Starting phenix.real_space_refine
on Fri May 16 03:23:23 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/8tx1_41674/05_2025/8tx1_41674.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/8tx1_41674/05_2025/8tx1_41674.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=3.62
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/cci-nas-00/data/ceres_data/8tx1_41674/05_2025/8tx1_41674.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/8tx1_41674/05_2025/8tx1_41674.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/8tx1_41674/05_2025/8tx1_41674.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/8tx1_41674/05_2025/8tx1_41674.cif"
  }
  resolution = 3.62
  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=   0.002 sd=   0.092
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: 4
    Type Number    sf(0)   Gaussians
     S      83      5.16       5
     C    8643      2.51       5
     N    2234      2.21       5
     O    2727      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 36 residue(s): 0.03s

  Monomer Library directory:
    "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/chem_data/mon_lib"
  Total number of atoms: 13687
  Number of models: 1
  Model: ""
    Number of chains: 1
    Chain: "A"
      Number of atoms: 13687
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 1894, 13687
          Classifications: {'peptide': 1894}
          Incomplete info: {'truncation_to_alanine': 12}
          Link IDs: {'PCIS': 4, 'PTRANS': 195, 'TRANS': 1694}
          Chain breaks: 4
          Unresolved chain link angles: 1
          Unresolved non-hydrogen bonds: 43
          Unresolved non-hydrogen angles: 54
          Unresolved non-hydrogen dihedrals: 33
          Unresolved non-hydrogen chiralities: 2
          Planarities with less than four sites: {'GLN:plan1': 1, 'ARG:plan': 3, 'ASN:plan1': 2, 'ASP:plan': 2}
          Unresolved non-hydrogen planarities: 31
  Time building chain proxies: 8.12, per 1000 atoms: 0.59
  Number of scatterers: 13687
  At special positions: 0
  Unit cell: (114.38, 113.05, 400.33, 90, 90, 90)
  Space group: P 1 (No. 1)
  Number of sites at special positions: 0
  Number of scattering types: 4
    Type Number    sf(0)
     S      83     16.00
     O    2727      8.00
     N    2234      7.00
     C    8643      6.00
    sf(0) = scattering factor at diffraction angle 0.

  Number of disulfides: simple=31, symmetry=0
    Simple disulfide: pdb=" SG  CYS A 534 " - pdb=" SG  CYS A 594 " distance=2.03
    Simple disulfide: pdb=" SG  CYS A 660 " - pdb=" SG  CYS A 700 " distance=2.03
    Simple disulfide: pdb=" SG  CYS A 790 " - pdb=" SG  CYS A 817 " distance=2.03
    Simple disulfide: pdb=" SG  CYS A 905 " - pdb=" SG  CYS A 947 " distance=2.03
    Simple disulfide: pdb=" SG  CYS A1052 " - pdb=" SG  CYS A1110 " distance=2.05
    Simple disulfide: pdb=" SG  CYS A1182 " - pdb=" SG  CYS A1213 " distance=2.03
    Simple disulfide: pdb=" SG  CYS A1216 " - pdb=" SG  CYS A1228 " distance=2.03
    Simple disulfide: pdb=" SG  CYS A1231 " - pdb=" SG  CYS A1244 " distance=2.03
    Simple disulfide: pdb=" SG  CYS A1247 " - pdb=" SG  CYS A1284 " distance=2.03
    Simple disulfide: pdb=" SG  CYS A1287 " - pdb=" SG  CYS A1301 " distance=2.03
    Simple disulfide: pdb=" SG  CYS A1304 " - pdb=" SG  CYS A1317 " distance=2.02
    Simple disulfide: pdb=" SG  CYS A1320 " - pdb=" SG  CYS A1358 " distance=2.03
    Simple disulfide: pdb=" SG  CYS A1361 " - pdb=" SG  CYS A1389 " distance=2.03
    Simple disulfide: pdb=" SG  CYS A1392 " - pdb=" SG  CYS A1405 " distance=2.03
    Simple disulfide: pdb=" SG  CYS A1408 " - pdb=" SG  CYS A1445 " distance=2.03
    Simple disulfide: pdb=" SG  CYS A1448 " - pdb=" SG  CYS A1462 " distance=2.03
    Simple disulfide: pdb=" SG  CYS A1465 " - pdb=" SG  CYS A1479 " distance=2.04
    Simple disulfide: pdb=" SG  CYS A1482 " - pdb=" SG  CYS A1546 " distance=2.03
    Simple disulfide: pdb=" SG  CYS A1566 " - pdb=" SG  CYS A1593 " distance=2.03
    Simple disulfide: pdb=" SG  CYS A1596 " - pdb=" SG  CYS A1610 " distance=2.03
    Simple disulfide: pdb=" SG  CYS A1613 " - pdb=" SG  CYS A1627 " distance=2.03
    Simple disulfide: pdb=" SG  CYS A1666 " - pdb=" SG  CYS A1680 " distance=2.03
    Simple disulfide: pdb=" SG  CYS A1683 " - pdb=" SG  CYS A1697 " distance=2.03
    Simple disulfide: pdb=" SG  CYS A1700 " - pdb=" SG  CYS A1714 " distance=2.03
    Simple disulfide: pdb=" SG  CYS A1717 " - pdb=" SG  CYS A1730 " distance=2.03
    Simple disulfide: pdb=" SG  CYS A1733 " - pdb=" SG  CYS A1747 " distance=2.03
    Simple disulfide: pdb=" SG  CYS A1750 " - pdb=" SG  CYS A1765 " distance=2.03
    Simple disulfide: pdb=" SG  CYS A1768 " - pdb=" SG  CYS A1794 " distance=2.03
    Simple disulfide: pdb=" SG  CYS A1797 " - pdb=" SG  CYS A1811 " distance=2.03
    Simple disulfide: pdb=" SG  CYS A1814 " - pdb=" SG  CYS A1837 " distance=2.03
    Simple disulfide: pdb=" SG  CYS A1828 " - pdb=" SG  CYS A1840 " 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=0, symmetry=0
  Time building additional restraints: 3.40
  Conformation dependent library (CDL) restraints added in 2.0 seconds
  

  3768 Ramachandran restraints generated.
    1884 Oldfield, 0 Emsley, 1884 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  3486

  Finding SS restraints...
    Secondary structure from input PDB file:
      9 helices and 39 sheets defined
      4.3% alpha, 17.8% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 2.04
  Creating SS restraints...
    Processing helix  chain 'A' and resid 265 through 269
    Processing helix  chain 'A' and resid 547 through 557
      removed outlier: 3.580A  pdb=" N   TRP A 551 " --> pdb=" O   ASP A 547 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 673 through 683
    Processing helix  chain 'A' and resid 822 through 827
      removed outlier: 4.035A  pdb=" N   THR A 825 " --> pdb=" O   ALA A 822 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 1073 through 1077
      removed outlier: 3.757A  pdb=" N   PHE A1077 " --> pdb=" O   TYR A1074 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 1343 through 1348
    Processing helix  chain 'A' and resid 1424 through 1428
      removed outlier: 3.638A  pdb=" N   THR A1428 " --> pdb=" O   PRO A1425 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 1492 through 1497
      removed outlier: 3.601A  pdb=" N   MET A1497 " --> pdb=" O   ARG A1493 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 1957 through 1982
      removed outlier: 3.772A  pdb=" N   GLN A1982 " --> pdb=" O   ASP A1978 " (cutoff:3.500A)
    Processing sheet with id=AA1, first strand: chain 'A' and resid 46 through 51
    Processing sheet with id=AA2, first strand: chain 'A' and resid 80 through 84
    Processing sheet with id=AA3, first strand: chain 'A' and resid 157 through 162
    Processing sheet with id=AA4, first strand: chain 'A' and resid 206 through 210
      removed outlier: 3.642A  pdb=" N   ILE A 209 " --> pdb=" O   MET A 189 " (cutoff:3.500A)
      removed outlier: 6.680A  pdb=" N   MET A 189 " --> pdb=" O   ILE A 209 " (cutoff:3.500A)
    Processing sheet with id=AA5, first strand: chain 'A' and resid 286 through 289
    Processing sheet with id=AA6, first strand: chain 'A' and resid 307 through 311
      removed outlier: 3.979A  pdb=" N   LEU A 363 " --> pdb=" O   ALA A 372 " (cutoff:3.500A)
      removed outlier: 4.115A  pdb=" N   ALA A 372 " --> pdb=" O   LEU A 363 " (cutoff:3.500A)
    Processing sheet with id=AA7, first strand: chain 'A' and resid 386 through 391
      removed outlier: 3.765A  pdb=" N   ILE A 403 " --> pdb=" O   ASN A 453 " (cutoff:3.500A)
      removed outlier: 3.524A  pdb=" N   PHE A 405 " --> pdb=" O   LEU A 451 " (cutoff:3.500A)
      removed outlier: 3.938A  pdb=" N   LEU A 451 " --> pdb=" O   PHE A 405 " (cutoff:3.500A)
    Processing sheet with id=AA8, first strand: chain 'A' and resid 419 through 423
    Processing sheet with id=AA9, first strand: chain 'A' and resid 495 through 501
    Processing sheet with id=AB1, first strand: chain 'A' and resid 530 through 534
      removed outlier: 4.073A  pdb=" N   GLU A 530 " --> pdb=" O   ILE A 565 " (cutoff:3.500A)
    Processing sheet with id=AB2, first strand: chain 'A' and resid 536 through 538
    Processing sheet with id=AB3, first strand: chain 'A' and resid 621 through 627
    Processing sheet with id=AB4, first strand: chain 'A' and resid 686 through 688
    Processing sheet with id=AB5, first strand: chain 'A' and resid 751 through 758
    Processing sheet with id=AB6, first strand: chain 'A' and resid 786 through 790
    Processing sheet with id=AB7, first strand: chain 'A' and resid 830 through 840
      removed outlier: 7.036A  pdb=" N   ASP A 840 " --> pdb=" O   THR A 844 " (cutoff:3.500A)
      removed outlier: 5.986A  pdb=" N   THR A 844 " --> pdb=" O   ASP A 840 " (cutoff:3.500A)
    Processing sheet with id=AB8, first strand: chain 'A' and resid 864 through 870
    Processing sheet with id=AB9, first strand: chain 'A' and resid 904 through 908
    Processing sheet with id=AC1, first strand: chain 'A' and resid 1006 through 1013
      removed outlier: 5.899A  pdb=" N   VAL A1008 " --> pdb=" O   LEU A1035 " (cutoff:3.500A)
      removed outlier: 6.507A  pdb=" N   LEU A1035 " --> pdb=" O   VAL A1008 " (cutoff:3.500A)
    Processing sheet with id=AC2, first strand: chain 'A' and resid 1094 through 1101
      removed outlier: 4.488A  pdb=" N   GLN A1049 " --> pdb=" O   TYR A1131 " (cutoff:3.500A)
      removed outlier: 8.244A  pdb=" N   VAL A1128 " --> pdb=" O   ASN A1139 " (cutoff:3.500A)
      removed outlier: 5.649A  pdb=" N   ASN A1139 " --> pdb=" O   VAL A1128 " (cutoff:3.500A)
      removed outlier: 5.508A  pdb=" N   GLU A1130 " --> pdb=" O   GLY A1137 " (cutoff:3.500A)
    Processing sheet with id=AC3, first strand: chain 'A' and resid 1187 through 1191
    Processing sheet with id=AC4, first strand: chain 'A' and resid 1302 through 1303
      removed outlier: 7.371A  pdb=" N   TYR A1291 " --> pdb=" O   ALA A1314 " (cutoff:3.500A)
    Processing sheet with id=AC5, first strand: chain 'A' and resid 1308 through 1309
    Processing sheet with id=AC6, first strand: chain 'A' and resid 1324 through 1327
    Processing sheet with id=AC7, first strand: chain 'A' and resid 1421 through 1422
      removed outlier: 3.549A  pdb=" N   GLN A1421 " --> pdb=" O   THR A1436 " (cutoff:3.500A)
    Processing sheet with id=AC8, first strand: chain 'A' and resid 1452 through 1453
      removed outlier: 3.543A  pdb=" N   LEU A1463 " --> pdb=" O   TYR A1453 " (cutoff:3.500A)
    Processing sheet with id=AC9, first strand: chain 'A' and resid 1469 through 1470
    Processing sheet with id=AD1, first strand: chain 'A' and resid 1486 through 1487
    Processing sheet with id=AD2, first strand: chain 'A' and resid 1570 through 1571
      removed outlier: 3.703A  pdb=" N   TYR A1594 " --> pdb=" O   PHE A1571 " (cutoff:3.500A)
    Processing sheet with id=AD3, first strand: chain 'A' and resid 1600 through 1601
    Processing sheet with id=AD4, first strand: chain 'A' and resid 1617 through 1618
      removed outlier: 3.597A  pdb=" N   GLU A1628 " --> pdb=" O   PHE A1618 " (cutoff:3.500A)
    Processing sheet with id=AD5, first strand: chain 'A' and resid 1634 through 1635
      removed outlier: 3.918A  pdb=" N   THR A1664 " --> pdb=" O   PHE A1635 " (cutoff:3.500A)
    Processing sheet with id=AD6, first strand: chain 'A' and resid 1645 through 1647
    Processing sheet with id=AD7, first strand: chain 'A' and resid 1670 through 1671
    Processing sheet with id=AD8, first strand: chain 'A' and resid 1704 through 1705
    Processing sheet with id=AD9, first strand: chain 'A' and resid 1721 through 1722
    Processing sheet with id=AE1, first strand: chain 'A' and resid 1754 through 1755
      removed outlier: 3.507A  pdb=" N   ARG A1766 " --> pdb=" O   TYR A1755 " (cutoff:3.500A)
    Processing sheet with id=AE2, first strand: chain 'A' and resid 1772 through 1773
    Processing sheet with id=AE3, first strand: chain 'A' and resid 1817 through 1818

