Starting phenix.real_space_refine
on Wed Mar  4 01:16:56 2026 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/9zjr_74339/03_2026/9zjr_74339.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/9zjr_74339/03_2026/9zjr_74339.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=2.53
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    model {
      file = "/net/cci-nas-00/data/ceres_data/9zjr_74339/03_2026/9zjr_74339.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/9zjr_74339/03_2026/9zjr_74339.cif"
    real_map_files = "/net/cci-nas-00/data/ceres_data/9zjr_74339/03_2026/9zjr_74339.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/9zjr_74339/03_2026/9zjr_74339.map"
  }
  resolution = 2.53
  write_initial_geo_file = False
  refinement {
    macro_cycles = 10
  }


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

Validating inputs
Origin is already at (0, 0, 0), no shifts will be applied
-------------------------------------------------------------------------------
Processing inputs
*****************
Set random seed
  Set to: 0
Set model cs if undefined
Decide on map wrapping
  Map wrapping is set to: False
Normalize map: mean=0, sd=1
  Input map: mean=  -0.000 sd=   0.055
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: 6
    Type Number    sf(0)   Gaussians
     P       3      5.49       5
     Mg      1      5.21       5
     S      41      5.16       5
     C    5936      2.51       5
     N    1524      2.21       5
     O    1886      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 6 residue(s): 0.01s

  Monomer Library directory:
    "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-5986/lib/python3.9/site-packages/chem_data/mon_lib"
  Total number of atoms: 9391
  Number of models: 1
  Model: ""
    Number of chains: 2
    Chain: "A"
      Number of atoms: 9181
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 1121, 9181
          Classifications: {'peptide': 1121}
          Modifications used: {'COO': 1}
          Link IDs: {'PTRANS': 39, 'TRANS': 1081}
          Chain breaks: 11
    Chain: "A"
      Number of atoms: 210
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 180, 210
          Unusual residues: {' MG': 1, 'ATP': 1}
          Classifications: {'undetermined': 2, 'water': 178}
          Link IDs: {None: 179}
  Time building chain proxies: 2.01, per 1000 atoms: 0.21
  Number of scatterers: 9391
  At special positions: 0
  Unit cell: (113.52, 112.86, 107.58, 90, 90, 90)
  Space group: P 1 (No. 1)
  Number of sites at special positions: 0
  Number of scattering types: 6
    Type Number    sf(0)
     S      41     16.00
     P       3     15.00
     Mg      1     11.99
     O    1886      8.00
     N    1524      7.00
     C    5936      6.00
    sf(0) = scattering factor at diffraction angle 0.

  Number of disulfides: simple=0, symmetry=0

  Automatic linking
    Parameters for automatic linking
      Linking & cutoffs
        Metal                : Auto  - 3.00
        Amino acid           : True  - 1.90
        Carbohydrate         : True  - 1.99
        Ligands              : True  - 1.99
        Small molecules      : False - 1.98
        Amino acid - RNA/DNA : False
      
  Number of custom bonds: simple=0, symmetry=0
  Time building additional restraints: 0.76
  Conformation dependent library (CDL) restraints added in 433.0 milliseconds
  

  2194 Ramachandran restraints generated.
    1097 Oldfield, 0 Emsley, 1097 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  2144

  Finding SS restraints...
    Secondary structure from input PDB file:
      57 helices and 6 sheets defined
      61.2% alpha, 10.3% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 0.39
  Creating SS restraints...
    Processing helix  chain 'A' and resid 389 through 400
      removed outlier: 4.053A  pdb=" N   LYS A 393 " --> pdb=" O   ARG A 389 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 421 through 434
      removed outlier: 3.955A  pdb=" N   LYS A 426 " --> pdb=" O   ASP A 423 " (cutoff:3.500A)
      removed outlier: 3.560A  pdb=" N   LEU A 428 " --> pdb=" O   THR A 425 " (cutoff:3.500A)
      removed outlier: 5.299A  pdb=" N   ASP A 429 " --> pdb=" O   LYS A 426 " (cutoff:3.500A)
      removed outlier: 5.052A  pdb=" N   PHE A 430 " --> pdb=" O   HIS A 427 " (cutoff:3.500A)
      removed outlier: 3.557A  pdb=" N   LEU A 431 " --> pdb=" O   LEU A 428 " (cutoff:3.500A)
      removed outlier: 3.807A  pdb=" N   ILE A 434 " --> pdb=" O   LEU A 431 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 445 through 450
    Processing helix  chain 'A' and resid 450 through 456
    Processing helix  chain 'A' and resid 465 through 470
    Processing helix  chain 'A' and resid 476 through 483
    Processing helix  chain 'A' and resid 509 through 517
    Processing helix  chain 'A' and resid 517 through 529
    Processing helix  chain 'A' and resid 554 through 568
    Processing helix  chain 'A' and resid 579 through 594
    Processing helix  chain 'A' and resid 601 through 603
      No H-bonds generated for 'chain 'A' and resid 601 through 603'
    Processing helix  chain 'A' and resid 610 through 620
      removed outlier: 3.645A  pdb=" N   LYS A 620 " --> pdb=" O   GLY A 616 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 642 through 647
    Processing helix  chain 'A' and resid 664 through 667
    Processing helix  chain 'A' and resid 668 through 686
      removed outlier: 3.607A  pdb=" N   GLY A 686 " --> pdb=" O   ASP A 682 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 690 through 699
      removed outlier: 3.820A  pdb=" N   PHE A 694 " --> pdb=" O   SER A 690 " (cutoff:3.500A)
      removed outlier: 3.736A  pdb=" N   SER A 697 " --> pdb=" O   ASN A 693 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 710 through 723
    Processing helix  chain 'A' and resid 742 through 754
    Processing helix  chain 'A' and resid 769 through 782
    Processing helix  chain 'A' and resid 804 through 821
      removed outlier: 4.339A  pdb=" N   TYR A 808 " --> pdb=" O   GLN A 804 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 840 through 845
    Processing helix  chain 'A' and resid 858 through 876
      removed outlier: 3.875A  pdb=" N   GLU A 874 " --> pdb=" O   LYS A 870 " (cutoff:3.500A)
      removed outlier: 3.900A  pdb=" N   GLN A 875 " --> pdb=" O   GLU A 871 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 878 through 881
    Processing helix  chain 'A' and resid 882 through 890
    Processing helix  chain 'A' and resid 893 through 906
    Processing helix  chain 'A' and resid 912 through 928
    Processing helix  chain 'A' and resid 935 through 943
    Processing helix  chain 'A' and resid 956 through 961
    Processing helix  chain 'A' and resid 962 through 965
      removed outlier: 3.788A  pdb=" N   THR A 965 " --> pdb=" O   THR A 962 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'A' and resid 962 through 965'
    Processing helix  chain 'A' and resid 985 through 1001
    Processing helix  chain 'A' and resid 1003 through 1013
    Processing helix  chain 'A' and resid 1023 through 1036
    Processing helix  chain 'A' and resid 1052 through 1062
    Processing helix  chain 'A' and resid 1063 through 1078
      removed outlier: 3.811A  pdb=" N   VAL A1067 " --> pdb=" O   GLY A1063 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 1081 through 1095
      removed outlier: 3.586A  pdb=" N   CYS A1085 " --> pdb=" O   ASN A1081 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 1098 through 1113
    Processing helix  chain 'A' and resid 1116 through 1139
      removed outlier: 3.854A  pdb=" N   LYS A1130 " --> pdb=" O   VAL A1126 " (cutoff:3.500A)
      removed outlier: 3.873A  pdb=" N   ILE A1131 " --> pdb=" O   TYR A1127 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 1145 through 1173
      removed outlier: 3.727A  pdb=" N   ARG A1173 " --> pdb=" O   GLN A1169 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 1194 through 1212
      removed outlier: 3.529A  pdb=" N   GLN A1198 " --> pdb=" O   ILE A1194 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 1213 through 1218
      removed outlier: 6.370A  pdb=" N   PHE A1216 " --> pdb=" O   LEU A1213 " (cutoff:3.500A)
      removed outlier: 3.682A  pdb=" N   ASP A1218 " --> pdb=" O   PRO A1215 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 1221 through 1233
    Processing helix  chain 'A' and resid 1244 through 1251
    Processing helix  chain 'A' and resid 1253 through 1258
    Processing helix  chain 'A' and resid 1259 through 1277
    Processing helix  chain 'A' and resid 1286 through 1308
    Processing helix  chain 'A' and resid 1325 through 1339
    Processing helix  chain 'A' and resid 1343 through 1349
    Processing helix  chain 'A' and resid 1350 through 1353
      removed outlier: 3.798A  pdb=" N   LYS A1353 " --> pdb=" O   TYR A1350 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'A' and resid 1350 through 1353'
    Processing helix  chain 'A' and resid 1354 through 1375
    Processing helix  chain 'A' and resid 1381 through 1399
    Processing helix  chain 'A' and resid 1407 through 1423
      Proline residue:  A1421  - end of helix
    Processing helix  chain 'A' and resid 1429 through 1439
    Processing helix  chain 'A' and resid 1449 through 1451
      No H-bonds generated for 'chain 'A' and resid 1449 through 1451'
    Processing helix  chain 'A' and resid 1452 through 1468
    Processing helix  chain 'A' and resid 1487 through 1490
    Processing helix  chain 'A' and resid 1495 through 1502
      removed outlier: 4.004A  pdb=" N   PHE A1502 " --> pdb=" O   ILE A1498 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 1520 through 1525
    Processing sheet with id=AA1, first strand: chain 'A' and resid 462 through 464
      removed outlier: 6.088A  pdb=" N   ASN A 462 " --> pdb=" O   TRP A 491 " (cutoff:3.500A)
      removed outlier: 7.245A  pdb=" N   PHE A 493 " --> pdb=" O   ASN A 462 " (cutoff:3.500A)
      removed outlier: 6.776A  pdb=" N   HIS A 464 " --> pdb=" O   PHE A 493 " (cutoff:3.500A)
      removed outlier: 7.065A  pdb=" N   TYR A 413 " --> pdb=" O   ALA A 438 " (cutoff:3.500A)
      removed outlier: 8.580A  pdb=" N   LEU A 440 " --> pdb=" O   TYR A 413 " (cutoff:3.500A)
      removed outlier: 6.826A  pdb=" N   LEU A 415 " --> pdb=" O   LEU A 440 " (cutoff:3.500A)
      removed outlier: 6.663A  pdb=" N   GLN A 412 " --> pdb=" O   LEU A 540 " (cutoff:3.500A)
      removed outlier: 7.939A  pdb=" N   VAL A 542 " --> pdb=" O   GLN A 412 " (cutoff:3.500A)
      removed outlier: 6.445A  pdb=" N   ILE A 414 " --> pdb=" O   VAL A 542 " (cutoff:3.500A)
      removed outlier: 7.355A  pdb=" N   LEU A 544 " --> pdb=" O   ILE A 414 " (cutoff:3.500A)
      removed outlier: 6.368A  pdb=" N   VAL A 416 " --> pdb=" O   LEU A 544 " (cutoff:3.500A)
    Processing sheet with id=AA2, first strand: chain 'A' and resid 631 through 632
    Processing sheet with id=AA3, first strand: chain 'A' and resid 652 through 655
      removed outlier: 4.202A  pdb=" N   CYS A 760 " --> pdb=" O   ILE A 655 " (cutoff:3.500A)
      removed outlier: 5.939A  pdb=" N   ARG A 759 " --> pdb=" O   LEU A 795 " (cutoff:3.500A)
      removed outlier: 7.556A  pdb=" N   LEU A 797 " --> pdb=" O   ARG A 759 " (cutoff:3.500A)
      removed outlier: 6.820A  pdb=" N   ALA A 761 " --> pdb=" O   LEU A 797 " (cutoff:3.500A)
      removed outlier: 8.467A  pdb=" N   ASP A 799 " --> pdb=" O   ALA A 761 " (cutoff:3.500A)
      removed outlier: 7.608A  pdb=" N   LEU A 763 " --> pdb=" O   ASP A 799 " (cutoff:3.500A)
      removed outlier: 6.362A  pdb=" N   VAL A 794 " --> pdb=" O   ILE A 831 " (cutoff:3.500A)
      removed outlier: 7.352A  pdb=" N   LEU A 833 " --> pdb=" O   VAL A 794 " (cutoff:3.500A)
      removed outlier: 6.486A  pdb=" N   LEU A 796 " --> pdb=" O   LEU A 833 " (cutoff:3.500A)
      removed outlier: 7.595A  pdb=" N   CYS A 835 " --> pdb=" O   LEU A 796 " (cutoff:3.500A)
      removed outlier: 6.715A  pdb=" N   VAL A 798 " --> pdb=" O   CYS A 835 " (cutoff:3.500A)
      removed outlier: 8.635A  pdb=" N   ARG A 837 " --> pdb=" O   VAL A 798 " (cutoff:3.500A)
      removed outlier: 6.563A  pdb=" N   LYS A 731 " --> pdb=" O   ILE A 832 " (cutoff:3.500A)
      removed outlier: 7.530A  pdb=" N   ASN A 834 " --> pdb=" O   LYS A 731 " (cutoff:3.500A)
      removed outlier: 6.528A  pdb=" N   ILE A 733 " --> pdb=" O   ASN A 834 " (cutoff:3.500A)
      removed outlier: 7.809A  pdb=" N   MET A 836 " --> pdb=" O   ILE A 733 " (cutoff:3.500A)
      removed outlier: 6.189A  pdb=" N   LEU A 735 " --> pdb=" O   MET A 836 " (cutoff:3.500A)
    Processing sheet with id=AA4, first strand: chain 'A' and resid 933 through 934
    Processing sheet with id=AA5, first strand: chain 'A' and resid 1278 through 1280
    Processing sheet with id=AA6, first strand: chain 'A' and resid 1492 through 1494
      removed outlier: 3.755A  pdb=" N   PHE A1481 " --> pdb=" O   PHE A1576 " (cutoff:3.500A)
      removed outlier: 5.472A  pdb=" N   LEU A1574 " --> pdb=" O   LEU A1483 " (cutoff:3.500A)
      removed outlier: 4.660A  pdb=" N   TYR A1573 " --> pdb=" O   ASP A1585 " (cutoff:3.500A)
      removed outlier: 5.414A  pdb=" N   ASP A1585 " --> pdb=" O   TYR A1573 " (cutoff:3.500A)
      removed outlier: 6.627A  pdb=" N   GLY A1575 " --> pdb=" O   ALA A1583 " (cutoff:3.500A)
      removed outlier: 5.403A  pdb=" N   ALA A1583 " --> pdb=" O   GLY A1575 " (cutoff:3.500A)
      removed outlier: 6.283A  pdb=" N   SER A1577 " --> pdb=" O   PRO A1581 " (cutoff:3.500A)
      removed outlier: 8.216A  pdb=" N   ALA A1583 " --> pdb=" O   PRO A1552 " (cutoff:3.500A)
      removed outlier: 7.215A  pdb=" N   THR A1554 " --> pdb=" O   ALA A1583 " (cutoff:3.500A)
      removed outlier: 9.207A  pdb=" N   ASP A1585 " --> pdb=" O   THR A1554 " (cutoff:3.500A)
      removed outlier: 5.444A  pdb=" N   GLU A1542 " --> pdb=" O   GLN A1531 " (cutoff:3.500A)
      removed outlier: 7.879A  pdb=" N   GLN A1531 " --> pdb=" O   GLU A1542 " (cutoff:3.500A)

