Starting phenix.real_space_refine
on Fri Feb 14 10:54:07 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/6uz3_20951/02_2025/6uz3_20951.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/6uz3_20951/02_2025/6uz3_20951.map

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

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

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/cci-nas-00/data/ceres_data/6uz3_20951/02_2025/6uz3_20951.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/6uz3_20951/02_2025/6uz3_20951.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/6uz3_20951/02_2025/6uz3_20951.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/6uz3_20951/02_2025/6uz3_20951.cif"
  }
  resolution = 3.5
  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=   0.024 sd=   0.849
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       5      5.49       5
     S      67      5.16       5
     C    6309      2.51       5
     N    1424      2.21       5
     O    1641      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 11 residue(s): 0.03s

  Monomer Library directory:
    "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5592/modules/chem_data/mon_lib"
  Total number of atoms: 9446
  Number of models: 1
  Model: ""
    Number of chains: 5
    Chain: "A"
      Number of atoms: 8887
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 1126, 8887
          Classifications: {'peptide': 1126}
          Incomplete info: {'truncation_to_alanine': 41}
          Link IDs: {'CIS': 1, 'PCIS': 1, 'PTRANS': 28, 'TRANS': 1095}
          Chain breaks: 7
          Unresolved non-hydrogen bonds: 169
          Unresolved non-hydrogen angles: 201
          Unresolved non-hydrogen dihedrals: 148
          Unresolved non-hydrogen chiralities: 6
          Planarities with less than four sites: {'GLN:plan1': 2, 'HIS:plan': 1, 'TYR:plan': 1, 'ASN:plan1': 2, 'ASP:plan': 2, 'PHE:plan': 3, 'GLU:plan': 6, 'ARG:plan': 3}
          Unresolved non-hydrogen planarities: 89
    Chain: "B"
      Number of atoms: 28
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 2, 28
          Unusual residues: {'NAG': 2}
          Classifications: {'undetermined': 2}
          Link IDs: {None: 1}
          Unresolved non-hydrogen bonds: 2
          Unresolved non-hydrogen angles: 4
          Unresolved non-hydrogen dihedrals: 6
          Unresolved non-hydrogen chiralities: 2
    Chain: "C"
      Number of atoms: 39
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 3, 39
          Unusual residues: {'BMA': 1, 'NAG': 2}
          Classifications: {'undetermined': 3}
          Link IDs: {None: 2}
          Unresolved non-hydrogen bonds: 3
          Unresolved non-hydrogen angles: 6
          Unresolved non-hydrogen dihedrals: 9
          Unresolved non-hydrogen chiralities: 3
    Chain: "D"
      Number of atoms: 28
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 2, 28
          Unusual residues: {'NAG': 2}
          Classifications: {'undetermined': 2}
          Link IDs: {None: 1}
          Unresolved non-hydrogen bonds: 2
          Unresolved non-hydrogen angles: 4
          Unresolved non-hydrogen dihedrals: 6
          Unresolved non-hydrogen chiralities: 2
    Chain: "A"
      Number of atoms: 464
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 18, 464
          Unusual residues: {'6OU': 11, '9Z9': 5, 'NAG': 2}
          Classifications: {'undetermined': 18}
          Link IDs: {None: 17}
          Unresolved non-hydrogen bonds: 302
          Unresolved non-hydrogen angles: 344
          Unresolved non-hydrogen dihedrals: 329
          Unresolved non-hydrogen chiralities: 12
          Planarities with less than four sites: {'6OU:plan-1': 9, '6OU:plan-2': 2, '6OU:plan-3': 1}
          Unresolved non-hydrogen planarities: 31
  Time building chain proxies: 6.26, per 1000 atoms: 0.66
  Number of scatterers: 9446
  At special positions: 0
  Unit cell: (135.168, 125.664, 110.88, 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      67     16.00
     P       5     15.00
     O    1641      8.00
     N    1424      7.00
     C    6309      6.00
    sf(0) = scattering factor at diffraction angle 0.

  Number of disulfides: simple=3, symmetry=0
    Simple disulfide: pdb=" SG  CYS A 327 " - pdb=" SG  CYS A 342 " distance=2.02
    Simple disulfide: pdb=" SG  CYS A 909 " - pdb=" SG  CYS A 918 " distance=2.02
    Simple disulfide: pdb=" SG  CYS A1730 " - pdb=" SG  CYS A1744 " distance=2.03

  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=3, symmetry=0
  Links applied
    BETA1-4
      " NAG B   1 " - " NAG B   2 "
      " NAG C   1 " - " NAG C   2 "
      " NAG C   2 " - " BMA C   3 "
      " NAG D   1 " - " NAG D   2 "
    NAG-ASN
      " NAG A3003 " - " ASN A 319 "
      " NAG A3009 " - " ASN A 284 "
      " NAG B   1 " - " ASN A1382 "
      " NAG C   1 " - " ASN A 329 "
      " NAG D   1 " - " ASN A1390 "
  Number of additional bonds: simple=3, symmetry=0
  Coordination:
  Other bonds:
  Time building additional restraints: 3.09
  Conformation dependent library (CDL) restraints added in 1.2 seconds
  

  2220 Ramachandran restraints generated.
    1110 Oldfield, 0 Emsley, 1110 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  2120

  Finding SS restraints...
    Secondary structure from input PDB file:
      62 helices and 2 sheets defined
      78.8% alpha, 0.5% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 0.92
  Creating SS restraints...
    Processing helix  chain 'A' and resid 121 through 130
    Processing helix  chain 'A' and resid 131 through 151
      removed outlier: 4.035A  pdb=" N   SER A 135 " --> pdb=" O   HIS A 131 " (cutoff:3.500A)
      removed outlier: 3.924A  pdb=" N   GLN A 151 " --> pdb=" O   VAL A 147 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 155 through 181
      removed outlier: 3.671A  pdb=" N   LYS A 159 " --> pdb=" O   PRO A 155 " (cutoff:3.500A)
      removed outlier: 3.984A  pdb=" N   TYR A 160 " --> pdb=" O   PRO A 156 " (cutoff:3.500A)
      removed outlier: 4.073A  pdb=" N   VAL A 161 " --> pdb=" O   TRP A 157 " (cutoff:3.500A)
      removed outlier: 3.614A  pdb=" N   GLU A 162 " --> pdb=" O   THR A 158 " (cutoff:3.500A)
      removed outlier: 4.131A  pdb=" N   TYR A 163 " --> pdb=" O   LYS A 159 " (cutoff:3.500A)
      removed outlier: 3.786A  pdb=" N   THR A 164 " --> pdb=" O   TYR A 160 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 182 through 191
    Processing helix  chain 'A' and resid 192 through 211
      removed outlier: 3.538A  pdb=" N   TRP A 196 " --> pdb=" O   ASP A 192 " (cutoff:3.500A)
      removed outlier: 3.967A  pdb=" N   LEU A 197 " --> pdb=" O   PRO A 193 " (cutoff:3.500A)
      removed outlier: 3.959A  pdb=" N   ASP A 198 " --> pdb=" O   TRP A 194 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 221 through 227
      removed outlier: 3.527A  pdb=" N   ARG A 226 " --> pdb=" O   ARG A 223 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 228 through 234
      removed outlier: 3.674A  pdb=" N   SER A 232 " --> pdb=" O   LEU A 228 " (cutoff:3.500A)
      removed outlier: 3.587A  pdb=" N   ILE A 234 " --> pdb=" O   THR A 230 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 236 through 251
      removed outlier: 4.007A  pdb=" N   GLN A 246 " --> pdb=" O   GLY A 242 " (cutoff:3.500A)
      removed outlier: 3.852A  pdb=" N   SER A 247 " --> pdb=" O   ALA A 243 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 251 through 273
    Processing helix  chain 'A' and resid 275 through 279
      removed outlier: 3.693A  pdb=" N   HIS A 279 " --> pdb=" O   ASN A 276 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 305 through 311
    Processing helix  chain 'A' and resid 312 through 315
    Processing helix  chain 'A' and resid 358 through 372
      removed outlier: 3.822A  pdb=" N   ALA A 362 " --> pdb=" O   SER A 358 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 374 through 386
      removed outlier: 3.766A  pdb=" N   LEU A 378 " --> pdb=" O   CYS A 374 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 387 through 389
      No H-bonds generated for 'chain 'A' and resid 387 through 389'
    Processing helix  chain 'A' and resid 390 through 401
    Processing helix  chain 'A' and resid 401 through 424
    Processing helix  chain 'A' and resid 700 through 716
    Processing helix  chain 'A' and resid 720 through 737
    Processing helix  chain 'A' and resid 743 through 772
      removed outlier: 3.660A  pdb=" N   ILE A 770 " --> pdb=" O   THR A 766 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 773 through 780
    Processing helix  chain 'A' and resid 780 through 798
    Processing helix  chain 'A' and resid 806 through 810
      removed outlier: 4.267A  pdb=" N   ARG A 809 " --> pdb=" O   SER A 806 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 815 through 817
      No H-bonds generated for 'chain 'A' and resid 815 through 817'
    Processing helix  chain 'A' and resid 818 through 823
      removed outlier: 4.113A  pdb=" N   SER A 822 " --> pdb=" O   LYS A 818 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 823 through 836
    Processing helix  chain 'A' and resid 840 through 858
      removed outlier: 3.607A  pdb=" N   VAL A 846 " --> pdb=" O   ASN A 842 " (cutoff:3.500A)
      removed outlier: 3.563A  pdb=" N   LEU A 847 " --> pdb=" O   LEU A 843 " (cutoff:3.500A)
      removed outlier: 3.638A  pdb=" N   VAL A 856 " --> pdb=" O   PHE A 852 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 858 through 867
      removed outlier: 5.426A  pdb=" N   LYS A 864 " --> pdb=" O   GLN A 860 " (cutoff:3.500A)
      removed outlier: 5.260A  pdb=" N   ASN A 865 " --> pdb=" O   LEU A 861 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 869 through 874
      removed outlier: 3.912A  pdb=" N   ILE A 873 " --> pdb=" O   LEU A 869 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 887 through 899
    Processing helix  chain 'A' and resid 902 through 913
      removed outlier: 4.502A  pdb=" N   ASP A 908 " --> pdb=" O   GLU A 904 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 914 through 944
      removed outlier: 3.629A  pdb=" N   LEU A 924 " --> pdb=" O   LEU A 920 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 1191 through 1205
    Processing helix  chain 'A' and resid 1206 through 1226
    Processing helix  chain 'A' and resid 1230 through 1233
    Processing helix  chain 'A' and resid 1234 through 1264
      removed outlier: 3.705A  pdb=" N   LYS A1238 " --> pdb=" O   ARG A1234 " (cutoff:3.500A)
      removed outlier: 3.509A  pdb=" N   VAL A1239 " --> pdb=" O   LYS A1235 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 1264 through 1271
      removed outlier: 3.874A  pdb=" N   ASN A1271 " --> pdb=" O   LYS A1267 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 1271 through 1293
    Processing helix  chain 'A' and resid 1305 through 1313
      removed outlier: 3.693A  pdb=" N   ARG A1308 " --> pdb=" O   ARG A1305 " (cutoff:3.500A)
      Proline residue:  A1312  - end of helix
    Processing helix  chain 'A' and resid 1314 through 1319
      removed outlier: 4.315A  pdb=" N   ARG A1318 " --> pdb=" O   ARG A1314 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 1321 through 1331
      removed outlier: 3.804A  pdb=" N   VAL A1325 " --> pdb=" O   GLY A1321 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 1332 through 1359
      removed outlier: 4.666A  pdb=" N   ASN A1338 " --> pdb=" O   PRO A1334 " (cutoff:3.500A)
      removed outlier: 4.190A  pdb=" N   VAL A1339 " --> pdb=" O   SER A1335 " (cutoff:3.500A)
      removed outlier: 4.429A  pdb=" N   PHE A1350 " --> pdb=" O   PHE A1346 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 1386 through 1390
    Processing helix  chain 'A' and resid 1407 through 1419
    Processing helix  chain 'A' and resid 1423 through 1432
    Processing helix  chain 'A' and resid 1445 through 1447
      No H-bonds generated for 'chain 'A' and resid 1445 through 1447'
    Processing helix  chain 'A' and resid 1448 through 1462
      removed outlier: 3.924A  pdb=" N   PHE A1452 " --> pdb=" O   MET A1448 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 1462 through 1482
      removed outlier: 3.517A  pdb=" N   ASP A1473 " --> pdb=" O   GLY A1469 " (cutoff:3.500A)
      removed outlier: 3.652A  pdb=" N   LYS A1480 " --> pdb=" O   ASN A1476 " (cutoff:3.500A)
      removed outlier: 3.773A  pdb=" N   LYS A1481 " --> pdb=" O   GLN A1477 " (cutoff:3.500A)
      removed outlier: 3.677A  pdb=" N   LEU A1482 " --> pdb=" O   GLN A1478 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 1490 through 1503
    Processing helix  chain 'A' and resid 1517 through 1528
    Processing helix  chain 'A' and resid 1529 through 1549
      removed outlier: 4.279A  pdb=" N   ASP A1533 " --> pdb=" O   LYS A1529 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 1555 through 1582
    Processing helix  chain 'A' and resid 1586 through 1591
      removed outlier: 4.272A  pdb=" N   ASN A1591 " --> pdb=" O   TYR A1587 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 1591 through 1617
      removed outlier: 3.879A  pdb=" N   ASP A1597 " --> pdb=" O   TRP A1593 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 1622 through 1628
    Processing helix  chain 'A' and resid 1629 through 1636
    Processing helix  chain 'A' and resid 1637 through 1642
    Processing helix  chain 'A' and resid 1643 through 1655
      removed outlier: 3.918A  pdb=" N   PHE A1650 " --> pdb=" O   ARG A1646 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 1655 through 1681
    Processing helix  chain 'A' and resid 1698 through 1711
      removed outlier: 3.542A  pdb=" N   SER A1702 " --> pdb=" O   THR A1698 " (cutoff:3.500A)
      removed outlier: 3.551A  pdb=" N   THR A1711 " --> pdb=" O   PHE A1707 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 1714 through 1724
      Proline residue:  A1721  - end of helix
      removed outlier: 3.847A  pdb=" N   ASN A1724 " --> pdb=" O   SER A1720 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 1746 through 1780
      removed outlier: 3.573A  pdb=" N   ALA A1780 " --> pdb=" O   ASN A1776 " (cutoff:3.500A)
    Processing sheet with id=AA1, first strand: chain 'A' and resid 280 through 282
    Processing sheet with id=AA2, first strand: chain 'A' and resid 1366 through 1367