    275 hydrogen bonds defined for protein.
    672 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: 5.86

  Time building geometry restraints manager: 4.01 seconds

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

  Histogram of bond lengths:
        0.99 -     1.16: 1
        1.16 -     1.33: 3260
        1.33 -     1.50: 5227
        1.50 -     1.67: 5475
        1.67 -     1.84: 104
  Bond restraints: 14067
  Sorted by residual:
  bond pdb=" CB  PRO A 902 "
       pdb=" CG  PRO A 902 "
    ideal  model  delta    sigma   weight residual
    1.492  0.991  0.501 5.00e-02 4.00e+02 1.00e+02
  bond pdb=" CG  PRO A 902 "
       pdb=" CD  PRO A 902 "
    ideal  model  delta    sigma   weight residual
    1.503  1.276  0.227 3.40e-02 8.65e+02 4.45e+01
  bond pdb=" CG  PRO A1528 "
       pdb=" CD  PRO A1528 "
    ideal  model  delta    sigma   weight residual
    1.503  1.412  0.091 3.40e-02 8.65e+02 7.09e+00
  bond pdb=" CB  PRO A 321 "
       pdb=" CG  PRO A 321 "
    ideal  model  delta    sigma   weight residual
    1.492  1.621 -0.129 5.00e-02 4.00e+02 6.69e+00
  bond pdb=" CB  PRO A1288 "
       pdb=" CG  PRO A1288 "
    ideal  model  delta    sigma   weight residual
    1.492  1.611 -0.119 5.00e-02 4.00e+02 5.65e+00
  ... (remaining 14062 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -    10.44: 19388
       10.44 -    20.87: 2
       20.87 -    31.31: 1
       31.31 -    41.74: 1
       41.74 -    52.18: 1
  Bond angle restraints: 19393
  Sorted by residual:
  angle pdb=" N   PRO A 902 "
        pdb=" CD  PRO A 902 "
        pdb=" CG  PRO A 902 "
      ideal   model   delta    sigma   weight residual
     103.20   74.15   29.05 1.50e+00 4.44e-01 3.75e+02
  angle pdb=" CA  PRO A 902 "
        pdb=" CB  PRO A 902 "
        pdb=" CG  PRO A 902 "
      ideal   model   delta    sigma   weight residual
     104.50   71.58   32.92 1.90e+00 2.77e-01 3.00e+02
  angle pdb=" CB  PRO A 902 "
        pdb=" CG  PRO A 902 "
        pdb=" CD  PRO A 902 "
      ideal   model   delta    sigma   weight residual
     106.10  158.28  -52.18 3.20e+00 9.77e-02 2.66e+02
  angle pdb=" CA  PRO A 902 "
        pdb=" N   PRO A 902 "
        pdb=" CD  PRO A 902 "
      ideal   model   delta    sigma   weight residual
     112.00   93.50   18.50 1.40e+00 5.10e-01 1.75e+02
  angle pdb=" CA  PRO A 266 "
        pdb=" N   PRO A 266 "
        pdb=" CD  PRO A 266 "
      ideal   model   delta    sigma   weight residual
     112.00  102.72    9.28 1.40e+00 5.10e-01 4.39e+01
  ... (remaining 19388 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    17.71: 7379
       17.71 -    35.42: 843
       35.42 -    53.13: 189
       53.13 -    70.84: 43
       70.84 -    88.55: 15
  Dihedral angle restraints: 8469
    sinusoidal: 3020
      harmonic: 5449
  Sorted by residual:
  dihedral pdb=" CB  CYS A1750 "
           pdb=" SG  CYS A1750 "
           pdb=" SG  CYS A1765 "
           pdb=" CB  CYS A1765 "
      ideal   model   delta sinusoidal    sigma   weight residual
     -86.00 -163.97   77.97     1      1.00e+01 1.00e-02 7.60e+01
  dihedral pdb=" CB  CYS A1320 "
           pdb=" SG  CYS A1320 "
           pdb=" SG  CYS A1358 "
           pdb=" CB  CYS A1358 "
      ideal   model   delta sinusoidal    sigma   weight residual
     -86.00 -160.13   74.13     1      1.00e+01 1.00e-02 6.97e+01
  dihedral pdb=" CB  CYS A1216 "
           pdb=" SG  CYS A1216 "
           pdb=" SG  CYS A1228 "
           pdb=" CB  CYS A1228 "
      ideal   model   delta sinusoidal    sigma   weight residual
      93.00  158.21  -65.21     1      1.00e+01 1.00e-02 5.57e+01
  ... (remaining 8466 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.043: 1757
       0.043 -    0.087: 379
       0.087 -    0.130: 159
       0.130 -    0.173: 7
       0.173 -    0.216: 1
  Chirality restraints: 2303
  Sorted by residual:
  chirality pdb=" CA  PRO A1939 "
            pdb=" N   PRO A1939 "
            pdb=" C   PRO A1939 "
            pdb=" CB  PRO A1939 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.72    2.50    0.22 2.00e-01 2.50e+01 1.17e+00
  chirality pdb=" CA  ILE A1013 "
            pdb=" N   ILE A1013 "
            pdb=" C   ILE A1013 "
            pdb=" CB  ILE A1013 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.43    2.60   -0.17 2.00e-01 2.50e+01 6.98e-01
  chirality pdb=" CA  SER A1014 "
            pdb=" N   SER A1014 "
            pdb=" C   SER A1014 "
            pdb=" CB  SER A1014 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.36    0.15 2.00e-01 2.50e+01 5.55e-01
  ... (remaining 2300 not shown)

  Planarity restraints: 2537
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   GLN A 901 "    0.093 5.00e-02 4.00e+02   1.25e-01 2.50e+01
        pdb=" N   PRO A 902 "   -0.215 5.00e-02 4.00e+02
        pdb=" CA  PRO A 902 "    0.054 5.00e-02 4.00e+02
        pdb=" CD  PRO A 902 "    0.068 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   CYS A1361 "   -0.078 5.00e-02 4.00e+02   1.17e-01 2.17e+01
        pdb=" N   PRO A1362 "    0.202 5.00e-02 4.00e+02
        pdb=" CA  PRO A1362 "   -0.062 5.00e-02 4.00e+02
        pdb=" CD  PRO A1362 "   -0.061 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   THR A 104 "   -0.077 5.00e-02 4.00e+02   1.11e-01 1.97e+01
        pdb=" N   PRO A 105 "    0.192 5.00e-02 4.00e+02
        pdb=" CA  PRO A 105 "   -0.056 5.00e-02 4.00e+02
        pdb=" CD  PRO A 105 "   -0.060 5.00e-02 4.00e+02
  ... (remaining 2534 not shown)

  Histogram of nonbonded interaction distances:
        2.14 -     2.69: 391
        2.69 -     3.24: 13332
        3.24 -     3.79: 20230
        3.79 -     4.35: 23857
        4.35 -     4.90: 39607
  Nonbonded interactions: 97417
  Sorted by model distance:
  nonbonded pdb=" OD1 ASN A1018 "
            pdb=" OG1 THR A1020 "
     model   vdw
     2.136 3.040
  nonbonded pdb=" O   PRO A1466 "
            pdb=" NZ  LYS A1542 "
     model   vdw
     2.166 3.120
  nonbonded pdb=" OG1 THR A 398 "
            pdb=" OD1 ASP A 400 "
     model   vdw
     2.203 3.040
  nonbonded pdb=" O   PRO A1484 "
            pdb=" OG1 THR A1555 "
     model   vdw
     2.225 3.040
  nonbonded pdb=" O   LYS A1567 "
            pdb=" OG1 THR A1570 "
     model   vdw
     2.237 3.040
  ... (remaining 97412 not shown)

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

  No NCS relation were found !!!