    485 hydrogen bonds defined for protein.
    1407 hydrogen bond angles defined for protein.
    Restraints generated for nucleic acids:
      0 hydrogen bonds
      0 hydrogen bond angles
      0 basepair planarities
      0 basepair parallelities
      0 stacking parallelities
  Total time for adding SS restraints: 1.88

  Time building geometry restraints manager: 1.04 seconds

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

  Histogram of bond lengths:
        1.20 -     1.32: 1531
        1.32 -     1.44: 2470
        1.44 -     1.56: 5342
        1.56 -     1.69: 5
        1.69 -     1.81: 59
  Bond restraints: 9407
  Sorted by residual:
  bond pdb=" CA  SER A1145 "
       pdb=" CB  SER A1145 "
    ideal  model  delta    sigma   weight residual
    1.531  1.470  0.062 1.58e-02 4.01e+03 1.52e+01
  bond pdb=" N   ILE A1284 "
       pdb=" CA  ILE A1284 "
    ideal  model  delta    sigma   weight residual
    1.456  1.495 -0.040 1.15e-02 7.56e+03 1.18e+01
  bond pdb=" C   ILE A 984 "
       pdb=" O   ILE A 984 "
    ideal  model  delta    sigma   weight residual
    1.237  1.197  0.041 1.23e-02 6.61e+03 1.10e+01
  bond pdb=" N   ILE A1150 "
       pdb=" CA  ILE A1150 "
    ideal  model  delta    sigma   weight residual
    1.461  1.498 -0.037 1.17e-02 7.31e+03 1.00e+01
  bond pdb=" N   ILE A1144 "
       pdb=" CA  ILE A1144 "
    ideal  model  delta    sigma   weight residual
    1.457  1.493 -0.036 1.14e-02 7.69e+03 9.87e+00
  ... (remaining 9402 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     1.26: 12250
        1.26 -     2.52: 311
        2.52 -     3.78: 91
        3.78 -     5.04: 20
        5.04 -     6.30: 10
  Bond angle restraints: 12682
  Sorted by residual:
  angle pdb=" N   ARG A1281 "
        pdb=" CA  ARG A1281 "
        pdb=" C   ARG A1281 "
      ideal   model   delta    sigma   weight residual
     110.50  104.20    6.30 1.41e+00 5.03e-01 2.00e+01
  angle pdb=" CA  HIS A 985 "
        pdb=" C   HIS A 985 "
        pdb=" O   HIS A 985 "
      ideal   model   delta    sigma   weight residual
     121.06  115.98    5.08 1.16e+00 7.43e-01 1.92e+01
  angle pdb=" N   ILE A 984 "
        pdb=" CA  ILE A 984 "
        pdb=" C   ILE A 984 "
      ideal   model   delta    sigma   weight residual
     111.05  116.23   -5.18 1.25e+00 6.40e-01 1.72e+01
  angle pdb=" CA  ARG A1281 "
        pdb=" C   ARG A1281 "
        pdb=" O   ARG A1281 "
      ideal   model   delta    sigma   weight residual
     121.56  117.09    4.47 1.09e+00 8.42e-01 1.69e+01
  angle pdb=" CA  ILE A1284 "
        pdb=" C   ILE A1284 "
        pdb=" O   ILE A1284 "
      ideal   model   delta    sigma   weight residual
     121.75  117.42    4.33 1.18e+00 7.18e-01 1.35e+01
  ... (remaining 12677 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    18.00: 4848
       18.00 -    36.00: 611
       36.00 -    53.99: 193
       53.99 -    71.99: 49
       71.99 -    89.99: 11
  Dihedral angle restraints: 5712
    sinusoidal: 2409
      harmonic: 3303
  Sorted by residual:
  dihedral pdb=" CA  SER A1354 "
           pdb=" C   SER A1354 "
           pdb=" N   GLN A1355 "
           pdb=" CA  GLN A1355 "
      ideal   model   delta  harmonic     sigma   weight residual
    -180.00 -162.40  -17.60     0      5.00e+00 4.00e-02 1.24e+01
  dihedral pdb=" CA  ASN A1219 "
           pdb=" CB  ASN A1219 "
           pdb=" CG  ASN A1219 "
           pdb=" OD1 ASN A1219 "
      ideal   model   delta sinusoidal    sigma   weight residual
     120.00 -165.02  -74.98     2      2.00e+01 2.50e-03 1.12e+01
  dihedral pdb=" CB  GLU A 715 "
           pdb=" CG  GLU A 715 "
           pdb=" CD  GLU A 715 "
           pdb=" OE1 GLU A 715 "
      ideal   model   delta sinusoidal    sigma   weight residual
       0.00   89.99  -89.99     1      3.00e+01 1.11e-03 1.07e+01
  ... (remaining 5709 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.045: 1060
       0.045 -    0.090: 238
       0.090 -    0.135: 82
       0.135 -    0.181: 5
       0.181 -    0.226: 5
  Chirality restraints: 1390
  Sorted by residual:
  chirality pdb=" CA  ILE A1284 "
            pdb=" N   ILE A1284 "
            pdb=" C   ILE A1284 "
            pdb=" CB  ILE A1284 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.43    2.66   -0.23 2.00e-01 2.50e+01 1.27e+00
  chirality pdb=" CB  ILE A 984 "
            pdb=" CA  ILE A 984 "
            pdb=" CG1 ILE A 984 "
            pdb=" CG2 ILE A 984 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.64    2.43    0.22 2.00e-01 2.50e+01 1.18e+00
  chirality pdb=" CA  ARG A1281 "
            pdb=" N   ARG A1281 "
            pdb=" C   ARG A1281 "
            pdb=" CB  ARG A1281 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.72   -0.21 2.00e-01 2.50e+01 1.09e+00
  ... (remaining 1387 not shown)

  Planarity restraints: 1600
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CD  ARG A1473 "   -0.212 9.50e-02 1.11e+02   9.53e-02 5.64e+00
        pdb=" NE  ARG A1473 "    0.014 2.00e-02 2.50e+03
        pdb=" CZ  ARG A1473 "   -0.003 2.00e-02 2.50e+03
        pdb=" NH1 ARG A1473 "    0.004 2.00e-02 2.50e+03
        pdb=" NH2 ARG A1473 "   -0.006 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  ILE A 983 "   -0.008 2.00e-02 2.50e+03   1.71e-02 2.92e+00
        pdb=" C   ILE A 983 "    0.030 2.00e-02 2.50e+03
        pdb=" O   ILE A 983 "   -0.011 2.00e-02 2.50e+03
        pdb=" N   ILE A 984 "   -0.010 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   ILE A1214 "    0.027 5.00e-02 4.00e+02   4.10e-02 2.69e+00
        pdb=" N   PRO A1215 "   -0.071 5.00e-02 4.00e+02
        pdb=" CA  PRO A1215 "    0.021 5.00e-02 4.00e+02
        pdb=" CD  PRO A1215 "    0.023 5.00e-02 4.00e+02
  ... (remaining 1597 not shown)

  Histogram of nonbonded interaction distances:
        1.99 -     2.58: 104
        2.58 -     3.16: 7003
        3.16 -     3.74: 14744
        3.74 -     4.32: 22163
        4.32 -     4.90: 35599
  Nonbonded interactions: 79613
  Sorted by model distance:
  nonbonded pdb=" O2G ATP A1601 "
            pdb="MG    MG A1602 "
     model   vdw
     1.995 2.170
  nonbonded pdb=" OE1 GLU A 411 "
            pdb=" O   HOH A1701 "
     model   vdw
     2.226 3.040
  nonbonded pdb=" OG  SER A1235 "
            pdb=" OD1 ASP A1237 "
     model   vdw
     2.233 3.040
  nonbonded pdb=" OD1 ASP A 800 "
            pdb=" O   HOH A1702 "
     model   vdw
     2.235 3.040
  nonbonded pdb=" OG  SER A1005 "
            pdb=" OE1 GLU A1062 "
     model   vdw
     2.242 3.040
  ... (remaining 79608 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 individual isotropic
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:             12.610
  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:          0.230
  Check model and map are aligned:         0.030
  Set scattering table:                    0.020
  Process input model:                     10.440
  Find NCS groups from input model:        0.040
  Set up NCS constraints:                  0.020
  Set refine NCS operators:                0.000
  Adjust number of macro_cycles:           0.000
  Reset NCS operators:                     0.000
  Extract rigid body selections:           0.000
  Check and reset occupancies:             0.000
  Load rotamer database and sin/cos tables:7.800
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   31.200
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8326
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      :  0.004   0.062   9407  Z= 0.223
  Angle     :  0.552   6.302  12682  Z= 0.338
  Chirality :  0.044   0.226   1390
  Planarity :  0.005   0.095   1600
  Dihedral  : 18.106  89.989   3568
  Min Nonbonded Distance : 1.995

Molprobity Statistics.
  All-atom Clashscore : 3.63
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.73 %
    Favored  : 98.27 %
  Rotamer:
    Outliers :  3.23 %
    Allowed  : 17.71 %
    Favored  : 79.06 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  1.53 (0.25), residues: 1097
  helix:  1.74 (0.21), residues: 604
  sheet:  1.07 (0.50), residues: 95
  loop : -0.06 (0.31), residues: 398

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.000   ARG A1473 
 TYR   0.013   0.001   TYR A1093 
 PHE   0.014   0.001   PHE A1083 
 TRP   0.016   0.001   TRP A 586 
 HIS   0.003   0.001   HIS A 737 

Details of bonding type rmsd
  covalent geometry    : bond        0.00362 ( 9407)
  covalent geometry    : angle       0.55228 (12682)
  hydrogen bonds       : bond        0.14717 (  485)
  hydrogen bonds       : angle       5.70773 ( 1407)