    599 hydrogen bonds defined for protein.
    1737 hydrogen bond angles defined for protein.
    Restraints generated for nucleic acids:
      0 hydrogen bonds
      0 hydrogen bond angles
      0 basepair planarities
      0 basepair parallelities
      0 stacking parallelities
  Total time for adding SS restraints: 2.88

  Time building geometry restraints manager: 3.42 seconds

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

  Histogram of bond lengths:
        1.13 -     1.27: 1406
        1.27 -     1.40: 2503
        1.40 -     1.54: 5535
        1.54 -     1.68: 102
        1.68 -     1.81: 124
  Bond restraints: 9670
  Sorted by residual:
  bond pdb=" C06 9Z9 A3014 "
       pdb=" C07 9Z9 A3014 "
    ideal  model  delta    sigma   weight residual
    1.520  1.131  0.389 2.00e-02 2.50e+03 3.78e+02
  bond pdb=" C06 9Z9 A3010 "
       pdb=" C07 9Z9 A3010 "
    ideal  model  delta    sigma   weight residual
    1.520  1.137  0.383 2.00e-02 2.50e+03 3.67e+02
  bond pdb=" C06 9Z9 A3011 "
       pdb=" C07 9Z9 A3011 "
    ideal  model  delta    sigma   weight residual
    1.520  1.138  0.382 2.00e-02 2.50e+03 3.65e+02
  bond pdb=" C06 9Z9 A3012 "
       pdb=" C07 9Z9 A3012 "
    ideal  model  delta    sigma   weight residual
    1.520  1.157  0.363 2.00e-02 2.50e+03 3.30e+02
  bond pdb=" C06 9Z9 A3013 "
       pdb=" C07 9Z9 A3013 "
    ideal  model  delta    sigma   weight residual
    1.520  1.160  0.360 2.00e-02 2.50e+03 3.23e+02
  ... (remaining 9665 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     4.09: 12819
        4.09 -     8.18: 240
        8.18 -    12.27: 42
       12.27 -    16.36: 5
       16.36 -    20.45: 2
  Bond angle restraints: 13108
  Sorted by residual:
  angle pdb=" N   LYS A1616 "
        pdb=" CA  LYS A1616 "
        pdb=" C   LYS A1616 "
      ideal   model   delta    sigma   weight residual
     111.36  122.77  -11.41 1.09e+00 8.42e-01 1.09e+02
  angle pdb=" N   LYS A1302 "
        pdb=" CA  LYS A1302 "
        pdb=" C   LYS A1302 "
      ideal   model   delta    sigma   weight residual
     113.18  102.85   10.33 1.21e+00 6.83e-01 7.28e+01
  angle pdb=" N   PRO A1621 "
        pdb=" CA  PRO A1621 "
        pdb=" CB  PRO A1621 "
      ideal   model   delta    sigma   weight residual
     103.25  111.59   -8.34 1.05e+00 9.07e-01 6.30e+01
  angle pdb=" N   THR A1622 "
        pdb=" CA  THR A1622 "
        pdb=" CB  THR A1622 "
      ideal   model   delta    sigma   weight residual
     110.81  100.46   10.35 1.48e+00 4.57e-01 4.89e+01
  angle pdb=" N   THR A1622 "
        pdb=" CA  THR A1622 "
        pdb=" C   THR A1622 "
      ideal   model   delta    sigma   weight residual
     114.04  105.84    8.20 1.24e+00 6.50e-01 4.37e+01
  ... (remaining 13103 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    35.96: 5829
       35.96 -    71.92: 254
       71.92 -   107.88: 26
      107.88 -   143.83: 12
      143.83 -   179.79: 7
  Dihedral angle restraints: 6128
    sinusoidal: 2849
      harmonic: 3279
  Sorted by residual:
  dihedral pdb=" CA  ARG A1364 "
           pdb=" C   ARG A1364 "
           pdb=" N   CYS A1365 "
           pdb=" CA  CYS A1365 "
      ideal   model   delta  harmonic     sigma   weight residual
    -180.00 -126.13  -53.87     0      5.00e+00 4.00e-02 1.16e+02
  dihedral pdb=" N   PRO A1621 "
           pdb=" C   PRO A1621 "
           pdb=" CA  PRO A1621 "
           pdb=" CB  PRO A1621 "
      ideal   model   delta  harmonic     sigma   weight residual
     115.10  141.39  -26.29     0      2.50e+00 1.60e-01 1.11e+02
  dihedral pdb=" C   PRO A1621 "
           pdb=" N   PRO A1621 "
           pdb=" CA  PRO A1621 "
           pdb=" CB  PRO A1621 "
      ideal   model   delta  harmonic     sigma   weight residual
    -120.70 -141.82   21.12     0      2.50e+00 1.60e-01 7.14e+01
  ... (remaining 6125 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.649: 1532
       0.649 -    1.298: 9
       1.298 -    1.947: 5
       1.947 -    2.596: 0
       2.596 -    3.245: 1
  Chirality restraints: 1547
  Sorted by residual:
  chirality pdb=" C1  NAG B   2 "
            pdb=" O4  NAG B   1 "
            pdb=" C2  NAG B   2 "
            pdb=" O5  NAG B   2 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.40   -0.78   -1.62 2.00e-02 2.50e+03 6.56e+03
  chirality pdb=" C1  BMA C   3 "
            pdb=" O4  NAG C   2 "
            pdb=" C2  BMA C   3 "
            pdb=" O5  BMA C   3 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.40   -2.00   -0.40 2.00e-02 2.50e+03 3.98e+02
  chirality pdb=" C1  NAG A3009 "
            pdb=" ND2 ASN A 284 "
            pdb=" C2  NAG A3009 "
            pdb=" O5  NAG A3009 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.40    0.84   -3.24 2.00e-01 2.50e+01 2.63e+02
  ... (remaining 1544 not shown)

  Planarity restraints: 1546
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C2  NAG D   1 "    0.361 2.00e-02 2.50e+03   3.10e-01 1.20e+03
        pdb=" C7  NAG D   1 "   -0.089 2.00e-02 2.50e+03
        pdb=" C8  NAG D   1 "    0.143 2.00e-02 2.50e+03
        pdb=" N2  NAG D   1 "   -0.550 2.00e-02 2.50e+03
        pdb=" O7  NAG D   1 "    0.135 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C2  NAG D   2 "   -0.352 2.00e-02 2.50e+03   3.04e-01 1.16e+03
        pdb=" C7  NAG D   2 "    0.083 2.00e-02 2.50e+03
        pdb=" C8  NAG D   2 "   -0.091 2.00e-02 2.50e+03
        pdb=" N2  NAG D   2 "    0.540 2.00e-02 2.50e+03
        pdb=" O7  NAG D   2 "   -0.179 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C2  NAG A3009 "   -0.260 2.00e-02 2.50e+03   2.23e-01 6.19e+02
        pdb=" C7  NAG A3009 "    0.056 2.00e-02 2.50e+03
        pdb=" C8  NAG A3009 "    0.028 2.00e-02 2.50e+03
        pdb=" N2  NAG A3009 "    0.372 2.00e-02 2.50e+03
        pdb=" O7  NAG A3009 "   -0.195 2.00e-02 2.50e+03
  ... (remaining 1543 not shown)