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

Found NCS groups:
  found none.
Set up NCS constraints
  No NCS constraints will be used in refinement.
Set refine NCS operators
Adjust number of macro_cycles
  Number of macro_cycles: 10
Reset NCS operators
Extract rigid body selections
Check and reset occupancies
  Occupancies: min=1.00 max=1.00 mean=1.00
Load rotamer database and sin/cos tables
Set ADP refinement strategy
  ADPs will be refined as group one per residue
Make a string to write initial .geo file
Internal consistency checks
Time:
  Set random seed:                         0.000
  Set model cs if undefined:               0.000
  Decide on map wrapping:                  0.000
  Normalize map: mean=0, sd=1:             3.270
  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:          0.560
  Check model and map are aligned:         0.120
  Set scattering table:                    0.130
  Process input model:                     34.520
  Find NCS groups from input model:        0.160
  Set up NCS constraints:                  0.060
  Set refine NCS operators:                0.000
  Adjust number of macro_cycles:           0.000
  Reset NCS operators:                     0.000
  Extract rigid body selections:           0.000
  Check and reset occupancies:             0.000
  Load rotamer database and sin/cos tables:2.760
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   41.590
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.5104
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      :  0.006   0.501  14098  Z= 0.202
  Angle     :  0.924  52.177  19455  Z= 0.474
  Chirality :  0.042   0.216   2303
  Planarity :  0.008   0.125   2537
  Dihedral  : 15.941  88.553   4890
  Min Nonbonded Distance : 2.136

Molprobity Statistics.
  All-atom Clashscore : 12.74
  Ramachandran Plot:
    Outliers :  0.21 %
    Allowed  :  6.58 %
    Favored  : 93.21 %
  Rotamer:
    Outliers :  0.20 %
    Allowed  : 30.85 %
    Favored  : 68.95 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.01 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.06 %

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:  0.18 (0.20), residues: 1884
  helix:  1.38 (0.63), residues: 68
  sheet:  1.65 (0.26), residues: 395
  loop : -0.42 (0.17), residues: 1421

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.047   0.002   TRP A 420 
 HIS   0.002   0.001   HIS A 847 
 PHE   0.017   0.001   PHE A1538 
 TYR   0.021   0.001   TYR A1208 
 ARG   0.010   0.001   ARG A1242 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.11986 (  275)
  hydrogen bonds       : angle       5.91239 (  672)
  SS BOND              : bond        0.00375 (   31)
  SS BOND              : angle       1.40323 (   62)
  covalent geometry    : bond        0.00639 (14067)
  covalent geometry    : angle       0.92167 (19393)

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

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

  3768 Ramachandran restraints generated.
    1884 Oldfield, 0 Emsley, 1884 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3768 Ramachandran restraints generated.
    1884 Oldfield, 0 Emsley, 1884 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  73 residues out of total 1500 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 3
    poor density    : 70
  time to evaluate  : 1.405 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  817 CYS cc_start: 0.1719 (OUTLIER) cc_final: 0.1476 (t)
REVERT: A  966 MET cc_start: -0.1974 (mtm) cc_final: -0.2311 (mtm)
REVERT: A 1101 MET cc_start: 0.6333 (mmp) cc_final: 0.5896 (mmp)
  outliers start: 3
  outliers final: 1
  residues processed: 73
  average time/residue: 0.2070
  time to fit residues: 25.0674
Evaluate side-chains
  66 residues out of total 1500 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 2
    poor density    : 64
  time to evaluate  : 1.406 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  817 CYS
Chi-restraints excluded: chain A residue 1394 ASP
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 189
   random chunks:
   chunk 159 optimal weight:    7.9990
   chunk 143 optimal weight:    0.9980
   chunk 79 optimal weight:    9.9990
   chunk 48 optimal weight:   10.0000
   chunk 96 optimal weight:    0.0000
   chunk 76 optimal weight:   10.0000
   chunk 148 optimal weight:    9.9990
   chunk 57 optimal weight:    0.0670
   chunk 90 optimal weight:    5.9990
   chunk 110 optimal weight:    3.9990
   chunk 171 optimal weight:   10.0000
   overall best weight:    2.2126

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

Flipped N/Q/H residues before XYZ refinement:
** A  57 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 162 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 311 ASN
A1061 ASN
** A1506 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
A1637 ASN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4705 r_free = 0.4705 target = 0.141391 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 45)----------------|
| r_work = 0.4527 r_free = 0.4527 target = 0.128139 restraints weight = 94300.593|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 25)----------------|
| r_work = 0.4476 r_free = 0.4476 target = 0.127328 restraints weight = 105911.363|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 27)----------------|
| r_work = 0.4484 r_free = 0.4484 target = 0.127497 restraints weight = 77209.305|
|-----------------------------------------------------------------------------|
r_work (final): 0.4459
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.5095
moved from start:          0.0918

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.067  14098  Z= 0.151
  Angle     :  0.649   8.888  19455  Z= 0.324
  Chirality :  0.043   0.173   2303
  Planarity :  0.006   0.081   2537
  Dihedral  :  4.588  36.662   2016
  Min Nonbonded Distance : 2.320

Molprobity Statistics.
  All-atom Clashscore : 10.14
  Ramachandran Plot:
    Outliers :  0.27 %
    Allowed  :  6.53 %
    Favored  : 93.21 %
  Rotamer:
    Outliers :  3.90 %
    Allowed  : 27.28 %
    Favored  : 68.82 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.01 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.03 (0.20), residues: 1884
  helix:  1.22 (0.63), residues: 68
  sheet:  1.47 (0.26), residues: 382
  loop : -0.48 (0.17), residues: 1434

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.018   0.002   TRP A 420 
 HIS   0.003   0.002   HIS A 411 
 PHE   0.018   0.001   PHE A1538 
 TYR   0.021   0.001   TYR A1208 
 ARG   0.008   0.001   ARG A1242 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.02659 (  275)
  hydrogen bonds       : angle       5.27585 (  672)
  SS BOND              : bond        0.00470 (   31)
  SS BOND              : angle       1.19404 (   62)
  covalent geometry    : bond        0.00356 (14067)
  covalent geometry    : angle       0.64640 (19393)

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

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

  3768 Ramachandran restraints generated.
    1884 Oldfield, 0 Emsley, 1884 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3768 Ramachandran restraints generated.
    1884 Oldfield, 0 Emsley, 1884 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  135 residues out of total 1500 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 58
    poor density    : 77
  time to evaluate  : 1.431 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  833 PHE cc_start: 0.7964 (m-80) cc_final: 0.7619 (m-10)
REVERT: A  966 MET cc_start: -0.1319 (mtm) cc_final: -0.1670 (mtm)
REVERT: A 1101 MET cc_start: 0.7069 (OUTLIER) cc_final: 0.6708 (mmp)
REVERT: A 1229 ILE cc_start: 0.2694 (OUTLIER) cc_final: 0.2160 (tp)
REVERT: A 1252 ILE cc_start: 0.5352 (OUTLIER) cc_final: 0.4970 (mm)
REVERT: A 1269 THR cc_start: 0.2614 (OUTLIER) cc_final: 0.2101 (p)
REVERT: A 1421 GLN cc_start: 0.4731 (OUTLIER) cc_final: 0.2825 (mt0)
REVERT: A 1480 GLN cc_start: 0.5444 (OUTLIER) cc_final: 0.3687 (tp40)
  outliers start: 58
  outliers final: 29
  residues processed: 124
  average time/residue: 0.1965
  time to fit residues: 40.1206
Evaluate side-chains
  103 residues out of total 1500 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 35
    poor density    : 68
  time to evaluate  : 1.487 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   48 THR
Chi-restraints excluded: chain A residue  241 TYR
Chi-restraints excluded: chain A residue  254 THR
Chi-restraints excluded: chain A residue  291 THR
Chi-restraints excluded: chain A residue  302 THR
Chi-restraints excluded: chain A residue  507 ILE
Chi-restraints excluded: chain A residue  536 PHE
Chi-restraints excluded: chain A residue  599 THR
Chi-restraints excluded: chain A residue  643 ILE
Chi-restraints excluded: chain A residue  863 THR
Chi-restraints excluded: chain A residue  867 THR
Chi-restraints excluded: chain A residue  961 PHE
Chi-restraints excluded: chain A residue 1026 ILE
Chi-restraints excluded: chain A residue 1052 CYS
Chi-restraints excluded: chain A residue 1064 SER
Chi-restraints excluded: chain A residue 1096 LEU
Chi-restraints excluded: chain A residue 1101 MET
Chi-restraints excluded: chain A residue 1128 VAL
Chi-restraints excluded: chain A residue 1201 VAL
Chi-restraints excluded: chain A residue 1229 ILE
Chi-restraints excluded: chain A residue 1245 THR
Chi-restraints excluded: chain A residue 1252 ILE
Chi-restraints excluded: chain A residue 1266 ILE
Chi-restraints excluded: chain A residue 1269 THR
Chi-restraints excluded: chain A residue 1317 CYS
Chi-restraints excluded: chain A residue 1324 THR
Chi-restraints excluded: chain A residue 1361 CYS
Chi-restraints excluded: chain A residue 1383 VAL
Chi-restraints excluded: chain A residue 1421 GLN
Chi-restraints excluded: chain A residue 1432 VAL
Chi-restraints excluded: chain A residue 1453 TYR
Chi-restraints excluded: chain A residue 1469 THR
Chi-restraints excluded: chain A residue 1480 GLN
Chi-restraints excluded: chain A residue 1506 ASN
Chi-restraints excluded: chain A residue 1588 VAL
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 189
   random chunks:
   chunk 49 optimal weight:    5.9990
   chunk 20 optimal weight:    0.6980
   chunk 2 optimal weight:   10.0000
   chunk 85 optimal weight:    9.9990
   chunk 144 optimal weight:    8.9990
   chunk 14 optimal weight:    7.9990
   chunk 53 optimal weight:   20.0000
   chunk 23 optimal weight:    6.9990
   chunk 172 optimal weight:    0.0060
   chunk 160 optimal weight:   30.0000
   chunk 31 optimal weight:    2.9990
   overall best weight:    3.3402

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

Flipped N/Q/H residues before XYZ refinement:
** A  57 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 162 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 446 ASN
A1058 GLN
** A1506 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 = 0.4663 r_free = 0.4663 target = 0.138699 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 78)----------------|
| r_work = 0.4452 r_free = 0.4452 target = 0.124073 restraints weight = 94957.389|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 29)----------------|
| r_work = 0.4395 r_free = 0.4395 target = 0.122551 restraints weight = 97473.321|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 27)----------------|
| r_work = 0.4403 r_free = 0.4403 target = 0.122736 restraints weight = 78943.085|
|-----------------------------------------------------------------------------|
r_work (final): 0.4357
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.5450
moved from start:          0.1992

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.100  14098  Z= 0.199
  Angle     :  0.702   8.656  19455  Z= 0.360
  Chirality :  0.045   0.204   2303
  Planarity :  0.006   0.081   2537
  Dihedral  :  5.033  29.728   2013
  Min Nonbonded Distance : 2.241

Molprobity Statistics.
  All-atom Clashscore : 12.55
  Ramachandran Plot:
    Outliers :  0.32 %
    Allowed  :  7.75 %
    Favored  : 91.93 %
  Rotamer:
    Outliers :  5.44 %
    Allowed  : 27.22 %
    Favored  : 67.34 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.01 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -0.37 (0.19), residues: 1884
  helix:  0.90 (0.64), residues: 68
  sheet:  1.01 (0.26), residues: 396
  loop : -0.72 (0.17), residues: 1420

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.018   0.002   TRP A1236 
 HIS   0.005   0.002   HIS A1272 
 PHE   0.021   0.002   PHE A1538 
 TYR   0.024   0.002   TYR A1453 
 ARG   0.009   0.001   ARG A1242 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03332 (  275)
  hydrogen bonds       : angle       5.78181 (  672)
  SS BOND              : bond        0.00528 (   31)
  SS BOND              : angle       1.39720 (   62)
  covalent geometry    : bond        0.00450 (14067)
  covalent geometry    : angle       0.69911 (19393)

