  covalent geometry    : angle       0.79999 (15708)
  hydrogen bonds       : bond        0.03183 (  369)
  hydrogen bonds       : angle       5.18623 ( 1047)

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

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

  2846 Ramachandran restraints generated.
    1423 Oldfield, 0 Emsley, 1423 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2846 Ramachandran restraints generated.
    1423 Oldfield, 0 Emsley, 1423 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  180 residues out of total 1167 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 23
    poor density    : 157
  time to evaluate  : 0.455 
Fit side-chains
REVERT: A   93 MET cc_start: 0.8316 (mmm) cc_final: 0.8112 (mmm)
REVERT: A  100 LYS cc_start: 0.8639 (mttt) cc_final: 0.8094 (tmmt)
REVERT: A  104 ASP cc_start: 0.8754 (m-30) cc_final: 0.8206 (m-30)
REVERT: A  118 GLU cc_start: 0.8159 (tt0) cc_final: 0.7858 (mm-30)
REVERT: A  183 THR cc_start: 0.5624 (p) cc_final: 0.5386 (p)
REVERT: A  486 LEU cc_start: 0.5929 (pp) cc_final: 0.5339 (tp)
REVERT: A  772 ASN cc_start: 0.7443 (t0) cc_final: 0.6863 (t0)
REVERT: A  795 MET cc_start: 0.7366 (mtp) cc_final: 0.7147 (mtp)
REVERT: A  960 ARG cc_start: 0.5620 (tpt90) cc_final: 0.4635 (mmm-85)
REVERT: A  985 ASP cc_start: 0.7839 (t70) cc_final: 0.7161 (m-30)
REVERT: A  991 GLN cc_start: 0.8295 (tp-100) cc_final: 0.7951 (tp-100)
REVERT: A 1011 MET cc_start: 0.8625 (ttt) cc_final: 0.8333 (ppp)
REVERT: A 1137 ARG cc_start: 0.7444 (tpt-90) cc_final: 0.6996 (tpt-90)
REVERT: A 1210 GLU cc_start: 0.8057 (mp0) cc_final: 0.7564 (mp0)
REVERT: A 1392 GLN cc_start: 0.8470 (mm-40) cc_final: 0.7756 (mp10)
REVERT: A 1453 TRP cc_start: 0.8112 (t60) cc_final: 0.7745 (t60)
  outliers start: 23
  outliers final: 17
  residues processed: 170
  average time/residue: 0.1163
  time to fit residues: 28.8020
Evaluate side-chains
  161 residues out of total 1167 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 17
    poor density    : 144
  time to evaluate  : 0.448 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  449 VAL
Chi-restraints excluded: chain A residue  503 SER
Chi-restraints excluded: chain A residue  532 VAL
Chi-restraints excluded: chain A residue  571 ILE
Chi-restraints excluded: chain A residue  616 SER
Chi-restraints excluded: chain A residue  791 SER
Chi-restraints excluded: chain A residue  812 VAL
Chi-restraints excluded: chain A residue  968 THR
Chi-restraints excluded: chain A residue 1065 THR
Chi-restraints excluded: chain A residue 1103 LEU
Chi-restraints excluded: chain A residue 1123 VAL
Chi-restraints excluded: chain A residue 1129 ILE
Chi-restraints excluded: chain A residue 1244 ILE
Chi-restraints excluded: chain A residue 1318 LEU
Chi-restraints excluded: chain A residue 1396 LEU
Chi-restraints excluded: chain A residue 1429 PHE
Chi-restraints excluded: chain A residue 1465 THR
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 144
   random chunks:
   chunk 88 optimal weight:    0.7980
   chunk 80 optimal weight:    2.9990
   chunk 28 optimal weight:    0.9990
   chunk 61 optimal weight:    4.9990
   chunk 91 optimal weight:    7.9990
   chunk 128 optimal weight:    0.6980
   chunk 96 optimal weight:    4.9990
   chunk 3 optimal weight:    2.9990
   chunk 62 optimal weight:    7.9990
   chunk 73 optimal weight:    6.9990
   chunk 27 optimal weight:    9.9990
   overall best weight:    1.6986

