Starting phenix.real_space_refine
on Wed Feb  4 12:15:41 2026 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/9qtb_53349/02_2026/9qtb_53349.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/9qtb_53349/02_2026/9qtb_53349.map

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

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

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    model {
      file = "/net/cci-nas-00/data/ceres_data/9qtb_53349/02_2026/9qtb_53349.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/9qtb_53349/02_2026/9qtb_53349.cif"
    real_map_files = "/net/cci-nas-00/data/ceres_data/9qtb_53349/02_2026/9qtb_53349.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/9qtb_53349/02_2026/9qtb_53349.map"
  }
  resolution = 3.5
  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=   0.002 sd=   0.031
Set stop_for_unknowns flag
  Set to: True
Assert model is a single copy model
Assert all atoms have isotropic ADPs
Construct map_model_manager
Extract box with map and model
Check model and map are aligned
Set scattering table
  Set to: electron
  Number of scattering types: 4
    Type Number    sf(0)   Gaussians
     S      76      5.16       5
     C    6568      2.51       5
     N    1755      2.21       5
     O    1890      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 5 residue(s): 0.01s

  Monomer Library directory:
    "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5952/lib/python3.9/site-packages/chem_data/mon_lib"
  Total number of atoms: 10289
  Number of models: 1
  Model: ""
    Number of chains: 1
    Chain: "A"
      Number of atoms: 10289
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 1283, 10289
          Classifications: {'peptide': 1283}
          Link IDs: {'PCIS': 1, 'PTRANS': 54, 'TRANS': 1227}
          Chain breaks: 7
  Time building chain proxies: 1.78, per 1000 atoms: 0.17
  Number of scatterers: 10289
  At special positions: 0
  Unit cell: (89.238, 99.246, 110.922, 90, 90, 90)
  Space group: P 1 (No. 1)
  Number of sites at special positions: 0
  Number of scattering types: 4
    Type Number    sf(0)
     S      76     16.00
     O    1890      8.00
     N    1755      7.00
     C    6568      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: 0.64
  Conformation dependent library (CDL) restraints added in 423.7 milliseconds
  

  2534 Ramachandran restraints generated.
    1267 Oldfield, 0 Emsley, 1267 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  2434