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

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

  2194 Ramachandran restraints generated.
    1097 Oldfield, 0 Emsley, 1097 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2194 Ramachandran restraints generated.
    1097 Oldfield, 0 Emsley, 1097 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  160 residues out of total 1022 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 33
    poor density    : 127
  time to evaluate  : 0.382 
Fit side-chains
   revert: symmetry clash
REVERT: A  396 LYS cc_start: 0.7818 (mttt) cc_final: 0.7148 (ttpp)
REVERT: A  453 LYS cc_start: 0.8405 (tmtt) cc_final: 0.7543 (tmmt)
REVERT: A  514 GLN cc_start: 0.7781 (mm-40) cc_final: 0.7143 (tp40)
REVERT: A  522 ARG cc_start: 0.8448 (OUTLIER) cc_final: 0.7923 (tmt-80)
REVERT: A  626 GLN cc_start: 0.8000 (tp-100) cc_final: 0.7318 (pt0)
REVERT: A  645 GLU cc_start: 0.8322 (OUTLIER) cc_final: 0.8007 (mp0)
REVERT: A  669 LYS cc_start: 0.7376 (mptp) cc_final: 0.6941 (mppt)
REVERT: A  671 LYS cc_start: 0.7969 (mttt) cc_final: 0.7576 (mmtp)
REVERT: A  682 ASP cc_start: 0.8536 (OUTLIER) cc_final: 0.8173 (t70)
REVERT: A  803 GLU cc_start: 0.7253 (mt-10) cc_final: 0.6983 (mt-10)
REVERT: A  804 GLN cc_start: 0.8049 (OUTLIER) cc_final: 0.7672 (mm-40)
REVERT: A  821 LYS cc_start: 0.6792 (mttt) cc_final: 0.6241 (mmtt)
REVERT: A  824 ARG cc_start: 0.6953 (mmt-90) cc_final: 0.6347 (ttm170)
REVERT: A  860 LYS cc_start: 0.7882 (OUTLIER) cc_final: 0.6525 (tptt)
REVERT: A  870 LYS cc_start: 0.8304 (tttt) cc_final: 0.7837 (ttmm)
REVERT: A  874 GLU cc_start: 0.7949 (mt-10) cc_final: 0.7282 (mm-30)
REVERT: A  997 LYS cc_start: 0.8115 (tttt) cc_final: 0.7566 (tptt)
REVERT: A  998 LYS cc_start: 0.7884 (tttt) cc_final: 0.7139 (ptpt)
REVERT: A 1187 ARG cc_start: 0.6584 (OUTLIER) cc_final: 0.4569 (mtm180)
REVERT: A 1200 GLU cc_start: 0.8711 (OUTLIER) cc_final: 0.8272 (tm-30)
REVERT: A 1301 LYS cc_start: 0.7985 (tttt) cc_final: 0.7408 (mtpt)
REVERT: A 1349 GLU cc_start: 0.8112 (tt0) cc_final: 0.6974 (pt0)
REVERT: A 1357 ASP cc_start: 0.7045 (m-30) cc_final: 0.6273 (p0)
REVERT: A 1452 GLN cc_start: 0.7278 (mp10) cc_final: 0.6792 (mp10)
  outliers start: 33
  outliers final: 19
  residues processed: 151
  average time/residue: 0.7331
  time to fit residues: 117.1347
Evaluate side-chains
  149 residues out of total 1022 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 26
    poor density    : 123
  time to evaluate  : 0.400 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  446 SER
Chi-restraints excluded: chain A residue  452 VAL
Chi-restraints excluded: chain A residue  470 VAL
Chi-restraints excluded: chain A residue  520 ASP
Chi-restraints excluded: chain A residue  522 ARG
Chi-restraints excluded: chain A residue  536 ARG
Chi-restraints excluded: chain A residue  634 SER
Chi-restraints excluded: chain A residue  645 GLU
Chi-restraints excluded: chain A residue  682 ASP
Chi-restraints excluded: chain A residue  751 LEU
Chi-restraints excluded: chain A residue  801 PHE
Chi-restraints excluded: chain A residue  804 GLN
Chi-restraints excluded: chain A residue  853 VAL
Chi-restraints excluded: chain A residue  860 LYS
Chi-restraints excluded: chain A residue  866 GLU
Chi-restraints excluded: chain A residue  970 THR
Chi-restraints excluded: chain A residue  986 SER
Chi-restraints excluded: chain A residue 1075 ILE
Chi-restraints excluded: chain A residue 1145 SER
Chi-restraints excluded: chain A residue 1173 ARG
Chi-restraints excluded: chain A residue 1187 ARG
Chi-restraints excluded: chain A residue 1191 THR
Chi-restraints excluded: chain A residue 1200 GLU
Chi-restraints excluded: chain A residue 1272 ASP
Chi-restraints excluded: chain A residue 1401 THR
Chi-restraints excluded: chain A residue 1571 SER
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 112
   random chunks:
   chunk 108 optimal weight:    5.9990
   chunk 49 optimal weight:    1.9990
   chunk 97 optimal weight:    4.9990
   chunk 53 optimal weight:    1.9990
   chunk 5 optimal weight:    1.9990
   chunk 33 optimal weight:    3.9990
   chunk 65 optimal weight:    0.6980
   chunk 62 optimal weight:    3.9990
   chunk 51 optimal weight:    2.9990
   chunk 100 optimal weight:    0.0870
   chunk 106 optimal weight:    5.9990
   overall best weight:    1.3564

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

Flipped N/Q/H residues before XYZ refinement:
A 421 HIS
A 565 GLN
A1230 ASN
A1287 ASN

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3714 r_free = 0.3714 target = 0.155321 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.3293 r_free = 0.3293 target = 0.118441 restraints weight = 8725.490|
|-----------------------------------------------------------------------------|
r_work (start): 0.3282 rms_B_bonded: 1.53
r_work: 0.3109 rms_B_bonded: 2.26 restraints_weight: 0.5000
r_work: 0.2973 rms_B_bonded: 3.60 restraints_weight: 0.2500
r_work (final): 0.2973
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8248
moved from start:          0.0593

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.034   9407  Z= 0.183
  Angle     :  0.535   5.905  12682  Z= 0.289
  Chirality :  0.044   0.154   1390
  Planarity :  0.005   0.040   1600
  Dihedral  :  9.691  87.731   1291
  Min Nonbonded Distance : 1.976

Molprobity Statistics.
  All-atom Clashscore : 2.55
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.46 %
    Favored  : 97.54 %
  Rotamer:
    Outliers :  4.60 %
    Allowed  : 16.54 %
    Favored  : 78.86 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  1.53 (0.25), residues: 1097
  helix:  1.82 (0.21), residues: 615
  sheet:  0.72 (0.49), residues: 98
  loop : -0.17 (0.31), residues: 384

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG A1473 
 TYR   0.014   0.002   TYR A 927 
 PHE   0.020   0.002   PHE A1083 
 TRP   0.016   0.002   TRP A1105 
 HIS   0.005   0.001   HIS A1494 

Details of bonding type rmsd
  covalent geometry    : bond        0.00424 ( 9407)
  covalent geometry    : angle       0.53466 (12682)
  hydrogen bonds       : bond        0.05779 (  485)
  hydrogen bonds       : angle       4.64594 ( 1407)

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

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

  2194 Ramachandran restraints generated.
    1097 Oldfield, 0 Emsley, 1097 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2194 Ramachandran restraints generated.
    1097 Oldfield, 0 Emsley, 1097 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  173 residues out of total 1022 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 47
    poor density    : 126
  time to evaluate  : 0.392 
Fit side-chains
REVERT: A  396 LYS cc_start: 0.7649 (mttt) cc_final: 0.7011 (ttpp)
REVERT: A  449 ASN cc_start: 0.7885 (t0) cc_final: 0.7117 (p0)
REVERT: A  453 LYS cc_start: 0.8369 (tmtt) cc_final: 0.7512 (tmmt)
REVERT: A  514 GLN cc_start: 0.7733 (mm-40) cc_final: 0.6985 (tp40)
REVERT: A  613 GLU cc_start: 0.8089 (mt-10) cc_final: 0.7569 (mt-10)
REVERT: A  626 GLN cc_start: 0.7919 (OUTLIER) cc_final: 0.7223 (pt0)
REVERT: A  669 LYS cc_start: 0.7369 (mptp) cc_final: 0.6935 (mppt)
REVERT: A  671 LYS cc_start: 0.7941 (mttt) cc_final: 0.7550 (mmtp)
REVERT: A  682 ASP cc_start: 0.8449 (OUTLIER) cc_final: 0.8098 (t70)
REVERT: A  803 GLU cc_start: 0.7294 (mt-10) cc_final: 0.7045 (mt-10)
REVERT: A  821 LYS cc_start: 0.6781 (mttt) cc_final: 0.6249 (mmtt)
REVERT: A  824 ARG cc_start: 0.6958 (mmt-90) cc_final: 0.6359 (ttm170)
REVERT: A  837 ARG cc_start: 0.8356 (OUTLIER) cc_final: 0.6684 (mtp180)
REVERT: A  860 LYS cc_start: 0.7879 (OUTLIER) cc_final: 0.6457 (tptt)
REVERT: A  870 LYS cc_start: 0.8261 (tttt) cc_final: 0.7775 (ttmm)
REVERT: A  874 GLU cc_start: 0.7862 (mt-10) cc_final: 0.7188 (mm-30)
REVERT: A  877 LYS cc_start: 0.8193 (mttt) cc_final: 0.7765 (mmtt)
REVERT: A  997 LYS cc_start: 0.7885 (tttt) cc_final: 0.7348 (tptt)
REVERT: A  998 LYS cc_start: 0.7852 (tttt) cc_final: 0.7066 (ptpt)
REVERT: A 1200 GLU cc_start: 0.8739 (OUTLIER) cc_final: 0.8249 (tm-30)
REVERT: A 1222 GLU cc_start: 0.6623 (OUTLIER) cc_final: 0.6396 (mp0)
REVERT: A 1230 ASN cc_start: 0.7981 (m110) cc_final: 0.7670 (m-40)
REVERT: A 1291 LYS cc_start: 0.7879 (mtmm) cc_final: 0.6850 (tptp)
REVERT: A 1301 LYS cc_start: 0.7940 (tttt) cc_final: 0.7353 (mtpt)
REVERT: A 1349 GLU cc_start: 0.8009 (tt0) cc_final: 0.6829 (pt0)
REVERT: A 1357 ASP cc_start: 0.7072 (m-30) cc_final: 0.6326 (p0)
REVERT: A 1471 MET cc_start: 0.8425 (OUTLIER) cc_final: 0.7178 (mmt)
  outliers start: 47
  outliers final: 19
  residues processed: 154
  average time/residue: 0.7079
  time to fit residues: 115.5640
Evaluate side-chains
  150 residues out of total 1022 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 26
    poor density    : 124
  time to evaluate  : 0.406 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  452 VAL
Chi-restraints excluded: chain A residue  470 VAL
Chi-restraints excluded: chain A residue  536 ARG
Chi-restraints excluded: chain A residue  550 ASP
Chi-restraints excluded: chain A residue  626 GLN
Chi-restraints excluded: chain A residue  634 SER
Chi-restraints excluded: chain A residue  682 ASP
Chi-restraints excluded: chain A residue  751 LEU
Chi-restraints excluded: chain A residue  801 PHE
Chi-restraints excluded: chain A residue  837 ARG
Chi-restraints excluded: chain A residue  860 LYS
Chi-restraints excluded: chain A residue  934 SER
Chi-restraints excluded: chain A residue  970 THR
Chi-restraints excluded: chain A residue 1049 ASN
Chi-restraints excluded: chain A residue 1145 SER
Chi-restraints excluded: chain A residue 1188 ARG
Chi-restraints excluded: chain A residue 1191 THR
Chi-restraints excluded: chain A residue 1200 GLU
Chi-restraints excluded: chain A residue 1222 GLU
Chi-restraints excluded: chain A residue 1272 ASP
Chi-restraints excluded: chain A residue 1362 MET
Chi-restraints excluded: chain A residue 1404 LEU
Chi-restraints excluded: chain A residue 1424 LEU
Chi-restraints excluded: chain A residue 1453 MET
Chi-restraints excluded: chain A residue 1471 MET
Chi-restraints excluded: chain A residue 1558 LEU
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 112
   random chunks:
   chunk 67 optimal weight:    0.0170
   chunk 16 optimal weight:    0.8980
   chunk 97 optimal weight:    3.9990
   chunk 23 optimal weight:    0.7980
   chunk 105 optimal weight:    5.9990
   chunk 86 optimal weight:    0.9990
   chunk 61 optimal weight:    0.6980
   chunk 78 optimal weight:    1.9990
   chunk 104 optimal weight:    1.9990
   chunk 18 optimal weight:    0.9980
   chunk 91 optimal weight:    0.9990
   overall best weight:    0.6818

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

Flipped N/Q/H residues before XYZ refinement:
A 565 GLN
A 804 GLN
A 862 GLN
A1168 GLN

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3744 r_free = 0.3744 target = 0.158230 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 35)----------------|
| r_work = 0.3383 r_free = 0.3383 target = 0.125842 restraints weight = 8860.488|
|-----------------------------------------------------------------------------|
r_work (start): 0.3372 rms_B_bonded: 1.82
r_work: 0.3125 rms_B_bonded: 2.57 restraints_weight: 0.5000
r_work: 0.2991 rms_B_bonded: 4.12 restraints_weight: 0.2500
r_work (final): 0.2991
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8364
moved from start:          0.0735

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.027   9407  Z= 0.119
  Angle     :  0.455   6.784  12682  Z= 0.246
  Chirality :  0.041   0.137   1390
  Planarity :  0.004   0.039   1600
  Dihedral  :  8.224  83.969   1261
  Min Nonbonded Distance : 2.022

Molprobity Statistics.
  All-atom Clashscore : 2.60
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.91 %
    Favored  : 98.09 %
  Rotamer:
    Outliers :  3.82 %
    Allowed  : 17.61 %
    Favored  : 78.57 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  1.87 (0.25), residues: 1097
  helix:  2.15 (0.21), residues: 615
  sheet:  0.85 (0.49), residues: 97
  loop : -0.11 (0.31), residues: 385

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG A1473 
 TYR   0.014   0.001   TYR A1093 
 PHE   0.013   0.001   PHE A1083 
 TRP   0.014   0.001   TRP A1105 
 HIS   0.003   0.001   HIS A1494 

Details of bonding type rmsd
  covalent geometry    : bond        0.00257 ( 9407)
  covalent geometry    : angle       0.45472 (12682)
  hydrogen bonds       : bond        0.04501 (  485)
  hydrogen bonds       : angle       4.36621 ( 1407)