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

Flipped N/Q/H residues before XYZ refinement:
** A 106 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 107 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 794 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 991 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A1241 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A1292 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A1295 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3718 r_free = 0.3718 target = 0.112515 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 36)----------------|
| r_work = 0.3349 r_free = 0.3349 target = 0.090859 restraints weight = 70541.974|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 37)----------------|
| r_work = 0.3430 r_free = 0.3430 target = 0.095308 restraints weight = 30194.534|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 26)----------------|
| r_work = 0.3461 r_free = 0.3461 target = 0.097176 restraints weight = 17085.144|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 32)----------------|
| r_work = 0.3507 r_free = 0.3507 target = 0.099879 restraints weight = 12037.215|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 31)----------------|
| r_work = 0.3530 r_free = 0.3530 target = 0.101218 restraints weight = 7602.983|
|-----------------------------------------------------------------------------|
r_work (final): 0.3531
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3531
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3531 r_free = 0.3531    target_work(ls_wunit_k1) = 0.101         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:       12 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3531 r_free = 0.3531    target_work(ls_wunit_k1) = 0.101         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:       12 |
|-----------------------------------------------------------------------------|
r_final: 0.3531
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7692
moved from start:          0.4608

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.049  11560  Z= 0.149
  Angle     :  0.810  16.734  15708  Z= 0.403
  Chirality :  0.045   0.182   1790
  Planarity :  0.005   0.063   2015
  Dihedral  : 12.401  88.989   1749
  Min Nonbonded Distance : 2.463

Molprobity Statistics.
  All-atom Clashscore : 10.75
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  : 12.96 %
    Favored  : 87.04 %
  Rotamer:
    Outliers :  2.05 %
    Allowed  : 13.69 %
    Favored  : 84.26 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 1.92 %
    Cis-general     : 0.51 %
    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: -2.75 (0.22), residues: 1423
  helix: -0.05 (0.23), residues: 527
  sheet: -1.98 (0.33), residues: 217
  loop : -3.34 (0.22), residues: 679

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.007   0.001   ARG A 934 
 TYR   0.022   0.002   TYR A 937 
 PHE   0.019   0.002   PHE A 894 
 TRP   0.056   0.002   TRP A1170 
 HIS   0.007   0.001   HIS A 528 

Details of bonding type rmsd
  covalent geometry    : bond        0.00337 (11560)
  covalent geometry    : angle       0.80950 (15708)
  hydrogen bonds       : bond        0.03274 (  369)
  hydrogen bonds       : angle       5.09938 ( 1047)