  Finding SS restraints...
    Secondary structure from input PDB file:
      64 helices and 9 sheets defined
      58.1% alpha, 8.4% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 0.46
  Creating SS restraints...
    Processing helix  chain 'A' and resid 215 through 228
    Processing helix  chain 'A' and resid 231 through 239
    Processing helix  chain 'A' and resid 243 through 253
      removed outlier: 3.652A  pdb=" N   PHE A 247 " --> pdb=" O   SER A 243 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 256 through 280
    Processing helix  chain 'A' and resid 286 through 311
    Processing helix  chain 'A' and resid 341 through 345
    Processing helix  chain 'A' and resid 353 through 369
    Processing helix  chain 'A' and resid 428 through 434
    Processing helix  chain 'A' and resid 435 through 437
      No H-bonds generated for 'chain 'A' and resid 435 through 437'
    Processing helix  chain 'A' and resid 447 through 455
      removed outlier: 3.617A  pdb=" N   SER A 451 " --> pdb=" O   VAL A 447 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 459 through 463
    Processing helix  chain 'A' and resid 475 through 487
      removed outlier: 4.255A  pdb=" N   HIS A 486 " --> pdb=" O   ALA A 482 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 487 through 494
      removed outlier: 3.903A  pdb=" N   ARG A 493 " --> pdb=" O   SER A 489 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 496 through 507
    Processing helix  chain 'A' and resid 508 through 529
      removed outlier: 3.947A  pdb=" N   LYS A 529 " --> pdb=" O   SER A 525 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 601 through 608
      removed outlier: 4.312A  pdb=" N   ASN A 605 " --> pdb=" O   SER A 601 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 608 through 624
    Processing helix  chain 'A' and resid 631 through 637
    Processing helix  chain 'A' and resid 640 through 660
    Processing helix  chain 'A' and resid 661 through 677
      removed outlier: 3.905A  pdb=" N   ALA A 671 " --> pdb=" O   LEU A 667 " (cutoff:3.500A)
      removed outlier: 4.533A  pdb=" N   ARG A 672 " --> pdb=" O   GLN A 668 " (cutoff:3.500A)
      removed outlier: 4.308A  pdb=" N   TYR A 673 " --> pdb=" O   THR A 669 " (cutoff:3.500A)
      removed outlier: 3.675A  pdb=" N   GLU A 677 " --> pdb=" O   TYR A 673 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 678 through 680
      No H-bonds generated for 'chain 'A' and resid 678 through 680'
    Processing helix  chain 'A' and resid 687 through 695
      removed outlier: 4.199A  pdb=" N   SER A 693 " --> pdb=" O   LYS A 690 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 701 through 721
    Processing helix  chain 'A' and resid 748 through 757
      removed outlier: 3.643A  pdb=" N   LEU A 752 " --> pdb=" O   ASP A 748 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 758 through 760
      No H-bonds generated for 'chain 'A' and resid 758 through 760'
    Processing helix  chain 'A' and resid 773 through 782
      removed outlier: 3.829A  pdb=" N   TYR A 777 " --> pdb=" O   LEU A 773 " (cutoff:3.500A)
      removed outlier: 3.610A  pdb=" N   ILE A 781 " --> pdb=" O   TYR A 777 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 783 through 787
    Processing helix  chain 'A' and resid 808 through 828
    Processing helix  chain 'A' and resid 830 through 845
    Processing helix  chain 'A' and resid 847 through 852
      removed outlier: 3.906A  pdb=" N   LEU A 851 " --> pdb=" O   THR A 847 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 861 through 865
    Processing helix  chain 'A' and resid 879 through 890
      removed outlier: 4.022A  pdb=" N   LYS A 883 " --> pdb=" O   LYS A 879 " (cutoff:3.500A)
      removed outlier: 3.681A  pdb=" N   GLU A 890 " --> pdb=" O   LYS A 886 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 894 through 897
    Processing helix  chain 'A' and resid 898 through 910
      removed outlier: 3.572A  pdb=" N   CYS A 902 " --> pdb=" O   LYS A 898 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 932 through 951
    Processing helix  chain 'A' and resid 960 through 980
      removed outlier: 3.605A  pdb=" N   LYS A 964 " --> pdb=" O   ASN A 960 " (cutoff:3.500A)
      removed outlier: 3.958A  pdb=" N   VAL A 965 " --> pdb=" O   PRO A 961 " (cutoff:3.500A)
      Proline residue:  A 968  - end of helix
      removed outlier: 4.082A  pdb=" N   GLY A 972 " --> pdb=" O   PRO A 968 " (cutoff:3.500A)
      removed outlier: 4.387A  pdb=" N   ILE A 973 " --> pdb=" O   GLU A 969 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 1001 through 1011
    Processing helix  chain 'A' and resid 1012 through 1015
      removed outlier: 6.187A  pdb=" N   LYS A1015 " --> pdb=" O   THR A1012 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'A' and resid 1012 through 1015'
    Processing helix  chain 'A' and resid 1016 through 1026
      removed outlier: 3.504A  pdb=" N   ARG A1022 " --> pdb=" O   PRO A1018 " (cutoff:3.500A)
      removed outlier: 3.637A  pdb=" N   MET A1026 " --> pdb=" O   ARG A1022 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 1035 through 1044
      removed outlier: 3.626A  pdb=" N   GLY A1044 " --> pdb=" O   LYS A1040 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 1052 through 1063
    Processing helix  chain 'A' and resid 1090 through 1116
      removed outlier: 3.620A  pdb=" N   VAL A1116 " --> pdb=" O   PHE A1112 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 1117 through 1124
      removed outlier: 3.740A  pdb=" N   MET A1120 " --> pdb=" O   ALA A1117 " (cutoff:3.500A)
      removed outlier: 4.468A  pdb=" N   SER A1121 " --> pdb=" O   PRO A1118 " (cutoff:3.500A)
      removed outlier: 3.842A  pdb=" N   LEU A1124 " --> pdb=" O   SER A1121 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 1145 through 1167
      removed outlier: 3.522A  pdb=" N   LYS A1164 " --> pdb=" O   PHE A1160 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 1168 through 1171
    Processing helix  chain 'A' and resid 1202 through 1209
      removed outlier: 3.602A  pdb=" N   ILE A1206 " --> pdb=" O   THR A1202 " (cutoff:3.500A)
      removed outlier: 3.926A  pdb=" N   ALA A1207 " --> pdb=" O   ILE A1203 " (cutoff:3.500A)
      removed outlier: 4.267A  pdb=" N   ALA A1208 " --> pdb=" O   ARG A1204 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 1217 through 1235
    Processing helix  chain 'A' and resid 1238 through 1257
      removed outlier: 3.588A  pdb=" N   MET A1257 " --> pdb=" O   HIS A1253 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 1264 through 1276
      removed outlier: 4.224A  pdb=" N   LYS A1274 " --> pdb=" O   LYS A1270 " (cutoff:3.500A)
      removed outlier: 3.634A  pdb=" N   TRP A1275 " --> pdb=" O   ALA A1271 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 1277 through 1281
    Processing helix  chain 'A' and resid 1287 through 1291
      removed outlier: 3.632A  pdb=" N   CYS A1291 " --> pdb=" O   PRO A1288 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 1294 through 1307
      removed outlier: 3.631A  pdb=" N   PHE A1298 " --> pdb=" O   GLY A1294 " (cutoff:3.500A)
      removed outlier: 3.796A  pdb=" N   ARG A1306 " --> pdb=" O   LYS A1302 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 1308 through 1318
      removed outlier: 3.920A  pdb=" N   LEU A1312 " --> pdb=" O   ASP A1308 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 1375 through 1381
    Processing helix  chain 'A' and resid 1382 through 1387
      removed outlier: 3.584A  pdb=" N   ARG A1387 " --> pdb=" O   VAL A1384 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 1391 through 1404
    Processing helix  chain 'A' and resid 1452 through 1459
    Processing helix  chain 'A' and resid 1460 through 1462
      No H-bonds generated for 'chain 'A' and resid 1460 through 1462'
    Processing helix  chain 'A' and resid 1469 through 1477
    Processing helix  chain 'A' and resid 1479 through 1491
      removed outlier: 3.839A  pdb=" N   ILE A1489 " --> pdb=" O   SER A1485 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 1524 through 1535
    Processing helix  chain 'A' and resid 1542 through 1557
    Processing helix  chain 'A' and resid 1563 through 1571
    Processing helix  chain 'A' and resid 1609 through 1616
    Processing sheet with id=AA1, first strand: chain 'A' and resid 330 through 332
    Processing sheet with id=AA2, first strand: chain 'A' and resid 538 through 541
    Processing sheet with id=AA3, first strand: chain 'A' and resid 538 through 541
    Processing sheet with id=AA4, first strand: chain 'A' and resid 724 through 726
    Processing sheet with id=AA5, first strand: chain 'A' and resid 927 through 930
      removed outlier: 5.728A  pdb=" N   MET A 912 " --> pdb=" O   ARG A1031 " (cutoff:3.500A)
      removed outlier: 7.195A  pdb=" N   MET A1033 " --> pdb=" O   MET A 912 " (cutoff:3.500A)
      removed outlier: 7.476A  pdb=" N   ILE A 914 " --> pdb=" O   MET A1033 " (cutoff:3.500A)
    Processing sheet with id=AA6, first strand: chain 'A' and resid 1125 through 1130
      removed outlier: 7.440A  pdb=" N   THR A 985 " --> pdb=" O   ASP A1183 " (cutoff:3.500A)
      removed outlier: 4.898A  pdb=" N   ASP A1183 " --> pdb=" O   THR A 985 " (cutoff:3.500A)
      removed outlier: 6.376A  pdb=" N   ALA A 987 " --> pdb=" O   ASN A1181 " (cutoff:3.500A)
    Processing sheet with id=AA7, first strand: chain 'A' and resid 1185 through 1188
    Processing sheet with id=AA8, first strand: chain 'A' and resid 1498 through 1500
    Processing sheet with id=AA9, first strand: chain 'A' and resid 1508 through 1513
      removed outlier: 3.569A  pdb=" N   VAL A1512 " --> pdb=" O   VAL A1593 " (cutoff:3.500A)
      removed outlier: 7.403A  pdb=" N   VAL A1593 " --> pdb=" O   VAL A1512 " (cutoff:3.500A)