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

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

  3768 Ramachandran restraints generated.
    1884 Oldfield, 0 Emsley, 1884 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3768 Ramachandran restraints generated.
    1884 Oldfield, 0 Emsley, 1884 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  155 residues out of total 1500 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 81
    poor density    : 74
  time to evaluate  : 1.445 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  662 PHE cc_start: -0.2098 (OUTLIER) cc_final: -0.2621 (m-80)
REVERT: A  833 PHE cc_start: 0.8262 (m-80) cc_final: 0.8045 (m-80)
REVERT: A  966 MET cc_start: -0.2065 (mtm) cc_final: -0.2328 (mtm)
REVERT: A 1101 MET cc_start: 0.7048 (mmp) cc_final: 0.6828 (mmp)
REVERT: A 1201 VAL cc_start: 0.3272 (OUTLIER) cc_final: 0.1765 (t)
REVERT: A 1229 ILE cc_start: 0.3137 (OUTLIER) cc_final: 0.2855 (tp)
REVERT: A 1252 ILE cc_start: 0.6160 (OUTLIER) cc_final: 0.5748 (mm)
REVERT: A 1270 THR cc_start: 0.6813 (OUTLIER) cc_final: 0.6584 (t)
REVERT: A 1421 GLN cc_start: 0.5615 (OUTLIER) cc_final: 0.3533 (mt0)
REVERT: A 1453 TYR cc_start: 0.5451 (OUTLIER) cc_final: 0.4479 (t80)
REVERT: A 1747 CYS cc_start: 0.3631 (OUTLIER) cc_final: 0.3017 (p)
  outliers start: 81
  outliers final: 44
  residues processed: 142
  average time/residue: 0.1850
  time to fit residues: 43.4896
Evaluate side-chains
  120 residues out of total 1500 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 52
    poor density    : 68
  time to evaluate  : 1.439 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   48 THR
Chi-restraints excluded: chain A residue   79 VAL
Chi-restraints excluded: chain A residue  205 SER
Chi-restraints excluded: chain A residue  241 TYR
Chi-restraints excluded: chain A residue  254 THR
Chi-restraints excluded: chain A residue  291 THR
Chi-restraints excluded: chain A residue  302 THR
Chi-restraints excluded: chain A residue  354 THR
Chi-restraints excluded: chain A residue  438 THR
Chi-restraints excluded: chain A residue  536 PHE
Chi-restraints excluded: chain A residue  594 CYS
Chi-restraints excluded: chain A residue  599 THR
Chi-restraints excluded: chain A residue  621 THR
Chi-restraints excluded: chain A residue  627 THR
Chi-restraints excluded: chain A residue  643 ILE
Chi-restraints excluded: chain A residue  662 PHE
Chi-restraints excluded: chain A residue  860 THR
Chi-restraints excluded: chain A residue  863 THR
Chi-restraints excluded: chain A residue  867 THR
Chi-restraints excluded: chain A residue 1024 THR
Chi-restraints excluded: chain A residue 1026 ILE
Chi-restraints excluded: chain A residue 1052 CYS
Chi-restraints excluded: chain A residue 1064 SER
Chi-restraints excluded: chain A residue 1073 VAL
Chi-restraints excluded: chain A residue 1096 LEU
Chi-restraints excluded: chain A residue 1109 SER
Chi-restraints excluded: chain A residue 1128 VAL
Chi-restraints excluded: chain A residue 1172 VAL
Chi-restraints excluded: chain A residue 1183 PHE
Chi-restraints excluded: chain A residue 1201 VAL
Chi-restraints excluded: chain A residue 1229 ILE
Chi-restraints excluded: chain A residue 1245 THR
Chi-restraints excluded: chain A residue 1252 ILE
Chi-restraints excluded: chain A residue 1266 ILE
Chi-restraints excluded: chain A residue 1270 THR
Chi-restraints excluded: chain A residue 1287 CYS
Chi-restraints excluded: chain A residue 1317 CYS
Chi-restraints excluded: chain A residue 1318 THR
Chi-restraints excluded: chain A residue 1324 THR
Chi-restraints excluded: chain A residue 1361 CYS
Chi-restraints excluded: chain A residue 1383 VAL
Chi-restraints excluded: chain A residue 1394 ASP
Chi-restraints excluded: chain A residue 1421 GLN
Chi-restraints excluded: chain A residue 1427 ILE
Chi-restraints excluded: chain A residue 1432 VAL
Chi-restraints excluded: chain A residue 1453 TYR
Chi-restraints excluded: chain A residue 1479 CYS
Chi-restraints excluded: chain A residue 1588 VAL
Chi-restraints excluded: chain A residue 1609 VAL
Chi-restraints excluded: chain A residue 1747 CYS
Chi-restraints excluded: chain A residue 1871 ARG
Chi-restraints excluded: chain A residue 1900 SER
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 189
   random chunks:
   chunk 141 optimal weight:    5.9990
   chunk 113 optimal weight:    0.7980
   chunk 17 optimal weight:    4.9990
   chunk 34 optimal weight:   10.0000
   chunk 184 optimal weight:    2.9990
   chunk 92 optimal weight:    7.9990
   chunk 145 optimal weight:    0.7980
   chunk 166 optimal weight:    0.0270
   chunk 172 optimal weight:    1.9990
   chunk 112 optimal weight:    0.2980
   chunk 65 optimal weight:   20.0000
   overall best weight:    0.7840

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

Flipped N/Q/H residues before XYZ refinement:
** A  57 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A1506 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4685 r_free = 0.4685 target = 0.140272 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 56)----------------|
| r_work = 0.4485 r_free = 0.4485 target = 0.126143 restraints weight = 94907.733|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 38)----------------|
| r_work = 0.4436 r_free = 0.4436 target = 0.124596 restraints weight = 84240.654|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 27)----------------|
| r_work = 0.4448 r_free = 0.4448 target = 0.125152 restraints weight = 66510.911|
|-----------------------------------------------------------------------------|
r_work (final): 0.4402
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.5326
moved from start:          0.2048

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.058  14098  Z= 0.109
  Angle     :  0.600   7.275  19455  Z= 0.297
  Chirality :  0.042   0.180   2303
  Planarity :  0.005   0.072   2537
  Dihedral  :  4.438  22.776   2013
  Min Nonbonded Distance : 2.300

Molprobity Statistics.
  All-atom Clashscore : 8.36
  Ramachandran Plot:
    Outliers :  0.27 %
    Allowed  :  5.73 %
    Favored  : 94.00 %
  Rotamer:
    Outliers :  3.49 %
    Allowed  : 28.49 %
    Favored  : 68.01 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.01 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -0.23 (0.20), residues: 1884
  helix:  1.31 (0.65), residues: 68
  sheet:  1.18 (0.27), residues: 380
  loop : -0.64 (0.17), residues: 1436

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.011   0.001   TRP A 639 
 HIS   0.002   0.001   HIS A 847 
 PHE   0.011   0.001   PHE A1538 
 TYR   0.019   0.001   TYR A 385 
 ARG   0.006   0.000   ARG A1242 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.02305 (  275)
  hydrogen bonds       : angle       5.16340 (  672)
  SS BOND              : bond        0.00295 (   31)
  SS BOND              : angle       0.82655 (   62)
  covalent geometry    : bond        0.00255 (14067)
  covalent geometry    : angle       0.59907 (19393)

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

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

  3768 Ramachandran restraints generated.
    1884 Oldfield, 0 Emsley, 1884 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3768 Ramachandran restraints generated.
    1884 Oldfield, 0 Emsley, 1884 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  124 residues out of total 1500 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 52
    poor density    : 72
  time to evaluate  : 1.557 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  662 PHE cc_start: -0.2224 (OUTLIER) cc_final: -0.2895 (m-80)
REVERT: A  753 ILE cc_start: 0.5842 (OUTLIER) cc_final: 0.5510 (pt)
REVERT: A 1421 GLN cc_start: 0.4671 (OUTLIER) cc_final: 0.2937 (tt0)
REVERT: A 1480 GLN cc_start: 0.5122 (OUTLIER) cc_final: 0.3237 (tp40)
REVERT: A 1747 CYS cc_start: 0.3278 (OUTLIER) cc_final: 0.2364 (p)
  outliers start: 52
  outliers final: 28
  residues processed: 110
  average time/residue: 0.1910
  time to fit residues: 35.2314
Evaluate side-chains
  96 residues out of total 1500 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 33
    poor density    : 63
  time to evaluate  : 1.537 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   48 THR
Chi-restraints excluded: chain A residue  241 TYR
Chi-restraints excluded: chain A residue  254 THR
Chi-restraints excluded: chain A residue  291 THR
Chi-restraints excluded: chain A residue  421 THR
Chi-restraints excluded: chain A residue  536 PHE
Chi-restraints excluded: chain A residue  594 CYS
Chi-restraints excluded: chain A residue  599 THR
Chi-restraints excluded: chain A residue  643 ILE
Chi-restraints excluded: chain A residue  662 PHE
Chi-restraints excluded: chain A residue  753 ILE
Chi-restraints excluded: chain A residue  863 THR
Chi-restraints excluded: chain A residue 1026 ILE
Chi-restraints excluded: chain A residue 1052 CYS
Chi-restraints excluded: chain A residue 1096 LEU
Chi-restraints excluded: chain A residue 1109 SER
Chi-restraints excluded: chain A residue 1172 VAL
Chi-restraints excluded: chain A residue 1201 VAL
Chi-restraints excluded: chain A residue 1270 THR
Chi-restraints excluded: chain A residue 1317 CYS
Chi-restraints excluded: chain A residue 1324 THR
Chi-restraints excluded: chain A residue 1361 CYS
Chi-restraints excluded: chain A residue 1383 VAL
Chi-restraints excluded: chain A residue 1394 ASP
Chi-restraints excluded: chain A residue 1421 GLN
Chi-restraints excluded: chain A residue 1432 VAL
Chi-restraints excluded: chain A residue 1479 CYS
Chi-restraints excluded: chain A residue 1480 GLN
Chi-restraints excluded: chain A residue 1557 VAL
Chi-restraints excluded: chain A residue 1588 VAL
Chi-restraints excluded: chain A residue 1747 CYS
Chi-restraints excluded: chain A residue 1871 ARG
Chi-restraints excluded: chain A residue 1981 MET
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 189
   random chunks:
   chunk 179 optimal weight:    4.9990
   chunk 143 optimal weight:    4.9990
   chunk 73 optimal weight:    7.9990
   chunk 170 optimal weight:   40.0000
   chunk 64 optimal weight:    5.9990
   chunk 144 optimal weight:    2.9990
   chunk 111 optimal weight:    4.9990
   chunk 119 optimal weight:    4.9990
   chunk 60 optimal weight:    5.9990
   chunk 138 optimal weight:    1.9990
   chunk 101 optimal weight:    6.9990
   overall best weight:    3.9990

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

Flipped N/Q/H residues before XYZ refinement:
** A  57 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 162 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A1506 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4640 r_free = 0.4640 target = 0.137206 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 54)----------------|
| r_work = 0.4438 r_free = 0.4438 target = 0.123204 restraints weight = 95083.724|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 27)----------------|
| r_work = 0.4380 r_free = 0.4380 target = 0.121918 restraints weight = 97160.073|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 27)----------------|
| r_work = 0.4388 r_free = 0.4388 target = 0.122137 restraints weight = 79129.355|
|-----------------------------------------------------------------------------|
r_work (final): 0.4359
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.5427
moved from start:          0.2894

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.106  14098  Z= 0.218
  Angle     :  0.710   8.579  19455  Z= 0.363
  Chirality :  0.045   0.255   2303
  Planarity :  0.006   0.076   2537
  Dihedral  :  5.190  28.342   2013
  Min Nonbonded Distance : 2.236