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

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

  2846 Ramachandran restraints generated.
    1423 Oldfield, 0 Emsley, 1423 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2846 Ramachandran restraints generated.
    1423 Oldfield, 0 Emsley, 1423 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  178 residues out of total 1167 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 24
    poor density    : 154
  time to evaluate  : 0.466 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   92 MET cc_start: 0.8786 (ttp) cc_final: 0.8445 (tmm)
REVERT: A  100 LYS cc_start: 0.8609 (mttt) cc_final: 0.8107 (tmmt)
REVERT: A  104 ASP cc_start: 0.8792 (m-30) cc_final: 0.8233 (m-30)
REVERT: A  183 THR cc_start: 0.5639 (p) cc_final: 0.5387 (p)
REVERT: A  548 MET cc_start: 0.6505 (tpp) cc_final: 0.6178 (tpp)
REVERT: A  772 ASN cc_start: 0.7554 (t0) cc_final: 0.6950 (t0)
REVERT: A  795 MET cc_start: 0.7368 (mtp) cc_final: 0.7037 (mtp)
REVERT: A  857 LYS cc_start: 0.8838 (tptp) cc_final: 0.8625 (tptm)
REVERT: A  960 ARG cc_start: 0.5640 (tpt90) cc_final: 0.4712 (mmm-85)
REVERT: A  985 ASP cc_start: 0.7919 (t70) cc_final: 0.7255 (m-30)
REVERT: A  991 GLN cc_start: 0.8333 (tp-100) cc_final: 0.7506 (tp-100)
REVERT: A 1011 MET cc_start: 0.8647 (ttt) cc_final: 0.8332 (ppp)
REVERT: A 1070 ASP cc_start: 0.8415 (p0) cc_final: 0.7675 (p0)
REVERT: A 1099 ASP cc_start: 0.5786 (t0) cc_final: 0.5411 (t0)
REVERT: A 1137 ARG cc_start: 0.7499 (tpt-90) cc_final: 0.7042 (mtt180)
REVERT: A 1210 GLU cc_start: 0.8068 (mp0) cc_final: 0.7576 (mp0)
  outliers start: 24
  outliers final: 18
  residues processed: 169
  average time/residue: 0.1134
  time to fit residues: 28.2217
Evaluate side-chains
  162 residues out of total 1167 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 18
    poor density    : 144
  time to evaluate  : 0.367 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   29 MET
Chi-restraints excluded: chain A residue  449 VAL
Chi-restraints excluded: chain A residue  503 SER
Chi-restraints excluded: chain A residue  532 VAL
Chi-restraints excluded: chain A residue  616 SER
Chi-restraints excluded: chain A residue  716 GLU
Chi-restraints excluded: chain A residue  791 SER
Chi-restraints excluded: chain A residue  812 VAL
Chi-restraints excluded: chain A residue  930 LEU
Chi-restraints excluded: chain A residue  968 THR
Chi-restraints excluded: chain A residue 1065 THR
Chi-restraints excluded: chain A residue 1103 LEU
Chi-restraints excluded: chain A residue 1182 SER
Chi-restraints excluded: chain A residue 1244 ILE
Chi-restraints excluded: chain A residue 1318 LEU
Chi-restraints excluded: chain A residue 1396 LEU
Chi-restraints excluded: chain A residue 1429 PHE
Chi-restraints excluded: chain A residue 1465 THR
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 144
   random chunks:
   chunk 14 optimal weight:    6.9990
   chunk 105 optimal weight:   20.0000
   chunk 76 optimal weight:    7.9990
   chunk 6 optimal weight:   20.0000
   chunk 30 optimal weight:    0.0470
   chunk 69 optimal weight:    0.9990
   chunk 103 optimal weight:    3.9990
   chunk 91 optimal weight:    0.0060
   chunk 74 optimal weight:    9.9990
   chunk 24 optimal weight:   10.0000
   chunk 70 optimal weight:   10.0000
   overall best weight:    2.4100

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

Flipped N/Q/H residues before XYZ refinement:
** A 106 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 107 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 794 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 856 GLN
A 861 HIS
** A 991 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A1292 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A1295 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3698 r_free = 0.3698 target = 0.111292 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 43)----------------|
| r_work = 0.3345 r_free = 0.3345 target = 0.090559 restraints weight = 55446.573|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 31)----------------|
| r_work = 0.3406 r_free = 0.3406 target = 0.094067 restraints weight = 26259.523|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 43)----------------|
| r_work = 0.3448 r_free = 0.3448 target = 0.096476 restraints weight = 15603.238|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 42)----------------|
| r_work = 0.3477 r_free = 0.3477 target = 0.098096 restraints weight = 10763.086|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 33)----------------|
| r_work = 0.3495 r_free = 0.3495 target = 0.099150 restraints weight = 8283.470|
|-----------------------------------------------------------------------------|
r_work (final): 0.3495
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3496
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3496 r_free = 0.3496    target_work(ls_wunit_k1) = 0.099         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:       12 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3496 r_free = 0.3496    target_work(ls_wunit_k1) = 0.099         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:       12 |
|-----------------------------------------------------------------------------|
r_final: 0.3496
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7730
moved from start:          0.4680

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.047  11560  Z= 0.170
  Angle     :  0.833  14.960  15708  Z= 0.413
  Chirality :  0.046   0.180   1790
  Planarity :  0.006   0.123   2015
  Dihedral  : 12.448  87.957   1749
  Min Nonbonded Distance : 2.453