  Histogram of nonbonded interaction distances:
        1.26 -     1.99: 6
        1.99 -     2.72: 770
        2.72 -     3.44: 14930
        3.44 -     4.17: 21633
        4.17 -     4.90: 38462
  Nonbonded interactions: 75801
  Sorted by model distance:
  nonbonded pdb=" O   LEU A 129 "
            pdb=" CE2 PHE A 134 "
     model   vdw
     1.260 3.340
  nonbonded pdb=" CD1 ILE A 138 "
            pdb=" OE2 GLU A 172 "
     model   vdw
     1.659 3.460
  nonbonded pdb=" O   LEU A 129 "
            pdb=" CZ  PHE A 134 "
     model   vdw
     1.838 3.340
  nonbonded pdb=" O   CYS A 342 "
            pdb=" O7  NAG C   1 "
     model   vdw
     1.942 3.040
  nonbonded pdb=" O   CYS A 342 "
            pdb=" C7  NAG C   1 "
     model   vdw
     1.953 3.270
  ... (remaining 75796 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
Found NCS groups:
ncs_group {
  reference = chain 'B'
  selection = chain 'D'
}

Set up NCS constraints
  No NCS constraints will be used in refinement.
Set refine NCS operators
Adjust number of macro_cycles
  Number of macro_cycles: 10
Reset NCS operators
Extract rigid body selections
Check and reset occupancies
  Occupancies: min=1.00 max=1.00 mean=1.00
Load rotamer database and sin/cos tables
Set ADP refinement strategy
  ADPs will be refined as group one per residue
Make a string to write initial .geo file
Internal consistency checks
Time:
  Set random seed:                         0.000
  Set model cs if undefined:               0.000
  Decide on map wrapping:                  0.000
  Normalize map: mean=0, sd=1:             1.190
  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:          0.360
  Check model and map are aligned:         0.070
  Set scattering table:                    0.090
  Process input model:                     25.160
  Find NCS groups from input model:        0.300
  Set up NCS constraints:                  0.030
  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:2.770
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   29.990
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7036
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      :  0.022   0.389   9670  Z= 1.610
  Angle     :  1.330  20.455  13108  Z= 0.622
  Chirality :  0.154   3.245   1547
  Planarity :  0.015   0.310   1541
  Dihedral  : 20.904 179.792   3999
  Min Nonbonded Distance : 1.260

Molprobity Statistics.
  All-atom Clashscore : 32.37
  Ramachandran Plot:
    Outliers :  0.36 %
    Allowed  : 11.17 %
    Favored  : 88.47 %
  Rotamer:
    Outliers :  1.05 %
    Allowed  : 12.12 %
    Favored  : 86.83 %
  Cbeta Deviations :  0.28 %
  Peptide Plane:
    Cis-proline     : 3.45 %
    Cis-general     : 0.09 %
    Twisted Proline : 0.00 %
    Twisted General : 0.28 %

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: -3.89 (0.22), residues: 1110
  helix: -2.29 (0.15), residues: 783
  sheet: -2.87 (1.28), residues: 10
  loop : -2.83 (0.37), residues: 317

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.058   0.003   TRP A1423 
 HIS   0.010   0.002   HIS A 351 
 PHE   0.030   0.003   PHE A 148 
 TYR   0.024   0.003   TYR A1201 
 ARG   0.010   0.001   ARG A 384 

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

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

  2220 Ramachandran restraints generated.
    1110 Oldfield, 0 Emsley, 1110 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2220 Ramachandran restraints generated.
    1110 Oldfield, 0 Emsley, 1110 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  268 residues out of total 990 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 258
  time to evaluate  : 0.952 
Fit side-chains
   revert: symmetry clash
REVERT: A  163 TYR cc_start: 0.7909 (m-80) cc_final: 0.7653 (m-80)
REVERT: A  251 LEU cc_start: 0.8831 (tp) cc_final: 0.8145 (tp)
REVERT: A  353 TYR cc_start: 0.7128 (m-80) cc_final: 0.6763 (m-80)
REVERT: A  404 TYR cc_start: 0.7439 (t80) cc_final: 0.7154 (t80)
REVERT: A  407 ASN cc_start: 0.8948 (t0) cc_final: 0.8601 (t0)
REVERT: A  422 GLN cc_start: 0.7161 (mt0) cc_final: 0.6877 (pp30)
REVERT: A  819 LEU cc_start: 0.8612 (tp) cc_final: 0.8233 (tp)
REVERT: A  907 TRP cc_start: 0.7849 (m-10) cc_final: 0.7482 (m-90)
REVERT: A 1274 CYS cc_start: 0.8066 (m) cc_final: 0.7744 (m)
REVERT: A 1323 ARG cc_start: 0.7497 (ttp80) cc_final: 0.6576 (ttp80)
REVERT: A 1496 TYR cc_start: 0.7900 (m-10) cc_final: 0.7537 (m-80)
REVERT: A 1497 TYR cc_start: 0.7653 (t80) cc_final: 0.7228 (t80)
REVERT: A 1500 MET cc_start: 0.6295 (ttm) cc_final: 0.5868 (ttp)
REVERT: A 1560 ASN cc_start: 0.8597 (t0) cc_final: 0.8342 (t0)
REVERT: A 1581 MET cc_start: 0.2436 (ttt) cc_final: 0.2228 (tpt)
REVERT: A 1588 TYR cc_start: 0.6200 (p90) cc_final: 0.5982 (p90)
REVERT: A 1622 THR cc_start: 0.7464 (m) cc_final: 0.7251 (t)
  outliers start: 10
  outliers final: 7
  residues processed: 264
  average time/residue: 0.2052
  time to fit residues: 76.8748
Evaluate side-chains
  221 residues out of total 990 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 7
    poor density    : 214
  time to evaluate  : 1.063 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue 1215 PHE
Chi-restraints excluded: chain A residue 1297 GLU
Chi-restraints excluded: chain A residue 1419 THR
Chi-restraints excluded: chain A residue 1421 LYS
Chi-restraints excluded: chain A residue 1618 PHE
Chi-restraints excluded: chain A residue 1626 VAL
Chi-restraints excluded: chain A residue 1711 THR
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 112
   random chunks:
   chunk 94 optimal weight:    0.9990
   chunk 84 optimal weight:    5.9990
   chunk 47 optimal weight:    0.9980
   chunk 28 optimal weight:    5.9990
   chunk 57 optimal weight:   10.0000
   chunk 45 optimal weight:    6.9990
   chunk 87 optimal weight:   10.0000
   chunk 33 optimal weight:    5.9990
   chunk 53 optimal weight:    2.9990
   chunk 65 optimal weight:    0.9980
   chunk 101 optimal weight:    0.9980
   overall best weight:    1.3984

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

Flipped N/Q/H residues before XYZ refinement:
A 195 ASN
A 314 ASN
** A 407 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 731 ASN
A 739 HIS
A 780 GLN
** A 860 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 871 HIS
** A 889 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
A 930 ASN
A1327 ASN
A1615 GLN
A1767 ASN

Total number of N/Q/H flips: 10

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4402 r_free = 0.4402 target = 0.175676 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 34)----------------|
| r_work = 0.4099 r_free = 0.4099 target = 0.146060 restraints weight = 16888.066|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 28)----------------|
| r_work = 0.4104 r_free = 0.4104 target = 0.149067 restraints weight = 8526.792|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 28)----------------|
| r_work = 0.4115 r_free = 0.4115 target = 0.150383 restraints weight = 5428.032|
|-----------------------------------------------------------------------------|
r_work (final): 0.4118
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6954
moved from start:          0.2073

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.050   9670  Z= 0.226
  Angle     :  0.818  10.293  13108  Z= 0.395
  Chirality :  0.047   0.483   1547
  Planarity :  0.005   0.048   1541
  Dihedral  : 19.519 178.038   2055
  Min Nonbonded Distance : 2.318

Molprobity Statistics.
  All-atom Clashscore : 15.51
  Ramachandran Plot:
    Outliers :  0.09 %
    Allowed  :  7.84 %
    Favored  : 92.07 %
  Rotamer:
    Outliers :  3.06 %
    Allowed  : 18.76 %
    Favored  : 78.19 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 3.45 %
    Cis-general     : 0.09 %
    Twisted Proline : 0.00 %
    Twisted General : 0.18 %

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: -1.96 (0.24), residues: 1110
  helix: -0.81 (0.17), residues: 785
  sheet: -2.59 (1.43), residues: 10
  loop : -2.21 (0.38), residues: 315

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.021   0.002   TRP A1423 
 HIS   0.006   0.001   HIS A 131 
 PHE   0.037   0.002   PHE A 785 
 TYR   0.023   0.002   TYR A 417 
 ARG   0.006   0.001   ARG A 384 

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

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

  2220 Ramachandran restraints generated.
    1110 Oldfield, 0 Emsley, 1110 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2220 Ramachandran restraints generated.
    1110 Oldfield, 0 Emsley, 1110 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  270 residues out of total 990 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 29
    poor density    : 241
  time to evaluate  : 1.061 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  159 LYS cc_start: 0.8529 (tptt) cc_final: 0.7640 (mtpp)
REVERT: A  404 TYR cc_start: 0.7409 (t80) cc_final: 0.6946 (t80)
REVERT: A  809 ARG cc_start: 0.8223 (mpt-90) cc_final: 0.7831 (mpp80)
REVERT: A 1265 PHE cc_start: 0.7304 (m-80) cc_final: 0.6667 (t80)
REVERT: A 1274 CYS cc_start: 0.8331 (m) cc_final: 0.7979 (m)
REVERT: A 1323 ARG cc_start: 0.7141 (ttp80) cc_final: 0.6413 (ttp80)
REVERT: A 1496 TYR cc_start: 0.7926 (m-10) cc_final: 0.7537 (m-80)
REVERT: A 1497 TYR cc_start: 0.7705 (t80) cc_final: 0.7274 (t80)
REVERT: A 1500 MET cc_start: 0.6262 (ttm) cc_final: 0.5912 (ttp)
REVERT: A 1588 TYR cc_start: 0.6082 (p90) cc_final: 0.5850 (p90)
REVERT: A 1629 LEU cc_start: 0.8649 (OUTLIER) cc_final: 0.8369 (tt)
REVERT: A 1671 PHE cc_start: 0.7715 (t80) cc_final: 0.7394 (t80)
REVERT: A 1729 TYR cc_start: 0.6086 (OUTLIER) cc_final: 0.5595 (p90)
REVERT: A 1765 VAL cc_start: 0.7512 (t) cc_final: 0.7001 (p)
  outliers start: 29
  outliers final: 14
  residues processed: 260
  average time/residue: 0.1956
  time to fit residues: 72.7913
Evaluate side-chains
  235 residues out of total 990 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 219
  time to evaluate  : 0.931 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  239 THR
Chi-restraints excluded: chain A residue  245 ILE
Chi-restraints excluded: chain A residue  306 ASP
Chi-restraints excluded: chain A residue  325 LEU
Chi-restraints excluded: chain A residue  327 CYS
Chi-restraints excluded: chain A residue  722 LEU
Chi-restraints excluded: chain A residue 1215 PHE
Chi-restraints excluded: chain A residue 1239 VAL
Chi-restraints excluded: chain A residue 1293 LEU
Chi-restraints excluded: chain A residue 1366 ILE
Chi-restraints excluded: chain A residue 1384 SER
Chi-restraints excluded: chain A residue 1597 ASP
Chi-restraints excluded: chain A residue 1626 VAL
Chi-restraints excluded: chain A residue 1629 LEU
Chi-restraints excluded: chain A residue 1729 TYR
Chi-restraints excluded: chain A residue 1744 CYS
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 112
   random chunks:
   chunk 81 optimal weight:    0.9980
   chunk 49 optimal weight:    0.7980
   chunk 72 optimal weight:    8.9990
   chunk 99 optimal weight:    5.9990
   chunk 110 optimal weight:    4.9990
   chunk 41 optimal weight:   20.0000
   chunk 92 optimal weight:    5.9990
   chunk 35 optimal weight:    3.9990
   chunk 111 optimal weight:    4.9990
   chunk 18 optimal weight:   10.0000
   chunk 78 optimal weight:    9.9990
   overall best weight:    3.1586