    532 hydrogen bonds defined for protein.
    1491 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: 1.61

  Time building geometry restraints manager: 0.89 seconds

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

  Histogram of bond lengths:
        1.22 -     1.34: 3313
        1.34 -     1.46: 2426
        1.46 -     1.58: 4657
        1.58 -     1.70: 0
        1.70 -     1.82: 121
  Bond restraints: 10517
  Sorted by residual:
  bond pdb=" C   LEU A1212 "
       pdb=" N   PRO A1213 "
    ideal  model  delta    sigma   weight residual
    1.326  1.346 -0.020 1.44e-02 4.82e+03 1.96e+00
  bond pdb=" N   LYS A 855 "
       pdb=" CA  LYS A 855 "
    ideal  model  delta    sigma   weight residual
    1.457  1.475 -0.017 1.29e-02 6.01e+03 1.79e+00
  bond pdb=" CG  ARG A 434 "
       pdb=" CD  ARG A 434 "
    ideal  model  delta    sigma   weight residual
    1.520  1.492  0.028 3.00e-02 1.11e+03 8.41e-01
  bond pdb=" CB  GLN A1101 "
       pdb=" CG  GLN A1101 "
    ideal  model  delta    sigma   weight residual
    1.520  1.493  0.027 3.00e-02 1.11e+03 7.83e-01
  bond pdb=" SD  MET A 613 "
       pdb=" CE  MET A 613 "
    ideal  model  delta    sigma   weight residual
    1.791  1.769  0.022 2.50e-02 1.60e+03 7.65e-01
  ... (remaining 10512 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     1.76: 13889
        1.76 -     3.52: 228
        3.52 -     5.28: 60
        5.28 -     7.04: 4
        7.04 -     8.80: 1
  Bond angle restraints: 14182
  Sorted by residual:
  angle pdb=" N   GLU A1214 "
        pdb=" CA  GLU A1214 "
        pdb=" CB  GLU A1214 "
      ideal   model   delta    sigma   weight residual
     114.17  109.19    4.98 1.14e+00 7.69e-01 1.91e+01
  angle pdb=" C   SER A1350 "
        pdb=" CA  SER A1350 "
        pdb=" CB  SER A1350 "
      ideal   model   delta    sigma   weight residual
     115.89  110.22    5.67 1.32e+00 5.74e-01 1.85e+01
  angle pdb=" C   ALA A 426 "
        pdb=" N   ASP A 427 "
        pdb=" CA  ASP A 427 "
      ideal   model   delta    sigma   weight residual
     121.54  127.52   -5.98 1.91e+00 2.74e-01 9.80e+00
  angle pdb=" CB  MET A 884 "
        pdb=" CG  MET A 884 "
        pdb=" SD  MET A 884 "
      ideal   model   delta    sigma   weight residual
     112.70  121.50   -8.80 3.00e+00 1.11e-01 8.60e+00
  angle pdb=" N   GLY A 421 "
        pdb=" CA  GLY A 421 "
        pdb=" C   GLY A 421 "
      ideal   model   delta    sigma   weight residual
     114.66  111.38    3.28 1.24e+00 6.50e-01 7.00e+00
  ... (remaining 14177 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    17.22: 5753
       17.22 -    34.45: 516
       34.45 -    51.67: 90
       51.67 -    68.90: 12
       68.90 -    86.12: 11
  Dihedral angle restraints: 6382
    sinusoidal: 2634
      harmonic: 3748
  Sorted by residual:
  dihedral pdb=" CA  LYS A 552 "
           pdb=" C   LYS A 552 "
           pdb=" N   PRO A 553 "
           pdb=" CA  PRO A 553 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  160.87   19.13     0      5.00e+00 4.00e-02 1.46e+01
  dihedral pdb=" CA  MET A1128 "
           pdb=" C   MET A1128 "
           pdb=" N   MET A1129 "
           pdb=" CA  MET A1129 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  161.01   18.99     0      5.00e+00 4.00e-02 1.44e+01
  dihedral pdb=" CA  VAL A 930 "
           pdb=" C   VAL A 930 "
           pdb=" N   MET A 931 "
           pdb=" CA  MET A 931 "
      ideal   model   delta  harmonic     sigma   weight residual
    -180.00 -162.27  -17.73     0      5.00e+00 4.00e-02 1.26e+01
  ... (remaining 6379 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.029: 988
       0.029 -    0.057: 379
       0.057 -    0.086: 117
       0.086 -    0.114: 59
       0.114 -    0.143: 10
  Chirality restraints: 1553
  Sorted by residual:
  chirality pdb=" CA  ILE A1499 "
            pdb=" N   ILE A1499 "
            pdb=" C   ILE A1499 "
            pdb=" CB  ILE A1499 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.43    2.58   -0.14 2.00e-01 2.50e+01 5.08e-01
  chirality pdb=" CA  ILE A1139 "
            pdb=" N   ILE A1139 "
            pdb=" C   ILE A1139 "
            pdb=" CB  ILE A1139 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.43    2.57   -0.14 2.00e-01 2.50e+01 4.74e-01
  chirality pdb=" CA  ILE A 626 "
            pdb=" N   ILE A 626 "
            pdb=" C   ILE A 626 "
            pdb=" CB  ILE A 626 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.43    2.57   -0.14 2.00e-01 2.50e+01 4.70e-01
  ... (remaining 1550 not shown)