Molprobity Statistics.
  All-atom Clashscore : 12.13
  Ramachandran Plot:
    Outliers :  0.07 %
    Allowed  : 13.31 %
    Favored  : 86.62 %
  Rotamer:
    Outliers :  1.97 %
    Allowed  : 14.29 %
    Favored  : 83.75 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 1.92 %
    Cis-general     : 0.51 %
    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: -2.72 (0.22), residues: 1423
  helix: -0.08 (0.23), residues: 528
  sheet: -1.90 (0.33), residues: 222
  loop : -3.31 (0.22), residues: 673

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.009   0.001   ARG A 934 
 TYR   0.027   0.002   TYR A 937 
 PHE   0.023   0.002   PHE A 894 
 TRP   0.041   0.002   TRP A1170 
 HIS   0.007   0.001   HIS A 528 

Details of bonding type rmsd
  covalent geometry    : bond        0.00386 (11560)
  covalent geometry    : angle       0.83322 (15708)
  hydrogen bonds       : bond        0.03310 (  369)
  hydrogen bonds       : angle       5.12135 ( 1047)

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

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

  2846 Ramachandran restraints generated.
    1423 Oldfield, 0 Emsley, 1423 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2846 Ramachandran restraints generated.
    1423 Oldfield, 0 Emsley, 1423 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  173 residues out of total 1167 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 23
    poor density    : 150
  time to evaluate  : 0.441 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  100 LYS cc_start: 0.8607 (mttt) cc_final: 0.8155 (tmmt)
REVERT: A  104 ASP cc_start: 0.8702 (m-30) cc_final: 0.8173 (m-30)
REVERT: A  183 THR cc_start: 0.5686 (p) cc_final: 0.5470 (p)
REVERT: A  486 LEU cc_start: 0.6021 (pp) cc_final: 0.5343 (tp)
REVERT: A  548 MET cc_start: 0.6563 (tpp) cc_final: 0.6249 (tpp)
REVERT: A  772 ASN cc_start: 0.7661 (t0) cc_final: 0.7076 (t0)
REVERT: A  856 GLN cc_start: 0.7837 (OUTLIER) cc_final: 0.7571 (mm-40)
REVERT: A  941 LYS cc_start: 0.8682 (mmmt) cc_final: 0.8091 (mmtm)
REVERT: A  960 ARG cc_start: 0.5721 (tpt90) cc_final: 0.4785 (mmm-85)
REVERT: A  985 ASP cc_start: 0.7805 (t70) cc_final: 0.7185 (m-30)
REVERT: A 1011 MET cc_start: 0.8647 (ttt) cc_final: 0.8339 (ppp)
REVERT: A 1070 ASP cc_start: 0.8409 (p0) cc_final: 0.7840 (p0)
REVERT: A 1141 TYR cc_start: 0.8006 (OUTLIER) cc_final: 0.7733 (m-80)
REVERT: A 1210 GLU cc_start: 0.8096 (mp0) cc_final: 0.7666 (mp0)
REVERT: A 1392 GLN cc_start: 0.8561 (mm-40) cc_final: 0.7873 (mp10)
  outliers start: 23
  outliers final: 20
  residues processed: 166
  average time/residue: 0.1160
  time to fit residues: 27.4471
Evaluate side-chains
  166 residues out of total 1167 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 22
    poor density    : 144
  time to evaluate  : 0.455 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   29 MET
Chi-restraints excluded: chain A residue  155 GLN
Chi-restraints excluded: chain A residue  449 VAL
Chi-restraints excluded: chain A residue  503 SER
Chi-restraints excluded: chain A residue  532 VAL
Chi-restraints excluded: chain A residue  616 SER
Chi-restraints excluded: chain A residue  716 GLU
Chi-restraints excluded: chain A residue  791 SER
Chi-restraints excluded: chain A residue  812 VAL
Chi-restraints excluded: chain A residue  856 GLN
Chi-restraints excluded: chain A residue  930 LEU
Chi-restraints excluded: chain A residue  968 THR
Chi-restraints excluded: chain A residue 1009 VAL
Chi-restraints excluded: chain A residue 1065 THR
Chi-restraints excluded: chain A residue 1103 LEU
Chi-restraints excluded: chain A residue 1141 TYR
Chi-restraints excluded: chain A residue 1182 SER
Chi-restraints excluded: chain A residue 1244 ILE
Chi-restraints excluded: chain A residue 1318 LEU
Chi-restraints excluded: chain A residue 1396 LEU
Chi-restraints excluded: chain A residue 1429 PHE
Chi-restraints excluded: chain A residue 1465 THR
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 144
   random chunks:
   chunk 70 optimal weight:    0.0670
   chunk 130 optimal weight:    9.9990
   chunk 21 optimal weight:    6.9990
   chunk 59 optimal weight:    1.9990
   chunk 38 optimal weight:    4.9990
   chunk 105 optimal weight:    9.9990
   chunk 128 optimal weight:    8.9990
   chunk 53 optimal weight:    2.9990
   chunk 94 optimal weight:    1.9990
   chunk 89 optimal weight:    9.9990
   chunk 141 optimal weight:    7.9990
   overall best weight:    2.4126