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

Flipped N/Q/H residues before XYZ refinement:
A 310 ASN
** A 407 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 731 ASN
** A 889 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** A1465 ASN ** 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 = 0.4389 r_free = 0.4389 target = 0.174667 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 43)----------------|
| r_work = 0.4020 r_free = 0.4020 target = 0.141359 restraints weight = 17303.674|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 32)----------------|
| r_work = 0.4065 r_free = 0.4065 target = 0.145279 restraints weight = 8585.090|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 46)----------------|
| r_work = 0.4093 r_free = 0.4093 target = 0.147825 restraints weight = 5625.614|
|-----------------------------------------------------------------------------|
r_work (final): 0.4092
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6996
moved from start:          0.2434

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.050   9670  Z= 0.252
  Angle     :  0.750  12.445  13108  Z= 0.367
  Chirality :  0.045   0.444   1547
  Planarity :  0.004   0.049   1541
  Dihedral  : 18.114 179.688   2044
  Min Nonbonded Distance : 2.391

Molprobity Statistics.
  All-atom Clashscore : 16.19
  Ramachandran Plot:
    Outliers :  0.09 %
    Allowed  :  7.48 %
    Favored  : 92.43 %
  Rotamer:
    Outliers :  3.90 %
    Allowed  : 20.44 %
    Favored  : 75.66 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 3.45 %
    Cis-general     : 0.09 %
    Twisted Proline : 0.00 %
    Twisted General : 0.18 %

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: -1.26 (0.25), residues: 1110
  helix: -0.30 (0.17), residues: 787
  sheet: -3.01 (1.32), residues: 10
  loop : -1.89 (0.40), residues: 313

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.020   0.002   TRP A1423 
 HIS   0.005   0.001   HIS A 279 
 PHE   0.019   0.002   PHE A1452 
 TYR   0.022   0.002   TYR A 308 
 ARG   0.006   0.000   ARG A 384 

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

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

  2220 Ramachandran restraints generated.
    1110 Oldfield, 0 Emsley, 1110 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2220 Ramachandran restraints generated.
    1110 Oldfield, 0 Emsley, 1110 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  270 residues out of total 990 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 37
    poor density    : 233
  time to evaluate  : 1.021 
Fit side-chains
   revert: symmetry clash
REVERT: A  159 LYS cc_start: 0.8610 (tptt) cc_final: 0.8141 (mttm)
REVERT: A  160 TYR cc_start: 0.6971 (OUTLIER) cc_final: 0.5740 (m-80)
REVERT: A  174 LEU cc_start: 0.8252 (tt) cc_final: 0.7843 (mt)
REVERT: A  404 TYR cc_start: 0.7446 (t80) cc_final: 0.7056 (t80)
REVERT: A  407 ASN cc_start: 0.8728 (t0) cc_final: 0.8267 (t0)
REVERT: A  422 GLN cc_start: 0.7141 (mt0) cc_final: 0.6827 (pp30)
REVERT: A 1215 PHE cc_start: 0.7361 (OUTLIER) cc_final: 0.6991 (t80)
REVERT: A 1265 PHE cc_start: 0.7348 (m-80) cc_final: 0.6657 (t80)
REVERT: A 1274 CYS cc_start: 0.8322 (m) cc_final: 0.7940 (m)
REVERT: A 1313 LEU cc_start: 0.8568 (OUTLIER) cc_final: 0.8349 (mp)
REVERT: A 1323 ARG cc_start: 0.7150 (ttp80) cc_final: 0.6447 (ttp80)
REVERT: A 1364 ARG cc_start: 0.6601 (pmt-80) cc_final: 0.6233 (pmt-80)
REVERT: A 1472 ILE cc_start: 0.8161 (mm) cc_final: 0.7959 (mt)
REVERT: A 1496 TYR cc_start: 0.7904 (m-10) cc_final: 0.7549 (m-80)
REVERT: A 1497 TYR cc_start: 0.7769 (t80) cc_final: 0.7336 (t80)
REVERT: A 1500 MET cc_start: 0.6334 (ttm) cc_final: 0.6112 (ttp)
REVERT: A 1588 TYR cc_start: 0.6259 (p90) cc_final: 0.5891 (p90)
REVERT: A 1671 PHE cc_start: 0.7838 (t80) cc_final: 0.7601 (t80)
REVERT: A 1729 TYR cc_start: 0.6023 (OUTLIER) cc_final: 0.5434 (p90)
  outliers start: 37
  outliers final: 24
  residues processed: 255
  average time/residue: 0.1992
  time to fit residues: 72.4148
Evaluate side-chains
  249 residues out of total 990 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 28
    poor density    : 221
  time to evaluate  : 1.026 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  160 TYR
Chi-restraints excluded: chain A residue  225 LEU
Chi-restraints excluded: chain A residue  237 LEU
Chi-restraints excluded: chain A residue  239 THR
Chi-restraints excluded: chain A residue  254 VAL
Chi-restraints excluded: chain A residue  306 ASP
Chi-restraints excluded: chain A residue  325 LEU
Chi-restraints excluded: chain A residue  327 CYS
Chi-restraints excluded: chain A residue  722 LEU
Chi-restraints excluded: chain A residue  733 LEU
Chi-restraints excluded: chain A residue  826 LEU
Chi-restraints excluded: chain A residue  849 ILE
Chi-restraints excluded: chain A residue  885 MET
Chi-restraints excluded: chain A residue 1215 PHE
Chi-restraints excluded: chain A residue 1260 TRP
Chi-restraints excluded: chain A residue 1293 LEU
Chi-restraints excluded: chain A residue 1313 LEU
Chi-restraints excluded: chain A residue 1324 VAL
Chi-restraints excluded: chain A residue 1366 ILE
Chi-restraints excluded: chain A residue 1384 SER
Chi-restraints excluded: chain A residue 1424 MET
Chi-restraints excluded: chain A residue 1487 ILE
Chi-restraints excluded: chain A residue 1597 ASP
Chi-restraints excluded: chain A residue 1626 VAL
Chi-restraints excluded: chain A residue 1685 LYS
Chi-restraints excluded: chain A residue 1711 THR
Chi-restraints excluded: chain A residue 1729 TYR
Chi-restraints excluded: chain A residue 1744 CYS
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 112
   random chunks:
   chunk 71 optimal weight:    1.9990
   chunk 37 optimal weight:    6.9990
   chunk 61 optimal weight:    9.9990
   chunk 43 optimal weight:    5.9990
   chunk 79 optimal weight:    6.9990
   chunk 69 optimal weight:    0.8980
   chunk 105 optimal weight:    6.9990
   chunk 46 optimal weight:    9.9990
   chunk 106 optimal weight:    0.9980
   chunk 101 optimal weight:    0.9990
   chunk 12 optimal weight:    1.9990
   overall best weight:    1.3786

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

Flipped N/Q/H residues before XYZ refinement:
** A 407 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 731 ASN
A 860 GLN
** A 889 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
A1327 ASN
** A1465 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4423 r_free = 0.4423 target = 0.178109 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 41)----------------|
| r_work = 0.4073 r_free = 0.4073 target = 0.145955 restraints weight = 16803.277|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 45)----------------|
| r_work = 0.4117 r_free = 0.4117 target = 0.149972 restraints weight = 8291.222|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 44)----------------|
| r_work = 0.4144 r_free = 0.4144 target = 0.152535 restraints weight = 5421.303|
|-----------------------------------------------------------------------------|
r_work (final): 0.4148
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6911
moved from start:          0.2949

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.052   9670  Z= 0.184
  Angle     :  0.719  12.414  13108  Z= 0.347
  Chirality :  0.044   0.376   1547
  Planarity :  0.004   0.047   1541
  Dihedral  : 16.735 176.570   2044
  Min Nonbonded Distance : 2.397

Molprobity Statistics.
  All-atom Clashscore : 14.25
  Ramachandran Plot:
    Outliers :  0.09 %
    Allowed  :  7.03 %
    Favored  : 92.88 %
  Rotamer:
    Outliers :  5.06 %
    Allowed  : 21.18 %
    Favored  : 73.76 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 3.45 %
    Cis-general     : 0.09 %
    Twisted Proline : 0.00 %
    Twisted General : 0.18 %

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: -0.59 (0.25), residues: 1110
  helix:  0.22 (0.18), residues: 781
  sheet: -2.90 (1.32), residues: 10
  loop : -1.66 (0.39), residues: 319

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.012   0.001   TRP A1715 
 HIS   0.004   0.001   HIS A 279 
 PHE   0.015   0.001   PHE A1753 
 TYR   0.024   0.002   TYR A 308 
 ARG   0.004   0.000   ARG A1318 