  Planarity restraints: 1803
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  ASP A 427 "   -0.011 2.00e-02 2.50e+03   2.24e-02 5.01e+00
        pdb=" C   ASP A 427 "    0.039 2.00e-02 2.50e+03
        pdb=" O   ASP A 427 "   -0.014 2.00e-02 2.50e+03
        pdb=" N   THR A 428 "   -0.013 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   LYS A 552 "   -0.031 5.00e-02 4.00e+02   4.79e-02 3.67e+00
        pdb=" N   PRO A 553 "    0.083 5.00e-02 4.00e+02
        pdb=" CA  PRO A 553 "   -0.025 5.00e-02 4.00e+02
        pdb=" CD  PRO A 553 "   -0.027 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   HIS A 353 "    0.031 5.00e-02 4.00e+02   4.67e-02 3.49e+00
        pdb=" N   PRO A 354 "   -0.081 5.00e-02 4.00e+02
        pdb=" CA  PRO A 354 "    0.024 5.00e-02 4.00e+02
        pdb=" CD  PRO A 354 "    0.026 5.00e-02 4.00e+02
  ... (remaining 1800 not shown)

  Histogram of nonbonded interaction distances:
        1.98 -     2.57: 86
        2.57 -     3.15: 9009
        3.15 -     3.73: 16334
        3.73 -     4.32: 21554
        4.32 -     4.90: 35804
  Nonbonded interactions: 82787
  Sorted by model distance:
  nonbonded pdb=" OH  TYR A 309 "
            pdb=" O   PRO A 696 "
     model   vdw
     1.982 3.040
  nonbonded pdb=" OD1 ASP A1531 "
            pdb=" OG1 THR A1536 "
     model   vdw
     2.130 3.040
  nonbonded pdb=" O   PHE A 250 "
            pdb=" NZ  LYS A 813 "
     model   vdw
     2.209 3.120
  nonbonded pdb=" OG1 THR A 988 "
            pdb=" O   THR A1179 "
     model   vdw
     2.274 3.040
  nonbonded pdb=" O   LEU A 214 "
            pdb=" NH1 ARG A 219 "
     model   vdw
     2.289 3.120
  ... (remaining 82782 not shown)

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

  No NCS relation were found !!!

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

Found NCS groups:
  found none.
Set up NCS constraints
  No NCS constraints will be used in refinement.
Set refine NCS operators
Adjust number of macro_cycles
  Number of macro_cycles: 10
Reset NCS operators
Extract rigid body selections
Check and reset occupancies
  Occupancies: min=1.00 max=1.00 mean=1.00
Load rotamer database and sin/cos tables
Set ADP refinement strategy
  ADPs will be refined as group one per residue
Make a string to write initial .geo file
Internal consistency checks
Time:
  Set random seed:                         0.000
  Set model cs if undefined:               0.000
  Decide on map wrapping:                  0.000
  Normalize map: mean=0, sd=1:             1.050
  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:             0.000
  Extract box with map and model:          0.100
  Check model and map are aligned:         0.020
  Set scattering table:                    0.010
  Process input model:                     9.250
  Find NCS groups from input model:        0.130
  Set up NCS constraints:                  0.010
  Set refine NCS operators:                0.000
  Adjust number of macro_cycles:           0.000
  Reset NCS operators:                     0.000
  Extract rigid body selections:           0.000
  Check and reset occupancies:             0.000
  Load rotamer database and sin/cos tables:1.240
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   11.810
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8495
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      :  0.003   0.028  10517  Z= 0.164
  Angle     :  0.613   8.799  14182  Z= 0.331
  Chirality :  0.038   0.143   1553
  Planarity :  0.004   0.048   1803
  Dihedral  : 13.535  86.120   3948
  Min Nonbonded Distance : 1.982

