Starting phenix.real_space_refine
on Tue Jul 29 12:31:47 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/5n8o_3601/07_2025/5n8o_3601_neut.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/5n8o_3601/07_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_3601/07_2025/5n8o_3601.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/5n8o_3601/07_2025/5n8o_3601.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/5n8o_3601/07_2025/5n8o_3601_neut.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/5n8o_3601/07_2025/5n8o_3601_neut.cif"
  }
  resolution = 3.9
  write_initial_geo_file = False
  refinement {
    macro_cycles = 10
  }
  qi {
    qm_restraints {
      package {
        program = *test
      }
    }
  }


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): 0.04s

  Monomer Library directory:
    "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5711/modules/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: 12.93, per 1000 atoms: 1.14
  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: 2.72
  Conformation dependent library (CDL) restraints added in 2.7 seconds
  

  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: 3.89
  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: 5.00

  Time building geometry restraints manager: 3.04 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:             0.680
  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:          0.460
  Check model and map are aligned:         0.090
  Set scattering table:                    0.110
  Process input model:                     40.320
  Find NCS groups from input model:        0.150
  Set up NCS constraints:                  0.080
  Set refine NCS operators:                0.000
  Adjust number of macro_cycles:           0.000
  Reset NCS operators:                     0.000
  Extract rigid body selections:           0.000
  Check and reset occupancies:             0.010
  Load rotamer database and sin/cos tables:3.110
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   45.020
-------------------------------------------------------------------------------
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 (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  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
 TRP   0.028   0.004   TRP A1280 
 HIS   0.012   0.002   HIS A 528 
 PHE   0.037   0.005   PHE A1412 
 TYR   0.021   0.003   TYR A 190 
 ARG   0.017   0.001   ARG A 934 

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

*********************** 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  : 1.462 
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: 0.3332
  time to fit residues: 131.4422
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  : 1.161 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 144
   random chunks:
   chunk 121 optimal weight:    4.9990
   chunk 109 optimal weight:   20.0000
   chunk 60 optimal weight:    7.9990
   chunk 37 optimal weight:    0.0070
   chunk 73 optimal weight:    5.9990
   chunk 58 optimal weight:    4.9990
   chunk 112 optimal weight:    4.9990
   chunk 43 optimal weight:    2.9990
   chunk 68 optimal weight:    8.9990
   chunk 84 optimal weight:    0.9980
   chunk 130 optimal weight:    0.8980
   overall best weight:    1.9802

-------------------------------------------------------------------------------
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
** 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: 7

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3718 r_free = 0.3718 target = 0.113067 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 42)----------------|
| r_work = 0.3373 r_free = 0.3373 target = 0.092296 restraints weight = 50732.393|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 38)----------------|
| r_work = 0.3434 r_free = 0.3434 target = 0.095780 restraints weight = 24862.939|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 38)----------------|
| r_work = 0.3475 r_free = 0.3475 target = 0.098171 restraints weight = 15044.490|
|-----------------------------------------------------------------------------|
r_work (final): 0.3477
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3476
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3476 r_free = 0.3476    target_work(ls_wunit_k1) = 0.098         |
| occupancies: max = 1.00  min = 0.50   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3471 r_free = 0.3471    target_work(ls_wunit_k1) = 0.098         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:       12 |
|-----------------------------------------------------------------------------|
r_final: 0.3471
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7741
moved from start:          0.2774

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.058  11560  Z= 0.176
  Angle     :  0.874  17.906  15708  Z= 0.447
  Chirality :  0.048   0.304   1790
  Planarity :  0.006   0.071   2015
  Dihedral  : 13.051  88.877   1749
  Min Nonbonded Distance : 2.426

Molprobity Statistics.
  All-atom Clashscore : 11.55
  Ramachandran Plot:
    Outliers :  0.07 %
    Allowed  : 13.24 %
    Favored  : 86.69 %
  Rotamer:
    Outliers :  1.97 %
    Allowed  :  9.50 %
    Favored  : 88.54 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 1.92 %
    Cis-general     : 0.51 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -4.36 (0.19), residues: 1423
  helix: -1.78 (0.20), residues: 525
  sheet: -2.94 (0.30), residues: 226
  loop : -3.86 (0.19), residues: 672

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.024   0.002   TRP A 560 
 HIS   0.009   0.001   HIS A  76 
 PHE   0.023   0.002   PHE A 894 
 TYR   0.025   0.002   TYR A1141 
 ARG   0.010   0.001   ARG A1093 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03957 (  369)
  hydrogen bonds       : angle       6.50788 ( 1047)
  covalent geometry    : bond        0.00390 (11560)
  covalent geometry    : angle       0.87413 (15708)

*********************** 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
  222 residues out of total 1167 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 23
    poor density    : 199
  time to evaluate  : 1.293 
Fit side-chains
   revert: symmetry clash
REVERT: A   59 ARG cc_start: 0.8334 (mtt90) cc_final: 0.7830 (ttm-80)
REVERT: A  100 LYS cc_start: 0.8811 (mttt) cc_final: 0.8220 (tmmt)
REVERT: A  104 ASP cc_start: 0.8561 (m-30) cc_final: 0.8138 (m-30)
REVERT: A  118 GLU cc_start: 0.8253 (tt0) cc_final: 0.7814 (mm-30)
REVERT: A  183 THR cc_start: 0.5846 (p) cc_final: 0.5601 (p)
REVERT: A  202 GLU cc_start: 0.8359 (tp30) cc_final: 0.8131 (mm-30)
REVERT: A  402 GLN cc_start: 0.8406 (mp-120) cc_final: 0.7917 (mp10)
REVERT: A  654 MET cc_start: 0.8440 (mmm) cc_final: 0.7999 (mmp)
REVERT: A  772 ASN cc_start: 0.7321 (t0) cc_final: 0.6897 (t0)
REVERT: A  795 MET cc_start: 0.7490 (mtp) cc_final: 0.7232 (mtp)
REVERT: A  838 GLU cc_start: 0.8118 (tp30) cc_final: 0.7861 (tp30)
REVERT: A  934 ARG cc_start: 0.6216 (OUTLIER) cc_final: 0.5534 (ptt90)
REVERT: A  979 MET cc_start: 0.7967 (mtt) cc_final: 0.7339 (mpp)
REVERT: A 1011 MET cc_start: 0.8861 (ttt) cc_final: 0.8394 (tmm)
REVERT: A 1070 ASP cc_start: 0.7996 (p0) cc_final: 0.7582 (p0)
REVERT: A 1099 ASP cc_start: 0.6367 (t70) cc_final: 0.5806 (t70)
REVERT: A 1195 MET cc_start: 0.7812 (mmm) cc_final: 0.7385 (mmt)
REVERT: A 1226 GLN cc_start: 0.6392 (tp-100) cc_final: 0.5804 (tt0)
REVERT: A 1273 GLU cc_start: 0.8092 (tt0) cc_final: 0.7858 (tt0)
REVERT: A 1447 THR cc_start: 0.7349 (p) cc_final: 0.7128 (p)
REVERT: A 1453 TRP cc_start: 0.8415 (t60) cc_final: 0.8213 (t60)
REVERT: A 1459 ASN cc_start: 0.8436 (m110) cc_final: 0.8110 (m-40)
  outliers start: 23
  outliers final: 13
  residues processed: 211
  average time/residue: 0.2656
  time to fit residues: 77.5123
Evaluate side-chains
  157 residues out of total 1167 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 143
  time to evaluate  : 1.144 
-------------------------------------------------------------------------------
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  616 SER
Chi-restraints excluded: chain A residue  696 SER
Chi-restraints excluded: chain A residue  791 SER
Chi-restraints excluded: chain A residue  932 VAL
Chi-restraints excluded: chain A residue  934 ARG
Chi-restraints excluded: chain A residue  938 GLU
Chi-restraints excluded: chain A residue  988 THR
Chi-restraints excluded: chain A residue 1114 LEU
Chi-restraints excluded: chain A residue 1396 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 100 optimal weight:    0.9990
   chunk 78 optimal weight:    9.9990
   chunk 86 optimal weight:    0.0570
   chunk 118 optimal weight:    4.9990
   chunk 14 optimal weight:    9.9990
   chunk 131 optimal weight:    0.3980
   chunk 79 optimal weight:    0.8980
   chunk 77 optimal weight:    2.9990
   chunk 58 optimal weight:    9.9990
   chunk 89 optimal weight:    0.9990
   chunk 126 optimal weight:    9.9990
   overall best weight:    0.6702