Molprobity Statistics.
  All-atom Clashscore : 13.41
  Ramachandran Plot:
    Outliers :  0.32 %
    Allowed  :  8.23 %
    Favored  : 91.45 %
  Rotamer:
    Outliers :  4.91 %
    Allowed  : 27.62 %
    Favored  : 67.47 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.01 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -0.70 (0.19), residues: 1884
  helix:  0.52 (0.62), residues: 74
  sheet:  0.79 (0.26), residues: 379
  loop : -0.94 (0.17), residues: 1431

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.019   0.002   TRP A1236 
 HIS   0.006   0.002   HIS A1276 
 PHE   0.019   0.002   PHE A1091 
 TYR   0.022   0.002   TYR A1291 
 ARG   0.006   0.001   ARG A1242 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03077 (  275)
  hydrogen bonds       : angle       5.79527 (  672)
  SS BOND              : bond        0.00556 (   31)
  SS BOND              : angle       1.56255 (   62)
  covalent geometry    : bond        0.00497 (14067)
  covalent geometry    : angle       0.70573 (19393)

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

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

  3768 Ramachandran restraints generated.
    1884 Oldfield, 0 Emsley, 1884 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3768 Ramachandran restraints generated.
    1884 Oldfield, 0 Emsley, 1884 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  142 residues out of total 1500 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 73
    poor density    : 69
  time to evaluate  : 1.406 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  229 ASN cc_start: 0.5961 (OUTLIER) cc_final: 0.5554 (t0)
REVERT: A  662 PHE cc_start: -0.2263 (OUTLIER) cc_final: -0.2752 (m-80)
REVERT: A  753 ILE cc_start: 0.5847 (OUTLIER) cc_final: 0.5403 (pt)
REVERT: A  966 MET cc_start: -0.0938 (mtm) cc_final: -0.1227 (mtm)
REVERT: A 1179 ARG cc_start: 0.8066 (OUTLIER) cc_final: 0.7470 (ptm160)
REVERT: A 1229 ILE cc_start: 0.3307 (OUTLIER) cc_final: 0.2887 (tp)
REVERT: A 1480 GLN cc_start: 0.5233 (OUTLIER) cc_final: 0.3235 (tp40)
REVERT: A 1747 CYS cc_start: 0.3220 (OUTLIER) cc_final: 0.2463 (p)
REVERT: A 1981 MET cc_start: 0.3587 (OUTLIER) cc_final: 0.3286 (ptt)
  outliers start: 73
  outliers final: 48
  residues processed: 130
  average time/residue: 0.1997
  time to fit residues: 42.7627
Evaluate side-chains
  121 residues out of total 1500 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 56
    poor density    : 65
  time to evaluate  : 1.388 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   48 THR
Chi-restraints excluded: chain A residue   79 VAL
Chi-restraints excluded: chain A residue  229 ASN
Chi-restraints excluded: chain A residue  241 TYR
Chi-restraints excluded: chain A residue  254 THR
Chi-restraints excluded: chain A residue  291 THR
Chi-restraints excluded: chain A residue  302 THR
Chi-restraints excluded: chain A residue  354 THR
Chi-restraints excluded: chain A residue  421 THR
Chi-restraints excluded: chain A residue  438 THR
Chi-restraints excluded: chain A residue  536 PHE
Chi-restraints excluded: chain A residue  594 CYS
Chi-restraints excluded: chain A residue  599 THR
Chi-restraints excluded: chain A residue  627 THR
Chi-restraints excluded: chain A residue  643 ILE
Chi-restraints excluded: chain A residue  662 PHE
Chi-restraints excluded: chain A residue  753 ILE
Chi-restraints excluded: chain A residue  790 CYS
Chi-restraints excluded: chain A residue  863 THR
Chi-restraints excluded: chain A residue  867 THR
Chi-restraints excluded: chain A residue  887 THR
Chi-restraints excluded: chain A residue 1024 THR
Chi-restraints excluded: chain A residue 1031 THR
Chi-restraints excluded: chain A residue 1052 CYS
Chi-restraints excluded: chain A residue 1073 VAL
Chi-restraints excluded: chain A residue 1096 LEU
Chi-restraints excluded: chain A residue 1109 SER
Chi-restraints excluded: chain A residue 1128 VAL
Chi-restraints excluded: chain A residue 1172 VAL
Chi-restraints excluded: chain A residue 1179 ARG
Chi-restraints excluded: chain A residue 1183 PHE
Chi-restraints excluded: chain A residue 1196 THR
Chi-restraints excluded: chain A residue 1201 VAL
Chi-restraints excluded: chain A residue 1229 ILE
Chi-restraints excluded: chain A residue 1266 ILE
Chi-restraints excluded: chain A residue 1269 THR
Chi-restraints excluded: chain A residue 1317 CYS
Chi-restraints excluded: chain A residue 1318 THR
Chi-restraints excluded: chain A residue 1324 THR
Chi-restraints excluded: chain A residue 1354 ILE
Chi-restraints excluded: chain A residue 1361 CYS
Chi-restraints excluded: chain A residue 1383 VAL
Chi-restraints excluded: chain A residue 1418 PHE
Chi-restraints excluded: chain A residue 1421 GLN
Chi-restraints excluded: chain A residue 1427 ILE
Chi-restraints excluded: chain A residue 1432 VAL
Chi-restraints excluded: chain A residue 1479 CYS
Chi-restraints excluded: chain A residue 1480 GLN
Chi-restraints excluded: chain A residue 1486 THR
Chi-restraints excluded: chain A residue 1506 ASN
Chi-restraints excluded: chain A residue 1550 LEU
Chi-restraints excluded: chain A residue 1588 VAL
Chi-restraints excluded: chain A residue 1609 VAL
Chi-restraints excluded: chain A residue 1747 CYS
Chi-restraints excluded: chain A residue 1871 ARG
Chi-restraints excluded: chain A residue 1981 MET
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 189
   random chunks:
   chunk 40 optimal weight:    3.9990
   chunk 132 optimal weight:    6.9990
   chunk 80 optimal weight:   30.0000
   chunk 43 optimal weight:   10.0000
   chunk 88 optimal weight:    9.9990
   chunk 77 optimal weight:    5.9990
   chunk 142 optimal weight:    7.9990
   chunk 7 optimal weight:    0.0040
   chunk 100 optimal weight:    0.9980
   chunk 152 optimal weight:   10.0000
   chunk 58 optimal weight:    6.9990
   overall best weight:    3.5998

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

Flipped N/Q/H residues before XYZ refinement:
** A  57 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 901 GLN
A1049 GLN
** A1506 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 = 0.4629 r_free = 0.4629 target = 0.136284 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 44)----------------|
| r_work = 0.4435 r_free = 0.4435 target = 0.123058 restraints weight = 95493.174|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 27)----------------|
| r_work = 0.4386 r_free = 0.4386 target = 0.121975 restraints weight = 89993.586|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 29)----------------|
| r_work = 0.4396 r_free = 0.4396 target = 0.122339 restraints weight = 72850.054|
|-----------------------------------------------------------------------------|
r_work (final): 0.4371
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.5394
moved from start:          0.3557

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.061  14098  Z= 0.192
  Angle     :  0.695   9.850  19455  Z= 0.353
  Chirality :  0.044   0.227   2303
  Planarity :  0.006   0.079   2537
  Dihedral  :  5.385  25.795   2013
  Min Nonbonded Distance : 2.235

Molprobity Statistics.
  All-atom Clashscore : 12.37
  Ramachandran Plot:
    Outliers :  0.32 %
    Allowed  :  7.06 %
    Favored  : 92.62 %
  Rotamer:
    Outliers :  4.77 %
    Allowed  : 28.49 %
    Favored  : 66.73 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.01 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -0.91 (0.19), residues: 1884
  helix:  0.77 (0.64), residues: 68
  sheet:  0.55 (0.26), residues: 386
  loop : -1.08 (0.17), residues: 1430

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.023   0.002   TRP A 771 
 HIS   0.007   0.002   HIS A1276 
 PHE   0.021   0.002   PHE A 202 
 TYR   0.022   0.002   TYR A1291 
 ARG   0.003   0.001   ARG A1712 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.02982 (  275)
  hydrogen bonds       : angle       5.89143 (  672)
  SS BOND              : bond        0.00475 (   31)
  SS BOND              : angle       1.20149 (   62)
  covalent geometry    : bond        0.00433 (14067)
  covalent geometry    : angle       0.69319 (19393)

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

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

  3768 Ramachandran restraints generated.
    1884 Oldfield, 0 Emsley, 1884 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3768 Ramachandran restraints generated.
    1884 Oldfield, 0 Emsley, 1884 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  141 residues out of total 1500 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 71
    poor density    : 70
  time to evaluate  : 1.581 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  306 LEU cc_start: 0.4932 (OUTLIER) cc_final: 0.4428 (mt)
REVERT: A  662 PHE cc_start: -0.2430 (OUTLIER) cc_final: -0.2856 (m-80)
REVERT: A  753 ILE cc_start: 0.5865 (OUTLIER) cc_final: 0.5437 (pt)
REVERT: A  817 CYS cc_start: 0.2765 (OUTLIER) cc_final: 0.2502 (t)
REVERT: A 1480 GLN cc_start: 0.5159 (OUTLIER) cc_final: 0.2937 (tp40)
REVERT: A 1747 CYS cc_start: 0.3138 (OUTLIER) cc_final: 0.2242 (p)
REVERT: A 1981 MET cc_start: 0.3493 (OUTLIER) cc_final: 0.3127 (ptt)
  outliers start: 71
  outliers final: 49
  residues processed: 130
  average time/residue: 0.1960
  time to fit residues: 41.9880
Evaluate side-chains
  120 residues out of total 1500 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 56
    poor density    : 64
  time to evaluate  : 1.424 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   48 THR
Chi-restraints excluded: chain A residue   79 VAL
Chi-restraints excluded: chain A residue  142 LEU
Chi-restraints excluded: chain A residue  188 ASP
Chi-restraints excluded: chain A residue  223 ILE
Chi-restraints excluded: chain A residue  241 TYR
Chi-restraints excluded: chain A residue  291 THR
Chi-restraints excluded: chain A residue  306 LEU
Chi-restraints excluded: chain A residue  354 THR
Chi-restraints excluded: chain A residue  421 THR
Chi-restraints excluded: chain A residue  462 LEU
Chi-restraints excluded: chain A residue  536 PHE
Chi-restraints excluded: chain A residue  594 CYS
Chi-restraints excluded: chain A residue  599 THR
Chi-restraints excluded: chain A residue  643 ILE
Chi-restraints excluded: chain A residue  662 PHE
Chi-restraints excluded: chain A residue  673 THR
Chi-restraints excluded: chain A residue  753 ILE
Chi-restraints excluded: chain A residue  791 GLN
Chi-restraints excluded: chain A residue  817 CYS
Chi-restraints excluded: chain A residue  863 THR
Chi-restraints excluded: chain A residue  867 THR
Chi-restraints excluded: chain A residue 1024 THR
Chi-restraints excluded: chain A residue 1026 ILE
Chi-restraints excluded: chain A residue 1031 THR
Chi-restraints excluded: chain A residue 1052 CYS
Chi-restraints excluded: chain A residue 1073 VAL
Chi-restraints excluded: chain A residue 1096 LEU
Chi-restraints excluded: chain A residue 1109 SER
Chi-restraints excluded: chain A residue 1128 VAL
Chi-restraints excluded: chain A residue 1172 VAL
Chi-restraints excluded: chain A residue 1196 THR
Chi-restraints excluded: chain A residue 1201 VAL
Chi-restraints excluded: chain A residue 1266 ILE
Chi-restraints excluded: chain A residue 1269 THR
Chi-restraints excluded: chain A residue 1317 CYS
Chi-restraints excluded: chain A residue 1324 THR
Chi-restraints excluded: chain A residue 1354 ILE
Chi-restraints excluded: chain A residue 1361 CYS
Chi-restraints excluded: chain A residue 1377 SER
Chi-restraints excluded: chain A residue 1383 VAL
Chi-restraints excluded: chain A residue 1418 PHE
Chi-restraints excluded: chain A residue 1421 GLN
Chi-restraints excluded: chain A residue 1432 VAL
Chi-restraints excluded: chain A residue 1479 CYS
Chi-restraints excluded: chain A residue 1480 GLN
Chi-restraints excluded: chain A residue 1486 THR
Chi-restraints excluded: chain A residue 1557 VAL
Chi-restraints excluded: chain A residue 1584 THR
Chi-restraints excluded: chain A residue 1588 VAL
Chi-restraints excluded: chain A residue 1609 VAL
Chi-restraints excluded: chain A residue 1651 LEU
Chi-restraints excluded: chain A residue 1747 CYS
Chi-restraints excluded: chain A residue 1871 ARG
Chi-restraints excluded: chain A residue 1975 VAL
Chi-restraints excluded: chain A residue 1981 MET
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 189
   random chunks:
   chunk 171 optimal weight:    0.9990
   chunk 111 optimal weight:    3.9990
   chunk 74 optimal weight:   20.0000
   chunk 108 optimal weight:    2.9990
   chunk 64 optimal weight:    6.9990
   chunk 77 optimal weight:    3.9990
   chunk 187 optimal weight:    5.9990
   chunk 103 optimal weight:    0.9980
   chunk 182 optimal weight:    5.9990
   chunk 101 optimal weight:    0.7980
   chunk 91 optimal weight:    9.9990
   overall best weight:    1.9586