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

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

  2194 Ramachandran restraints generated.
    1097 Oldfield, 0 Emsley, 1097 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2194 Ramachandran restraints generated.
    1097 Oldfield, 0 Emsley, 1097 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  170 residues out of total 1022 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 39
    poor density    : 131
  time to evaluate  : 0.383 
Fit side-chains
   revert: symmetry clash
REVERT: A  396 LYS cc_start: 0.7807 (mttt) cc_final: 0.7229 (ttpp)
REVERT: A  419 LYS cc_start: 0.8077 (OUTLIER) cc_final: 0.7806 (tttp)
REVERT: A  423 ASP cc_start: 0.7095 (t0) cc_final: 0.6844 (t70)
REVERT: A  449 ASN cc_start: 0.7838 (t0) cc_final: 0.7165 (p0)
REVERT: A  453 LYS cc_start: 0.8426 (tmtt) cc_final: 0.7659 (tmmt)
REVERT: A  514 GLN cc_start: 0.7840 (mm-40) cc_final: 0.7128 (tp40)
REVERT: A  522 ARG cc_start: 0.8452 (OUTLIER) cc_final: 0.8218 (tmt-80)
REVERT: A  558 GLU cc_start: 0.7811 (tp30) cc_final: 0.6972 (mp0)
REVERT: A  613 GLU cc_start: 0.8254 (mt-10) cc_final: 0.7853 (mt-10)
REVERT: A  626 GLN cc_start: 0.7995 (OUTLIER) cc_final: 0.7405 (pt0)
REVERT: A  635 ILE cc_start: 0.7666 (OUTLIER) cc_final: 0.7304 (mm)
REVERT: A  669 LYS cc_start: 0.7407 (mptp) cc_final: 0.7037 (mppt)
REVERT: A  671 LYS cc_start: 0.8071 (mttt) cc_final: 0.7618 (mmtm)
REVERT: A  682 ASP cc_start: 0.8468 (OUTLIER) cc_final: 0.8197 (t70)
REVERT: A  803 GLU cc_start: 0.7239 (OUTLIER) cc_final: 0.6977 (mt-10)
REVERT: A  821 LYS cc_start: 0.6895 (mttt) cc_final: 0.6371 (mmtt)
REVERT: A  824 ARG cc_start: 0.6969 (mmt-90) cc_final: 0.6458 (ttm170)
REVERT: A  837 ARG cc_start: 0.8439 (OUTLIER) cc_final: 0.6806 (mtp180)
REVERT: A  860 LYS cc_start: 0.7984 (OUTLIER) cc_final: 0.6700 (tptt)
REVERT: A  870 LYS cc_start: 0.8320 (tttt) cc_final: 0.7951 (ttmm)
REVERT: A  874 GLU cc_start: 0.7980 (mt-10) cc_final: 0.7329 (mm-30)
REVERT: A  877 LYS cc_start: 0.8223 (mttt) cc_final: 0.7806 (mmpt)
REVERT: A  997 LYS cc_start: 0.8002 (tttt) cc_final: 0.7541 (tptt)
REVERT: A  998 LYS cc_start: 0.7870 (tttt) cc_final: 0.7124 (ptpt)
REVERT: A 1200 GLU cc_start: 0.8713 (OUTLIER) cc_final: 0.8297 (tm-30)
REVERT: A 1225 LYS cc_start: 0.7278 (OUTLIER) cc_final: 0.6422 (tmtt)
REVERT: A 1230 ASN cc_start: 0.8151 (m110) cc_final: 0.7842 (m-40)
REVERT: A 1301 LYS cc_start: 0.8057 (tttt) cc_final: 0.7501 (mtpt)
REVERT: A 1349 GLU cc_start: 0.8088 (tt0) cc_final: 0.6990 (pt0)
REVERT: A 1357 ASP cc_start: 0.7205 (m-30) cc_final: 0.6486 (p0)
REVERT: A 1452 GLN cc_start: 0.7418 (mp10) cc_final: 0.6948 (mp10)
REVERT: A 1471 MET cc_start: 0.8490 (OUTLIER) cc_final: 0.7279 (mmt)
  outliers start: 39
  outliers final: 14
  residues processed: 153
  average time/residue: 0.7403
  time to fit residues: 119.6871
Evaluate side-chains
  148 residues out of total 1022 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 25
    poor density    : 123
  time to evaluate  : 0.383 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  419 LYS
Chi-restraints excluded: chain A residue  452 VAL
Chi-restraints excluded: chain A residue  470 VAL
Chi-restraints excluded: chain A residue  522 ARG
Chi-restraints excluded: chain A residue  526 SER
Chi-restraints excluded: chain A residue  536 ARG
Chi-restraints excluded: chain A residue  550 ASP
Chi-restraints excluded: chain A residue  626 GLN
Chi-restraints excluded: chain A residue  635 ILE
Chi-restraints excluded: chain A residue  682 ASP
Chi-restraints excluded: chain A residue  751 LEU
Chi-restraints excluded: chain A residue  801 PHE
Chi-restraints excluded: chain A residue  803 GLU
Chi-restraints excluded: chain A residue  837 ARG
Chi-restraints excluded: chain A residue  860 LYS
Chi-restraints excluded: chain A residue  934 SER
Chi-restraints excluded: chain A residue 1049 ASN
Chi-restraints excluded: chain A residue 1075 ILE
Chi-restraints excluded: chain A residue 1113 GLU
Chi-restraints excluded: chain A residue 1191 THR
Chi-restraints excluded: chain A residue 1200 GLU
Chi-restraints excluded: chain A residue 1225 LYS
Chi-restraints excluded: chain A residue 1272 ASP
Chi-restraints excluded: chain A residue 1471 MET
Chi-restraints excluded: chain A residue 1558 LEU
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 112
   random chunks:
   chunk 59 optimal weight:    3.9990
   chunk 68 optimal weight:    1.9990
   chunk 47 optimal weight:    1.9990
   chunk 75 optimal weight:    1.9990
   chunk 44 optimal weight:    0.9980
   chunk 100 optimal weight:    3.9990
   chunk 102 optimal weight:    3.9990
   chunk 85 optimal weight:    2.9990
   chunk 60 optimal weight:    2.9990
   chunk 8 optimal weight:    3.9990
   chunk 55 optimal weight:    2.9990
   overall best weight:    1.9988

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

Flipped N/Q/H residues before XYZ refinement:
A 565 GLN
A 804 GLN
A1168 GLN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3702 r_free = 0.3702 target = 0.154443 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 40)----------------|
| r_work = 0.3324 r_free = 0.3324 target = 0.121124 restraints weight = 8883.480|
|-----------------------------------------------------------------------------|
r_work (start): 0.3315 rms_B_bonded: 1.77
r_work: 0.3068 rms_B_bonded: 2.58 restraints_weight: 0.5000
r_work: 0.2934 rms_B_bonded: 4.10 restraints_weight: 0.2500
r_work (final): 0.2934
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8424
moved from start:          0.0800

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.006   0.042   9407  Z= 0.245
  Angle     :  0.599   7.518  12682  Z= 0.322
  Chirality :  0.048   0.197   1390
  Planarity :  0.005   0.042   1600
  Dihedral  :  8.577  88.596   1258
  Min Nonbonded Distance : 1.960

Molprobity Statistics.
  All-atom Clashscore : 2.82
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.92 %
    Favored  : 97.08 %
  Rotamer:
    Outliers :  4.89 %
    Allowed  : 17.03 %
    Favored  : 78.08 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  1.46 (0.25), residues: 1097
  helix:  1.83 (0.20), residues: 607
  sheet:  0.80 (0.49), residues: 96
  loop : -0.31 (0.30), residues: 394

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.001   ARG A 713 
 TYR   0.016   0.002   TYR A 896 
 PHE   0.022   0.003   PHE A1083 
 TRP   0.017   0.002   TRP A1105 
 HIS   0.006   0.001   HIS A1494 

Details of bonding type rmsd
  covalent geometry    : bond        0.00585 ( 9407)
  covalent geometry    : angle       0.59940 (12682)
  hydrogen bonds       : bond        0.06415 (  485)
  hydrogen bonds       : angle       4.60416 ( 1407)

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

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

  2194 Ramachandran restraints generated.
    1097 Oldfield, 0 Emsley, 1097 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2194 Ramachandran restraints generated.
    1097 Oldfield, 0 Emsley, 1097 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  171 residues out of total 1022 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 50
    poor density    : 121
  time to evaluate  : 0.374 
Fit side-chains
REVERT: A  396 LYS cc_start: 0.7875 (mttt) cc_final: 0.7283 (tttm)
REVERT: A  419 LYS cc_start: 0.8217 (OUTLIER) cc_final: 0.7876 (tttp)
REVERT: A  453 LYS cc_start: 0.8553 (tmtt) cc_final: 0.7810 (tmmt)
REVERT: A  514 GLN cc_start: 0.7873 (mm-40) cc_final: 0.7158 (tp40)
REVERT: A  522 ARG cc_start: 0.8504 (OUTLIER) cc_final: 0.8194 (tmt-80)
REVERT: A  558 GLU cc_start: 0.7900 (tp30) cc_final: 0.7015 (mp0)
REVERT: A  613 GLU cc_start: 0.8256 (mt-10) cc_final: 0.7846 (mt-10)
REVERT: A  626 GLN cc_start: 0.8016 (OUTLIER) cc_final: 0.7407 (pt0)
REVERT: A  635 ILE cc_start: 0.7744 (OUTLIER) cc_final: 0.7334 (mm)
REVERT: A  645 GLU cc_start: 0.8314 (OUTLIER) cc_final: 0.7778 (mm-30)
REVERT: A  669 LYS cc_start: 0.7564 (mptp) cc_final: 0.7143 (mppt)
REVERT: A  671 LYS cc_start: 0.8094 (mttt) cc_final: 0.7744 (mmtp)
REVERT: A  682 ASP cc_start: 0.8513 (OUTLIER) cc_final: 0.8200 (t70)
REVERT: A  803 GLU cc_start: 0.7479 (OUTLIER) cc_final: 0.7232 (mt-10)
REVERT: A  821 LYS cc_start: 0.6998 (mttt) cc_final: 0.6498 (mmtt)
REVERT: A  824 ARG cc_start: 0.7048 (mmt-90) cc_final: 0.6463 (ttm170)
REVERT: A  837 ARG cc_start: 0.8502 (OUTLIER) cc_final: 0.6853 (mtp180)
REVERT: A  860 LYS cc_start: 0.8135 (OUTLIER) cc_final: 0.6764 (tptt)
REVERT: A  870 LYS cc_start: 0.8344 (tttt) cc_final: 0.7943 (ttmm)
REVERT: A  874 GLU cc_start: 0.7984 (mt-10) cc_final: 0.7364 (mm-30)
REVERT: A  877 LYS cc_start: 0.8275 (mttt) cc_final: 0.7858 (mmpt)
REVERT: A  997 LYS cc_start: 0.8090 (tttt) cc_final: 0.7612 (tptt)
REVERT: A  998 LYS cc_start: 0.8017 (tttt) cc_final: 0.7233 (ptpt)
REVERT: A 1200 GLU cc_start: 0.8890 (OUTLIER) cc_final: 0.8473 (tm-30)
REVERT: A 1222 GLU cc_start: 0.6694 (OUTLIER) cc_final: 0.6457 (mp0)
REVERT: A 1225 LYS cc_start: 0.7277 (OUTLIER) cc_final: 0.6420 (tmtt)
REVERT: A 1230 ASN cc_start: 0.8243 (m110) cc_final: 0.7957 (m-40)
REVERT: A 1301 LYS cc_start: 0.8161 (tttt) cc_final: 0.7625 (mtpt)
REVERT: A 1355 GLN cc_start: 0.6269 (OUTLIER) cc_final: 0.5985 (tp40)
REVERT: A 1357 ASP cc_start: 0.7259 (m-30) cc_final: 0.6580 (p0)
REVERT: A 1471 MET cc_start: 0.8541 (OUTLIER) cc_final: 0.7330 (mmt)
  outliers start: 50
  outliers final: 20
  residues processed: 152
  average time/residue: 0.7575
  time to fit residues: 121.6318
Evaluate side-chains
  153 residues out of total 1022 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 34
    poor density    : 119
  time to evaluate  : 0.400 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  419 LYS
Chi-restraints excluded: chain A residue  452 VAL
Chi-restraints excluded: chain A residue  470 VAL
Chi-restraints excluded: chain A residue  475 THR
Chi-restraints excluded: chain A residue  522 ARG
Chi-restraints excluded: chain A residue  526 SER
Chi-restraints excluded: chain A residue  536 ARG
Chi-restraints excluded: chain A residue  550 ASP
Chi-restraints excluded: chain A residue  626 GLN
Chi-restraints excluded: chain A residue  635 ILE
Chi-restraints excluded: chain A residue  645 GLU
Chi-restraints excluded: chain A residue  682 ASP
Chi-restraints excluded: chain A residue  751 LEU
Chi-restraints excluded: chain A residue  801 PHE
Chi-restraints excluded: chain A residue  803 GLU
Chi-restraints excluded: chain A residue  837 ARG
Chi-restraints excluded: chain A residue  860 LYS
Chi-restraints excluded: chain A residue  934 SER
Chi-restraints excluded: chain A residue  970 THR
Chi-restraints excluded: chain A residue 1049 ASN
Chi-restraints excluded: chain A residue 1075 ILE
Chi-restraints excluded: chain A residue 1188 ARG
Chi-restraints excluded: chain A residue 1191 THR
Chi-restraints excluded: chain A residue 1200 GLU
Chi-restraints excluded: chain A residue 1208 ILE
Chi-restraints excluded: chain A residue 1222 GLU
Chi-restraints excluded: chain A residue 1225 LYS
Chi-restraints excluded: chain A residue 1272 ASP
Chi-restraints excluded: chain A residue 1355 GLN
Chi-restraints excluded: chain A residue 1362 MET
Chi-restraints excluded: chain A residue 1404 LEU
Chi-restraints excluded: chain A residue 1424 LEU
Chi-restraints excluded: chain A residue 1471 MET
Chi-restraints excluded: chain A residue 1558 LEU
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 112
   random chunks:
   chunk 2 optimal weight:    0.9990
   chunk 62 optimal weight:    2.9990
   chunk 1 optimal weight:    0.9990
   chunk 64 optimal weight:    0.9990
   chunk 70 optimal weight:    0.9980
   chunk 87 optimal weight:    0.6980
   chunk 58 optimal weight:    0.7980
   chunk 89 optimal weight:    0.8980
   chunk 68 optimal weight:    0.8980
   chunk 22 optimal weight:    1.9990
   chunk 8 optimal weight:    2.9990
   overall best weight:    0.8580