-------------------------------------------------------------------------------
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**
** A1116 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A1292 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A1403 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 = 0.3756 r_free = 0.3756 target = 0.115167 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 43)----------------|
| r_work = 0.3442 r_free = 0.3442 target = 0.096119 restraints weight = 40531.537|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 28)----------------|
| r_work = 0.3497 r_free = 0.3497 target = 0.099312 restraints weight = 20758.789|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 36)----------------|
| r_work = 0.3533 r_free = 0.3533 target = 0.101471 restraints weight = 12911.757|
|-----------------------------------------------------------------------------|
r_work (final): 0.3535
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3533
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3533 r_free = 0.3533    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 = 0.3533 r_free = 0.3533    target_work(ls_wunit_k1) = 0.101         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:       12 |
|-----------------------------------------------------------------------------|
r_final: 0.3533
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7663
moved from start:          0.3588

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.044  11560  Z= 0.138
  Angle     :  0.804  17.726  15708  Z= 0.406
  Chirality :  0.045   0.227   1790
  Planarity :  0.005   0.065   2015
  Dihedral  : 12.706  88.475   1749
  Min Nonbonded Distance : 2.475

Molprobity Statistics.
  All-atom Clashscore : 10.84
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  : 12.61 %
    Favored  : 87.39 %
  Rotamer:
    Outliers :  1.97 %
    Allowed  : 11.55 %
    Favored  : 86.48 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 1.92 %
    Cis-general     : 0.51 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -3.61 (0.20), residues: 1423
  helix: -0.87 (0.22), residues: 520
  sheet: -2.43 (0.31), residues: 221
  loop : -3.72 (0.19), residues: 682

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.019   0.001   TRP A 702 
 HIS   0.005   0.001   HIS A 528 
 PHE   0.020   0.002   PHE A1112 
 TYR   0.015   0.002   TYR A1141 
 ARG   0.007   0.001   ARG A1093 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03538 (  369)
  hydrogen bonds       : angle       5.76258 ( 1047)
  covalent geometry    : bond        0.00299 (11560)
  covalent geometry    : angle       0.80404 (15708)

*********************** 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
  208 residues out of total 1167 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 23
    poor density    : 185
  time to evaluate  : 1.283 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   59 ARG cc_start: 0.8208 (mtt90) cc_final: 0.7915 (ttm-80)
REVERT: A  100 LYS cc_start: 0.8710 (mttt) cc_final: 0.8141 (tmmt)
REVERT: A  104 ASP cc_start: 0.8641 (m-30) cc_final: 0.8164 (m-30)
REVERT: A  118 GLU cc_start: 0.8118 (tt0) cc_final: 0.7846 (mm-30)
REVERT: A  183 THR cc_start: 0.5462 (p) cc_final: 0.5262 (p)
REVERT: A  226 MET cc_start: 0.8285 (mtt) cc_final: 0.8080 (mtt)
REVERT: A  486 LEU cc_start: 0.6086 (pp) cc_final: 0.5402 (tp)
REVERT: A  772 ASN cc_start: 0.7315 (t0) cc_final: 0.6764 (t0)
REVERT: A  884 MET cc_start: 0.6365 (mmm) cc_final: 0.6095 (mmm)
REVERT: A 1011 MET cc_start: 0.8803 (ttt) cc_final: 0.8452 (tmm)
REVERT: A 1033 MET cc_start: 0.7935 (mtp) cc_final: 0.7281 (mtp)
REVERT: A 1068 LEU cc_start: 0.8711 (OUTLIER) cc_final: 0.8471 (mm)
REVERT: A 1099 ASP cc_start: 0.6181 (t70) cc_final: 0.5403 (t0)
REVERT: A 1226 GLN cc_start: 0.6418 (tp-100) cc_final: 0.6145 (tt0)
REVERT: A 1270 ARG cc_start: 0.7559 (mtt180) cc_final: 0.7316 (mtt180)
REVERT: A 1392 GLN cc_start: 0.8509 (mm-40) cc_final: 0.7732 (mp10)
REVERT: A 1459 ASN cc_start: 0.8391 (m110) cc_final: 0.8112 (m-40)
  outliers start: 23
  outliers final: 9
  residues processed: 200
  average time/residue: 0.2643
  time to fit residues: 73.5531
Evaluate side-chains
  154 residues out of total 1167 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 144
  time to evaluate  : 1.207 
-------------------------------------------------------------------------------
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  812 VAL
Chi-restraints excluded: chain A residue  934 ARG
Chi-restraints excluded: chain A residue  974 ARG
Chi-restraints excluded: chain A residue 1065 THR
Chi-restraints excluded: chain A residue 1068 LEU
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=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 144
   random chunks:
   chunk 67 optimal weight:    9.9990
   chunk 26 optimal weight:   10.0000
   chunk 19 optimal weight:    0.9980
   chunk 75 optimal weight:    4.9990
   chunk 62 optimal weight:    9.9990
   chunk 50 optimal weight:    6.9990
   chunk 58 optimal weight:    5.9990
   chunk 47 optimal weight:    0.6980
   chunk 130 optimal weight:    9.9990
   chunk 48 optimal weight:    0.7980
   chunk 98 optimal weight:    1.9990
   overall best weight:    1.8984