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

Flipped N/Q/H residues before XYZ refinement:
** A  57 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A1506 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4637 r_free = 0.4637 target = 0.136683 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 42)----------------|
| r_work = 0.4445 r_free = 0.4445 target = 0.123248 restraints weight = 95745.989|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 34)----------------|
| r_work = 0.4389 r_free = 0.4389 target = 0.121966 restraints weight = 87062.650|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 29)----------------|
| r_work = 0.4402 r_free = 0.4402 target = 0.122502 restraints weight = 66052.700|
|-----------------------------------------------------------------------------|
r_work (final): 0.4374
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.5388
moved from start:          0.3682

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.066  14098  Z= 0.136
  Angle     :  0.632   8.938  19455  Z= 0.317
  Chirality :  0.042   0.169   2303
  Planarity :  0.006   0.080   2537
  Dihedral  :  4.986  24.269   2013
  Min Nonbonded Distance : 2.258

Molprobity Statistics.
  All-atom Clashscore : 10.29
  Ramachandran Plot:
    Outliers :  0.32 %
    Allowed  :  7.48 %
    Favored  : 92.20 %
  Rotamer:
    Outliers :  4.03 %
    Allowed  : 29.37 %
    Favored  : 66.60 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.01 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -0.84 (0.19), residues: 1884
  helix:  0.97 (0.64), residues: 68
  sheet:  0.54 (0.26), residues: 393
  loop : -1.03 (0.17), residues: 1423

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.021   0.002   TRP A 771 
 HIS   0.005   0.002   HIS A 847 
 PHE   0.013   0.001   PHE A1418 
 TYR   0.017   0.001   TYR A1029 
 ARG   0.004   0.000   ARG A1179 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.02532 (  275)
  hydrogen bonds       : angle       5.56261 (  672)
  SS BOND              : bond        0.00351 (   31)
  SS BOND              : angle       0.91848 (   62)
  covalent geometry    : bond        0.00317 (14067)
  covalent geometry    : angle       0.63128 (19393)

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

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

  3768 Ramachandran restraints generated.
    1884 Oldfield, 0 Emsley, 1884 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3768 Ramachandran restraints generated.
    1884 Oldfield, 0 Emsley, 1884 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  122 residues out of total 1500 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 60
    poor density    : 62
  time to evaluate  : 1.413 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  175 PHE cc_start: 0.6621 (OUTLIER) cc_final: 0.6083 (m-10)
REVERT: A  606 TYR cc_start: 0.0761 (OUTLIER) cc_final: 0.0283 (m-10)
REVERT: A  662 PHE cc_start: -0.2698 (OUTLIER) cc_final: -0.3049 (m-80)
REVERT: A  753 ILE cc_start: 0.5904 (OUTLIER) cc_final: 0.5539 (pt)
REVERT: A  792 MET cc_start: -0.0262 (mtm) cc_final: -0.0835 (mtm)
REVERT: A  817 CYS cc_start: 0.2854 (OUTLIER) cc_final: 0.2640 (t)
REVERT: A 1229 ILE cc_start: 0.2078 (OUTLIER) cc_final: 0.1679 (tp)
REVERT: A 1286 LYS cc_start: 0.7893 (tppt) cc_final: 0.7583 (tptt)
REVERT: A 1480 GLN cc_start: 0.5057 (OUTLIER) cc_final: 0.2798 (tp40)
REVERT: A 1747 CYS cc_start: 0.3123 (OUTLIER) cc_final: 0.2241 (p)
REVERT: A 1981 MET cc_start: 0.3148 (OUTLIER) cc_final: 0.2642 (ptt)
  outliers start: 60
  outliers final: 47
  residues processed: 115
  average time/residue: 0.1998
  time to fit residues: 37.6054
Evaluate side-chains
  115 residues out of total 1500 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 56
    poor density    : 59
  time to evaluate  : 1.528 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   48 THR
Chi-restraints excluded: chain A residue   79 VAL
Chi-restraints excluded: chain A residue  142 LEU
Chi-restraints excluded: chain A residue  175 PHE
Chi-restraints excluded: chain A residue  223 ILE
Chi-restraints excluded: chain A residue  241 TYR
Chi-restraints excluded: chain A residue  254 THR
Chi-restraints excluded: chain A residue  291 THR
Chi-restraints excluded: chain A residue  354 THR
Chi-restraints excluded: chain A residue  421 THR
Chi-restraints excluded: chain A residue  438 THR
Chi-restraints excluded: chain A residue  536 PHE
Chi-restraints excluded: chain A residue  594 CYS
Chi-restraints excluded: chain A residue  599 THR
Chi-restraints excluded: chain A residue  606 TYR
Chi-restraints excluded: chain A residue  621 THR
Chi-restraints excluded: chain A residue  643 ILE
Chi-restraints excluded: chain A residue  662 PHE
Chi-restraints excluded: chain A residue  753 ILE
Chi-restraints excluded: chain A residue  817 CYS
Chi-restraints excluded: chain A residue  863 THR
Chi-restraints excluded: chain A residue  867 THR
Chi-restraints excluded: chain A residue  952 TYR
Chi-restraints excluded: chain A residue 1031 THR
Chi-restraints excluded: chain A residue 1052 CYS
Chi-restraints excluded: chain A residue 1073 VAL
Chi-restraints excluded: chain A residue 1096 LEU
Chi-restraints excluded: chain A residue 1109 SER
Chi-restraints excluded: chain A residue 1128 VAL
Chi-restraints excluded: chain A residue 1162 ILE
Chi-restraints excluded: chain A residue 1172 VAL
Chi-restraints excluded: chain A residue 1183 PHE
Chi-restraints excluded: chain A residue 1201 VAL
Chi-restraints excluded: chain A residue 1229 ILE
Chi-restraints excluded: chain A residue 1317 CYS
Chi-restraints excluded: chain A residue 1318 THR
Chi-restraints excluded: chain A residue 1324 THR
Chi-restraints excluded: chain A residue 1354 ILE
Chi-restraints excluded: chain A residue 1361 CYS
Chi-restraints excluded: chain A residue 1377 SER
Chi-restraints excluded: chain A residue 1383 VAL
Chi-restraints excluded: chain A residue 1418 PHE
Chi-restraints excluded: chain A residue 1421 GLN
Chi-restraints excluded: chain A residue 1432 VAL
Chi-restraints excluded: chain A residue 1465 CYS
Chi-restraints excluded: chain A residue 1479 CYS
Chi-restraints excluded: chain A residue 1480 GLN
Chi-restraints excluded: chain A residue 1486 THR
Chi-restraints excluded: chain A residue 1520 VAL
Chi-restraints excluded: chain A residue 1557 VAL
Chi-restraints excluded: chain A residue 1588 VAL
Chi-restraints excluded: chain A residue 1609 VAL
Chi-restraints excluded: chain A residue 1747 CYS
Chi-restraints excluded: chain A residue 1871 ARG
Chi-restraints excluded: chain A residue 1900 SER
Chi-restraints excluded: chain A residue 1981 MET
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 189
   random chunks:
   chunk 121 optimal weight:    0.3980
   chunk 18 optimal weight:    0.6980
   chunk 21 optimal weight:    4.9990
   chunk 152 optimal weight:    4.9990
   chunk 184 optimal weight:    0.0770
   chunk 37 optimal weight:    8.9990
   chunk 33 optimal weight:    4.9990
   chunk 42 optimal weight:    7.9990
   chunk 130 optimal weight:    7.9990
   chunk 175 optimal weight:   50.0000
   chunk 120 optimal weight:    5.9990
   overall best weight:    2.2342

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

Flipped N/Q/H residues before XYZ refinement:
** A  57 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A1506 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4630 r_free = 0.4630 target = 0.136012 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 53)----------------|
| r_work = 0.4441 r_free = 0.4441 target = 0.122794 restraints weight = 94288.699|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 27)----------------|
| r_work = 0.4385 r_free = 0.4385 target = 0.121514 restraints weight = 90551.623|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 29)----------------|
| r_work = 0.4399 r_free = 0.4399 target = 0.121979 restraints weight = 71923.082|
|-----------------------------------------------------------------------------|
r_work (final): 0.4372
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.5386
moved from start:          0.3924

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.065  14098  Z= 0.146
  Angle     :  0.637   9.674  19455  Z= 0.320
  Chirality :  0.043   0.163   2303
  Planarity :  0.006   0.077   2537
  Dihedral  :  4.957  25.788   2013
  Min Nonbonded Distance : 2.264

Molprobity Statistics.
  All-atom Clashscore : 11.03
  Ramachandran Plot:
    Outliers :  0.32 %
    Allowed  :  7.43 %
    Favored  : 92.25 %
  Rotamer:
    Outliers :  4.44 %
    Allowed  : 29.03 %
    Favored  : 66.53 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.01 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -0.84 (0.19), residues: 1884
  helix:  0.97 (0.64), residues: 68
  sheet:  0.58 (0.26), residues: 386
  loop : -1.03 (0.17), residues: 1430

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.012   0.001   TRP A1397 
 HIS   0.005   0.002   HIS A1276 
 PHE   0.012   0.001   PHE A1538 
 TYR   0.014   0.001   TYR A1291 
 ARG   0.004   0.000   ARG A 130 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.02659 (  275)
  hydrogen bonds       : angle       5.53995 (  672)
  SS BOND              : bond        0.00389 (   31)
  SS BOND              : angle       0.94430 (   62)
  covalent geometry    : bond        0.00337 (14067)
  covalent geometry    : angle       0.63593 (19393)