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

Flipped N/Q/H residues before XYZ refinement:
** A 106 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 107 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 794 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 856 GLN
** A 991 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
A1077 ASN
** A1292 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A1295 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3691 r_free = 0.3691 target = 0.110823 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 35)----------------|
| r_work = 0.3328 r_free = 0.3328 target = 0.089625 restraints weight = 59598.522|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 34)----------------|
| r_work = 0.3392 r_free = 0.3392 target = 0.093267 restraints weight = 27618.735|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 35)----------------|
| r_work = 0.3435 r_free = 0.3435 target = 0.095729 restraints weight = 16169.844|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 45)----------------|
| r_work = 0.3465 r_free = 0.3465 target = 0.097435 restraints weight = 11074.016|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 21)----------------|
| r_work = 0.3483 r_free = 0.3483 target = 0.098499 restraints weight = 8443.599|
|-----------------------------------------------------------------------------|
r_work (final): 0.3484
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3485
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3485 r_free = 0.3485    target_work(ls_wunit_k1) = 0.098         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:       12 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3485 r_free = 0.3485    target_work(ls_wunit_k1) = 0.098         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:       12 |
|-----------------------------------------------------------------------------|
r_final: 0.3485
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7743
moved from start:          0.4794

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.050  11560  Z= 0.171
  Angle     :  0.839  17.013  15708  Z= 0.416
  Chirality :  0.046   0.181   1790
  Planarity :  0.005   0.061   2015
  Dihedral  : 12.444  86.642   1749
  Min Nonbonded Distance : 2.452

Molprobity Statistics.
  All-atom Clashscore : 12.22
  Ramachandran Plot:
    Outliers :  0.07 %
    Allowed  : 13.80 %
    Favored  : 86.13 %
  Rotamer:
    Outliers :  1.97 %
    Allowed  : 14.80 %
    Favored  : 83.23 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 1.92 %
    Cis-general     : 0.51 %
    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: -2.72 (0.22), residues: 1423
  helix: -0.08 (0.23), residues: 525
  sheet: -1.95 (0.33), residues: 217
  loop : -3.28 (0.22), residues: 681

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.009   0.001   ARG A 934 
 TYR   0.022   0.002   TYR A 937 
 PHE   0.023   0.002   PHE A 894 
 TRP   0.039   0.002   TRP A1170 
 HIS   0.007   0.001   HIS A 528 

Details of bonding type rmsd
  covalent geometry    : bond        0.00390 (11560)
  covalent geometry    : angle       0.83921 (15708)
  hydrogen bonds       : bond        0.03336 (  369)
  hydrogen bonds       : angle       5.13576 ( 1047)