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

Flipped N/Q/H residues before XYZ refinement:
A 565 GLN
A 804 GLN
A1168 GLN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3733 r_free = 0.3733 target = 0.157242 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 29)----------------|
| r_work = 0.3372 r_free = 0.3372 target = 0.125045 restraints weight = 8837.672|
|-----------------------------------------------------------------------------|
r_work (start): 0.3364 rms_B_bonded: 1.69
r_work: 0.3123 rms_B_bonded: 2.46 restraints_weight: 0.5000
r_work: 0.2992 rms_B_bonded: 3.90 restraints_weight: 0.2500
r_work (final): 0.2992
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8367
moved from start:          0.0766

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.029   9407  Z= 0.132
  Angle     :  0.477   7.037  12682  Z= 0.258
  Chirality :  0.042   0.142   1390
  Planarity :  0.004   0.040   1600
  Dihedral  :  8.218  87.427   1258
  Min Nonbonded Distance : 2.000

Molprobity Statistics.
  All-atom Clashscore : 2.77
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.01 %
    Favored  : 97.99 %
  Rotamer:
    Outliers :  4.01 %
    Allowed  : 17.91 %
    Favored  : 78.08 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  1.75 (0.25), residues: 1097
  helix:  2.07 (0.21), residues: 614
  sheet:  0.81 (0.49), residues: 96
  loop : -0.20 (0.30), residues: 387

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG A 713 
 TYR   0.013   0.001   TYR A1093 
 PHE   0.015   0.002   PHE A1083 
 TRP   0.015   0.002   TRP A1105 
 HIS   0.003   0.001   HIS A1494 

Details of bonding type rmsd
  covalent geometry    : bond        0.00293 ( 9407)
  covalent geometry    : angle       0.47713 (12682)
  hydrogen bonds       : bond        0.04761 (  485)
  hydrogen bonds       : angle       4.37778 ( 1407)

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

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

  2194 Ramachandran restraints generated.
    1097 Oldfield, 0 Emsley, 1097 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2194 Ramachandran restraints generated.
    1097 Oldfield, 0 Emsley, 1097 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  164 residues out of total 1022 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 41
    poor density    : 123
  time to evaluate  : 0.369 
Fit side-chains
REVERT: A  396 LYS cc_start: 0.7814 (mttt) cc_final: 0.7230 (ttpp)
REVERT: A  419 LYS cc_start: 0.8152 (OUTLIER) cc_final: 0.7847 (tttp)
REVERT: A  449 ASN cc_start: 0.7821 (t0) cc_final: 0.7193 (p0)
REVERT: A  453 LYS cc_start: 0.8476 (tmtt) cc_final: 0.7728 (tmmt)
REVERT: A  514 GLN cc_start: 0.7839 (mm-40) cc_final: 0.7130 (tp40)
REVERT: A  522 ARG cc_start: 0.8435 (OUTLIER) cc_final: 0.8201 (tmt-80)
REVERT: A  558 GLU cc_start: 0.7826 (tp30) cc_final: 0.6975 (mp0)
REVERT: A  613 GLU cc_start: 0.8240 (mt-10) cc_final: 0.7805 (mt-10)
REVERT: A  626 GLN cc_start: 0.7983 (OUTLIER) cc_final: 0.7402 (pt0)
REVERT: A  635 ILE cc_start: 0.7561 (OUTLIER) cc_final: 0.7214 (mm)
REVERT: A  645 GLU cc_start: 0.8303 (OUTLIER) cc_final: 0.7801 (mm-30)
REVERT: A  669 LYS cc_start: 0.7432 (mptp) cc_final: 0.7066 (mppt)
REVERT: A  671 LYS cc_start: 0.8058 (mttt) cc_final: 0.7634 (mmtm)
REVERT: A  682 ASP cc_start: 0.8434 (OUTLIER) cc_final: 0.8150 (t70)
REVERT: A  803 GLU cc_start: 0.7284 (OUTLIER) cc_final: 0.7018 (mt-10)
REVERT: A  821 LYS cc_start: 0.6965 (mttt) cc_final: 0.6456 (mmtt)
REVERT: A  824 ARG cc_start: 0.6982 (mmt-90) cc_final: 0.6434 (ttm170)
REVERT: A  837 ARG cc_start: 0.8451 (OUTLIER) cc_final: 0.6812 (mtp180)
REVERT: A  860 LYS cc_start: 0.7998 (OUTLIER) cc_final: 0.6697 (tptt)
REVERT: A  870 LYS cc_start: 0.8318 (tttt) cc_final: 0.7903 (ttmm)
REVERT: A  874 GLU cc_start: 0.7959 (mt-10) cc_final: 0.7333 (mm-30)
REVERT: A  877 LYS cc_start: 0.8201 (mttt) cc_final: 0.7803 (mmpt)
REVERT: A  997 LYS cc_start: 0.8011 (tttt) cc_final: 0.7560 (tptt)
REVERT: A  998 LYS cc_start: 0.7863 (tttt) cc_final: 0.7136 (ptpt)
REVERT: A 1200 GLU cc_start: 0.8736 (OUTLIER) cc_final: 0.8327 (tm-30)
REVERT: A 1225 LYS cc_start: 0.7311 (OUTLIER) cc_final: 0.6465 (tmtt)
REVERT: A 1230 ASN cc_start: 0.8188 (m110) cc_final: 0.7895 (m-40)
REVERT: A 1291 LYS cc_start: 0.7946 (mtmm) cc_final: 0.6995 (tptp)
REVERT: A 1301 LYS cc_start: 0.8074 (tttt) cc_final: 0.7536 (mtpt)
REVERT: A 1349 GLU cc_start: 0.8058 (tt0) cc_final: 0.6963 (pt0)
REVERT: A 1355 GLN cc_start: 0.6215 (OUTLIER) cc_final: 0.5971 (tp40)
REVERT: A 1357 ASP cc_start: 0.7235 (m-30) cc_final: 0.6554 (p0)
REVERT: A 1471 MET cc_start: 0.8506 (OUTLIER) cc_final: 0.7266 (mmt)
  outliers start: 41
  outliers final: 15
  residues processed: 148
  average time/residue: 0.7303
  time to fit residues: 114.2810
Evaluate side-chains
  148 residues out of total 1022 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 28
    poor density    : 120
  time to evaluate  : 0.477 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  419 LYS
Chi-restraints excluded: chain A residue  452 VAL
Chi-restraints excluded: chain A residue  470 VAL
Chi-restraints excluded: chain A residue  475 THR
Chi-restraints excluded: chain A residue  522 ARG
Chi-restraints excluded: chain A residue  526 SER
Chi-restraints excluded: chain A residue  536 ARG
Chi-restraints excluded: chain A residue  550 ASP
Chi-restraints excluded: chain A residue  626 GLN
Chi-restraints excluded: chain A residue  635 ILE
Chi-restraints excluded: chain A residue  645 GLU
Chi-restraints excluded: chain A residue  682 ASP
Chi-restraints excluded: chain A residue  751 LEU
Chi-restraints excluded: chain A residue  801 PHE
Chi-restraints excluded: chain A residue  803 GLU
Chi-restraints excluded: chain A residue  837 ARG
Chi-restraints excluded: chain A residue  860 LYS
Chi-restraints excluded: chain A residue  934 SER
Chi-restraints excluded: chain A residue 1075 ILE
Chi-restraints excluded: chain A residue 1113 GLU
Chi-restraints excluded: chain A residue 1191 THR
Chi-restraints excluded: chain A residue 1200 GLU
Chi-restraints excluded: chain A residue 1225 LYS
Chi-restraints excluded: chain A residue 1272 ASP
Chi-restraints excluded: chain A residue 1355 GLN
Chi-restraints excluded: chain A residue 1436 SER
Chi-restraints excluded: chain A residue 1471 MET
Chi-restraints excluded: chain A residue 1558 LEU
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 112
   random chunks:
   chunk 44 optimal weight:    3.9990
   chunk 24 optimal weight:    0.5980
   chunk 72 optimal weight:    0.9990
   chunk 56 optimal weight:    4.9990
   chunk 58 optimal weight:    0.8980
   chunk 25 optimal weight:    1.9990
   chunk 33 optimal weight:    1.9990
   chunk 88 optimal weight:    0.8980
   chunk 37 optimal weight:    0.5980
   chunk 101 optimal weight:    0.8980
   chunk 111 optimal weight:    1.9990
   overall best weight:    0.7780

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

Flipped N/Q/H residues before XYZ refinement:
A 565 GLN
A 804 GLN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3739 r_free = 0.3739 target = 0.157861 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 29)----------------|
| r_work = 0.3381 r_free = 0.3381 target = 0.125739 restraints weight = 8822.188|
|-----------------------------------------------------------------------------|
r_work (start): 0.3373 rms_B_bonded: 1.69
r_work: 0.3131 rms_B_bonded: 2.46 restraints_weight: 0.5000
r_work: 0.2998 rms_B_bonded: 3.94 restraints_weight: 0.2500
r_work (final): 0.2998
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8360
moved from start:          0.0832

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.028   9407  Z= 0.125
  Angle     :  0.462   7.156  12682  Z= 0.250
  Chirality :  0.041   0.137   1390
  Planarity :  0.004   0.039   1600
  Dihedral  :  8.105  85.875   1258
  Min Nonbonded Distance : 2.013

Molprobity Statistics.
  All-atom Clashscore : 2.71
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.28 %
    Favored  : 97.72 %
  Rotamer:
    Outliers :  4.01 %
    Allowed  : 17.71 %
    Favored  : 78.28 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  1.88 (0.25), residues: 1097
  helix:  2.19 (0.21), residues: 614
  sheet:  0.81 (0.50), residues: 96
  loop : -0.14 (0.31), residues: 387

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG A1473 
 TYR   0.014   0.001   TYR A1093 
 PHE   0.015   0.002   PHE A1083 
 TRP   0.014   0.001   TRP A1105 
 HIS   0.003   0.001   HIS A1494 

Details of bonding type rmsd
  covalent geometry    : bond        0.00276 ( 9407)
  covalent geometry    : angle       0.46157 (12682)
  hydrogen bonds       : bond        0.04548 (  485)
  hydrogen bonds       : angle       4.29902 ( 1407)

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

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

  2194 Ramachandran restraints generated.
    1097 Oldfield, 0 Emsley, 1097 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2194 Ramachandran restraints generated.
    1097 Oldfield, 0 Emsley, 1097 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  163 residues out of total 1022 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 41
    poor density    : 122
  time to evaluate  : 0.397 
Fit side-chains
   revert: symmetry clash
REVERT: A  396 LYS cc_start: 0.7794 (mttt) cc_final: 0.7228 (ttpp)
REVERT: A  419 LYS cc_start: 0.8152 (OUTLIER) cc_final: 0.7819 (tttp)
REVERT: A  449 ASN cc_start: 0.7920 (t0) cc_final: 0.7234 (p0)
REVERT: A  453 LYS cc_start: 0.8437 (tmtt) cc_final: 0.7672 (tmmt)
REVERT: A  514 GLN cc_start: 0.7785 (mm-40) cc_final: 0.7083 (tp40)
REVERT: A  558 GLU cc_start: 0.7828 (tp30) cc_final: 0.6947 (mp0)
REVERT: A  613 GLU cc_start: 0.8258 (mt-10) cc_final: 0.7868 (mt-10)
REVERT: A  626 GLN cc_start: 0.8001 (OUTLIER) cc_final: 0.7410 (pt0)
REVERT: A  635 ILE cc_start: 0.7554 (OUTLIER) cc_final: 0.7224 (mm)
REVERT: A  669 LYS cc_start: 0.7414 (mptp) cc_final: 0.7059 (mppt)
REVERT: A  671 LYS cc_start: 0.8080 (mttt) cc_final: 0.7643 (mmtm)
REVERT: A  682 ASP cc_start: 0.8437 (OUTLIER) cc_final: 0.8162 (t70)
REVERT: A  803 GLU cc_start: 0.7225 (OUTLIER) cc_final: 0.6977 (mt-10)
REVERT: A  821 LYS cc_start: 0.6890 (mttt) cc_final: 0.6377 (mmtt)
REVERT: A  824 ARG cc_start: 0.6961 (mmt-90) cc_final: 0.6422 (ttm170)
REVERT: A  837 ARG cc_start: 0.8456 (OUTLIER) cc_final: 0.6821 (mtp180)
REVERT: A  860 LYS cc_start: 0.7971 (OUTLIER) cc_final: 0.6705 (tptt)
REVERT: A  870 LYS cc_start: 0.8315 (tttt) cc_final: 0.7900 (ttmm)
REVERT: A  874 GLU cc_start: 0.7975 (mt-10) cc_final: 0.7322 (mm-30)
REVERT: A  877 LYS cc_start: 0.8203 (mttt) cc_final: 0.7812 (mmtt)
REVERT: A  997 LYS cc_start: 0.8007 (tttt) cc_final: 0.7550 (tptt)
REVERT: A  998 LYS cc_start: 0.7845 (tttt) cc_final: 0.7112 (ptpt)
REVERT: A 1173 ARG cc_start: 0.7980 (OUTLIER) cc_final: 0.7439 (ttp-170)
REVERT: A 1200 GLU cc_start: 0.8724 (OUTLIER) cc_final: 0.8316 (tm-30)
REVERT: A 1225 LYS cc_start: 0.7254 (OUTLIER) cc_final: 0.6401 (tmtt)
REVERT: A 1230 ASN cc_start: 0.8194 (m110) cc_final: 0.7899 (m-40)
REVERT: A 1279 LYS cc_start: 0.8668 (OUTLIER) cc_final: 0.8364 (ptmt)
REVERT: A 1291 LYS cc_start: 0.7928 (mtmm) cc_final: 0.6975 (tptp)
REVERT: A 1301 LYS cc_start: 0.8052 (tttt) cc_final: 0.7511 (mtpt)
REVERT: A 1349 GLU cc_start: 0.8073 (tt0) cc_final: 0.6973 (pt0)
REVERT: A 1355 GLN cc_start: 0.6143 (OUTLIER) cc_final: 0.5913 (tp40)
REVERT: A 1357 ASP cc_start: 0.7226 (m-30) cc_final: 0.6524 (p0)
REVERT: A 1452 GLN cc_start: 0.7403 (mp10) cc_final: 0.6916 (mp10)
REVERT: A 1471 MET cc_start: 0.8496 (OUTLIER) cc_final: 0.7252 (mmt)
  outliers start: 41
  outliers final: 16
  residues processed: 150
  average time/residue: 0.7443
  time to fit residues: 117.9851
Evaluate side-chains
  148 residues out of total 1022 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 29
    poor density    : 119
  time to evaluate  : 0.368 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  419 LYS
Chi-restraints excluded: chain A residue  452 VAL
Chi-restraints excluded: chain A residue  475 THR
Chi-restraints excluded: chain A residue  526 SER
Chi-restraints excluded: chain A residue  536 ARG
Chi-restraints excluded: chain A residue  550 ASP
Chi-restraints excluded: chain A residue  626 GLN
Chi-restraints excluded: chain A residue  635 ILE
Chi-restraints excluded: chain A residue  682 ASP
Chi-restraints excluded: chain A residue  751 LEU
Chi-restraints excluded: chain A residue  801 PHE
Chi-restraints excluded: chain A residue  803 GLU
Chi-restraints excluded: chain A residue  837 ARG
Chi-restraints excluded: chain A residue  860 LYS
Chi-restraints excluded: chain A residue  934 SER
Chi-restraints excluded: chain A residue  970 THR
Chi-restraints excluded: chain A residue 1049 ASN
Chi-restraints excluded: chain A residue 1075 ILE
Chi-restraints excluded: chain A residue 1173 ARG
Chi-restraints excluded: chain A residue 1191 THR
Chi-restraints excluded: chain A residue 1200 GLU
Chi-restraints excluded: chain A residue 1208 ILE
Chi-restraints excluded: chain A residue 1225 LYS
Chi-restraints excluded: chain A residue 1272 ASP
Chi-restraints excluded: chain A residue 1279 LYS
Chi-restraints excluded: chain A residue 1355 GLN
Chi-restraints excluded: chain A residue 1436 SER
Chi-restraints excluded: chain A residue 1471 MET
Chi-restraints excluded: chain A residue 1558 LEU
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 112
   random chunks:
   chunk 37 optimal weight:    1.9990
   chunk 74 optimal weight:    1.9990
   chunk 16 optimal weight:    0.8980
   chunk 10 optimal weight:    1.9990
   chunk 95 optimal weight:    2.9990
   chunk 108 optimal weight:    5.9990
   chunk 109 optimal weight:    0.6980
   chunk 87 optimal weight:    0.5980
   chunk 35 optimal weight:    0.4980
   chunk 73 optimal weight:    2.9990
   chunk 76 optimal weight:    1.9990
   overall best weight:    0.9382