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

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

  3768 Ramachandran restraints generated.
    1884 Oldfield, 0 Emsley, 1884 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3768 Ramachandran restraints generated.
    1884 Oldfield, 0 Emsley, 1884 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  128 residues out of total 1500 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 66
    poor density    : 62
  time to evaluate  : 1.390 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  175 PHE cc_start: 0.6679 (OUTLIER) cc_final: 0.6110 (m-10)
REVERT: A  306 LEU cc_start: 0.4933 (OUTLIER) cc_final: 0.4459 (mt)
REVERT: A  606 TYR cc_start: 0.0780 (OUTLIER) cc_final: 0.0284 (m-10)
REVERT: A  662 PHE cc_start: -0.2700 (OUTLIER) cc_final: -0.3071 (m-80)
REVERT: A  753 ILE cc_start: 0.5885 (OUTLIER) cc_final: 0.5503 (pt)
REVERT: A 1229 ILE cc_start: 0.2408 (OUTLIER) cc_final: 0.1990 (tp)
REVERT: A 1286 LYS cc_start: 0.7770 (tppt) cc_final: 0.7480 (tptt)
REVERT: A 1480 GLN cc_start: 0.5035 (OUTLIER) cc_final: 0.2773 (tp40)
REVERT: A 1747 CYS cc_start: 0.3085 (OUTLIER) cc_final: 0.2200 (p)
REVERT: A 1981 MET cc_start: 0.3153 (OUTLIER) cc_final: 0.2640 (ptt)
  outliers start: 66
  outliers final: 49
  residues processed: 121
  average time/residue: 0.1916
  time to fit residues: 38.9503
Evaluate side-chains
  116 residues out of total 1500 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 58
    poor density    : 58
  time to evaluate  : 1.402 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   48 THR
Chi-restraints excluded: chain A residue   79 VAL
Chi-restraints excluded: chain A residue  142 LEU
Chi-restraints excluded: chain A residue  175 PHE
Chi-restraints excluded: chain A residue  223 ILE
Chi-restraints excluded: chain A residue  241 TYR
Chi-restraints excluded: chain A residue  254 THR
Chi-restraints excluded: chain A residue  291 THR
Chi-restraints excluded: chain A residue  306 LEU
Chi-restraints excluded: chain A residue  354 THR
Chi-restraints excluded: chain A residue  421 THR
Chi-restraints excluded: chain A residue  536 PHE
Chi-restraints excluded: chain A residue  594 CYS
Chi-restraints excluded: chain A residue  599 THR
Chi-restraints excluded: chain A residue  606 TYR
Chi-restraints excluded: chain A residue  621 THR
Chi-restraints excluded: chain A residue  643 ILE
Chi-restraints excluded: chain A residue  662 PHE
Chi-restraints excluded: chain A residue  673 THR
Chi-restraints excluded: chain A residue  753 ILE
Chi-restraints excluded: chain A residue  860 THR
Chi-restraints excluded: chain A residue  863 THR
Chi-restraints excluded: chain A residue  952 TYR
Chi-restraints excluded: chain A residue 1031 THR
Chi-restraints excluded: chain A residue 1052 CYS
Chi-restraints excluded: chain A residue 1073 VAL
Chi-restraints excluded: chain A residue 1084 VAL
Chi-restraints excluded: chain A residue 1096 LEU
Chi-restraints excluded: chain A residue 1109 SER
Chi-restraints excluded: chain A residue 1128 VAL
Chi-restraints excluded: chain A residue 1162 ILE
Chi-restraints excluded: chain A residue 1172 VAL
Chi-restraints excluded: chain A residue 1201 VAL
Chi-restraints excluded: chain A residue 1229 ILE
Chi-restraints excluded: chain A residue 1266 ILE
Chi-restraints excluded: chain A residue 1300 VAL
Chi-restraints excluded: chain A residue 1317 CYS
Chi-restraints excluded: chain A residue 1318 THR
Chi-restraints excluded: chain A residue 1324 THR
Chi-restraints excluded: chain A residue 1354 ILE
Chi-restraints excluded: chain A residue 1361 CYS
Chi-restraints excluded: chain A residue 1377 SER
Chi-restraints excluded: chain A residue 1383 VAL
Chi-restraints excluded: chain A residue 1418 PHE
Chi-restraints excluded: chain A residue 1421 GLN
Chi-restraints excluded: chain A residue 1427 ILE
Chi-restraints excluded: chain A residue 1432 VAL
Chi-restraints excluded: chain A residue 1479 CYS
Chi-restraints excluded: chain A residue 1480 GLN
Chi-restraints excluded: chain A residue 1486 THR
Chi-restraints excluded: chain A residue 1520 VAL
Chi-restraints excluded: chain A residue 1557 VAL
Chi-restraints excluded: chain A residue 1588 VAL
Chi-restraints excluded: chain A residue 1609 VAL
Chi-restraints excluded: chain A residue 1747 CYS
Chi-restraints excluded: chain A residue 1871 ARG
Chi-restraints excluded: chain A residue 1900 SER
Chi-restraints excluded: chain A residue 1981 MET
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 189
   random chunks:
   chunk 20 optimal weight:    8.9990
   chunk 158 optimal weight:   20.0000
   chunk 139 optimal weight:    6.9990
   chunk 39 optimal weight:   20.0000
   chunk 164 optimal weight:    6.9990
   chunk 123 optimal weight:    0.7980
   chunk 19 optimal weight:    7.9990
   chunk 70 optimal weight:    2.9990
   chunk 105 optimal weight:    1.9990
   chunk 65 optimal weight:   10.0000
   chunk 40 optimal weight:    0.0670
   overall best weight:    2.5724

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

Flipped N/Q/H residues before XYZ refinement:
** A  57 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A1506 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A1580 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4622 r_free = 0.4622 target = 0.135573 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 72)----------------|
| r_work = 0.4420 r_free = 0.4420 target = 0.121760 restraints weight = 94166.496|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 34)----------------|
| r_work = 0.4363 r_free = 0.4363 target = 0.120361 restraints weight = 100420.214|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 27)----------------|
| r_work = 0.4369 r_free = 0.4369 target = 0.120601 restraints weight = 77655.507|
|-----------------------------------------------------------------------------|
r_work (final): 0.4343
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.5481
moved from start:          0.4216

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.062  14098  Z= 0.156
  Angle     :  0.666  15.827  19455  Z= 0.330
  Chirality :  0.043   0.179   2303
  Planarity :  0.006   0.077   2537
  Dihedral  :  5.066  24.972   2013
  Min Nonbonded Distance : 2.244

Molprobity Statistics.
  All-atom Clashscore : 11.81
  Ramachandran Plot:
    Outliers :  0.32 %
    Allowed  :  7.75 %
    Favored  : 91.93 %
  Rotamer:
    Outliers :  4.50 %
    Allowed  : 28.83 %
    Favored  : 66.67 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.01 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -0.90 (0.19), residues: 1884
  helix:  0.94 (0.64), residues: 68
  sheet:  0.49 (0.26), residues: 386
  loop : -1.07 (0.17), residues: 1430

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.016   0.002   TRP A1397 
 HIS   0.005   0.001   HIS A 847 
 PHE   0.018   0.001   PHE A 886 
 TYR   0.019   0.001   TYR A1029 
 ARG   0.003   0.000   ARG A1712 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.02731 (  275)
  hydrogen bonds       : angle       5.69066 (  672)
  SS BOND              : bond        0.00485 (   31)
  SS BOND              : angle       0.95205 (   62)
  covalent geometry    : bond        0.00358 (14067)
  covalent geometry    : angle       0.66526 (19393)

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

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

  3768 Ramachandran restraints generated.
    1884 Oldfield, 0 Emsley, 1884 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3768 Ramachandran restraints generated.
    1884 Oldfield, 0 Emsley, 1884 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  127 residues out of total 1500 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 67
    poor density    : 60
  time to evaluate  : 1.523 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  175 PHE cc_start: 0.6762 (OUTLIER) cc_final: 0.6115 (m-10)
REVERT: A  306 LEU cc_start: 0.4853 (OUTLIER) cc_final: 0.4401 (mt)
REVERT: A  606 TYR cc_start: 0.0429 (OUTLIER) cc_final: -0.0071 (m-10)
REVERT: A  662 PHE cc_start: -0.2786 (OUTLIER) cc_final: -0.3164 (m-80)
REVERT: A  753 ILE cc_start: 0.5956 (OUTLIER) cc_final: 0.5624 (pt)
REVERT: A  792 MET cc_start: -0.0098 (mtm) cc_final: -0.0778 (mtp)
REVERT: A 1229 ILE cc_start: 0.2479 (OUTLIER) cc_final: 0.2023 (tp)
REVERT: A 1286 LYS cc_start: 0.7931 (tppt) cc_final: 0.7684 (tptt)
REVERT: A 1480 GLN cc_start: 0.4999 (OUTLIER) cc_final: 0.2685 (tp40)
REVERT: A 1747 CYS cc_start: 0.3130 (OUTLIER) cc_final: 0.2233 (p)
REVERT: A 1981 MET cc_start: 0.3286 (OUTLIER) cc_final: 0.2722 (ptt)
  outliers start: 67
  outliers final: 51
  residues processed: 121
  average time/residue: 0.1962
  time to fit residues: 38.9578
Evaluate side-chains
  117 residues out of total 1500 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 60
    poor density    : 57
  time to evaluate  : 1.383 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   48 THR
Chi-restraints excluded: chain A residue   79 VAL
Chi-restraints excluded: chain A residue  142 LEU
Chi-restraints excluded: chain A residue  175 PHE
Chi-restraints excluded: chain A residue  223 ILE
Chi-restraints excluded: chain A residue  241 TYR
Chi-restraints excluded: chain A residue  291 THR
Chi-restraints excluded: chain A residue  306 LEU
Chi-restraints excluded: chain A residue  354 THR
Chi-restraints excluded: chain A residue  421 THR
Chi-restraints excluded: chain A residue  536 PHE
Chi-restraints excluded: chain A residue  594 CYS
Chi-restraints excluded: chain A residue  599 THR
Chi-restraints excluded: chain A residue  606 TYR
Chi-restraints excluded: chain A residue  621 THR
Chi-restraints excluded: chain A residue  643 ILE
Chi-restraints excluded: chain A residue  662 PHE
Chi-restraints excluded: chain A residue  673 THR
Chi-restraints excluded: chain A residue  753 ILE
Chi-restraints excluded: chain A residue  860 THR
Chi-restraints excluded: chain A residue  863 THR
Chi-restraints excluded: chain A residue  867 THR
Chi-restraints excluded: chain A residue  952 TYR
Chi-restraints excluded: chain A residue 1031 THR
Chi-restraints excluded: chain A residue 1052 CYS
Chi-restraints excluded: chain A residue 1073 VAL
Chi-restraints excluded: chain A residue 1084 VAL
Chi-restraints excluded: chain A residue 1096 LEU
Chi-restraints excluded: chain A residue 1109 SER
Chi-restraints excluded: chain A residue 1128 VAL
Chi-restraints excluded: chain A residue 1162 ILE
Chi-restraints excluded: chain A residue 1172 VAL
Chi-restraints excluded: chain A residue 1183 PHE
Chi-restraints excluded: chain A residue 1196 THR
Chi-restraints excluded: chain A residue 1201 VAL
Chi-restraints excluded: chain A residue 1229 ILE
Chi-restraints excluded: chain A residue 1266 ILE
Chi-restraints excluded: chain A residue 1300 VAL
Chi-restraints excluded: chain A residue 1317 CYS
Chi-restraints excluded: chain A residue 1318 THR
Chi-restraints excluded: chain A residue 1324 THR
Chi-restraints excluded: chain A residue 1354 ILE
Chi-restraints excluded: chain A residue 1361 CYS
Chi-restraints excluded: chain A residue 1377 SER
Chi-restraints excluded: chain A residue 1383 VAL
Chi-restraints excluded: chain A residue 1418 PHE
Chi-restraints excluded: chain A residue 1421 GLN
Chi-restraints excluded: chain A residue 1427 ILE
Chi-restraints excluded: chain A residue 1432 VAL
Chi-restraints excluded: chain A residue 1479 CYS
Chi-restraints excluded: chain A residue 1480 GLN
Chi-restraints excluded: chain A residue 1486 THR
Chi-restraints excluded: chain A residue 1520 VAL
Chi-restraints excluded: chain A residue 1557 VAL
Chi-restraints excluded: chain A residue 1588 VAL
Chi-restraints excluded: chain A residue 1609 VAL
Chi-restraints excluded: chain A residue 1747 CYS
Chi-restraints excluded: chain A residue 1871 ARG
Chi-restraints excluded: chain A residue 1900 SER
Chi-restraints excluded: chain A residue 1981 MET
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 189
   random chunks:
   chunk 178 optimal weight:    3.9990
   chunk 74 optimal weight:    6.9990
   chunk 11 optimal weight:   10.0000
   chunk 37 optimal weight:    5.9990
   chunk 94 optimal weight:    0.7980
   chunk 55 optimal weight:    7.9990
   chunk 13 optimal weight:    2.9990
   chunk 150 optimal weight:    9.9990
   chunk 38 optimal weight:    1.9990
   chunk 173 optimal weight:    9.9990
   chunk 9 optimal weight:    0.0570
   overall best weight:    1.9704