Molprobity Statistics.
  All-atom Clashscore : 4.76
  Ramachandran Plot:
    Outliers :  0.08 %
    Allowed  :  4.18 %
    Favored  : 95.74 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  0.00 %
    Favored  : 100.00 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 1.82 %
    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:  0.91 (0.25), residues: 1267
  helix:  1.77 (0.21), residues: 635
  sheet: -0.69 (0.51), residues: 98
  loop : -0.55 (0.29), residues: 534

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.001   ARG A1511 
 TYR   0.012   0.001   TYR A 648 
 PHE   0.011   0.001   PHE A1112 
 TRP   0.005   0.001   TRP A 620 
 HIS   0.006   0.001   HIS A 424 

Details of bonding type rmsd
  covalent geometry    : bond        0.00343 (10517)
  covalent geometry    : angle       0.61272 (14182)
  hydrogen bonds       : bond        0.15436 (  522)
  hydrogen bonds       : angle       6.13479 ( 1491)

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

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

  2534 Ramachandran restraints generated.
    1267 Oldfield, 0 Emsley, 1267 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2534 Ramachandran restraints generated.
    1267 Oldfield, 0 Emsley, 1267 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  99 residues out of total 1140 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 99
  time to evaluate  : 0.319 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  246 MET cc_start: 0.9112 (mmm) cc_final: 0.8684 (mmm)
REVERT: A  355 MET cc_start: 0.9498 (mmm) cc_final: 0.8619 (mmm)
REVERT: A  433 MET cc_start: 0.9666 (mmp) cc_final: 0.9458 (mmp)
REVERT: A  622 GLU cc_start: 0.9601 (tm-30) cc_final: 0.9203 (tm-30)
REVERT: A  644 MET cc_start: 0.9194 (mpp) cc_final: 0.8827 (mpp)
REVERT: A  666 GLU cc_start: 0.9463 (mp0) cc_final: 0.9203 (mp0)
REVERT: A  674 ILE cc_start: 0.9586 (mm) cc_final: 0.9331 (mm)
REVERT: A  748 ASP cc_start: 0.9203 (m-30) cc_final: 0.8995 (t0)
REVERT: A  769 GLU cc_start: 0.8819 (tp30) cc_final: 0.8187 (tp30)
REVERT: A  912 MET cc_start: 0.8230 (mmt) cc_final: 0.7904 (mmt)
REVERT: A 1032 MET cc_start: 0.9228 (mpp) cc_final: 0.8903 (mpp)
REVERT: A 1085 MET cc_start: 0.8671 (mpp) cc_final: 0.8260 (mpp)
REVERT: A 1101 GLN cc_start: 0.8897 (mt0) cc_final: 0.8327 (mt0)
REVERT: A 1120 MET cc_start: 0.9592 (mtp) cc_final: 0.9372 (mtp)
REVERT: A 1128 MET cc_start: 0.8139 (mmp) cc_final: 0.7598 (mmp)
REVERT: A 1186 MET cc_start: 0.8136 (tmm) cc_final: 0.7496 (tmm)
REVERT: A 1223 GLU cc_start: 0.9571 (pt0) cc_final: 0.9288 (pt0)
REVERT: A 1227 ASN cc_start: 0.9446 (m110) cc_final: 0.9202 (m110)
REVERT: A 1402 LYS cc_start: 0.9613 (mmmt) cc_final: 0.9321 (mmmm)
  outliers start: 0
  outliers final: 0
  residues processed: 99
  average time/residue: 0.0838
  time to fit residues: 12.1012
Evaluate side-chains
  82 residues out of total 1140 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 82
  time to evaluate  : 0.415 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 128
   random chunks:
   chunk 98 optimal weight:   10.0000
   chunk 107 optimal weight:    6.9990
   chunk 10 optimal weight:   20.0000
   chunk 66 optimal weight:   20.0000
   chunk 124 optimal weight:    5.9990
   chunk 103 optimal weight:    4.9990
   chunk 77 optimal weight:    7.9990
   chunk 122 optimal weight:    7.9990
   chunk 91 optimal weight:    1.9990
   chunk 55 optimal weight:    8.9990
   chunk 35 optimal weight:    0.9990
   overall best weight:    4.1990

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

Flipped N/Q/H residues before XYZ refinement:
A 334 HIS
A 502 HIS
A 805 HIS

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3009 r_free = 0.3009 target = 0.050775 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 32)----------------|
| r_work = 0.2574 r_free = 0.2574 target = 0.036207 restraints weight = 49936.220|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 31)----------------|
| r_work = 0.2621 r_free = 0.2621 target = 0.037624 restraints weight = 26783.335|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 32)----------------|
| r_work = 0.2651 r_free = 0.2651 target = 0.038602 restraints weight = 17850.419|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 36)----------------|
| r_work = 0.2672 r_free = 0.2672 target = 0.039272 restraints weight = 13529.008|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 21)----------------|
| r_work = 0.2685 r_free = 0.2685 target = 0.039732 restraints weight = 11172.881|
|-----------------------------------------------------------------------------|
r_work (final): 0.2648
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8592
moved from start:          0.1179

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.038  10517  Z= 0.226
  Angle     :  0.618   6.621  14182  Z= 0.321
  Chirality :  0.041   0.172   1553
  Planarity :  0.004   0.045   1803
  Dihedral  :  4.232  19.516   1385
  Min Nonbonded Distance : 2.467