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

Flipped N/Q/H residues before XYZ refinement:
A 477 ASN
A 565 GLN
A 804 GLN
A1168 GLN

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3733 r_free = 0.3733 target = 0.157207 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 29)----------------|
| r_work = 0.3374 r_free = 0.3374 target = 0.125242 restraints weight = 8783.763|
|-----------------------------------------------------------------------------|
r_work (start): 0.3367 rms_B_bonded: 1.73
r_work: 0.3116 rms_B_bonded: 2.51 restraints_weight: 0.5000
r_work: 0.2980 rms_B_bonded: 4.04 restraints_weight: 0.2500
r_work (final): 0.2980
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8376
moved from start:          0.0840

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.030   9407  Z= 0.139
  Angle     :  0.478   6.946  12682  Z= 0.258
  Chirality :  0.042   0.139   1390
  Planarity :  0.004   0.039   1600
  Dihedral  :  8.150  86.639   1257
  Min Nonbonded Distance : 2.000

Molprobity Statistics.
  All-atom Clashscore : 2.49
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.19 %
    Favored  : 97.81 %
  Rotamer:
    Outliers :  4.50 %
    Allowed  : 17.42 %
    Favored  : 78.08 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  1.83 (0.25), residues: 1097
  helix:  2.15 (0.21), residues: 614
  sheet:  0.79 (0.50), residues: 96
  loop : -0.17 (0.30), residues: 387

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARG A 522 
 TYR   0.013   0.001   TYR A1093 
 PHE   0.017   0.002   PHE A1083 
 TRP   0.015   0.001   TRP A1105 
 HIS   0.003   0.001   HIS A1494 

Details of bonding type rmsd
  covalent geometry    : bond        0.00313 ( 9407)
  covalent geometry    : angle       0.47803 (12682)
  hydrogen bonds       : bond        0.04803 (  485)
  hydrogen bonds       : angle       4.33315 ( 1407)

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

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

  2194 Ramachandran restraints generated.
    1097 Oldfield, 0 Emsley, 1097 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2194 Ramachandran restraints generated.
    1097 Oldfield, 0 Emsley, 1097 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  169 residues out of total 1022 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 46
    poor density    : 123
  time to evaluate  : 0.358 
Fit side-chains
REVERT: A  396 LYS cc_start: 0.7803 (mttt) cc_final: 0.7222 (ttpp)
REVERT: A  419 LYS cc_start: 0.8165 (OUTLIER) cc_final: 0.7849 (tttp)
REVERT: A  449 ASN cc_start: 0.7854 (t0) cc_final: 0.7194 (p0)
REVERT: A  453 LYS cc_start: 0.8488 (tmtt) cc_final: 0.7716 (tmmt)
REVERT: A  514 GLN cc_start: 0.7815 (mm-40) cc_final: 0.6838 (mm110)
REVERT: A  516 GLU cc_start: 0.7232 (mp0) cc_final: 0.6646 (mp0)
REVERT: A  558 GLU cc_start: 0.7848 (tp30) cc_final: 0.7002 (mp0)
REVERT: A  613 GLU cc_start: 0.8252 (mt-10) cc_final: 0.7848 (mt-10)
REVERT: A  626 GLN cc_start: 0.8011 (OUTLIER) cc_final: 0.7404 (pt0)
REVERT: A  635 ILE cc_start: 0.7583 (OUTLIER) cc_final: 0.7247 (mm)
REVERT: A  645 GLU cc_start: 0.8297 (OUTLIER) cc_final: 0.7814 (mm-30)
REVERT: A  669 LYS cc_start: 0.7453 (mptp) cc_final: 0.7086 (mppt)
REVERT: A  671 LYS cc_start: 0.8064 (mttt) cc_final: 0.7617 (mmtm)
REVERT: A  682 ASP cc_start: 0.8472 (OUTLIER) cc_final: 0.8195 (t70)
REVERT: A  803 GLU cc_start: 0.7287 (OUTLIER) cc_final: 0.7008 (mt-10)
REVERT: A  821 LYS cc_start: 0.6911 (mttt) cc_final: 0.6400 (mmtt)
REVERT: A  824 ARG cc_start: 0.6973 (mmt-90) cc_final: 0.6415 (ttm170)
REVERT: A  837 ARG cc_start: 0.8465 (OUTLIER) cc_final: 0.6835 (mtp180)
REVERT: A  860 LYS cc_start: 0.7985 (OUTLIER) cc_final: 0.6709 (tptt)
REVERT: A  870 LYS cc_start: 0.8327 (tttt) cc_final: 0.7913 (ttmm)
REVERT: A  874 GLU cc_start: 0.7983 (mt-10) cc_final: 0.7327 (mm-30)
REVERT: A  877 LYS cc_start: 0.8257 (mttt) cc_final: 0.7853 (mmtt)
REVERT: A  997 LYS cc_start: 0.8000 (tttt) cc_final: 0.7529 (tptt)
REVERT: A  998 LYS cc_start: 0.7891 (tttt) cc_final: 0.7168 (ptpt)
REVERT: A 1173 ARG cc_start: 0.7998 (OUTLIER) cc_final: 0.7394 (ttp-170)
REVERT: A 1200 GLU cc_start: 0.8769 (OUTLIER) cc_final: 0.8372 (tm-30)
REVERT: A 1222 GLU cc_start: 0.6610 (OUTLIER) cc_final: 0.6386 (mp0)
REVERT: A 1225 LYS cc_start: 0.7255 (OUTLIER) cc_final: 0.6395 (tmtt)
REVERT: A 1230 ASN cc_start: 0.8191 (m110) cc_final: 0.7890 (m-40)
REVERT: A 1279 LYS cc_start: 0.8680 (OUTLIER) cc_final: 0.8382 (ptmt)
REVERT: A 1291 LYS cc_start: 0.7939 (mtmm) cc_final: 0.6952 (tptp)
REVERT: A 1301 LYS cc_start: 0.8075 (tttt) cc_final: 0.7539 (mtpt)
REVERT: A 1349 GLU cc_start: 0.8091 (tt0) cc_final: 0.7024 (pt0)
REVERT: A 1355 GLN cc_start: 0.6147 (OUTLIER) cc_final: 0.5913 (tp40)
REVERT: A 1357 ASP cc_start: 0.7237 (m-30) cc_final: 0.6535 (p0)
REVERT: A 1452 GLN cc_start: 0.7430 (mp10) cc_final: 0.6935 (mp10)
REVERT: A 1471 MET cc_start: 0.8494 (OUTLIER) cc_final: 0.7270 (mmt)
  outliers start: 46
  outliers final: 22
  residues processed: 151
  average time/residue: 0.7100
  time to fit residues: 113.4990
Evaluate side-chains
  161 residues out of total 1022 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 37
    poor density    : 124
  time to evaluate  : 0.299 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  419 LYS
Chi-restraints excluded: chain A residue  446 SER
Chi-restraints excluded: chain A residue  452 VAL
Chi-restraints excluded: chain A residue  475 THR
Chi-restraints excluded: chain A residue  526 SER
Chi-restraints excluded: chain A residue  536 ARG
Chi-restraints excluded: chain A residue  550 ASP
Chi-restraints excluded: chain A residue  626 GLN
Chi-restraints excluded: chain A residue  635 ILE
Chi-restraints excluded: chain A residue  645 GLU
Chi-restraints excluded: chain A residue  682 ASP
Chi-restraints excluded: chain A residue  728 THR
Chi-restraints excluded: chain A residue  751 LEU
Chi-restraints excluded: chain A residue  801 PHE
Chi-restraints excluded: chain A residue  803 GLU
Chi-restraints excluded: chain A residue  837 ARG
Chi-restraints excluded: chain A residue  844 SER
Chi-restraints excluded: chain A residue  860 LYS
Chi-restraints excluded: chain A residue  934 SER
Chi-restraints excluded: chain A residue  970 THR
Chi-restraints excluded: chain A residue 1049 ASN
Chi-restraints excluded: chain A residue 1075 ILE
Chi-restraints excluded: chain A residue 1113 GLU
Chi-restraints excluded: chain A residue 1173 ARG
Chi-restraints excluded: chain A residue 1191 THR
Chi-restraints excluded: chain A residue 1200 GLU
Chi-restraints excluded: chain A residue 1208 ILE
Chi-restraints excluded: chain A residue 1222 GLU
Chi-restraints excluded: chain A residue 1225 LYS
Chi-restraints excluded: chain A residue 1272 ASP
Chi-restraints excluded: chain A residue 1279 LYS
Chi-restraints excluded: chain A residue 1355 GLN
Chi-restraints excluded: chain A residue 1404 LEU
Chi-restraints excluded: chain A residue 1424 LEU
Chi-restraints excluded: chain A residue 1436 SER
Chi-restraints excluded: chain A residue 1471 MET
Chi-restraints excluded: chain A residue 1558 LEU
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 112
   random chunks:
   chunk 71 optimal weight:    0.7980
   chunk 65 optimal weight:    0.6980
   chunk 36 optimal weight:    2.9990
   chunk 21 optimal weight:    1.9990
   chunk 17 optimal weight:    2.9990
   chunk 94 optimal weight:    1.9990
   chunk 40 optimal weight:    2.9990
   chunk 33 optimal weight:    2.9990
   chunk 93 optimal weight:    0.8980
   chunk 106 optimal weight:    6.9990
   chunk 56 optimal weight:    1.9990
   overall best weight:    1.2784

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

Flipped N/Q/H residues before XYZ refinement:
A 477 ASN
A 565 GLN
A 804 GLN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3721 r_free = 0.3721 target = 0.156206 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 35)----------------|
| r_work = 0.3355 r_free = 0.3355 target = 0.123636 restraints weight = 8740.322|
|-----------------------------------------------------------------------------|
r_work (start): 0.3346 rms_B_bonded: 1.87
r_work: 0.3089 rms_B_bonded: 2.60 restraints_weight: 0.5000
r_work: 0.2955 rms_B_bonded: 4.15 restraints_weight: 0.2500
r_work (final): 0.2955
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8397
moved from start:          0.0866

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.034   9407  Z= 0.172
  Angle     :  0.518   6.626  12682  Z= 0.279
  Chirality :  0.044   0.147   1390
  Planarity :  0.004   0.040   1600
  Dihedral  :  8.316  88.247   1257
  Min Nonbonded Distance : 1.977