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

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

  2220 Ramachandran restraints generated.
    1110 Oldfield, 0 Emsley, 1110 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2220 Ramachandran restraints generated.
    1110 Oldfield, 0 Emsley, 1110 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  288 residues out of total 990 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 48
    poor density    : 240
  time to evaluate  : 0.944 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  159 LYS cc_start: 0.8554 (tptt) cc_final: 0.8125 (mttm)
REVERT: A  160 TYR cc_start: 0.6821 (OUTLIER) cc_final: 0.5682 (m-80)
REVERT: A  174 LEU cc_start: 0.8113 (tt) cc_final: 0.7624 (mt)
REVERT: A  400 LEU cc_start: 0.7278 (OUTLIER) cc_final: 0.6642 (mm)
REVERT: A  404 TYR cc_start: 0.7452 (t80) cc_final: 0.7011 (t80)
REVERT: A  422 GLN cc_start: 0.7121 (mt0) cc_final: 0.6804 (pp30)
REVERT: A 1215 PHE cc_start: 0.7301 (OUTLIER) cc_final: 0.6896 (t80)
REVERT: A 1265 PHE cc_start: 0.7282 (m-80) cc_final: 0.6694 (t80)
REVERT: A 1274 CYS cc_start: 0.8183 (m) cc_final: 0.7823 (m)
REVERT: A 1323 ARG cc_start: 0.6963 (ttp80) cc_final: 0.6285 (ttp80)
REVERT: A 1364 ARG cc_start: 0.6851 (pmt-80) cc_final: 0.6192 (pmt-80)
REVERT: A 1497 TYR cc_start: 0.7762 (t80) cc_final: 0.7269 (t80)
REVERT: A 1613 ILE cc_start: 0.7230 (OUTLIER) cc_final: 0.6977 (mp)
REVERT: A 1729 TYR cc_start: 0.6051 (OUTLIER) cc_final: 0.5492 (p90)
  outliers start: 48
  outliers final: 25
  residues processed: 271
  average time/residue: 0.1855
  time to fit residues: 72.7773
Evaluate side-chains
  249 residues out of total 990 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 30
    poor density    : 219
  time to evaluate  : 1.042 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  160 TYR
Chi-restraints excluded: chain A residue  225 LEU
Chi-restraints excluded: chain A residue  230 THR
Chi-restraints excluded: chain A residue  237 LEU
Chi-restraints excluded: chain A residue  239 THR
Chi-restraints excluded: chain A residue  306 ASP
Chi-restraints excluded: chain A residue  325 LEU
Chi-restraints excluded: chain A residue  327 CYS
Chi-restraints excluded: chain A residue  385 SER
Chi-restraints excluded: chain A residue  400 LEU
Chi-restraints excluded: chain A residue  722 LEU
Chi-restraints excluded: chain A residue  733 LEU
Chi-restraints excluded: chain A residue  826 LEU
Chi-restraints excluded: chain A residue  849 ILE
Chi-restraints excluded: chain A residue  878 LEU
Chi-restraints excluded: chain A residue 1215 PHE
Chi-restraints excluded: chain A residue 1226 PHE
Chi-restraints excluded: chain A residue 1261 VAL
Chi-restraints excluded: chain A residue 1293 LEU
Chi-restraints excluded: chain A residue 1324 VAL
Chi-restraints excluded: chain A residue 1366 ILE
Chi-restraints excluded: chain A residue 1384 SER
Chi-restraints excluded: chain A residue 1487 ILE
Chi-restraints excluded: chain A residue 1503 LEU
Chi-restraints excluded: chain A residue 1544 MET
Chi-restraints excluded: chain A residue 1613 ILE
Chi-restraints excluded: chain A residue 1624 PHE
Chi-restraints excluded: chain A residue 1685 LYS
Chi-restraints excluded: chain A residue 1729 TYR
Chi-restraints excluded: chain A residue 1744 CYS
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 112
   random chunks:
   chunk 40 optimal weight:    1.9990
   chunk 13 optimal weight:    4.9990
   chunk 82 optimal weight:   20.0000
   chunk 43 optimal weight:    6.9990
   chunk 14 optimal weight:    6.9990
   chunk 62 optimal weight:    9.9990
   chunk 4 optimal weight:   10.0000
   chunk 8 optimal weight:    6.9990
   chunk 106 optimal weight:    0.8980
   chunk 7 optimal weight:    5.9990
   chunk 105 optimal weight:    1.9990
   overall best weight:    3.1788

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

Flipped N/Q/H residues before XYZ refinement:
** A 407 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 731 ASN
** A 889 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** A1465 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
A1586 HIS
** A1736 ASN ** 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 = 0.4399 r_free = 0.4399 target = 0.175538 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 46)----------------|
| r_work = 0.4041 r_free = 0.4041 target = 0.143105 restraints weight = 16996.634|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 40)----------------|
| r_work = 0.4086 r_free = 0.4086 target = 0.147025 restraints weight = 8319.456|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 44)----------------|
| r_work = 0.4114 r_free = 0.4114 target = 0.149539 restraints weight = 5454.594|
|-----------------------------------------------------------------------------|
r_work (final): 0.4114
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6978
moved from start:          0.3060

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.052   9670  Z= 0.245
  Angle     :  0.748  12.552  13108  Z= 0.363
  Chirality :  0.045   0.399   1547
  Planarity :  0.004   0.045   1541
  Dihedral  : 16.258 173.943   2043
  Min Nonbonded Distance : 2.405

Molprobity Statistics.
  All-atom Clashscore : 14.98
  Ramachandran Plot:
    Outliers :  0.09 %
    Allowed  :  7.12 %
    Favored  : 92.79 %
  Rotamer:
    Outliers :  5.06 %
    Allowed  : 23.92 %
    Favored  : 71.02 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 3.45 %
    Cis-general     : 0.09 %
    Twisted Proline : 0.00 %
    Twisted General : 0.18 %

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: -0.39 (0.26), residues: 1110
  helix:  0.36 (0.18), residues: 783
  sheet: -2.83 (1.35), residues: 10
  loop : -1.55 (0.39), residues: 317

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.014   0.001   TRP A1442 
 HIS   0.003   0.001   HIS A 351 
 PHE   0.020   0.002   PHE A1762 
 TYR   0.017   0.002   TYR A1588 
 ARG   0.006   0.000   ARG A1640 

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

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

  2220 Ramachandran restraints generated.
    1110 Oldfield, 0 Emsley, 1110 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2220 Ramachandran restraints generated.
    1110 Oldfield, 0 Emsley, 1110 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  276 residues out of total 990 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 48
    poor density    : 228
  time to evaluate  : 1.017 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  159 LYS cc_start: 0.8603 (tptt) cc_final: 0.8148 (mttm)
REVERT: A  160 TYR cc_start: 0.6891 (OUTLIER) cc_final: 0.5748 (m-80)
REVERT: A  174 LEU cc_start: 0.7988 (tt) cc_final: 0.7500 (mt)
REVERT: A  404 TYR cc_start: 0.7500 (t80) cc_final: 0.7083 (t80)
REVERT: A  407 ASN cc_start: 0.8773 (t0) cc_final: 0.8570 (t0)
REVERT: A  422 GLN cc_start: 0.7088 (mt0) cc_final: 0.6794 (pp30)
REVERT: A  785 PHE cc_start: 0.7707 (p90) cc_final: 0.7498 (p90)
REVERT: A 1215 PHE cc_start: 0.7258 (OUTLIER) cc_final: 0.6825 (t80)
REVERT: A 1265 PHE cc_start: 0.7295 (m-80) cc_final: 0.6689 (t80)
REVERT: A 1274 CYS cc_start: 0.8170 (m) cc_final: 0.7799 (m)
REVERT: A 1364 ARG cc_start: 0.6715 (pmt-80) cc_final: 0.6290 (pmt-80)
REVERT: A 1496 TYR cc_start: 0.7703 (m-80) cc_final: 0.7393 (m-80)
REVERT: A 1497 TYR cc_start: 0.7758 (t80) cc_final: 0.7274 (t80)
REVERT: A 1613 ILE cc_start: 0.7354 (OUTLIER) cc_final: 0.7075 (mp)
REVERT: A 1656 LEU cc_start: 0.8229 (OUTLIER) cc_final: 0.7926 (mm)
REVERT: A 1729 TYR cc_start: 0.6069 (OUTLIER) cc_final: 0.5520 (p90)
  outliers start: 48
  outliers final: 26
  residues processed: 257
  average time/residue: 0.2017
  time to fit residues: 75.5418
Evaluate side-chains
  249 residues out of total 990 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 31
    poor density    : 218
  time to evaluate  : 1.002 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  122 ARG
Chi-restraints excluded: chain A residue  160 TYR
Chi-restraints excluded: chain A residue  225 LEU
Chi-restraints excluded: chain A residue  228 LEU
Chi-restraints excluded: chain A residue  237 LEU
Chi-restraints excluded: chain A residue  239 THR
Chi-restraints excluded: chain A residue  325 LEU
Chi-restraints excluded: chain A residue  327 CYS
Chi-restraints excluded: chain A residue  385 SER
Chi-restraints excluded: chain A residue  722 LEU
Chi-restraints excluded: chain A residue  878 LEU
Chi-restraints excluded: chain A residue  885 MET
Chi-restraints excluded: chain A residue  940 LEU
Chi-restraints excluded: chain A residue 1215 PHE
Chi-restraints excluded: chain A residue 1260 TRP
Chi-restraints excluded: chain A residue 1261 VAL
Chi-restraints excluded: chain A residue 1275 TRP
Chi-restraints excluded: chain A residue 1293 LEU
Chi-restraints excluded: chain A residue 1324 VAL
Chi-restraints excluded: chain A residue 1366 ILE
Chi-restraints excluded: chain A residue 1384 SER
Chi-restraints excluded: chain A residue 1424 MET
Chi-restraints excluded: chain A residue 1452 PHE
Chi-restraints excluded: chain A residue 1487 ILE
Chi-restraints excluded: chain A residue 1490 THR
Chi-restraints excluded: chain A residue 1544 MET
Chi-restraints excluded: chain A residue 1613 ILE
Chi-restraints excluded: chain A residue 1624 PHE
Chi-restraints excluded: chain A residue 1656 LEU
Chi-restraints excluded: chain A residue 1729 TYR
Chi-restraints excluded: chain A residue 1744 CYS
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 112
   random chunks:
   chunk 2 optimal weight:    8.9990
   chunk 3 optimal weight:    2.9990
   chunk 46 optimal weight:    7.9990
   chunk 107 optimal weight:    6.9990
   chunk 59 optimal weight:    5.9990
   chunk 94 optimal weight:    2.9990
   chunk 71 optimal weight:    0.0970
   chunk 69 optimal weight:    0.9990
   chunk 68 optimal weight:    2.9990
   chunk 81 optimal weight:    2.9990
   chunk 77 optimal weight:    5.9990
   overall best weight:    2.0186

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

Flipped N/Q/H residues before XYZ refinement:
** A 407 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 731 ASN
** A 889 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** A1465 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
A1586 HIS
** A1736 ASN ** 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 = 0.4421 r_free = 0.4421 target = 0.177463 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 42)----------------|
| r_work = 0.4068 r_free = 0.4068 target = 0.145277 restraints weight = 16764.493|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 44)----------------|
| r_work = 0.4114 r_free = 0.4114 target = 0.149291 restraints weight = 8236.501|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 45)----------------|
| r_work = 0.4141 r_free = 0.4141 target = 0.151850 restraints weight = 5368.310|
|-----------------------------------------------------------------------------|
r_work (final): 0.4143
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6923
moved from start:          0.3322

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.051   9670  Z= 0.197
  Angle     :  0.733  12.439  13108  Z= 0.352
  Chirality :  0.045   0.368   1547
  Planarity :  0.004   0.043   1541
  Dihedral  : 15.437 171.144   2043
  Min Nonbonded Distance : 2.409

Molprobity Statistics.
  All-atom Clashscore : 14.93
  Ramachandran Plot:
    Outliers :  0.09 %
    Allowed  :  6.67 %
    Favored  : 93.24 %
  Rotamer:
    Outliers :  4.53 %
    Allowed  : 25.82 %
    Favored  : 69.65 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 3.45 %
    Cis-general     : 0.09 %
    Twisted Proline : 0.00 %
    Twisted General : 0.18 %

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: -0.29 (0.26), residues: 1110
  helix:  0.46 (0.18), residues: 795
  sheet: -2.85 (1.30), residues: 10
  loop : -1.70 (0.39), residues: 305