-------------------------------------------------------------------------------
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 ** both conformations clash, **PLEASE CHECK MANUALLY**
A 780 HIS
A 856 GLN
** 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: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3718 r_free = 0.3718 target = 0.112684 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 43)----------------|
| r_work = 0.3373 r_free = 0.3373 target = 0.092195 restraints weight = 54733.273|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 39)----------------|
| r_work = 0.3436 r_free = 0.3436 target = 0.095760 restraints weight = 25966.520|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 34)----------------|
| r_work = 0.3477 r_free = 0.3477 target = 0.098152 restraints weight = 15341.291|
|-----------------------------------------------------------------------------|
r_work (final): 0.3477
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3477
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3477 r_free = 0.3477    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 = 0.3477 r_free = 0.3477    target_work(ls_wunit_k1) = 0.098         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:       12 |
|-----------------------------------------------------------------------------|
r_final: 0.3477
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7745
moved from start:          0.3933

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.038  11560  Z= 0.157
  Angle     :  0.806  16.738  15708  Z= 0.406
  Chirality :  0.046   0.181   1790
  Planarity :  0.005   0.064   2015
  Dihedral  : 12.591  89.299   1749
  Min Nonbonded Distance : 2.467

Molprobity Statistics.
  All-atom Clashscore : 12.13
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  : 12.89 %
    Favored  : 87.11 %
  Rotamer:
    Outliers :  2.40 %
    Allowed  : 12.66 %
    Favored  : 84.94 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 1.92 %
    Cis-general     : 0.51 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -3.29 (0.21), residues: 1423
  helix: -0.52 (0.23), residues: 522
  sheet: -2.35 (0.33), residues: 208
  loop : -3.58 (0.20), residues: 693

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.032   0.002   TRP A1170 
 HIS   0.007   0.001   HIS A 528 
 PHE   0.022   0.002   PHE A 894 
 TYR   0.016   0.002   TYR A1209 
 ARG   0.008   0.001   ARG A1146 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03385 (  369)
  hydrogen bonds       : angle       5.40885 ( 1047)
  covalent geometry    : bond        0.00351 (11560)
  covalent geometry    : angle       0.80562 (15708)

*********************** 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
  189 residues out of total 1167 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 28
    poor density    : 161
  time to evaluate  : 1.145 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   59 ARG cc_start: 0.8422 (mtt90) cc_final: 0.8000 (ttm-80)
REVERT: A  100 LYS cc_start: 0.8708 (mttt) cc_final: 0.8143 (tmmt)
REVERT: A  104 ASP cc_start: 0.8696 (m-30) cc_final: 0.8212 (m-30)
REVERT: A  118 GLU cc_start: 0.8252 (tt0) cc_final: 0.7918 (mm-30)
REVERT: A  183 THR cc_start: 0.5747 (p) cc_final: 0.5540 (p)
REVERT: A  486 LEU cc_start: 0.6352 (pp) cc_final: 0.5657 (tp)
REVERT: A  772 ASN cc_start: 0.7364 (t0) cc_final: 0.6850 (t0)
REVERT: A  884 MET cc_start: 0.6434 (mmm) cc_final: 0.6091 (mmm)
REVERT: A  934 ARG cc_start: 0.6156 (OUTLIER) cc_final: 0.5414 (ptt90)
REVERT: A 1011 MET cc_start: 0.8785 (ttt) cc_final: 0.8402 (ppp)
REVERT: A 1099 ASP cc_start: 0.6016 (t70) cc_final: 0.5698 (t70)
REVERT: A 1210 GLU cc_start: 0.8336 (mp0) cc_final: 0.7954 (mp0)
REVERT: A 1226 GLN cc_start: 0.6474 (tp-100) cc_final: 0.6258 (tt0)
REVERT: A 1392 GLN cc_start: 0.8576 (mm-40) cc_final: 0.7741 (mp10)
REVERT: A 1423 ARG cc_start: 0.6028 (ptm160) cc_final: 0.5454 (ttp-170)
REVERT: A 1451 GLN cc_start: 0.7197 (OUTLIER) cc_final: 0.6955 (tp40)
REVERT: A 1459 ASN cc_start: 0.8402 (m110) cc_final: 0.8180 (m-40)
  outliers start: 28
  outliers final: 14
  residues processed: 179
  average time/residue: 0.2614
  time to fit residues: 65.4974
Evaluate side-chains
  164 residues out of total 1167 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 148
  time to evaluate  : 1.302 
-------------------------------------------------------------------------------
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  532 VAL
Chi-restraints excluded: chain A residue  547 LEU
Chi-restraints excluded: chain A residue  791 SER
Chi-restraints excluded: chain A residue  812 VAL
Chi-restraints excluded: chain A residue  934 ARG
Chi-restraints excluded: chain A residue 1009 VAL
Chi-restraints excluded: chain A residue 1065 THR
Chi-restraints excluded: chain A residue 1114 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 1396 LEU
Chi-restraints excluded: chain A residue 1451 GLN
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 144
   random chunks:
   chunk 71 optimal weight:    7.9990
   chunk 83 optimal weight:    0.9980
   chunk 7 optimal weight:    0.8980
   chunk 16 optimal weight:    9.9990
   chunk 79 optimal weight:   10.0000
   chunk 112 optimal weight:    2.9990
   chunk 100 optimal weight:    0.0970
   chunk 5 optimal weight:    3.9990
   chunk 84 optimal weight:    4.9990
   chunk 103 optimal weight:    3.9990
   chunk 80 optimal weight:    0.8980
   overall best weight:    1.1780

-------------------------------------------------------------------------------
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**
** 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 = 0.3740 r_free = 0.3740 target = 0.113998 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 38)----------------|
| r_work = 0.3380 r_free = 0.3380 target = 0.092495 restraints weight = 70252.530|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 34)----------------|
| r_work = 0.3451 r_free = 0.3451 target = 0.096509 restraints weight = 30274.023|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 29)----------------|
| r_work = 0.3499 r_free = 0.3499 target = 0.099209 restraints weight = 16915.128|
|-----------------------------------------------------------------------------|
r_work (final): 0.3500
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3499
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3499 r_free = 0.3499    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 = 0.3499 r_free = 0.3499    target_work(ls_wunit_k1) = 0.099         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:       12 |
|-----------------------------------------------------------------------------|
r_final: 0.3499
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7716
moved from start:          0.4252