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

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

  2846 Ramachandran restraints generated.
    1423 Oldfield, 0 Emsley, 1423 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2846 Ramachandran restraints generated.
    1423 Oldfield, 0 Emsley, 1423 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  172 residues out of total 1167 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 23
    poor density    : 149
  time to evaluate  : 0.479 
Fit side-chains
   revert: symmetry clash
REVERT: A   59 ARG cc_start: 0.8366 (mtt90) cc_final: 0.7982 (ttm-80)
REVERT: A  100 LYS cc_start: 0.8633 (mttt) cc_final: 0.8178 (tmmt)
REVERT: A  104 ASP cc_start: 0.8703 (m-30) cc_final: 0.8174 (m-30)
REVERT: A  183 THR cc_start: 0.5710 (p) cc_final: 0.5495 (p)
REVERT: A  486 LEU cc_start: 0.6069 (pp) cc_final: 0.5404 (tp)
REVERT: A  548 MET cc_start: 0.6594 (tpp) cc_final: 0.6282 (tpp)
REVERT: A  772 ASN cc_start: 0.7691 (t0) cc_final: 0.7180 (t0)
REVERT: A  960 ARG cc_start: 0.5729 (tpt90) cc_final: 0.4824 (mmm-85)
REVERT: A  985 ASP cc_start: 0.7945 (t70) cc_final: 0.7294 (m-30)
REVERT: A 1011 MET cc_start: 0.8640 (ttt) cc_final: 0.8341 (ppp)
REVERT: A 1070 ASP cc_start: 0.8407 (p0) cc_final: 0.7903 (p0)
REVERT: A 1210 GLU cc_start: 0.8066 (mp0) cc_final: 0.7618 (mp0)
REVERT: A 1392 GLN cc_start: 0.8564 (mm-40) cc_final: 0.7886 (mp10)
  outliers start: 23
  outliers final: 20
  residues processed: 166
  average time/residue: 0.1221
  time to fit residues: 28.3306
Evaluate side-chains
  164 residues out of total 1167 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 20
    poor density    : 144
  time to evaluate  : 0.436 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   29 MET
Chi-restraints excluded: chain A residue  449 VAL
Chi-restraints excluded: chain A residue  503 SER
Chi-restraints excluded: chain A residue  532 VAL
Chi-restraints excluded: chain A residue  616 SER
Chi-restraints excluded: chain A residue  716 GLU
Chi-restraints excluded: chain A residue  791 SER
Chi-restraints excluded: chain A residue  812 VAL
Chi-restraints excluded: chain A residue  930 LEU
Chi-restraints excluded: chain A residue  968 THR
Chi-restraints excluded: chain A residue 1009 VAL
Chi-restraints excluded: chain A residue 1065 THR
Chi-restraints excluded: chain A residue 1103 LEU
Chi-restraints excluded: chain A residue 1129 ILE
Chi-restraints excluded: chain A residue 1182 SER
Chi-restraints excluded: chain A residue 1244 ILE
Chi-restraints excluded: chain A residue 1318 LEU
Chi-restraints excluded: chain A residue 1396 LEU
Chi-restraints excluded: chain A residue 1429 PHE
Chi-restraints excluded: chain A residue 1465 THR
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 144
   random chunks:
   chunk 121 optimal weight:    0.8980
   chunk 50 optimal weight:    0.0470
   chunk 82 optimal weight:    6.9990
   chunk 56 optimal weight:    3.9990
   chunk 62 optimal weight:    8.9990
   chunk 97 optimal weight:    0.4980
   chunk 32 optimal weight:    2.9990
   chunk 143 optimal weight:   10.0000
   chunk 118 optimal weight:    0.6980
   chunk 130 optimal weight:    6.9990
   chunk 103 optimal weight:    0.9990
   overall best weight:    0.6280

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

Flipped N/Q/H residues before XYZ refinement:
** A 106 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 107 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 794 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 991 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A1292 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A1295 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3748 r_free = 0.3748 target = 0.114671 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 40)----------------|
| r_work = 0.3401 r_free = 0.3401 target = 0.093724 restraints weight = 59973.659|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 34)----------------|
| r_work = 0.3466 r_free = 0.3466 target = 0.097426 restraints weight = 27885.670|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 32)----------------|
| r_work = 0.3509 r_free = 0.3509 target = 0.099963 restraints weight = 16336.882|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 29)----------------|
| r_work = 0.3538 r_free = 0.3538 target = 0.101700 restraints weight = 11101.924|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 37)----------------|
| r_work = 0.3559 r_free = 0.3559 target = 0.102894 restraints weight = 8417.698|
|-----------------------------------------------------------------------------|
r_work (final): 0.3560
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3560
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3560 r_free = 0.3560    target_work(ls_wunit_k1) = 0.103         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:       12 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3560 r_free = 0.3560    target_work(ls_wunit_k1) = 0.103         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:       12 |
|-----------------------------------------------------------------------------|
r_final: 0.3560
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7643
moved from start:          0.5094