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.016   0.001   TRP A1442 
 HIS   0.002   0.001   HIS A 351 
 PHE   0.016   0.001   PHE A1762 
 TYR   0.015   0.001   TYR A 308 
 ARG   0.004   0.000   ARG A 384 

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

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

  2220 Ramachandran restraints generated.
    1110 Oldfield, 0 Emsley, 1110 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2220 Ramachandran restraints generated.
    1110 Oldfield, 0 Emsley, 1110 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  272 residues out of total 990 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 43
    poor density    : 229
  time to evaluate  : 0.948 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  159 LYS cc_start: 0.8544 (tptt) cc_final: 0.8090 (mttm)
REVERT: A  160 TYR cc_start: 0.6669 (OUTLIER) cc_final: 0.5446 (m-80)
REVERT: A  174 LEU cc_start: 0.7955 (OUTLIER) cc_final: 0.7551 (mt)
REVERT: A  382 THR cc_start: 0.8342 (m) cc_final: 0.8110 (m)
REVERT: A  404 TYR cc_start: 0.7423 (t80) cc_final: 0.7062 (t80)
REVERT: A  422 GLN cc_start: 0.7106 (mt0) cc_final: 0.6796 (pp30)
REVERT: A 1215 PHE cc_start: 0.7172 (OUTLIER) cc_final: 0.6495 (t80)
REVERT: A 1265 PHE cc_start: 0.7244 (m-80) cc_final: 0.6657 (t80)
REVERT: A 1274 CYS cc_start: 0.8167 (m) cc_final: 0.7815 (m)
REVERT: A 1496 TYR cc_start: 0.7683 (m-80) cc_final: 0.7177 (m-80)
REVERT: A 1497 TYR cc_start: 0.7759 (t80) cc_final: 0.7235 (t80)
REVERT: A 1613 ILE cc_start: 0.7304 (OUTLIER) cc_final: 0.6999 (mp)
REVERT: A 1656 LEU cc_start: 0.8092 (OUTLIER) cc_final: 0.7812 (mm)
REVERT: A 1729 TYR cc_start: 0.6263 (OUTLIER) cc_final: 0.5681 (p90)
  outliers start: 43
  outliers final: 25
  residues processed: 253
  average time/residue: 0.1870
  time to fit residues: 68.9483
Evaluate side-chains
  245 residues out of total 990 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 31
    poor density    : 214
  time to evaluate  : 1.026 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  122 ARG
Chi-restraints excluded: chain A residue  160 TYR
Chi-restraints excluded: chain A residue  164 THR
Chi-restraints excluded: chain A residue  174 LEU
Chi-restraints excluded: chain A residue  225 LEU
Chi-restraints excluded: chain A residue  237 LEU
Chi-restraints excluded: chain A residue  239 THR
Chi-restraints excluded: chain A residue  254 VAL
Chi-restraints excluded: chain A residue  325 LEU
Chi-restraints excluded: chain A residue  327 CYS
Chi-restraints excluded: chain A residue  385 SER
Chi-restraints excluded: chain A residue  722 LEU
Chi-restraints excluded: chain A residue  878 LEU
Chi-restraints excluded: chain A residue  940 LEU
Chi-restraints excluded: chain A residue 1215 PHE
Chi-restraints excluded: chain A residue 1260 TRP
Chi-restraints excluded: chain A residue 1261 VAL
Chi-restraints excluded: chain A residue 1293 LEU
Chi-restraints excluded: chain A residue 1324 VAL
Chi-restraints excluded: chain A residue 1366 ILE
Chi-restraints excluded: chain A residue 1384 SER
Chi-restraints excluded: chain A residue 1446 LEU
Chi-restraints excluded: chain A residue 1452 PHE
Chi-restraints excluded: chain A residue 1487 ILE
Chi-restraints excluded: chain A residue 1503 LEU
Chi-restraints excluded: chain A residue 1613 ILE
Chi-restraints excluded: chain A residue 1624 PHE
Chi-restraints excluded: chain A residue 1656 LEU
Chi-restraints excluded: chain A residue 1708 GLN
Chi-restraints excluded: chain A residue 1729 TYR
Chi-restraints excluded: chain A residue 1744 CYS
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 112
   random chunks:
   chunk 41 optimal weight:   10.0000
   chunk 76 optimal weight:    0.9980
   chunk 89 optimal weight:   10.0000
   chunk 66 optimal weight:    0.6980
   chunk 36 optimal weight:    8.9990
   chunk 73 optimal weight:   10.0000
   chunk 62 optimal weight:    5.9990
   chunk 67 optimal weight:    6.9990
   chunk 92 optimal weight:    7.9990
   chunk 107 optimal weight:    2.9990
   chunk 79 optimal weight:    0.9980
   overall best weight:    2.3384

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

Flipped N/Q/H residues before XYZ refinement:
** A 407 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 731 ASN
** A 889 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** A1465 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
A1586 HIS
** A1736 ASN ** 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 = 0.4417 r_free = 0.4417 target = 0.177062 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 46)----------------|
| r_work = 0.4067 r_free = 0.4067 target = 0.145230 restraints weight = 16948.251|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 38)----------------|
| r_work = 0.4113 r_free = 0.4113 target = 0.149234 restraints weight = 8266.719|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 43)----------------|
| r_work = 0.4142 r_free = 0.4142 target = 0.151844 restraints weight = 5373.609|
|-----------------------------------------------------------------------------|
r_work (final): 0.4143
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6926
moved from start:          0.3483

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.052   9670  Z= 0.212
  Angle     :  0.740  12.824  13108  Z= 0.358
  Chirality :  0.045   0.374   1547
  Planarity :  0.004   0.041   1541
  Dihedral  : 14.820 168.799   2043
  Min Nonbonded Distance : 2.414

Molprobity Statistics.
  All-atom Clashscore : 15.03
  Ramachandran Plot:
    Outliers :  0.09 %
    Allowed  :  6.49 %
    Favored  : 93.42 %
  Rotamer:
    Outliers :  4.74 %
    Allowed  : 26.03 %
    Favored  : 69.23 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 3.45 %
    Cis-general     : 0.09 %
    Twisted Proline : 0.00 %
    Twisted General : 0.18 %

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: -0.16 (0.26), residues: 1110
  helix:  0.56 (0.18), residues: 791
  sheet: -2.91 (1.26), residues: 10
  loop : -1.63 (0.38), residues: 309

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.013   0.001   TRP A 782 
 HIS   0.003   0.001   HIS A 351 
 PHE   0.013   0.001   PHE A1753 
 TYR   0.016   0.001   TYR A 163 
 ARG   0.008   0.000   ARG A1640 

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

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

  2220 Ramachandran restraints generated.
    1110 Oldfield, 0 Emsley, 1110 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2220 Ramachandran restraints generated.
    1110 Oldfield, 0 Emsley, 1110 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  271 residues out of total 990 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 45
    poor density    : 226
  time to evaluate  : 0.952 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  159 LYS cc_start: 0.8593 (tptt) cc_final: 0.8099 (mttm)
REVERT: A  160 TYR cc_start: 0.6531 (OUTLIER) cc_final: 0.5193 (m-80)
REVERT: A  174 LEU cc_start: 0.8111 (OUTLIER) cc_final: 0.7784 (mt)
REVERT: A  404 TYR cc_start: 0.7402 (t80) cc_final: 0.7123 (t80)
REVERT: A  407 ASN cc_start: 0.8651 (t0) cc_final: 0.8437 (t0)
REVERT: A  422 GLN cc_start: 0.7082 (mt0) cc_final: 0.6786 (pp30)
REVERT: A  705 MET cc_start: 0.8031 (mmm) cc_final: 0.7771 (mmp)
REVERT: A 1215 PHE cc_start: 0.7150 (OUTLIER) cc_final: 0.6442 (t80)
REVERT: A 1265 PHE cc_start: 0.7239 (m-80) cc_final: 0.6661 (t80)
REVERT: A 1274 CYS cc_start: 0.8150 (m) cc_final: 0.7803 (m)
REVERT: A 1472 ILE cc_start: 0.8038 (OUTLIER) cc_final: 0.7796 (tt)
REVERT: A 1496 TYR cc_start: 0.7687 (m-80) cc_final: 0.7201 (m-80)
REVERT: A 1497 TYR cc_start: 0.7762 (t80) cc_final: 0.7273 (t80)
REVERT: A 1613 ILE cc_start: 0.7272 (OUTLIER) cc_final: 0.6974 (mp)
REVERT: A 1656 LEU cc_start: 0.8118 (OUTLIER) cc_final: 0.7876 (mm)
REVERT: A 1729 TYR cc_start: 0.6396 (OUTLIER) cc_final: 0.5828 (p90)
  outliers start: 45
  outliers final: 32
  residues processed: 250
  average time/residue: 0.2014
  time to fit residues: 73.2849
Evaluate side-chains
  258 residues out of total 990 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 39
    poor density    : 219
  time to evaluate  : 0.974 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  122 ARG
Chi-restraints excluded: chain A residue  160 TYR
Chi-restraints excluded: chain A residue  164 THR
Chi-restraints excluded: chain A residue  174 LEU
Chi-restraints excluded: chain A residue  225 LEU
Chi-restraints excluded: chain A residue  237 LEU
Chi-restraints excluded: chain A residue  239 THR
Chi-restraints excluded: chain A residue  254 VAL
Chi-restraints excluded: chain A residue  325 LEU
Chi-restraints excluded: chain A residue  327 CYS
Chi-restraints excluded: chain A residue  385 SER
Chi-restraints excluded: chain A residue  400 LEU
Chi-restraints excluded: chain A residue  722 LEU
Chi-restraints excluded: chain A residue  826 LEU
Chi-restraints excluded: chain A residue  923 LEU
Chi-restraints excluded: chain A residue  940 LEU
Chi-restraints excluded: chain A residue 1215 PHE
Chi-restraints excluded: chain A residue 1226 PHE
Chi-restraints excluded: chain A residue 1260 TRP
Chi-restraints excluded: chain A residue 1261 VAL
Chi-restraints excluded: chain A residue 1275 TRP
Chi-restraints excluded: chain A residue 1293 LEU
Chi-restraints excluded: chain A residue 1324 VAL
Chi-restraints excluded: chain A residue 1366 ILE
Chi-restraints excluded: chain A residue 1424 MET
Chi-restraints excluded: chain A residue 1446 LEU
Chi-restraints excluded: chain A residue 1452 PHE
Chi-restraints excluded: chain A residue 1472 ILE
Chi-restraints excluded: chain A residue 1487 ILE
Chi-restraints excluded: chain A residue 1490 THR
Chi-restraints excluded: chain A residue 1503 LEU
Chi-restraints excluded: chain A residue 1613 ILE
Chi-restraints excluded: chain A residue 1624 PHE
Chi-restraints excluded: chain A residue 1649 LEU
Chi-restraints excluded: chain A residue 1656 LEU
Chi-restraints excluded: chain A residue 1708 GLN
Chi-restraints excluded: chain A residue 1711 THR
Chi-restraints excluded: chain A residue 1729 TYR
Chi-restraints excluded: chain A residue 1744 CYS
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 112
   random chunks:
   chunk 62 optimal weight:    3.9990
   chunk 0 optimal weight:   30.0000
   chunk 7 optimal weight:    5.9990
   chunk 54 optimal weight:   20.0000
   chunk 74 optimal weight:    3.9990
   chunk 111 optimal weight:    0.9980
   chunk 50 optimal weight:    9.9990
   chunk 59 optimal weight:    6.9990
   chunk 35 optimal weight:    5.9990
   chunk 42 optimal weight:    9.9990
   chunk 55 optimal weight:    5.9990
   overall best weight:    4.1988