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.061  11560  Z= 0.135
  Angle     :  0.791  15.437  15708  Z= 0.395
  Chirality :  0.044   0.191   1790
  Planarity :  0.005   0.065   2015
  Dihedral  : 12.475  89.884   1749
  Min Nonbonded Distance : 2.446

Molprobity Statistics.
  All-atom Clashscore : 11.42
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  : 12.11 %
    Favored  : 87.89 %
  Rotamer:
    Outliers :  2.14 %
    Allowed  : 13.43 %
    Favored  : 84.43 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 1.92 %
    Cis-general     : 0.51 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -3.02 (0.21), residues: 1423
  helix: -0.22 (0.23), residues: 524
  sheet: -2.20 (0.33), residues: 218
  loop : -3.50 (0.20), residues: 681

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.056   0.003   TRP A1453 
 HIS   0.006   0.001   HIS A 528 
 PHE   0.018   0.002   PHE A1412 
 TYR   0.010   0.001   TYR A 213 
 ARG   0.005   0.001   ARG A1093 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03221 (  369)
  hydrogen bonds       : angle       5.25463 ( 1047)
  covalent geometry    : bond        0.00303 (11560)
  covalent geometry    : angle       0.79118 (15708)

*********************** 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
  190 residues out of total 1167 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 25
    poor density    : 165
  time to evaluate  : 1.370 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   59 ARG cc_start: 0.8434 (mtt90) cc_final: 0.7942 (ttm-80)
REVERT: A  100 LYS cc_start: 0.8654 (mttt) cc_final: 0.8111 (tmmt)
REVERT: A  104 ASP cc_start: 0.8668 (m-30) cc_final: 0.8166 (m-30)
REVERT: A  118 GLU cc_start: 0.8142 (tt0) cc_final: 0.7888 (mm-30)
REVERT: A  183 THR cc_start: 0.5574 (p) cc_final: 0.5346 (p)
REVERT: A  486 LEU cc_start: 0.6375 (pp) cc_final: 0.5843 (tp)
REVERT: A  772 ASN cc_start: 0.7309 (t0) cc_final: 0.6797 (t0)
REVERT: A  884 MET cc_start: 0.6352 (mmm) cc_final: 0.6052 (mmm)
REVERT: A  934 ARG cc_start: 0.5930 (OUTLIER) cc_final: 0.5375 (ptt90)
REVERT: A  978 ARG cc_start: 0.8467 (ttt180) cc_final: 0.8060 (ttm170)
REVERT: A  979 MET cc_start: 0.7973 (mtt) cc_final: 0.7594 (mmm)
REVERT: A  985 ASP cc_start: 0.7796 (t70) cc_final: 0.7097 (m-30)
REVERT: A 1011 MET cc_start: 0.8732 (ttt) cc_final: 0.8165 (tmm)
REVERT: A 1099 ASP cc_start: 0.5924 (t70) cc_final: 0.5415 (t0)
REVERT: A 1210 GLU cc_start: 0.8206 (mp0) cc_final: 0.7842 (mp0)
REVERT: A 1392 GLN cc_start: 0.8526 (mm-40) cc_final: 0.7747 (mp10)
REVERT: A 1423 ARG cc_start: 0.5941 (ptm160) cc_final: 0.5451 (ttp-170)
  outliers start: 25
  outliers final: 15
  residues processed: 183
  average time/residue: 0.2743
  time to fit residues: 70.8814
Evaluate side-chains
  159 residues out of total 1167 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 143
  time to evaluate  : 1.288 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  347 LEU
Chi-restraints excluded: chain A residue  449 VAL
Chi-restraints excluded: chain A residue  469 ASP
Chi-restraints excluded: chain A residue  503 SER
Chi-restraints excluded: chain A residue  547 LEU
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  934 ARG
Chi-restraints excluded: chain A residue 1009 VAL
Chi-restraints excluded: chain A residue 1065 THR
Chi-restraints excluded: chain A residue 1114 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 1396 LEU
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 144
   random chunks:
   chunk 122 optimal weight:    9.9990
   chunk 127 optimal weight:    6.9990
   chunk 132 optimal weight:    2.9990
   chunk 112 optimal weight:    7.9990
   chunk 68 optimal weight:   10.0000
   chunk 46 optimal weight:    1.9990
   chunk 17 optimal weight:   10.0000
   chunk 30 optimal weight:    3.9990
   chunk 131 optimal weight:    6.9990
   chunk 8 optimal weight:    0.9990
   chunk 15 optimal weight:    9.9990
   overall best weight:    3.3990

-------------------------------------------------------------------------------
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 509 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 529 ASN
** A 794 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 ** 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 = 0.3658 r_free = 0.3658 target = 0.108873 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 34)----------------|
| r_work = 0.3287 r_free = 0.3287 target = 0.087488 restraints weight = 76787.754|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 31)----------------|
| r_work = 0.3379 r_free = 0.3379 target = 0.092752 restraints weight = 31689.977|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 32)----------------|
| r_work = 0.3414 r_free = 0.3414 target = 0.094804 restraints weight = 14566.658|
|-----------------------------------------------------------------------------|
r_work (final): 0.3415
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3415
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3415 r_free = 0.3415    target_work(ls_wunit_k1) = 0.094         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:       12 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3415 r_free = 0.3415    target_work(ls_wunit_k1) = 0.094         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:       12 |
|-----------------------------------------------------------------------------|
r_final: 0.3415
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7833
moved from start:          0.4305

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.060  11560  Z= 0.209
  Angle     :  0.850  14.406  15708  Z= 0.429
  Chirality :  0.047   0.190   1790
  Planarity :  0.005   0.063   2015
  Dihedral  : 12.636  87.962   1749
  Min Nonbonded Distance : 2.483

Molprobity Statistics.
  All-atom Clashscore : 13.42
  Ramachandran Plot:
    Outliers :  0.14 %
    Allowed  : 13.94 %
    Favored  : 85.92 %
  Rotamer:
    Outliers :  2.40 %
    Allowed  : 14.37 %
    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 (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -2.99 (0.21), residues: 1423
  helix: -0.22 (0.23), residues: 531
  sheet: -2.20 (0.32), residues: 229
  loop : -3.50 (0.21), residues: 663

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.040   0.002   TRP A1170 
 HIS   0.009   0.001   HIS A 528 
 PHE   0.032   0.002   PHE A 894 
 TYR   0.013   0.002   TYR A1398 
 ARG   0.007   0.001   ARG A1146 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03461 (  369)
  hydrogen bonds       : angle       5.30663 ( 1047)
  covalent geometry    : bond        0.00472 (11560)
  covalent geometry    : angle       0.84952 (15708)