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.054  11560  Z= 0.131
  Angle     :  0.808  16.469  15708  Z= 0.397
  Chirality :  0.044   0.180   1790
  Planarity :  0.005   0.061   2015
  Dihedral  : 12.248  86.827   1749
  Min Nonbonded Distance : 2.452

Molprobity Statistics.
  All-atom Clashscore : 10.97
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  : 12.32 %
    Favored  : 87.68 %
  Rotamer:
    Outliers :  1.37 %
    Allowed  : 15.14 %
    Favored  : 83.49 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 1.92 %
    Cis-general     : 0.51 %
    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: -2.52 (0.22), residues: 1423
  helix:  0.08 (0.23), residues: 520
  sheet: -1.86 (0.35), residues: 206
  loop : -3.12 (0.22), residues: 697

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.010   0.001   ARG A 694 
 TYR   0.025   0.001   TYR A 937 
 PHE   0.023   0.002   PHE A1112 
 TRP   0.032   0.002   TRP A1170 
 HIS   0.005   0.001   HIS A1232 

Details of bonding type rmsd
  covalent geometry    : bond        0.00295 (11560)
  covalent geometry    : angle       0.80757 (15708)
  hydrogen bonds       : bond        0.03082 (  369)
  hydrogen bonds       : angle       5.01477 ( 1047)

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

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

  2846 Ramachandran restraints generated.
    1423 Oldfield, 0 Emsley, 1423 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2846 Ramachandran restraints generated.
    1423 Oldfield, 0 Emsley, 1423 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  180 residues out of total 1167 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 164
  time to evaluate  : 0.345 
Fit side-chains
   revert: symmetry clash
REVERT: A   59 ARG cc_start: 0.8176 (mtt90) cc_final: 0.7910 (ttm-80)
REVERT: A  100 LYS cc_start: 0.8566 (mttt) cc_final: 0.8167 (tmmt)
REVERT: A  104 ASP cc_start: 0.8520 (m-30) cc_final: 0.8084 (m-30)
REVERT: A  183 THR cc_start: 0.5533 (p) cc_final: 0.5303 (p)
REVERT: A  278 MET cc_start: 0.7669 (tmm) cc_final: 0.7433 (tmm)
REVERT: A  478 GLN cc_start: 0.7921 (mp10) cc_final: 0.7636 (pt0)
REVERT: A  486 LEU cc_start: 0.5890 (pp) cc_final: 0.5387 (tp)
REVERT: A  548 MET cc_start: 0.6422 (tpp) cc_final: 0.6133 (tpp)
REVERT: A  772 ASN cc_start: 0.7555 (t0) cc_final: 0.7020 (t0)
REVERT: A  960 ARG cc_start: 0.5378 (tpt90) cc_final: 0.4661 (mmm-85)
REVERT: A  985 ASP cc_start: 0.7737 (t70) cc_final: 0.7168 (m-30)
REVERT: A  991 GLN cc_start: 0.8049 (tp-100) cc_final: 0.7640 (tp40)
REVERT: A 1070 ASP cc_start: 0.8313 (p0) cc_final: 0.7928 (p0)
REVERT: A 1182 SER cc_start: 0.6586 (OUTLIER) cc_final: 0.6092 (p)
REVERT: A 1210 GLU cc_start: 0.7894 (mp0) cc_final: 0.7482 (mp0)
REVERT: A 1392 GLN cc_start: 0.8455 (mm-40) cc_final: 0.7769 (mp10)
  outliers start: 16
  outliers final: 14
  residues processed: 176
  average time/residue: 0.1272
  time to fit residues: 31.5784
Evaluate side-chains
  165 residues out of total 1167 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 15
    poor density    : 150
  time to evaluate  : 0.582 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  155 GLN
Chi-restraints excluded: chain A residue  503 SER
Chi-restraints excluded: chain A residue  616 SER
Chi-restraints excluded: chain A residue  791 SER
Chi-restraints excluded: chain A residue  812 VAL
Chi-restraints excluded: chain A residue  968 THR
Chi-restraints excluded: chain A residue 1065 THR
Chi-restraints excluded: chain A residue 1103 LEU
Chi-restraints excluded: chain A residue 1129 ILE
Chi-restraints excluded: chain A residue 1182 SER
Chi-restraints excluded: chain A residue 1244 ILE
Chi-restraints excluded: chain A residue 1318 LEU
Chi-restraints excluded: chain A residue 1396 LEU
Chi-restraints excluded: chain A residue 1429 PHE
Chi-restraints excluded: chain A residue 1465 THR
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 144
   random chunks:
   chunk 85 optimal weight:    0.4980
   chunk 10 optimal weight:    6.9990
   chunk 45 optimal weight:    2.9990
   chunk 58 optimal weight:    9.9990
   chunk 101 optimal weight:    0.0980
   chunk 107 optimal weight:    0.7980
   chunk 109 optimal weight:    5.9990
   chunk 5 optimal weight:   10.0000
   chunk 57 optimal weight:    4.9990
   chunk 105 optimal weight:    6.9990
   chunk 73 optimal weight:    2.9990
   overall best weight:    1.4784