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

Flipped N/Q/H residues before XYZ refinement:
** A 407 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 731 ASN
** A 889 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** A1465 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
A1586 HIS
** A1736 ASN ** 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 = 0.4393 r_free = 0.4393 target = 0.174614 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 41)----------------|
| r_work = 0.4032 r_free = 0.4032 target = 0.142317 restraints weight = 17117.486|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 49)----------------|
| r_work = 0.4078 r_free = 0.4078 target = 0.146260 restraints weight = 8378.595|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 50)----------------|
| r_work = 0.4107 r_free = 0.4107 target = 0.148787 restraints weight = 5448.390|
|-----------------------------------------------------------------------------|
r_work (final): 0.4107
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6981
moved from start:          0.3437

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.052   9670  Z= 0.285
  Angle     :  0.783  13.822  13108  Z= 0.379
  Chirality :  0.046   0.401   1547
  Planarity :  0.004   0.040   1541
  Dihedral  : 14.725 169.200   2043
  Min Nonbonded Distance : 2.412

Molprobity Statistics.
  All-atom Clashscore : 16.98
  Ramachandran Plot:
    Outliers :  0.09 %
    Allowed  :  7.30 %
    Favored  : 92.61 %
  Rotamer:
    Outliers :  5.06 %
    Allowed  : 26.13 %
    Favored  : 68.81 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 3.45 %
    Cis-general     : 0.09 %
    Twisted Proline : 0.00 %
    Twisted General : 0.18 %

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: -0.17 (0.26), residues: 1110
  helix:  0.51 (0.18), residues: 783
  sheet: -3.06 (1.22), residues: 10
  loop : -1.43 (0.40), residues: 317

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.011   0.001   TRP A1442 
 HIS   0.004   0.001   HIS A 351 
 PHE   0.019   0.002   PHE A1762 
 TYR   0.016   0.002   TYR A 379 
 ARG   0.007   0.000   ARG A 815 

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

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

  2220 Ramachandran restraints generated.
    1110 Oldfield, 0 Emsley, 1110 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2220 Ramachandran restraints generated.
    1110 Oldfield, 0 Emsley, 1110 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  277 residues out of total 990 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 48
    poor density    : 229
  time to evaluate  : 0.990 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  159 LYS cc_start: 0.8625 (tptt) cc_final: 0.8139 (mttm)
REVERT: A  160 TYR cc_start: 0.6222 (OUTLIER) cc_final: 0.4947 (m-80)
REVERT: A  174 LEU cc_start: 0.8111 (OUTLIER) cc_final: 0.7786 (mt)
REVERT: A  404 TYR cc_start: 0.7596 (t80) cc_final: 0.7175 (t80)
REVERT: A  422 GLN cc_start: 0.7110 (mt0) cc_final: 0.6799 (pp30)
REVERT: A  705 MET cc_start: 0.8085 (mmm) cc_final: 0.7877 (mmp)
REVERT: A  862 PHE cc_start: 0.7737 (m-80) cc_final: 0.7533 (m-80)
REVERT: A 1212 PHE cc_start: 0.7233 (OUTLIER) cc_final: 0.6731 (t80)
REVERT: A 1215 PHE cc_start: 0.7156 (OUTLIER) cc_final: 0.6368 (t80)
REVERT: A 1265 PHE cc_start: 0.7246 (m-80) cc_final: 0.6649 (t80)
REVERT: A 1274 CYS cc_start: 0.8170 (m) cc_final: 0.7815 (m)
REVERT: A 1348 LEU cc_start: 0.7881 (OUTLIER) cc_final: 0.7644 (tp)
REVERT: A 1496 TYR cc_start: 0.7703 (m-80) cc_final: 0.7221 (m-80)
REVERT: A 1497 TYR cc_start: 0.7780 (t80) cc_final: 0.7259 (t80)
REVERT: A 1613 ILE cc_start: 0.7288 (OUTLIER) cc_final: 0.6978 (mp)
REVERT: A 1656 LEU cc_start: 0.8147 (OUTLIER) cc_final: 0.7916 (mm)
REVERT: A 1729 TYR cc_start: 0.6513 (OUTLIER) cc_final: 0.5941 (p90)
  outliers start: 48
  outliers final: 34
  residues processed: 257
  average time/residue: 0.1778
  time to fit residues: 67.5723
Evaluate side-chains
  264 residues out of total 990 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 42
    poor density    : 222
  time to evaluate  : 1.055 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  122 ARG
Chi-restraints excluded: chain A residue  160 TYR
Chi-restraints excluded: chain A residue  164 THR
Chi-restraints excluded: chain A residue  174 LEU
Chi-restraints excluded: chain A residue  184 LEU
Chi-restraints excluded: chain A residue  225 LEU
Chi-restraints excluded: chain A residue  237 LEU
Chi-restraints excluded: chain A residue  239 THR
Chi-restraints excluded: chain A residue  254 VAL
Chi-restraints excluded: chain A residue  325 LEU
Chi-restraints excluded: chain A residue  327 CYS
Chi-restraints excluded: chain A residue  369 LEU
Chi-restraints excluded: chain A residue  400 LEU
Chi-restraints excluded: chain A residue  722 LEU
Chi-restraints excluded: chain A residue  826 LEU
Chi-restraints excluded: chain A residue  885 MET
Chi-restraints excluded: chain A residue  940 LEU
Chi-restraints excluded: chain A residue 1212 PHE
Chi-restraints excluded: chain A residue 1215 PHE
Chi-restraints excluded: chain A residue 1260 TRP
Chi-restraints excluded: chain A residue 1261 VAL
Chi-restraints excluded: chain A residue 1275 TRP
Chi-restraints excluded: chain A residue 1293 LEU
Chi-restraints excluded: chain A residue 1324 VAL
Chi-restraints excluded: chain A residue 1333 ILE
Chi-restraints excluded: chain A residue 1348 LEU
Chi-restraints excluded: chain A residue 1366 ILE
Chi-restraints excluded: chain A residue 1419 THR
Chi-restraints excluded: chain A residue 1424 MET
Chi-restraints excluded: chain A residue 1446 LEU
Chi-restraints excluded: chain A residue 1452 PHE
Chi-restraints excluded: chain A residue 1487 ILE
Chi-restraints excluded: chain A residue 1490 THR
Chi-restraints excluded: chain A residue 1503 LEU
Chi-restraints excluded: chain A residue 1613 ILE
Chi-restraints excluded: chain A residue 1624 PHE
Chi-restraints excluded: chain A residue 1649 LEU
Chi-restraints excluded: chain A residue 1656 LEU
Chi-restraints excluded: chain A residue 1708 GLN
Chi-restraints excluded: chain A residue 1711 THR
Chi-restraints excluded: chain A residue 1729 TYR
Chi-restraints excluded: chain A residue 1744 CYS
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 112
   random chunks:
   chunk 26 optimal weight:    0.7980
   chunk 31 optimal weight:   10.0000
   chunk 111 optimal weight:    1.9990
   chunk 47 optimal weight:    5.9990
   chunk 61 optimal weight:    6.9990
   chunk 56 optimal weight:    5.9990
   chunk 86 optimal weight:    0.3980
   chunk 69 optimal weight:    0.6980
   chunk 48 optimal weight:    0.9990
   chunk 105 optimal weight:    4.9990
   chunk 71 optimal weight:    4.9990
   overall best weight:    0.9784

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

Flipped N/Q/H residues before XYZ refinement:
** A 407 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 731 ASN
** A 889 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** A1376 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A1465 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
A1586 HIS
** A1736 ASN ** 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 = 0.4438 r_free = 0.4438 target = 0.178977 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 54)----------------|
| r_work = 0.4096 r_free = 0.4096 target = 0.147425 restraints weight = 17018.463|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 45)----------------|
| r_work = 0.4141 r_free = 0.4141 target = 0.151522 restraints weight = 8190.835|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 45)----------------|
| r_work = 0.4170 r_free = 0.4170 target = 0.154159 restraints weight = 5300.740|
|-----------------------------------------------------------------------------|
r_work (final): 0.4172
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6887
moved from start:          0.3771

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.055   9670  Z= 0.188
  Angle     :  0.766  15.286  13108  Z= 0.368
  Chirality :  0.044   0.348   1547
  Planarity :  0.004   0.040   1541
  Dihedral  : 14.061 169.549   2043
  Min Nonbonded Distance : 2.418

Molprobity Statistics.
  All-atom Clashscore : 14.77
  Ramachandran Plot:
    Outliers :  0.09 %
    Allowed  :  6.04 %
    Favored  : 93.87 %
  Rotamer:
    Outliers :  4.00 %
    Allowed  : 28.24 %
    Favored  : 67.76 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 3.45 %
    Cis-general     : 0.09 %
    Twisted Proline : 0.00 %
    Twisted General : 0.18 %

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: -0.05 (0.26), residues: 1110
  helix:  0.65 (0.18), residues: 780
  sheet: -2.93 (1.22), residues: 10
  loop : -1.52 (0.38), residues: 320

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.014   0.001   TRP A 375 
 HIS   0.002   0.001   HIS A 279 
 PHE   0.016   0.001   PHE A1212 
 TYR   0.016   0.001   TYR A 417 
 ARG   0.008   0.000   ARG A1640 