*********************** 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
  171 residues out of total 1167 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 28
    poor density    : 143
  time to evaluate  : 1.128 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   59 ARG cc_start: 0.8471 (mtt90) cc_final: 0.7988 (ttm-80)
REVERT: A   92 MET cc_start: 0.8736 (ttp) cc_final: 0.8415 (tmm)
REVERT: A  100 LYS cc_start: 0.8702 (mttt) cc_final: 0.8094 (tmmt)
REVERT: A  104 ASP cc_start: 0.8670 (m-30) cc_final: 0.8174 (m-30)
REVERT: A  118 GLU cc_start: 0.8233 (tt0) cc_final: 0.7996 (mm-30)
REVERT: A  183 THR cc_start: 0.6025 (p) cc_final: 0.5805 (p)
REVERT: A  486 LEU cc_start: 0.6327 (pp) cc_final: 0.5730 (tp)
REVERT: A  631 MET cc_start: 0.8184 (tpt) cc_final: 0.7581 (tpt)
REVERT: A  772 ASN cc_start: 0.7688 (t0) cc_final: 0.7174 (t0)
REVERT: A  884 MET cc_start: 0.6165 (mmm) cc_final: 0.5848 (mmm)
REVERT: A  934 ARG cc_start: 0.6314 (OUTLIER) cc_final: 0.5700 (ptt90)
REVERT: A  978 ARG cc_start: 0.8613 (ttt180) cc_final: 0.8376 (ttm170)
REVERT: A  979 MET cc_start: 0.8048 (mtt) cc_final: 0.7656 (mmm)
REVERT: A 1011 MET cc_start: 0.8791 (ttt) cc_final: 0.8383 (ppp)
REVERT: A 1167 GLU cc_start: 0.8101 (pt0) cc_final: 0.7320 (tm-30)
REVERT: A 1210 GLU cc_start: 0.8262 (mp0) cc_final: 0.7864 (mp0)
  outliers start: 28
  outliers final: 18
  residues processed: 161
  average time/residue: 0.3196
  time to fit residues: 73.0101
Evaluate side-chains
  155 residues out of total 1167 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 19
    poor density    : 136
  time to evaluate  : 1.216 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  449 VAL
Chi-restraints excluded: chain A residue  469 ASP
Chi-restraints excluded: chain A residue  503 SER
Chi-restraints excluded: chain A residue  532 VAL
Chi-restraints excluded: chain A residue  547 LEU
Chi-restraints excluded: chain A residue  571 ILE
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  934 ARG
Chi-restraints excluded: chain A residue 1009 VAL
Chi-restraints excluded: chain A residue 1065 THR
Chi-restraints excluded: chain A residue 1114 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 1396 LEU
Chi-restraints excluded: chain A residue 1429 PHE
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 144
   random chunks:
   chunk 65 optimal weight:    3.9990
   chunk 46 optimal weight:    5.9990
   chunk 0 optimal weight:   10.0000
   chunk 61 optimal weight:    0.8980
   chunk 111 optimal weight:    0.0050
   chunk 72 optimal weight:    4.9990
   chunk 42 optimal weight:   10.0000
   chunk 137 optimal weight:    0.9980
   chunk 70 optimal weight:    0.7980
   chunk 78 optimal weight:    0.6980
   chunk 106 optimal weight:    1.9990
   overall best weight:    0.6794

-------------------------------------------------------------------------------
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**
** 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

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3738 r_free = 0.3738 target = 0.113977 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 44)----------------|
| r_work = 0.3396 r_free = 0.3396 target = 0.093389 restraints weight = 56733.498|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 39)----------------|
| r_work = 0.3459 r_free = 0.3459 target = 0.097064 restraints weight = 26289.880|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 36)----------------|
| r_work = 0.3502 r_free = 0.3502 target = 0.099542 restraints weight = 15398.915|
|-----------------------------------------------------------------------------|
r_work (final): 0.3503
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3503
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3503 r_free = 0.3503    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 = 0.3503 r_free = 0.3503    target_work(ls_wunit_k1) = 0.099         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:       12 |
|-----------------------------------------------------------------------------|
r_final: 0.3503
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7709
moved from start:          0.4660

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.045  11560  Z= 0.129
  Angle     :  0.790  17.041  15708  Z= 0.394
  Chirality :  0.044   0.181   1790
  Planarity :  0.005   0.065   2015
  Dihedral  : 12.393  87.726   1749
  Min Nonbonded Distance : 2.466

Molprobity Statistics.
  All-atom Clashscore : 10.97
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  : 11.69 %
    Favored  : 88.31 %
  Rotamer:
    Outliers :  1.88 %
    Allowed  : 14.29 %
    Favored  : 83.83 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 1.92 %
    Cis-general     : 0.51 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -2.75 (0.22), residues: 1423
  helix: -0.00 (0.23), residues: 525
  sheet: -2.19 (0.32), residues: 222
  loop : -3.29 (0.22), residues: 676

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.054   0.002   TRP A1170 
 HIS   0.005   0.001   HIS A 528 
 PHE   0.018   0.002   PHE A1412 
 TYR   0.010   0.001   TYR A1209 
 ARG   0.006   0.000   ARG A 694 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03078 (  369)
  hydrogen bonds       : angle       5.04293 ( 1047)
  covalent geometry    : bond        0.00286 (11560)
  covalent geometry    : angle       0.79027 (15708)