Molprobity Statistics.
  All-atom Clashscore : 2.66
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.46 %
    Favored  : 97.54 %
  Rotamer:
    Outliers :  4.79 %
    Allowed  : 17.12 %
    Favored  : 78.08 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  1.66 (0.25), residues: 1097
  helix:  2.01 (0.21), residues: 613
  sheet:  0.76 (0.49), residues: 96
  loop : -0.24 (0.30), residues: 388

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.000   ARG A 522 
 TYR   0.013   0.002   TYR A 927 
 PHE   0.019   0.002   PHE A1083 
 TRP   0.015   0.002   TRP A1105 
 HIS   0.004   0.001   HIS A1494 

Details of bonding type rmsd
  covalent geometry    : bond        0.00399 ( 9407)
  covalent geometry    : angle       0.51838 (12682)
  hydrogen bonds       : bond        0.05348 (  485)
  hydrogen bonds       : angle       4.42476 ( 1407)

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

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

  2194 Ramachandran restraints generated.
    1097 Oldfield, 0 Emsley, 1097 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2194 Ramachandran restraints generated.
    1097 Oldfield, 0 Emsley, 1097 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  173 residues out of total 1022 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 49
    poor density    : 124
  time to evaluate  : 0.397 
Fit side-chains
REVERT: A  396 LYS cc_start: 0.7804 (mttt) cc_final: 0.7200 (ttpp)
REVERT: A  419 LYS cc_start: 0.8193 (OUTLIER) cc_final: 0.7842 (tttp)
REVERT: A  449 ASN cc_start: 0.7949 (t0) cc_final: 0.7259 (p0)
REVERT: A  453 LYS cc_start: 0.8521 (tmtt) cc_final: 0.7759 (tmmt)
REVERT: A  514 GLN cc_start: 0.7868 (mm-40) cc_final: 0.7147 (tp40)
REVERT: A  558 GLU cc_start: 0.7858 (tp30) cc_final: 0.6956 (mp0)
REVERT: A  613 GLU cc_start: 0.8257 (mt-10) cc_final: 0.7840 (mt-10)
REVERT: A  626 GLN cc_start: 0.8020 (OUTLIER) cc_final: 0.7397 (pt0)
REVERT: A  635 ILE cc_start: 0.7668 (OUTLIER) cc_final: 0.7282 (mm)
REVERT: A  645 GLU cc_start: 0.8307 (OUTLIER) cc_final: 0.7799 (mm-30)
REVERT: A  669 LYS cc_start: 0.7480 (mptp) cc_final: 0.7094 (mppt)
REVERT: A  671 LYS cc_start: 0.8065 (mttt) cc_final: 0.7634 (mmtm)
REVERT: A  682 ASP cc_start: 0.8496 (OUTLIER) cc_final: 0.8197 (t70)
REVERT: A  731 LYS cc_start: 0.6897 (OUTLIER) cc_final: 0.6598 (tptt)
REVERT: A  803 GLU cc_start: 0.7365 (OUTLIER) cc_final: 0.7086 (mt-10)
REVERT: A  821 LYS cc_start: 0.6925 (mttt) cc_final: 0.6395 (mmtt)
REVERT: A  824 ARG cc_start: 0.6996 (mmt-90) cc_final: 0.6435 (ttm170)
REVERT: A  837 ARG cc_start: 0.8485 (OUTLIER) cc_final: 0.6865 (mtp180)
REVERT: A  860 LYS cc_start: 0.8037 (OUTLIER) cc_final: 0.6699 (tptt)
REVERT: A  870 LYS cc_start: 0.8353 (tttt) cc_final: 0.7936 (ttmm)
REVERT: A  874 GLU cc_start: 0.8005 (mt-10) cc_final: 0.7349 (mm-30)
REVERT: A  877 LYS cc_start: 0.8211 (mttt) cc_final: 0.7814 (mmtt)
REVERT: A  997 LYS cc_start: 0.8037 (tttt) cc_final: 0.7553 (tptt)
REVERT: A  998 LYS cc_start: 0.7948 (tttt) cc_final: 0.7212 (ptpt)
REVERT: A 1173 ARG cc_start: 0.8009 (OUTLIER) cc_final: 0.7354 (ttp-170)
REVERT: A 1200 GLU cc_start: 0.8830 (OUTLIER) cc_final: 0.8389 (tm-30)
REVERT: A 1222 GLU cc_start: 0.6605 (OUTLIER) cc_final: 0.6383 (mp0)
REVERT: A 1225 LYS cc_start: 0.7248 (OUTLIER) cc_final: 0.6393 (tmtt)
REVERT: A 1230 ASN cc_start: 0.8229 (m110) cc_final: 0.7927 (m-40)
REVERT: A 1279 LYS cc_start: 0.8697 (OUTLIER) cc_final: 0.8411 (ptmt)
REVERT: A 1291 LYS cc_start: 0.7936 (mtmm) cc_final: 0.7009 (tptp)
REVERT: A 1301 LYS cc_start: 0.8115 (tttt) cc_final: 0.7581 (mtpt)
REVERT: A 1349 GLU cc_start: 0.8107 (tt0) cc_final: 0.7020 (pt0)
REVERT: A 1355 GLN cc_start: 0.6168 (OUTLIER) cc_final: 0.5927 (tp40)
REVERT: A 1357 ASP cc_start: 0.7258 (m-30) cc_final: 0.6567 (p0)
REVERT: A 1471 MET cc_start: 0.8516 (OUTLIER) cc_final: 0.7302 (mmt)
  outliers start: 49
  outliers final: 23
  residues processed: 151
  average time/residue: 0.7228
  time to fit residues: 115.3104
Evaluate side-chains
  160 residues out of total 1022 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 39
    poor density    : 121
  time to evaluate  : 0.370 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  419 LYS
Chi-restraints excluded: chain A residue  446 SER
Chi-restraints excluded: chain A residue  452 VAL
Chi-restraints excluded: chain A residue  475 THR
Chi-restraints excluded: chain A residue  526 SER
Chi-restraints excluded: chain A residue  536 ARG
Chi-restraints excluded: chain A residue  550 ASP
Chi-restraints excluded: chain A residue  626 GLN
Chi-restraints excluded: chain A residue  635 ILE
Chi-restraints excluded: chain A residue  645 GLU
Chi-restraints excluded: chain A residue  682 ASP
Chi-restraints excluded: chain A residue  728 THR
Chi-restraints excluded: chain A residue  731 LYS
Chi-restraints excluded: chain A residue  751 LEU
Chi-restraints excluded: chain A residue  801 PHE
Chi-restraints excluded: chain A residue  803 GLU
Chi-restraints excluded: chain A residue  837 ARG
Chi-restraints excluded: chain A residue  844 SER
Chi-restraints excluded: chain A residue  860 LYS
Chi-restraints excluded: chain A residue  934 SER
Chi-restraints excluded: chain A residue  970 THR
Chi-restraints excluded: chain A residue 1049 ASN
Chi-restraints excluded: chain A residue 1075 ILE
Chi-restraints excluded: chain A residue 1173 ARG
Chi-restraints excluded: chain A residue 1191 THR
Chi-restraints excluded: chain A residue 1200 GLU
Chi-restraints excluded: chain A residue 1208 ILE
Chi-restraints excluded: chain A residue 1222 GLU
Chi-restraints excluded: chain A residue 1225 LYS
Chi-restraints excluded: chain A residue 1272 ASP
Chi-restraints excluded: chain A residue 1279 LYS
Chi-restraints excluded: chain A residue 1355 GLN
Chi-restraints excluded: chain A residue 1362 MET
Chi-restraints excluded: chain A residue 1404 LEU
Chi-restraints excluded: chain A residue 1424 LEU
Chi-restraints excluded: chain A residue 1436 SER
Chi-restraints excluded: chain A residue 1453 MET
Chi-restraints excluded: chain A residue 1471 MET
Chi-restraints excluded: chain A residue 1558 LEU
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 112
   random chunks:
   chunk 11 optimal weight:    0.6980
   chunk 93 optimal weight:    0.6980
   chunk 41 optimal weight:    0.0270
   chunk 78 optimal weight:    1.9990
   chunk 96 optimal weight:    1.9990
   chunk 4 optimal weight:    1.9990
   chunk 10 optimal weight:    0.8980
   chunk 47 optimal weight:    0.9990
   chunk 92 optimal weight:    0.9980
   chunk 105 optimal weight:    1.9990
   chunk 45 optimal weight:    0.0570
   overall best weight:    0.4756

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

Flipped N/Q/H residues before XYZ refinement:
A 477 ASN
A 565 GLN
A 804 GLN
A 862 GLN
A1168 GLN

Total number of N/Q/H flips: 5

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3754 r_free = 0.3754 target = 0.159059 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 32)----------------|
| r_work = 0.3347 r_free = 0.3347 target = 0.122707 restraints weight = 8728.844|
|-----------------------------------------------------------------------------|
r_work (start): 0.3336 rms_B_bonded: 1.53
r_work: 0.3151 rms_B_bonded: 2.35 restraints_weight: 0.5000
r_work: 0.3015 rms_B_bonded: 3.77 restraints_weight: 0.2500
r_work (final): 0.3015
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8175
moved from start:          0.0988

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.024   9407  Z= 0.100
  Angle     :  0.433   7.617  12682  Z= 0.235
  Chirality :  0.040   0.132   1390
  Planarity :  0.004   0.038   1600
  Dihedral  :  7.903  83.637   1257
  Min Nonbonded Distance : 2.048

Molprobity Statistics.
  All-atom Clashscore : 2.39
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.10 %
    Favored  : 97.90 %
  Rotamer:
    Outliers :  3.72 %
    Allowed  : 18.20 %
    Favored  : 78.08 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  2.04 (0.25), residues: 1097
  helix:  2.32 (0.21), residues: 613
  sheet:  0.85 (0.50), residues: 96
  loop : -0.06 (0.31), residues: 388

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG A1331 
 TYR   0.015   0.001   TYR A1093 
 PHE   0.012   0.001   PHE A 675 
 TRP   0.014   0.001   TRP A1105 
 HIS   0.002   0.001   HIS A 581 

Details of bonding type rmsd
  covalent geometry    : bond        0.00204 ( 9407)
  covalent geometry    : angle       0.43302 (12682)
  hydrogen bonds       : bond        0.03975 (  485)
  hydrogen bonds       : angle       4.23525 ( 1407)

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

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

  2194 Ramachandran restraints generated.
    1097 Oldfield, 0 Emsley, 1097 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2194 Ramachandran restraints generated.
    1097 Oldfield, 0 Emsley, 1097 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  162 residues out of total 1022 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 38
    poor density    : 124
  time to evaluate  : 0.367 
Fit side-chains
   revert: symmetry clash
REVERT: A  396 LYS cc_start: 0.7551 (mttt) cc_final: 0.6859 (ttpp)
REVERT: A  419 LYS cc_start: 0.7962 (OUTLIER) cc_final: 0.7669 (tttp)
REVERT: A  449 ASN cc_start: 0.7684 (t0) cc_final: 0.6897 (p0)
REVERT: A  453 LYS cc_start: 0.8181 (tmtt) cc_final: 0.7325 (tmmt)
REVERT: A  514 GLN cc_start: 0.7573 (mm-40) cc_final: 0.6556 (mm110)
REVERT: A  516 GLU cc_start: 0.7029 (mp0) cc_final: 0.6407 (mp0)
REVERT: A  558 GLU cc_start: 0.7576 (tp30) cc_final: 0.6683 (mp0)
REVERT: A  613 GLU cc_start: 0.8043 (mt-10) cc_final: 0.7587 (mt-10)
REVERT: A  626 GLN cc_start: 0.7894 (OUTLIER) cc_final: 0.7168 (pt0)
REVERT: A  669 LYS cc_start: 0.7247 (mptp) cc_final: 0.6849 (mppt)
REVERT: A  671 LYS cc_start: 0.7865 (mttt) cc_final: 0.7384 (mmtm)
REVERT: A  682 ASP cc_start: 0.8403 (OUTLIER) cc_final: 0.8110 (t70)
REVERT: A  731 LYS cc_start: 0.6718 (OUTLIER) cc_final: 0.6453 (tptt)
REVERT: A  803 GLU cc_start: 0.7051 (OUTLIER) cc_final: 0.6764 (mt-10)
REVERT: A  821 LYS cc_start: 0.6632 (mttt) cc_final: 0.6184 (mptt)
REVERT: A  824 ARG cc_start: 0.6867 (mmt-90) cc_final: 0.6297 (ttm170)
REVERT: A  837 ARG cc_start: 0.8338 (OUTLIER) cc_final: 0.6625 (mtp180)
REVERT: A  860 LYS cc_start: 0.7663 (OUTLIER) cc_final: 0.6337 (tptt)
REVERT: A  870 LYS cc_start: 0.8209 (tttt) cc_final: 0.7707 (ttmm)
REVERT: A  874 GLU cc_start: 0.7891 (mt-10) cc_final: 0.7146 (mm-30)
REVERT: A  877 LYS cc_start: 0.8104 (mttt) cc_final: 0.7661 (mmtt)
REVERT: A  888 MET cc_start: 0.8585 (mmt) cc_final: 0.7990 (mmt)
REVERT: A  997 LYS cc_start: 0.7778 (tttt) cc_final: 0.7216 (tptt)
REVERT: A  998 LYS cc_start: 0.7683 (tttt) cc_final: 0.6927 (ptpt)
REVERT: A 1200 GLU cc_start: 0.8596 (OUTLIER) cc_final: 0.8086 (tm-30)
REVERT: A 1225 LYS cc_start: 0.7047 (OUTLIER) cc_final: 0.6173 (tptm)
REVERT: A 1230 ASN cc_start: 0.7936 (m110) cc_final: 0.7594 (m-40)
REVERT: A 1291 LYS cc_start: 0.7702 (mtmm) cc_final: 0.6694 (tptp)
REVERT: A 1301 LYS cc_start: 0.7854 (tttt) cc_final: 0.7208 (mtpt)
REVERT: A 1349 GLU cc_start: 0.7999 (tt0) cc_final: 0.6792 (pt0)
REVERT: A 1355 GLN cc_start: 0.5950 (OUTLIER) cc_final: 0.5744 (tp40)
REVERT: A 1357 ASP cc_start: 0.7067 (m-30) cc_final: 0.6346 (p0)
REVERT: A 1452 GLN cc_start: 0.7176 (mp10) cc_final: 0.6667 (mp10)
REVERT: A 1471 MET cc_start: 0.8359 (OUTLIER) cc_final: 0.7123 (mmt)
  outliers start: 38
  outliers final: 17
  residues processed: 145
  average time/residue: 0.7187
  time to fit residues: 110.2705
Evaluate side-chains
  151 residues out of total 1022 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 28
    poor density    : 123
  time to evaluate  : 0.362 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  419 LYS
Chi-restraints excluded: chain A residue  446 SER
Chi-restraints excluded: chain A residue  452 VAL
Chi-restraints excluded: chain A residue  475 THR
Chi-restraints excluded: chain A residue  526 SER
Chi-restraints excluded: chain A residue  536 ARG
Chi-restraints excluded: chain A residue  550 ASP
Chi-restraints excluded: chain A residue  626 GLN
Chi-restraints excluded: chain A residue  682 ASP
Chi-restraints excluded: chain A residue  731 LYS
Chi-restraints excluded: chain A residue  751 LEU
Chi-restraints excluded: chain A residue  801 PHE
Chi-restraints excluded: chain A residue  803 GLU
Chi-restraints excluded: chain A residue  837 ARG
Chi-restraints excluded: chain A residue  844 SER
Chi-restraints excluded: chain A residue  860 LYS
Chi-restraints excluded: chain A residue  934 SER
Chi-restraints excluded: chain A residue  970 THR
Chi-restraints excluded: chain A residue 1049 ASN
Chi-restraints excluded: chain A residue 1075 ILE
Chi-restraints excluded: chain A residue 1191 THR
Chi-restraints excluded: chain A residue 1200 GLU
Chi-restraints excluded: chain A residue 1225 LYS
Chi-restraints excluded: chain A residue 1272 ASP
Chi-restraints excluded: chain A residue 1355 GLN
Chi-restraints excluded: chain A residue 1424 LEU
Chi-restraints excluded: chain A residue 1471 MET
Chi-restraints excluded: chain A residue 1558 LEU
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 112
   random chunks:
   chunk 72 optimal weight:    2.9990
   chunk 5 optimal weight:    0.9980
   chunk 63 optimal weight:    1.9990
   chunk 26 optimal weight:    0.8980
   chunk 107 optimal weight:    0.3980
   chunk 104 optimal weight:    5.9990
   chunk 41 optimal weight:    0.2980
   chunk 33 optimal weight:    2.9990
   chunk 4 optimal weight:    0.9990
   chunk 65 optimal weight:    0.9980
   chunk 40 optimal weight:    0.5980
   overall best weight:    0.6380