Molprobity Statistics.
  All-atom Clashscore : 5.25
  Ramachandran Plot:
    Outliers :  0.16 %
    Allowed  :  3.79 %
    Favored  : 96.05 %
  Rotamer:
    Outliers :  0.35 %
    Allowed  :  4.56 %
    Favored  : 95.09 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 1.82 %
    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:  0.95 (0.24), residues: 1267
  helix:  1.79 (0.20), residues: 658
  sheet: -0.46 (0.50), residues: 103
  loop : -0.66 (0.29), residues: 506

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG A 479 
 TYR   0.013   0.001   TYR A 760 
 PHE   0.012   0.001   PHE A1054 
 TRP   0.007   0.001   TRP A 359 
 HIS   0.005   0.001   HIS A 913 

Details of bonding type rmsd
  covalent geometry    : bond        0.00487 (10517)
  covalent geometry    : angle       0.61815 (14182)
  hydrogen bonds       : bond        0.04767 (  522)
  hydrogen bonds       : angle       4.75909 ( 1491)

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

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

  2534 Ramachandran restraints generated.
    1267 Oldfield, 0 Emsley, 1267 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2534 Ramachandran restraints generated.
    1267 Oldfield, 0 Emsley, 1267 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  98 residues out of total 1140 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 4
    poor density    : 94
  time to evaluate  : 0.249 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  246 MET cc_start: 0.9170 (mmm) cc_final: 0.8904 (mmm)
REVERT: A  427 ASP cc_start: 0.8753 (t0) cc_final: 0.8524 (m-30)
REVERT: A  622 GLU cc_start: 0.9591 (tm-30) cc_final: 0.9235 (tm-30)
REVERT: A  644 MET cc_start: 0.9253 (mpp) cc_final: 0.9007 (mmt)
REVERT: A  748 ASP cc_start: 0.9224 (m-30) cc_final: 0.8975 (t0)
REVERT: A  769 GLU cc_start: 0.8917 (tp30) cc_final: 0.8336 (tp30)
REVERT: A  903 MET cc_start: 0.9330 (ttm) cc_final: 0.8785 (ttt)
REVERT: A  912 MET cc_start: 0.8553 (mmt) cc_final: 0.8331 (mmt)
REVERT: A 1085 MET cc_start: 0.8789 (mpp) cc_final: 0.8278 (mpp)
REVERT: A 1120 MET cc_start: 0.9515 (mtp) cc_final: 0.9204 (mtp)
REVERT: A 1137 MET cc_start: 0.8775 (tpp) cc_final: 0.8507 (tpp)
REVERT: A 1186 MET cc_start: 0.8447 (tmm) cc_final: 0.7736 (tmm)
REVERT: A 1223 GLU cc_start: 0.9566 (pt0) cc_final: 0.9305 (pt0)
REVERT: A 1227 ASN cc_start: 0.9475 (m110) cc_final: 0.9225 (m110)
REVERT: A 1229 MET cc_start: 0.9347 (mmm) cc_final: 0.9119 (mmm)
REVERT: A 1459 TYR cc_start: 0.9274 (m-80) cc_final: 0.9000 (m-80)
  outliers start: 4
  outliers final: 1
  residues processed: 97
  average time/residue: 0.0840
  time to fit residues: 12.1353
Evaluate side-chains
  83 residues out of total 1140 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 82
  time to evaluate  : 0.327 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  519 LEU
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 128
   random chunks:
   chunk 62 optimal weight:   10.0000
   chunk 32 optimal weight:    7.9990
   chunk 25 optimal weight:    3.9990
   chunk 88 optimal weight:   10.0000
   chunk 53 optimal weight:    6.9990
   chunk 48 optimal weight:    4.9990
   chunk 105 optimal weight:    3.9990
   chunk 41 optimal weight:    4.9990
   chunk 111 optimal weight:    0.9990
   chunk 4 optimal weight:    1.9990
   chunk 70 optimal weight:    5.9990
   overall best weight:    3.1990

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3016 r_free = 0.3016 target = 0.050975 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.2589 r_free = 0.2589 target = 0.036427 restraints weight = 49430.555|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 24)----------------|
| r_work = 0.2633 r_free = 0.2633 target = 0.037841 restraints weight = 26370.416|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 28)----------------|
| r_work = 0.2663 r_free = 0.2663 target = 0.038803 restraints weight = 17566.931|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 38)----------------|
| r_work = 0.2683 r_free = 0.2683 target = 0.039469 restraints weight = 13341.981|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 28)----------------|
| r_work = 0.2696 r_free = 0.2696 target = 0.039926 restraints weight = 11047.385|
|-----------------------------------------------------------------------------|
r_work (final): 0.2648
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8589
moved from start:          0.1544

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.032  10517  Z= 0.180
  Angle     :  0.577   7.573  14182  Z= 0.298
  Chirality :  0.040   0.178   1553
  Planarity :  0.004   0.043   1803
  Dihedral  :  4.185  20.514   1385
  Min Nonbonded Distance : 2.503

Molprobity Statistics.
  All-atom Clashscore : 6.32
  Ramachandran Plot:
    Outliers :  0.16 %
    Allowed  :  4.03 %
    Favored  : 95.82 %
  Rotamer:
    Outliers :  0.79 %
    Allowed  :  7.28 %
    Favored  : 91.93 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 1.82 %
    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:  0.99 (0.24), residues: 1267
  helix:  1.77 (0.20), residues: 659
  sheet: -0.34 (0.50), residues: 103
  loop : -0.61 (0.29), residues: 505

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.006   0.000   ARG A1297 
 TYR   0.010   0.001   TYR A1103 
 PHE   0.015   0.001   PHE A1465 
 TRP   0.008   0.001   TRP A 359 
 HIS   0.003   0.001   HIS A 818 