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

Flipped N/Q/H residues before XYZ refinement:
** A 106 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 107 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 794 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 991 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A1292 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A1295 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3722 r_free = 0.3722 target = 0.113101 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.3395 r_free = 0.3395 target = 0.093309 restraints weight = 48433.734|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 35)----------------|
| r_work = 0.3452 r_free = 0.3452 target = 0.096601 restraints weight = 24233.895|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 38)----------------|
| r_work = 0.3491 r_free = 0.3491 target = 0.098874 restraints weight = 14912.559|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 42)----------------|
| r_work = 0.3518 r_free = 0.3518 target = 0.100435 restraints weight = 10476.914|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 23)----------------|
| r_work = 0.3534 r_free = 0.3534 target = 0.101426 restraints weight = 8135.598|
|-----------------------------------------------------------------------------|
r_work (final): 0.3536
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3536
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3536 r_free = 0.3536    target_work(ls_wunit_k1) = 0.101         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:       12 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3536 r_free = 0.3536    target_work(ls_wunit_k1) = 0.101         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:       12 |
|-----------------------------------------------------------------------------|
r_final: 0.3536
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7678
moved from start:          0.5177

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.053  11560  Z= 0.144
  Angle     :  0.819  15.758  15708  Z= 0.404
  Chirality :  0.045   0.179   1790
  Planarity :  0.005   0.069   2015
  Dihedral  : 12.278  86.528   1749
  Min Nonbonded Distance : 2.448

Molprobity Statistics.
  All-atom Clashscore : 11.82
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  : 13.52 %
    Favored  : 86.48 %
  Rotamer:
    Outliers :  1.37 %
    Allowed  : 15.83 %
    Favored  : 82.81 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 1.92 %
    Cis-general     : 0.51 %
    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: -2.48 (0.22), residues: 1423
  helix:  0.15 (0.23), residues: 519
  sheet: -1.83 (0.35), residues: 206
  loop : -3.11 (0.22), residues: 698

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.014   0.001   ARG A 694 
 TYR   0.021   0.002   TYR A 937 
 PHE   0.020   0.002   PHE A1412 
 TRP   0.079   0.002   TRP A1453 
 HIS   0.009   0.001   HIS A 528 

Details of bonding type rmsd
  covalent geometry    : bond        0.00328 (11560)
  covalent geometry    : angle       0.81851 (15708)
  hydrogen bonds       : bond        0.03109 (  369)
  hydrogen bonds       : angle       4.99099 ( 1047)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 1999.36 seconds
wall clock time: 35 minutes 19.14 seconds (2119.14 seconds total)