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

Flipped N/Q/H residues before XYZ refinement:
A 477 ASN
A 565 GLN
A 804 GLN
A 862 GLN

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3751 r_free = 0.3751 target = 0.158679 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 29)----------------|
| r_work = 0.3395 r_free = 0.3395 target = 0.126820 restraints weight = 8780.505|
|-----------------------------------------------------------------------------|
r_work (start): 0.3388 rms_B_bonded: 1.70
r_work: 0.3141 rms_B_bonded: 2.49 restraints_weight: 0.5000
r_work: 0.3007 rms_B_bonded: 3.99 restraints_weight: 0.2500
r_work (final): 0.3007
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8349
moved from start:          0.0996

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.026   9407  Z= 0.112
  Angle     :  0.448   7.565  12682  Z= 0.242
  Chirality :  0.041   0.134   1390
  Planarity :  0.004   0.039   1600
  Dihedral  :  7.951  84.144   1257
  Min Nonbonded Distance : 2.026

Molprobity Statistics.
  All-atom Clashscore : 2.55
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.28 %
    Favored  : 97.72 %
  Rotamer:
    Outliers :  2.94 %
    Allowed  : 19.08 %
    Favored  : 77.98 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  2.05 (0.25), residues: 1097
  helix:  2.30 (0.21), residues: 615
  sheet:  0.86 (0.50), residues: 96
  loop : -0.03 (0.31), residues: 386

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG A1473 
 TYR   0.014   0.001   TYR A1093 
 PHE   0.014   0.001   PHE A1083 
 TRP   0.014   0.001   TRP A1105 
 HIS   0.002   0.001   HIS A 581 

Details of bonding type rmsd
  covalent geometry    : bond        0.00243 ( 9407)
  covalent geometry    : angle       0.44788 (12682)
  hydrogen bonds       : bond        0.04241 (  485)
  hydrogen bonds       : angle       4.23917 ( 1407)

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

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

  2194 Ramachandran restraints generated.
    1097 Oldfield, 0 Emsley, 1097 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2194 Ramachandran restraints generated.
    1097 Oldfield, 0 Emsley, 1097 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  154 residues out of total 1022 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 30
    poor density    : 124
  time to evaluate  : 0.389 
Fit side-chains
REVERT: A  396 LYS cc_start: 0.7773 (mttt) cc_final: 0.7213 (ttpp)
REVERT: A  419 LYS cc_start: 0.8122 (OUTLIER) cc_final: 0.7801 (tttp)
REVERT: A  449 ASN cc_start: 0.7875 (t0) cc_final: 0.7198 (p0)
REVERT: A  453 LYS cc_start: 0.8423 (tmtt) cc_final: 0.7656 (tmmt)
REVERT: A  514 GLN cc_start: 0.7743 (mm-40) cc_final: 0.6794 (mm110)
REVERT: A  558 GLU cc_start: 0.7809 (tp30) cc_final: 0.6998 (mp0)
REVERT: A  613 GLU cc_start: 0.8275 (mt-10) cc_final: 0.7876 (mt-10)
REVERT: A  626 GLN cc_start: 0.7999 (OUTLIER) cc_final: 0.7405 (pt0)
REVERT: A  669 LYS cc_start: 0.7408 (mptp) cc_final: 0.7064 (mppt)
REVERT: A  671 LYS cc_start: 0.8054 (mttt) cc_final: 0.7612 (mmtm)
REVERT: A  682 ASP cc_start: 0.8430 (OUTLIER) cc_final: 0.8115 (t70)
REVERT: A  731 LYS cc_start: 0.6920 (OUTLIER) cc_final: 0.6623 (tptt)
REVERT: A  803 GLU cc_start: 0.7219 (OUTLIER) cc_final: 0.6955 (mt-10)
REVERT: A  821 LYS cc_start: 0.6880 (mttt) cc_final: 0.6369 (mmtt)
REVERT: A  824 ARG cc_start: 0.6914 (mmt-90) cc_final: 0.6427 (ttm170)
REVERT: A  837 ARG cc_start: 0.8468 (OUTLIER) cc_final: 0.6835 (mtp180)
REVERT: A  860 LYS cc_start: 0.7947 (OUTLIER) cc_final: 0.6706 (tptt)
REVERT: A  870 LYS cc_start: 0.8325 (tttt) cc_final: 0.7904 (ttmm)
REVERT: A  874 GLU cc_start: 0.7984 (mt-10) cc_final: 0.7325 (mm-30)
REVERT: A  877 LYS cc_start: 0.8260 (mttt) cc_final: 0.7860 (mmtt)
REVERT: A  888 MET cc_start: 0.8639 (mmt) cc_final: 0.8096 (mmt)
REVERT: A  997 LYS cc_start: 0.8010 (tttt) cc_final: 0.7542 (tptt)
REVERT: A  998 LYS cc_start: 0.7826 (tttt) cc_final: 0.7091 (ptpt)
REVERT: A 1200 GLU cc_start: 0.8695 (OUTLIER) cc_final: 0.8283 (tm-30)
REVERT: A 1225 LYS cc_start: 0.7217 (OUTLIER) cc_final: 0.6385 (tmtt)
REVERT: A 1230 ASN cc_start: 0.8157 (m110) cc_final: 0.7853 (m-40)
REVERT: A 1279 LYS cc_start: 0.8664 (OUTLIER) cc_final: 0.8382 (ptmt)
REVERT: A 1291 LYS cc_start: 0.7935 (mtmm) cc_final: 0.6977 (tptp)
REVERT: A 1301 LYS cc_start: 0.8057 (tttt) cc_final: 0.7508 (mtpt)
REVERT: A 1349 GLU cc_start: 0.8121 (tt0) cc_final: 0.7046 (pt0)
REVERT: A 1355 GLN cc_start: 0.6095 (OUTLIER) cc_final: 0.5829 (tp40)
REVERT: A 1357 ASP cc_start: 0.7229 (m-30) cc_final: 0.6538 (p0)
REVERT: A 1452 GLN cc_start: 0.7412 (mp10) cc_final: 0.6925 (mp10)
REVERT: A 1471 MET cc_start: 0.8480 (OUTLIER) cc_final: 0.7232 (mmt)
  outliers start: 30
  outliers final: 15
  residues processed: 143
  average time/residue: 0.7619
  time to fit residues: 115.0736
Evaluate side-chains
  149 residues out of total 1022 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 27
    poor density    : 122
  time to evaluate  : 0.379 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  419 LYS
Chi-restraints excluded: chain A residue  446 SER
Chi-restraints excluded: chain A residue  452 VAL
Chi-restraints excluded: chain A residue  475 THR
Chi-restraints excluded: chain A residue  526 SER
Chi-restraints excluded: chain A residue  536 ARG
Chi-restraints excluded: chain A residue  550 ASP
Chi-restraints excluded: chain A residue  626 GLN
Chi-restraints excluded: chain A residue  682 ASP
Chi-restraints excluded: chain A residue  731 LYS
Chi-restraints excluded: chain A residue  751 LEU
Chi-restraints excluded: chain A residue  801 PHE
Chi-restraints excluded: chain A residue  803 GLU
Chi-restraints excluded: chain A residue  837 ARG
Chi-restraints excluded: chain A residue  860 LYS
Chi-restraints excluded: chain A residue  934 SER
Chi-restraints excluded: chain A residue  970 THR
Chi-restraints excluded: chain A residue 1049 ASN
Chi-restraints excluded: chain A residue 1075 ILE
Chi-restraints excluded: chain A residue 1191 THR
Chi-restraints excluded: chain A residue 1200 GLU
Chi-restraints excluded: chain A residue 1225 LYS
Chi-restraints excluded: chain A residue 1272 ASP
Chi-restraints excluded: chain A residue 1279 LYS
Chi-restraints excluded: chain A residue 1355 GLN
Chi-restraints excluded: chain A residue 1471 MET
Chi-restraints excluded: chain A residue 1558 LEU
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 112
   random chunks:
   chunk 95 optimal weight:    0.5980
   chunk 108 optimal weight:    4.9990
   chunk 92 optimal weight:    0.5980
   chunk 69 optimal weight:    0.9980
   chunk 7 optimal weight:    2.9990
   chunk 23 optimal weight:    0.6980
   chunk 55 optimal weight:    1.9990
   chunk 37 optimal weight:    0.6980
   chunk 63 optimal weight:    1.9990
   chunk 44 optimal weight:    3.9990
   chunk 58 optimal weight:    0.9990
   overall best weight:    0.7180

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

Flipped N/Q/H residues before XYZ refinement:
A 477 ASN
A 804 GLN
A 862 GLN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3747 r_free = 0.3747 target = 0.158305 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 29)----------------|
| r_work = 0.3387 r_free = 0.3387 target = 0.126197 restraints weight = 8817.463|
|-----------------------------------------------------------------------------|
r_work (start): 0.3380 rms_B_bonded: 1.69
r_work: 0.3139 rms_B_bonded: 2.46 restraints_weight: 0.5000
r_work: 0.3005 rms_B_bonded: 3.95 restraints_weight: 0.2500
r_work (final): 0.3005
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8351
moved from start:          0.0981

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.027   9407  Z= 0.119
  Angle     :  0.456   7.462  12682  Z= 0.246
  Chirality :  0.041   0.142   1390
  Planarity :  0.004   0.039   1600
  Dihedral  :  7.987  84.327   1257
  Min Nonbonded Distance : 2.021

Molprobity Statistics.
  All-atom Clashscore : 2.55
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.91 %
    Favored  : 98.09 %
  Rotamer:
    Outliers :  3.33 %
    Allowed  : 18.69 %
    Favored  : 77.98 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  2.05 (0.25), residues: 1097
  helix:  2.27 (0.21), residues: 615
  sheet:  0.85 (0.49), residues: 103
  loop :  0.02 (0.31), residues: 379

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG A 522 
 TYR   0.016   0.001   TYR A1246 
 PHE   0.014   0.001   PHE A1083 
 TRP   0.014   0.001   TRP A1105 
 HIS   0.003   0.001   HIS A1494 

Details of bonding type rmsd
  covalent geometry    : bond        0.00260 ( 9407)
  covalent geometry    : angle       0.45633 (12682)
  hydrogen bonds       : bond        0.04367 (  485)
  hydrogen bonds       : angle       4.26724 ( 1407)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 4622.23 seconds
wall clock time: 79 minutes 20.75 seconds (4760.75 seconds total)