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

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

  2220 Ramachandran restraints generated.
    1110 Oldfield, 0 Emsley, 1110 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2220 Ramachandran restraints generated.
    1110 Oldfield, 0 Emsley, 1110 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  279 residues out of total 990 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 38
    poor density    : 241
  time to evaluate  : 1.067 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  160 TYR cc_start: 0.6309 (OUTLIER) cc_final: 0.5051 (m-80)
REVERT: A  174 LEU cc_start: 0.7955 (OUTLIER) cc_final: 0.7635 (mt)
REVERT: A  382 THR cc_start: 0.8313 (m) cc_final: 0.8072 (m)
REVERT: A  422 GLN cc_start: 0.7067 (mt0) cc_final: 0.6787 (pp30)
REVERT: A  926 MET cc_start: 0.7909 (tpt) cc_final: 0.7073 (tpt)
REVERT: A 1215 PHE cc_start: 0.7068 (OUTLIER) cc_final: 0.6269 (t80)
REVERT: A 1265 PHE cc_start: 0.7127 (m-80) cc_final: 0.6576 (t80)
REVERT: A 1274 CYS cc_start: 0.8129 (m) cc_final: 0.7790 (m)
REVERT: A 1472 ILE cc_start: 0.7939 (mp) cc_final: 0.7678 (tt)
REVERT: A 1496 TYR cc_start: 0.7729 (m-80) cc_final: 0.7298 (m-80)
REVERT: A 1497 TYR cc_start: 0.7774 (t80) cc_final: 0.7269 (t80)
REVERT: A 1603 LEU cc_start: 0.8946 (mm) cc_final: 0.8532 (mm)
REVERT: A 1613 ILE cc_start: 0.7124 (OUTLIER) cc_final: 0.6818 (mp)
REVERT: A 1729 TYR cc_start: 0.6365 (OUTLIER) cc_final: 0.5768 (p90)
  outliers start: 38
  outliers final: 23
  residues processed: 261
  average time/residue: 0.1896
  time to fit residues: 71.6520
Evaluate side-chains
  255 residues out of total 990 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 28
    poor density    : 227
  time to evaluate  : 0.928 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  122 ARG
Chi-restraints excluded: chain A residue  160 TYR
Chi-restraints excluded: chain A residue  164 THR
Chi-restraints excluded: chain A residue  174 LEU
Chi-restraints excluded: chain A residue  225 LEU
Chi-restraints excluded: chain A residue  237 LEU
Chi-restraints excluded: chain A residue  239 THR
Chi-restraints excluded: chain A residue  254 VAL
Chi-restraints excluded: chain A residue  325 LEU
Chi-restraints excluded: chain A residue  327 CYS
Chi-restraints excluded: chain A residue  722 LEU
Chi-restraints excluded: chain A residue  826 LEU
Chi-restraints excluded: chain A residue 1215 PHE
Chi-restraints excluded: chain A residue 1226 PHE
Chi-restraints excluded: chain A residue 1260 TRP
Chi-restraints excluded: chain A residue 1261 VAL
Chi-restraints excluded: chain A residue 1293 LEU
Chi-restraints excluded: chain A residue 1324 VAL
Chi-restraints excluded: chain A residue 1366 ILE
Chi-restraints excluded: chain A residue 1446 LEU
Chi-restraints excluded: chain A residue 1452 PHE
Chi-restraints excluded: chain A residue 1487 ILE
Chi-restraints excluded: chain A residue 1503 LEU
Chi-restraints excluded: chain A residue 1613 ILE
Chi-restraints excluded: chain A residue 1624 PHE
Chi-restraints excluded: chain A residue 1708 GLN
Chi-restraints excluded: chain A residue 1729 TYR
Chi-restraints excluded: chain A residue 1744 CYS
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 112
   random chunks:
   chunk 48 optimal weight:    1.9990
   chunk 20 optimal weight:    5.9990
   chunk 12 optimal weight:    2.9990
   chunk 90 optimal weight:    8.9990
   chunk 73 optimal weight:    5.9990
   chunk 110 optimal weight:    1.9990
   chunk 64 optimal weight:   20.0000
   chunk 37 optimal weight:    8.9990
   chunk 74 optimal weight:    3.9990
   chunk 10 optimal weight:   20.0000
   chunk 65 optimal weight:    4.9990
   overall best weight:    3.1990

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

Flipped N/Q/H residues before XYZ refinement:
** A 407 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 731 ASN
** A 889 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** A1376 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A1465 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
A1586 HIS
** A1736 ASN ** 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 = 0.4412 r_free = 0.4412 target = 0.176399 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 53)----------------|
| r_work = 0.4059 r_free = 0.4059 target = 0.144468 restraints weight = 17223.924|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 39)----------------|
| r_work = 0.4105 r_free = 0.4105 target = 0.148421 restraints weight = 8332.279|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 35)----------------|
| r_work = 0.4133 r_free = 0.4133 target = 0.150968 restraints weight = 5429.612|
|-----------------------------------------------------------------------------|
r_work (final): 0.4135
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6942
moved from start:          0.3787

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.059   9670  Z= 0.257
  Angle     :  0.818  15.093  13108  Z= 0.395
  Chirality :  0.049   0.548   1547
  Planarity :  0.004   0.040   1541
  Dihedral  : 13.910 169.572   2043
  Min Nonbonded Distance : 2.414

Molprobity Statistics.
  All-atom Clashscore : 16.09
  Ramachandran Plot:
    Outliers :  0.09 %
    Allowed  :  7.03 %
    Favored  : 92.88 %
  Rotamer:
    Outliers :  3.37 %
    Allowed  : 28.77 %
    Favored  : 67.86 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 3.45 %
    Cis-general     : 0.09 %
    Twisted Proline : 0.00 %
    Twisted General : 0.18 %

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: -0.17 (0.26), residues: 1110
  helix:  0.53 (0.18), residues: 789
  sheet: -3.11 (1.16), residues: 10
  loop : -1.51 (0.39), residues: 311

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.009   0.001   TRP A1442 
 HIS   0.003   0.001   HIS A 351 
 PHE   0.016   0.002   PHE A1346 
 TYR   0.016   0.002   TYR A 417 
 ARG   0.008   0.000   ARG A 815 

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

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

  2220 Ramachandran restraints generated.
    1110 Oldfield, 0 Emsley, 1110 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2220 Ramachandran restraints generated.
    1110 Oldfield, 0 Emsley, 1110 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  260 residues out of total 990 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 32
    poor density    : 228
  time to evaluate  : 1.010 
Fit side-chains
   revert: symmetry clash
REVERT: A  160 TYR cc_start: 0.6219 (OUTLIER) cc_final: 0.4866 (m-80)
REVERT: A  174 LEU cc_start: 0.7959 (OUTLIER) cc_final: 0.7653 (mt)
REVERT: A  422 GLN cc_start: 0.7024 (mt0) cc_final: 0.6783 (pp30)
REVERT: A 1215 PHE cc_start: 0.7151 (OUTLIER) cc_final: 0.6322 (t80)
REVERT: A 1265 PHE cc_start: 0.7187 (m-80) cc_final: 0.6613 (t80)
REVERT: A 1274 CYS cc_start: 0.8175 (m) cc_final: 0.7819 (m)
REVERT: A 1472 ILE cc_start: 0.8067 (mp) cc_final: 0.7818 (tt)
REVERT: A 1496 TYR cc_start: 0.7736 (m-80) cc_final: 0.7307 (m-80)
REVERT: A 1497 TYR cc_start: 0.7789 (t80) cc_final: 0.7270 (t80)
REVERT: A 1613 ILE cc_start: 0.7182 (OUTLIER) cc_final: 0.6876 (mp)
REVERT: A 1729 TYR cc_start: 0.6431 (OUTLIER) cc_final: 0.5838 (p90)
  outliers start: 32
  outliers final: 24
  residues processed: 249
  average time/residue: 0.1822
  time to fit residues: 66.2749
Evaluate side-chains
  252 residues out of total 990 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 29
    poor density    : 223
  time to evaluate  : 0.936 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  122 ARG
Chi-restraints excluded: chain A residue  160 TYR
Chi-restraints excluded: chain A residue  164 THR
Chi-restraints excluded: chain A residue  174 LEU
Chi-restraints excluded: chain A residue  225 LEU
Chi-restraints excluded: chain A residue  237 LEU
Chi-restraints excluded: chain A residue  239 THR
Chi-restraints excluded: chain A residue  254 VAL
Chi-restraints excluded: chain A residue  325 LEU
Chi-restraints excluded: chain A residue  327 CYS
Chi-restraints excluded: chain A residue  369 LEU
Chi-restraints excluded: chain A residue  385 SER
Chi-restraints excluded: chain A residue  722 LEU
Chi-restraints excluded: chain A residue  826 LEU
Chi-restraints excluded: chain A residue 1215 PHE
Chi-restraints excluded: chain A residue 1260 TRP
Chi-restraints excluded: chain A residue 1261 VAL
Chi-restraints excluded: chain A residue 1293 LEU
Chi-restraints excluded: chain A residue 1324 VAL
Chi-restraints excluded: chain A residue 1366 ILE
Chi-restraints excluded: chain A residue 1446 LEU
Chi-restraints excluded: chain A residue 1452 PHE
Chi-restraints excluded: chain A residue 1487 ILE
Chi-restraints excluded: chain A residue 1503 LEU
Chi-restraints excluded: chain A residue 1613 ILE
Chi-restraints excluded: chain A residue 1624 PHE
Chi-restraints excluded: chain A residue 1708 GLN
Chi-restraints excluded: chain A residue 1729 TYR
Chi-restraints excluded: chain A residue 1744 CYS
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 112
   random chunks:
   chunk 43 optimal weight:    6.9990
   chunk 63 optimal weight:    8.9990
   chunk 55 optimal weight:    2.9990
   chunk 51 optimal weight:    0.9980
   chunk 36 optimal weight:    8.9990
   chunk 49 optimal weight:    4.9990
   chunk 50 optimal weight:    9.9990
   chunk 109 optimal weight:    5.9990
   chunk 107 optimal weight:    4.9990
   chunk 0 optimal weight:   30.0000
   chunk 103 optimal weight:    0.9990
   overall best weight:    2.9988

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

Flipped N/Q/H residues before XYZ refinement:
** A 407 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 731 ASN
** A 860 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 889 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
A1586 HIS
** A1736 ASN ** 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 = 0.4413 r_free = 0.4413 target = 0.176525 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 41)----------------|
| r_work = 0.4059 r_free = 0.4059 target = 0.144505 restraints weight = 17015.652|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 55)----------------|
| r_work = 0.4106 r_free = 0.4106 target = 0.148498 restraints weight = 8293.398|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 39)----------------|
| r_work = 0.4134 r_free = 0.4134 target = 0.151052 restraints weight = 5397.154|
|-----------------------------------------------------------------------------|
r_work (final): 0.4136
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6940
moved from start:          0.3845

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.052   9670  Z= 0.245
  Angle     :  0.811  15.237  13108  Z= 0.392
  Chirality :  0.048   0.468   1547
  Planarity :  0.004   0.039   1541
  Dihedral  : 13.697 169.291   2043
  Min Nonbonded Distance : 2.413

Molprobity Statistics.
  All-atom Clashscore : 16.14
  Ramachandran Plot:
    Outliers :  0.09 %
    Allowed  :  6.94 %
    Favored  : 92.97 %
  Rotamer:
    Outliers :  3.58 %
    Allowed  : 29.29 %
    Favored  : 67.12 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 3.45 %
    Cis-general     : 0.09 %
    Twisted Proline : 0.00 %
    Twisted General : 0.18 %

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: -0.21 (0.26), residues: 1110
  helix:  0.48 (0.18), residues: 789
  sheet: -3.15 (1.15), residues: 10
  loop : -1.46 (0.39), residues: 311

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.011   0.001   TRP A1442 
 HIS   0.003   0.001   HIS A 351 
 PHE   0.017   0.002   PHE A 148 
 TYR   0.016   0.001   TYR A 417 
 ARG   0.004   0.000   ARG A 384 
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 3331.39 seconds
wall clock time: 60 minutes 20.52 seconds (3620.52 seconds total)