*********************** 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
  183 residues out of total 1167 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 22
    poor density    : 161
  time to evaluate  : 1.449 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   92 MET cc_start: 0.8700 (ttp) cc_final: 0.8388 (tmm)
REVERT: A  100 LYS cc_start: 0.8590 (mttt) cc_final: 0.8104 (tmmt)
REVERT: A  104 ASP cc_start: 0.8692 (m-30) cc_final: 0.8165 (m-30)
REVERT: A  118 GLU cc_start: 0.8090 (tt0) cc_final: 0.7796 (mm-30)
REVERT: A  183 THR cc_start: 0.5476 (p) cc_final: 0.5261 (p)
REVERT: A  278 MET cc_start: 0.8062 (tmm) cc_final: 0.7788 (tmm)
REVERT: A  486 LEU cc_start: 0.6232 (pp) cc_final: 0.5772 (tp)
REVERT: A  631 MET cc_start: 0.8185 (tpt) cc_final: 0.7571 (tpt)
REVERT: A  772 ASN cc_start: 0.7500 (t0) cc_final: 0.6886 (t0)
REVERT: A  884 MET cc_start: 0.6376 (mmm) cc_final: 0.6026 (mmm)
REVERT: A  934 ARG cc_start: 0.5860 (OUTLIER) cc_final: 0.5266 (ptt90)
REVERT: A  960 ARG cc_start: 0.5938 (tpt-90) cc_final: 0.5513 (mmm-85)
REVERT: A  974 ARG cc_start: 0.7224 (tpt170) cc_final: 0.6914 (tpt170)
REVERT: A  985 ASP cc_start: 0.7936 (t70) cc_final: 0.7276 (m-30)
REVERT: A 1137 ARG cc_start: 0.7278 (tpt-90) cc_final: 0.6488 (mmt90)
REVERT: A 1167 GLU cc_start: 0.7970 (pt0) cc_final: 0.7293 (tm-30)
REVERT: A 1210 GLU cc_start: 0.7893 (mp0) cc_final: 0.7426 (mp0)
REVERT: A 1392 GLN cc_start: 0.8406 (mm-40) cc_final: 0.7647 (mp10)
  outliers start: 22
  outliers final: 14
  residues processed: 173
  average time/residue: 0.3702
  time to fit residues: 91.4659
Evaluate side-chains
  161 residues out of total 1167 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 15
    poor density    : 146
  time to evaluate  : 1.679 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  347 LEU
Chi-restraints excluded: chain A residue  449 VAL
Chi-restraints excluded: chain A residue  503 SER
Chi-restraints excluded: chain A residue  547 LEU
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  934 ARG
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 1114 LEU
Chi-restraints excluded: chain A residue 1318 LEU
Chi-restraints excluded: chain A residue 1396 LEU
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 51 optimal weight:    2.9990
   chunk 6 optimal weight:    2.9990
   chunk 109 optimal weight:    3.9990
   chunk 121 optimal weight:    0.0970
   chunk 33 optimal weight:    3.9990
   chunk 37 optimal weight:    7.9990
   chunk 77 optimal weight:    5.9990
   chunk 3 optimal weight:   10.0000
   chunk 113 optimal weight:    6.9990
   chunk 54 optimal weight:    0.7980
   chunk 124 optimal weight:    2.9990
   overall best weight:    1.9784

-------------------------------------------------------------------------------
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 794 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 856 GLN
** A1116 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 = 0.3702 r_free = 0.3702 target = 0.111757 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 42)----------------|
| r_work = 0.3375 r_free = 0.3375 target = 0.092219 restraints weight = 45576.267|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 28)----------------|
| r_work = 0.3431 r_free = 0.3431 target = 0.095481 restraints weight = 22855.360|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 41)----------------|
| r_work = 0.3470 r_free = 0.3470 target = 0.097687 restraints weight = 14071.047|
|-----------------------------------------------------------------------------|
r_work (final): 0.3470
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3471
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3471 r_free = 0.3471    target_work(ls_wunit_k1) = 0.097         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:       12 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3470 r_free = 0.3470    target_work(ls_wunit_k1) = 0.097         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:       12 |
|-----------------------------------------------------------------------------|
r_final: 0.3470
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7760
moved from start:          0.4755

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.049  11560  Z= 0.157
  Angle     :  0.808  14.722  15708  Z= 0.404
  Chirality :  0.046   0.193   1790
  Planarity :  0.005   0.063   2015
  Dihedral  : 12.419  86.311   1749
  Min Nonbonded Distance : 2.435

Molprobity Statistics.
  All-atom Clashscore : 11.99
  Ramachandran Plot:
    Outliers :  0.07 %
    Allowed  : 13.24 %
    Favored  : 86.69 %
  Rotamer:
    Outliers :  1.88 %
    Allowed  : 15.40 %
    Favored  : 82.72 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 1.92 %
    Cis-general     : 0.51 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -2.72 (0.22), residues: 1423
  helix:  0.01 (0.23), residues: 526
  sheet: -2.12 (0.32), residues: 228
  loop : -3.29 (0.22), residues: 669

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.056   0.002   TRP A1170 
 HIS   0.015   0.001   HIS A  76 
 PHE   0.021   0.002   PHE A 894 
 TYR   0.025   0.002   TYR A 937 
 ARG   0.011   0.001   ARG A 298 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03274 (  369)
  hydrogen bonds       : angle       5.08350 ( 1047)
  covalent geometry    : bond        0.00356 (11560)
  covalent geometry    : angle       0.80825 (15708)

*********************** 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
  172 residues out of total 1167 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 22
    poor density    : 150
  time to evaluate  : 2.189 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   92 MET cc_start: 0.8702 (ttp) cc_final: 0.8379 (tmm)
REVERT: A  100 LYS cc_start: 0.8581 (mttt) cc_final: 0.8120 (tmmt)
REVERT: A  104 ASP cc_start: 0.8685 (m-30) cc_final: 0.8175 (m-30)
REVERT: A  118 GLU cc_start: 0.8230 (tt0) cc_final: 0.7939 (mm-30)
REVERT: A  183 THR cc_start: 0.5599 (p) cc_final: 0.5382 (p)
REVERT: A  278 MET cc_start: 0.8005 (tmm) cc_final: 0.7648 (tmm)
REVERT: A  486 LEU cc_start: 0.6247 (pp) cc_final: 0.5786 (tp)
REVERT: A  631 MET cc_start: 0.8173 (tpt) cc_final: 0.7482 (tpt)
REVERT: A  772 ASN cc_start: 0.7627 (t0) cc_final: 0.7052 (t0)
REVERT: A  884 MET cc_start: 0.6273 (mmm) cc_final: 0.5846 (mmm)
REVERT: A  934 ARG cc_start: 0.6174 (OUTLIER) cc_final: 0.5624 (ptt90)
REVERT: A  960 ARG cc_start: 0.6121 (tpt-90) cc_final: 0.5542 (mmm-85)
REVERT: A  985 ASP cc_start: 0.7892 (t70) cc_final: 0.7224 (m-30)
REVERT: A 1099 ASP cc_start: 0.5606 (t0) cc_final: 0.5383 (t0)
REVERT: A 1137 ARG cc_start: 0.7373 (tpt-90) cc_final: 0.6574 (mmt90)
REVERT: A 1167 GLU cc_start: 0.8061 (pt0) cc_final: 0.7553 (tm-30)
REVERT: A 1210 GLU cc_start: 0.7935 (mp0) cc_final: 0.7487 (mp0)
REVERT: A 1392 GLN cc_start: 0.8360 (mm-40) cc_final: 0.7589 (mp10)
  outliers start: 22
  outliers final: 14
  residues processed: 166
  average time/residue: 0.3823
  time to fit residues: 92.5316
Evaluate side-chains
  156 residues out of total 1167 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 15
    poor density    : 141
  time to evaluate  : 2.920 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  469 ASP
Chi-restraints excluded: chain A residue  503 SER
Chi-restraints excluded: chain A residue  547 LEU
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  930 LEU
Chi-restraints excluded: chain A residue  934 ARG
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 1182 SER
Chi-restraints excluded: chain A residue 1318 LEU
Chi-restraints excluded: chain A residue 1396 LEU
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 39 optimal weight:    4.9990
   chunk 29 optimal weight:    0.9990
   chunk 89 optimal weight:   10.0000
   chunk 78 optimal weight:    0.0570
   chunk 77 optimal weight:    0.9990
   chunk 17 optimal weight:    8.9990
   chunk 109 optimal weight:    0.9980
   chunk 42 optimal weight:    0.1980
   chunk 114 optimal weight:    3.9990
   chunk 84 optimal weight:    0.9990
   chunk 30 optimal weight:    0.7980
   overall best weight:    0.6100