Details of bonding type rmsd
  covalent geometry    : bond        0.00394 (10517)
  covalent geometry    : angle       0.57717 (14182)
  hydrogen bonds       : bond        0.04139 (  522)
  hydrogen bonds       : angle       4.46960 ( 1491)

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

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

  2534 Ramachandran restraints generated.
    1267 Oldfield, 0 Emsley, 1267 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2534 Ramachandran restraints generated.
    1267 Oldfield, 0 Emsley, 1267 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  101 residues out of total 1140 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 9
    poor density    : 92
  time to evaluate  : 0.270 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  246 MET cc_start: 0.9182 (mmm) cc_final: 0.8875 (mmm)
REVERT: A  427 ASP cc_start: 0.8874 (t0) cc_final: 0.8586 (m-30)
REVERT: A  622 GLU cc_start: 0.9558 (tm-30) cc_final: 0.9148 (tm-30)
REVERT: A  674 ILE cc_start: 0.9477 (mm) cc_final: 0.9101 (mm)
REVERT: A  748 ASP cc_start: 0.9213 (m-30) cc_final: 0.8977 (t0)
REVERT: A  769 GLU cc_start: 0.8962 (tp30) cc_final: 0.8412 (tp30)
REVERT: A  804 MET cc_start: 0.8969 (tpp) cc_final: 0.8723 (tpp)
REVERT: A  927 GLU cc_start: 0.9272 (mp0) cc_final: 0.8818 (pm20)
REVERT: A  931 MET cc_start: 0.7882 (ppp) cc_final: 0.7679 (tmm)
REVERT: A 1032 MET cc_start: 0.8891 (mpp) cc_final: 0.8622 (mpp)
REVERT: A 1085 MET cc_start: 0.8810 (mpp) cc_final: 0.8271 (mpp)
REVERT: A 1120 MET cc_start: 0.9471 (mtp) cc_final: 0.9186 (mtp)
REVERT: A 1129 MET cc_start: 0.8440 (mtt) cc_final: 0.8064 (mtp)
REVERT: A 1186 MET cc_start: 0.8526 (tmm) cc_final: 0.7920 (tmm)
REVERT: A 1223 GLU cc_start: 0.9532 (pt0) cc_final: 0.9285 (pt0)
REVERT: A 1227 ASN cc_start: 0.9467 (m110) cc_final: 0.9212 (m110)
REVERT: A 1229 MET cc_start: 0.9381 (mmm) cc_final: 0.9124 (mmm)
REVERT: A 1459 TYR cc_start: 0.9267 (m-80) cc_final: 0.8998 (m-80)
  outliers start: 9
  outliers final: 3
  residues processed: 100
  average time/residue: 0.0821
  time to fit residues: 12.3005
Evaluate side-chains
  88 residues out of total 1140 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 3
    poor density    : 85
  time to evaluate  : 0.262 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  519 LEU
Chi-restraints excluded: chain A residue  538 VAL
Chi-restraints excluded: chain A residue  870 VAL
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 128
   random chunks:
   chunk 3 optimal weight:    5.9990
   chunk 19 optimal weight:    9.9990
   chunk 109 optimal weight:    0.0170
   chunk 43 optimal weight:    3.9990
   chunk 85 optimal weight:    0.8980
   chunk 117 optimal weight:    0.7980
   chunk 122 optimal weight:    0.0470
   chunk 64 optimal weight:    0.7980
   chunk 46 optimal weight:    0.8980
   chunk 9 optimal weight:    0.9980
   chunk 34 optimal weight:    3.9990
   overall best weight:    0.5116

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

Flipped N/Q/H residues before XYZ refinement:
A 531 HIS
A1101 GLN
A1189 ASN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3078 r_free = 0.3078 target = 0.052639 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 35)----------------|
| r_work = 0.2664 r_free = 0.2664 target = 0.037997 restraints weight = 48661.402|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 23)----------------|
| r_work = 0.2706 r_free = 0.2706 target = 0.039461 restraints weight = 25836.250|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 36)----------------|
| r_work = 0.2737 r_free = 0.2737 target = 0.040517 restraints weight = 17164.962|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 36)----------------|
| r_work = 0.2759 r_free = 0.2759 target = 0.041242 restraints weight = 12915.973|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 38)----------------|
| r_work = 0.2773 r_free = 0.2773 target = 0.041738 restraints weight = 10580.182|
|-----------------------------------------------------------------------------|
r_work (final): 0.2738
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8587
moved from start:          0.1808

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.032  10517  Z= 0.104
  Angle     :  0.562   8.663  14182  Z= 0.282
  Chirality :  0.039   0.152   1553
  Planarity :  0.004   0.043   1803
  Dihedral  :  4.004  18.247   1385
  Min Nonbonded Distance : 2.520

Molprobity Statistics.
  All-atom Clashscore : 5.49
  Ramachandran Plot:
    Outliers :  0.08 %
    Allowed  :  3.71 %
    Favored  : 96.21 %
  Rotamer:
    Outliers :  0.96 %
    Allowed  :  8.42 %
    Favored  : 90.61 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 1.82 %
    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:  1.22 (0.25), residues: 1267
  helix:  1.89 (0.20), residues: 649
  sheet: -0.15 (0.51), residues: 104
  loop : -0.35 (0.30), residues: 514

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARG A1297 
 TYR   0.013   0.001   TYR A 648 
 PHE   0.015   0.001   PHE A1265 
 TRP   0.010   0.001   TRP A 359 
 HIS   0.003   0.001   HIS A 531 