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

Flipped N/Q/H residues before XYZ refinement:
** A  57 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A1506 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4627 r_free = 0.4627 target = 0.135811 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 58)----------------|
| r_work = 0.4429 r_free = 0.4429 target = 0.121914 restraints weight = 94231.013|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 27)----------------|
| r_work = 0.4371 r_free = 0.4371 target = 0.120698 restraints weight = 101481.433|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 27)----------------|
| r_work = 0.4385 r_free = 0.4385 target = 0.121130 restraints weight = 73517.133|
|-----------------------------------------------------------------------------|
r_work (final): 0.4354
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.5465
moved from start:          0.4297

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.065  14098  Z= 0.136
  Angle     :  0.658  16.718  19455  Z= 0.323
  Chirality :  0.043   0.159   2303
  Planarity :  0.006   0.080   2537
  Dihedral  :  4.922  27.071   2013
  Min Nonbonded Distance : 2.280

Molprobity Statistics.
  All-atom Clashscore : 10.96
  Ramachandran Plot:
    Outliers :  0.32 %
    Allowed  :  7.11 %
    Favored  : 92.57 %
  Rotamer:
    Outliers :  4.03 %
    Allowed  : 29.10 %
    Favored  : 66.87 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.01 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -0.90 (0.19), residues: 1884
  helix:  1.06 (0.65), residues: 68
  sheet:  0.42 (0.26), residues: 388
  loop : -1.05 (0.17), residues: 1428

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.016   0.001   TRP A 771 
 HIS   0.005   0.002   HIS A1276 
 PHE   0.011   0.001   PHE A1538 
 TYR   0.014   0.001   TYR A1291 
 ARG   0.004   0.000   ARG A1179 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.02546 (  275)
  hydrogen bonds       : angle       5.54625 (  672)
  SS BOND              : bond        0.00402 (   31)
  SS BOND              : angle       0.91355 (   62)
  covalent geometry    : bond        0.00316 (14067)
  covalent geometry    : angle       0.65667 (19393)

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

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

  3768 Ramachandran restraints generated.
    1884 Oldfield, 0 Emsley, 1884 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3768 Ramachandran restraints generated.
    1884 Oldfield, 0 Emsley, 1884 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  120 residues out of total 1500 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 60
    poor density    : 60
  time to evaluate  : 1.523 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  175 PHE cc_start: 0.6689 (OUTLIER) cc_final: 0.6082 (m-10)
REVERT: A  306 LEU cc_start: 0.4833 (OUTLIER) cc_final: 0.4374 (mt)
REVERT: A  606 TYR cc_start: 0.0023 (OUTLIER) cc_final: -0.0457 (m-10)
REVERT: A  662 PHE cc_start: -0.2874 (OUTLIER) cc_final: -0.3251 (m-80)
REVERT: A  753 ILE cc_start: 0.5928 (OUTLIER) cc_final: 0.5588 (pt)
REVERT: A 1101 MET cc_start: 0.5496 (mmp) cc_final: 0.5204 (mmp)
REVERT: A 1229 ILE cc_start: 0.2515 (OUTLIER) cc_final: 0.2086 (tp)
REVERT: A 1480 GLN cc_start: 0.4957 (OUTLIER) cc_final: 0.2682 (tp40)
REVERT: A 1747 CYS cc_start: 0.3004 (OUTLIER) cc_final: 0.2196 (p)
REVERT: A 1981 MET cc_start: 0.3212 (OUTLIER) cc_final: 0.2628 (ptt)
  outliers start: 60
  outliers final: 49
  residues processed: 114
  average time/residue: 0.2100
  time to fit residues: 39.0958
Evaluate side-chains
  113 residues out of total 1500 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 58
    poor density    : 55
  time to evaluate  : 1.453 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   48 THR
Chi-restraints excluded: chain A residue  175 PHE
Chi-restraints excluded: chain A residue  223 ILE
Chi-restraints excluded: chain A residue  241 TYR
Chi-restraints excluded: chain A residue  291 THR
Chi-restraints excluded: chain A residue  306 LEU
Chi-restraints excluded: chain A residue  354 THR
Chi-restraints excluded: chain A residue  421 THR
Chi-restraints excluded: chain A residue  536 PHE
Chi-restraints excluded: chain A residue  594 CYS
Chi-restraints excluded: chain A residue  599 THR
Chi-restraints excluded: chain A residue  606 TYR
Chi-restraints excluded: chain A residue  621 THR
Chi-restraints excluded: chain A residue  643 ILE
Chi-restraints excluded: chain A residue  662 PHE
Chi-restraints excluded: chain A residue  673 THR
Chi-restraints excluded: chain A residue  753 ILE
Chi-restraints excluded: chain A residue  860 THR
Chi-restraints excluded: chain A residue  863 THR
Chi-restraints excluded: chain A residue  867 THR
Chi-restraints excluded: chain A residue  952 TYR
Chi-restraints excluded: chain A residue 1031 THR
Chi-restraints excluded: chain A residue 1052 CYS
Chi-restraints excluded: chain A residue 1073 VAL
Chi-restraints excluded: chain A residue 1084 VAL
Chi-restraints excluded: chain A residue 1096 LEU
Chi-restraints excluded: chain A residue 1109 SER
Chi-restraints excluded: chain A residue 1128 VAL
Chi-restraints excluded: chain A residue 1162 ILE
Chi-restraints excluded: chain A residue 1172 VAL
Chi-restraints excluded: chain A residue 1183 PHE
Chi-restraints excluded: chain A residue 1196 THR
Chi-restraints excluded: chain A residue 1201 VAL
Chi-restraints excluded: chain A residue 1229 ILE
Chi-restraints excluded: chain A residue 1266 ILE
Chi-restraints excluded: chain A residue 1300 VAL
Chi-restraints excluded: chain A residue 1317 CYS
Chi-restraints excluded: chain A residue 1318 THR
Chi-restraints excluded: chain A residue 1324 THR
Chi-restraints excluded: chain A residue 1354 ILE
Chi-restraints excluded: chain A residue 1361 CYS
Chi-restraints excluded: chain A residue 1377 SER
Chi-restraints excluded: chain A residue 1383 VAL
Chi-restraints excluded: chain A residue 1418 PHE
Chi-restraints excluded: chain A residue 1421 GLN
Chi-restraints excluded: chain A residue 1427 ILE
Chi-restraints excluded: chain A residue 1432 VAL
Chi-restraints excluded: chain A residue 1479 CYS
Chi-restraints excluded: chain A residue 1480 GLN
Chi-restraints excluded: chain A residue 1486 THR
Chi-restraints excluded: chain A residue 1520 VAL
Chi-restraints excluded: chain A residue 1557 VAL
Chi-restraints excluded: chain A residue 1588 VAL
Chi-restraints excluded: chain A residue 1609 VAL
Chi-restraints excluded: chain A residue 1747 CYS
Chi-restraints excluded: chain A residue 1871 ARG
Chi-restraints excluded: chain A residue 1900 SER
Chi-restraints excluded: chain A residue 1981 MET
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 189
   random chunks:
   chunk 53 optimal weight:   20.0000
   chunk 58 optimal weight:    1.9990
   chunk 179 optimal weight:    0.0030
   chunk 144 optimal weight:    7.9990
   chunk 171 optimal weight:    0.9990
   chunk 69 optimal weight:   20.0000
   chunk 37 optimal weight:    9.9990
   chunk 124 optimal weight:    0.9980
   chunk 83 optimal weight:    5.9990
   chunk 125 optimal weight:    0.0570
   chunk 73 optimal weight:    6.9990
   overall best weight:    0.8112

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

Flipped N/Q/H residues before XYZ refinement:
A  57 ASN
** A1506 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4644 r_free = 0.4644 target = 0.136616 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 78)----------------|
| r_work = 0.4390 r_free = 0.4390 target = 0.120208 restraints weight = 96379.564|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 30)----------------|
| r_work = 0.4394 r_free = 0.4394 target = 0.120769 restraints weight = 79468.272|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 30)----------------|
| r_work = 0.4405 r_free = 0.4405 target = 0.120897 restraints weight = 57190.023|
|-----------------------------------------------------------------------------|
r_work (final): 0.4345
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.5613
moved from start:          0.4274

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.063  14098  Z= 0.112
  Angle     :  0.638  17.311  19455  Z= 0.309
  Chirality :  0.042   0.160   2303
  Planarity :  0.006   0.078   2537
  Dihedral  :  4.571  23.504   2013
  Min Nonbonded Distance : 2.316

Molprobity Statistics.
  All-atom Clashscore : 8.73
  Ramachandran Plot:
    Outliers :  0.32 %
    Allowed  :  6.90 %
    Favored  : 92.78 %
  Rotamer:
    Outliers :  3.56 %
    Allowed  : 29.64 %
    Favored  : 66.80 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.01 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -0.79 (0.20), residues: 1884
  helix:  1.29 (0.66), residues: 68
  sheet:  0.53 (0.26), residues: 378
  loop : -0.98 (0.17), residues: 1438

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.012   0.002   TRP A1417 
 HIS   0.006   0.001   HIS A 847 
 PHE   0.009   0.001   PHE A 172 
 TYR   0.013   0.001   TYR A 385 
 ARG   0.004   0.000   ARG A1179 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.02287 (  275)
  hydrogen bonds       : angle       5.16849 (  672)
  SS BOND              : bond        0.00295 (   31)
  SS BOND              : angle       0.84226 (   62)
  covalent geometry    : bond        0.00265 (14067)
  covalent geometry    : angle       0.63768 (19393)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 5097.65 seconds
wall clock time: 89 minutes 51.54 seconds (5391.54 seconds total)