-------------------------------------------------------------------------------
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**
** 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 = 0.3763 r_free = 0.3763 target = 0.115641 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 45)----------------|
| r_work = 0.3430 r_free = 0.3430 target = 0.095343 restraints weight = 59961.040|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 26)----------------|
| r_work = 0.3493 r_free = 0.3493 target = 0.099018 restraints weight = 27794.200|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 37)----------------|
| r_work = 0.3535 r_free = 0.3535 target = 0.101565 restraints weight = 16229.848|
|-----------------------------------------------------------------------------|
r_work (final): 0.3537
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3537
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3537 r_free = 0.3537    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 = 0.3537 r_free = 0.3537    target_work(ls_wunit_k1) = 0.101         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:       12 |
|-----------------------------------------------------------------------------|
r_final: 0.3537
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7666
moved from start:          0.5099

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.046  11560  Z= 0.128
  Angle     :  0.786  17.099  15708  Z= 0.391
  Chirality :  0.044   0.193   1790
  Planarity :  0.005   0.071   2015
  Dihedral  : 12.215  89.110   1749
  Min Nonbonded Distance : 2.463

Molprobity Statistics.
  All-atom Clashscore : 10.62
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  : 11.55 %
    Favored  : 88.45 %
  Rotamer:
    Outliers :  1.71 %
    Allowed  : 15.74 %
    Favored  : 82.55 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 1.92 %
    Cis-general     : 0.51 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -2.51 (0.22), residues: 1423
  helix:  0.10 (0.23), residues: 529
  sheet: -1.80 (0.35), residues: 202
  loop : -3.16 (0.22), residues: 692

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.038   0.002   TRP A1170 
 HIS   0.005   0.001   HIS A 528 
 PHE   0.017   0.001   PHE A1412 
 TYR   0.026   0.001   TYR A 937 
 ARG   0.017   0.001   ARG A 974 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.02972 (  369)
  hydrogen bonds       : angle       4.88845 ( 1047)
  covalent geometry    : bond        0.00285 (11560)
  covalent geometry    : angle       0.78589 (15708)

*********************** 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
  190 residues out of total 1167 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 20
    poor density    : 170
  time to evaluate  : 2.377 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  278 MET cc_start: 0.8007 (tmm) cc_final: 0.7628 (tmm)
REVERT: A  478 GLN cc_start: 0.7891 (mp10) cc_final: 0.7649 (pt0)
REVERT: A  486 LEU cc_start: 0.6105 (pp) cc_final: 0.5648 (tp)
REVERT: A  631 MET cc_start: 0.8168 (tpt) cc_final: 0.7491 (tpt)
REVERT: A  772 ASN cc_start: 0.7475 (t0) cc_final: 0.6895 (t0)
REVERT: A  884 MET cc_start: 0.6186 (mmm) cc_final: 0.5841 (mmm)
REVERT: A  934 ARG cc_start: 0.5781 (OUTLIER) cc_final: 0.5118 (ptt90)
REVERT: A  974 ARG cc_start: 0.6952 (tpt170) cc_final: 0.6622 (tmt-80)
REVERT: A  985 ASP cc_start: 0.7871 (t70) cc_final: 0.7293 (m-30)
REVERT: A 1070 ASP cc_start: 0.8226 (p0) cc_final: 0.7737 (p0)
REVERT: A 1137 ARG cc_start: 0.7226 (tpt-90) cc_final: 0.6543 (mmt90)
REVERT: A 1182 SER cc_start: 0.6673 (OUTLIER) cc_final: 0.6224 (p)
REVERT: A 1210 GLU cc_start: 0.7691 (mp0) cc_final: 0.7236 (mp0)
REVERT: A 1238 ARG cc_start: 0.7514 (ttm-80) cc_final: 0.7149 (ttt-90)
REVERT: A 1345 MET cc_start: 0.8353 (tpp) cc_final: 0.7982 (mmt)
REVERT: A 1392 GLN cc_start: 0.8191 (mm-40) cc_final: 0.7653 (mp10)
REVERT: A 1425 LEU cc_start: 0.6872 (mm) cc_final: 0.6600 (mt)
  outliers start: 20
  outliers final: 13
  residues processed: 182
  average time/residue: 0.4060
  time to fit residues: 104.5259
Evaluate side-chains
  166 residues out of total 1167 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 15
    poor density    : 151
  time to evaluate  : 1.072 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   23 TYR
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  934 ARG
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 1114 LEU
Chi-restraints excluded: chain A residue 1182 SER
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 125 optimal weight:    7.9990
   chunk 103 optimal weight:    1.9990
   chunk 56 optimal weight:    2.9990
   chunk 16 optimal weight:    2.9990
   chunk 12 optimal weight:    8.9990
   chunk 105 optimal weight:    9.9990
   chunk 53 optimal weight:    3.9990
   chunk 94 optimal weight:    9.9990
   chunk 42 optimal weight:    4.9990
   chunk 29 optimal weight:    0.9980
   chunk 132 optimal weight:    0.0980
   overall best weight:    1.8186

-------------------------------------------------------------------------------
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 317 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 528 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 794 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 = 0.3728 r_free = 0.3728 target = 0.113542 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 40)----------------|
| r_work = 0.3381 r_free = 0.3381 target = 0.092581 restraints weight = 63827.574|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 37)----------------|
| r_work = 0.3446 r_free = 0.3446 target = 0.096295 restraints weight = 29093.637|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 40)----------------|
| r_work = 0.3490 r_free = 0.3490 target = 0.098850 restraints weight = 16891.449|
|-----------------------------------------------------------------------------|
r_work (final): 0.3489
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3489
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3489 r_free = 0.3489    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 = 0.3489 r_free = 0.3489    target_work(ls_wunit_k1) = 0.099         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:       12 |
|-----------------------------------------------------------------------------|
r_final: 0.3489
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7732
moved from start:          0.5157

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.052  11560  Z= 0.150
  Angle     :  0.817  16.442  15708  Z= 0.405
  Chirality :  0.045   0.183   1790
  Planarity :  0.005   0.064   2015
  Dihedral  : 12.265  88.076   1749
  Min Nonbonded Distance : 2.443

Molprobity Statistics.
  All-atom Clashscore : 11.33
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  : 11.97 %
    Favored  : 88.03 %
  Rotamer:
    Outliers :  1.71 %
    Allowed  : 16.60 %
    Favored  : 81.69 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 1.92 %
    Cis-general     : 0.51 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -2.48 (0.22), residues: 1423
  helix:  0.16 (0.23), residues: 527
  sheet: -1.79 (0.36), residues: 200
  loop : -3.17 (0.22), residues: 696

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.040   0.002   TRP A1170 
 HIS   0.007   0.001   HIS A 528 
 PHE   0.020   0.002   PHE A 894 
 TYR   0.023   0.002   TYR A 937 
 ARG   0.008   0.001   ARG A 974 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03088 (  369)
  hydrogen bonds       : angle       4.94024 ( 1047)
  covalent geometry    : bond        0.00344 (11560)
  covalent geometry    : angle       0.81744 (15708)

********************** 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
  175 residues out of total 1167 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 20
    poor density    : 155
  time to evaluate  : 1.354 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   59 ARG cc_start: 0.8228 (mtt90) cc_final: 0.7932 (ttm-80)
REVERT: A   93 MET cc_start: 0.8241 (mmm) cc_final: 0.7917 (mmm)
REVERT: A  278 MET cc_start: 0.7974 (tmm) cc_final: 0.7630 (tmm)
REVERT: A  478 GLN cc_start: 0.7924 (mp10) cc_final: 0.7680 (pt0)
REVERT: A  486 LEU cc_start: 0.6093 (pp) cc_final: 0.5640 (tp)
REVERT: A  631 MET cc_start: 0.8175 (tpt) cc_final: 0.7545 (tpt)
REVERT: A  772 ASN cc_start: 0.7623 (t0) cc_final: 0.7064 (t0)
REVERT: A  884 MET cc_start: 0.6304 (mmm) cc_final: 0.5966 (mmm)
REVERT: A  934 ARG cc_start: 0.5889 (OUTLIER) cc_final: 0.5471 (ptt90)
REVERT: A  979 MET cc_start: 0.7650 (mmm) cc_final: 0.6885 (mpp)
REVERT: A  985 ASP cc_start: 0.7839 (t70) cc_final: 0.7239 (m-30)
REVERT: A 1070 ASP cc_start: 0.8293 (p0) cc_final: 0.7763 (p0)
REVERT: A 1182 SER cc_start: 0.6687 (OUTLIER) cc_final: 0.6230 (p)
REVERT: A 1210 GLU cc_start: 0.7894 (mp0) cc_final: 0.7488 (mp0)
REVERT: A 1238 ARG cc_start: 0.7586 (ttm-80) cc_final: 0.7215 (ttt-90)
REVERT: A 1345 MET cc_start: 0.8355 (tpp) cc_final: 0.7979 (mmt)
REVERT: A 1392 GLN cc_start: 0.8277 (mm-40) cc_final: 0.7676 (mp10)
REVERT: A 1425 LEU cc_start: 0.6961 (mm) cc_final: 0.6667 (mt)
  outliers start: 20
  outliers final: 13
  residues processed: 166
  average time/residue: 0.3132
  time to fit residues: 76.0510
Evaluate side-chains
  163 residues out of total 1167 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 15
    poor density    : 148
  time to evaluate  : 1.441 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   23 TYR
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  934 ARG
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 1114 LEU
Chi-restraints excluded: chain A residue 1182 SER
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 124 optimal weight:    5.9990
   chunk 88 optimal weight:    6.9990
   chunk 48 optimal weight:    5.9990
   chunk 115 optimal weight:    8.9990
   chunk 63 optimal weight:    4.9990
   chunk 104 optimal weight:    5.9990
   chunk 33 optimal weight:    1.9990
   chunk 17 optimal weight:    5.9990
   chunk 11 optimal weight:    0.4980
   chunk 128 optimal weight:    0.0050
   chunk 40 optimal weight:    5.9990
   overall best weight:    2.7000

-------------------------------------------------------------------------------
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 528 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 794 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 861 HIS
** A1292 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A1295 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
A1467 HIS

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3687 r_free = 0.3687 target = 0.111092 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 41)----------------|
| r_work = 0.3338 r_free = 0.3338 target = 0.090293 restraints weight = 59793.191|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 34)----------------|
| r_work = 0.3400 r_free = 0.3400 target = 0.093815 restraints weight = 28343.171|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 42)----------------|
| r_work = 0.3443 r_free = 0.3443 target = 0.096258 restraints weight = 16877.017|
|-----------------------------------------------------------------------------|
r_work (final): 0.3444
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3444
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3444 r_free = 0.3444    target_work(ls_wunit_k1) = 0.096         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:       12 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3444 r_free = 0.3444    target_work(ls_wunit_k1) = 0.096         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:       12 |
|-----------------------------------------------------------------------------|
r_final: 0.3444
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7791
moved from start:          0.5189

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= 0.182
  Angle     :  0.844  15.820  15708  Z= 0.423
  Chirality :  0.047   0.173   1790
  Planarity :  0.005   0.085   2015
  Dihedral  : 12.384  86.944   1749
  Min Nonbonded Distance : 2.412

Molprobity Statistics.
  All-atom Clashscore : 13.24
  Ramachandran Plot:
    Outliers :  0.07 %
    Allowed  : 12.68 %
    Favored  : 87.25 %
  Rotamer:
    Outliers :  1.71 %
    Allowed  : 16.85 %
    Favored  : 81.44 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 1.92 %
    Cis-general     : 0.51 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -2.60 (0.22), residues: 1423
  helix:  0.04 (0.23), residues: 532
  sheet: -1.75 (0.35), residues: 210
  loop : -3.29 (0.22), residues: 681

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.042   0.002   TRP A1170 
 HIS   0.006   0.001   HIS A1467 
 PHE   0.037   0.002   PHE A 499 
 TYR   0.021   0.002   TYR A 937 
 ARG   0.010   0.001   ARG A 974 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03283 (  369)
  hydrogen bonds       : angle       4.99659 ( 1047)
  covalent geometry    : bond        0.00414 (11560)
  covalent geometry    : angle       0.84442 (15708)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 4606.33 seconds
wall clock time: 85 minutes 32.46 seconds (5132.46 seconds total)