Details of bonding type rmsd
  covalent geometry    : bond        0.00222 (10517)
  covalent geometry    : angle       0.56179 (14182)
  hydrogen bonds       : bond        0.03605 (  522)
  hydrogen bonds       : angle       4.15987 ( 1491)

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

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

  2534 Ramachandran restraints generated.
    1267 Oldfield, 0 Emsley, 1267 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2534 Ramachandran restraints generated.
    1267 Oldfield, 0 Emsley, 1267 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  107 residues out of total 1140 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 96
  time to evaluate  : 0.370 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  246 MET cc_start: 0.9176 (mmm) cc_final: 0.8623 (mmm)
REVERT: A  355 MET cc_start: 0.9502 (mmm) cc_final: 0.8872 (mmm)
REVERT: A  427 ASP cc_start: 0.8625 (t0) cc_final: 0.8361 (m-30)
REVERT: A  622 GLU cc_start: 0.9437 (tm-30) cc_final: 0.9019 (tm-30)
REVERT: A  674 ILE cc_start: 0.9442 (mm) cc_final: 0.9137 (mm)
REVERT: A  691 MET cc_start: 0.9078 (tpp) cc_final: 0.8816 (mpp)
REVERT: A  769 GLU cc_start: 0.8937 (tp30) cc_final: 0.8445 (tp30)
REVERT: A  804 MET cc_start: 0.8998 (tpp) cc_final: 0.8716 (tpp)
REVERT: A  931 MET cc_start: 0.8102 (ppp) cc_final: 0.7795 (tmm)
REVERT: A 1032 MET cc_start: 0.8921 (mpp) cc_final: 0.8666 (mpp)
REVERT: A 1085 MET cc_start: 0.8778 (mpp) cc_final: 0.8163 (mpp)
REVERT: A 1120 MET cc_start: 0.9420 (mtp) cc_final: 0.9144 (mtp)
REVERT: A 1186 MET cc_start: 0.8589 (tmm) cc_final: 0.7973 (tmm)
REVERT: A 1223 GLU cc_start: 0.9516 (pt0) cc_final: 0.9243 (pt0)
REVERT: A 1227 ASN cc_start: 0.9435 (m110) cc_final: 0.9176 (m110)
REVERT: A 1459 TYR cc_start: 0.9207 (m-80) cc_final: 0.8950 (m-80)
REVERT: A 1465 PHE cc_start: 0.8711 (p90) cc_final: 0.8392 (t80)
  outliers start: 11
  outliers final: 5
  residues processed: 102
  average time/residue: 0.0781
  time to fit residues: 11.8370
Evaluate side-chains
  91 residues out of total 1140 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 5
    poor density    : 86
  time to evaluate  : 0.244 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  519 LEU
Chi-restraints excluded: chain A residue  538 VAL
Chi-restraints excluded: chain A residue  776 MET
Chi-restraints excluded: chain A residue  870 VAL
Chi-restraints excluded: chain A residue 1512 VAL
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 128
   random chunks:
   chunk 40 optimal weight:    0.9980
   chunk 58 optimal weight:    6.9990
   chunk 8 optimal weight:    3.9990
   chunk 30 optimal weight:    9.9990
   chunk 32 optimal weight:   10.0000
   chunk 106 optimal weight:   30.0000
   chunk 50 optimal weight:    2.9990
   chunk 37 optimal weight:    0.4980
   chunk 80 optimal weight:    0.8980
   chunk 111 optimal weight:    9.9990
   chunk 74 optimal weight:    9.9990
   overall best weight:    1.8784

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3040 r_free = 0.3040 target = 0.051238 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 26)----------------|
| r_work = 0.2612 r_free = 0.2612 target = 0.036070 restraints weight = 48328.504|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 23)----------------|
| r_work = 0.2654 r_free = 0.2654 target = 0.037523 restraints weight = 25943.346|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 31)----------------|
| r_work = 0.2683 r_free = 0.2683 target = 0.038528 restraints weight = 17361.152|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 35)----------------|
| r_work = 0.2704 r_free = 0.2704 target = 0.039228 restraints weight = 13182.065|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 29)----------------|
| r_work = 0.2717 r_free = 0.2717 target = 0.039669 restraints weight = 10885.117|
|-----------------------------------------------------------------------------|
r_work (final): 0.2681
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8558
moved from start:          0.1924

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.029  10517  Z= 0.127
  Angle     :  0.566   8.711  14182  Z= 0.284
  Chirality :  0.039   0.195   1553
  Planarity :  0.004   0.044   1803
  Dihedral  :  3.929  17.893   1385
  Min Nonbonded Distance : 2.513

Molprobity Statistics.
  All-atom Clashscore : 6.37
  Ramachandran Plot:
    Outliers :  0.16 %
    Allowed  :  3.79 %
    Favored  : 96.05 %
  Rotamer:
    Outliers :  0.88 %
    Allowed  : 10.00 %
    Favored  : 89.12 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 1.82 %
    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:  1.25 (0.25), residues: 1267
  helix:  1.91 (0.20), residues: 650
  sheet: -0.12 (0.51), residues: 104
  loop : -0.32 (0.29), residues: 513

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG A1297 
 TYR   0.012   0.001   TYR A 648 
 PHE   0.013   0.001   PHE A1265 
 TRP   0.008   0.001   TRP A 359 
 HIS   0.003   0.001   HIS A 818 

Details of bonding type rmsd
  covalent geometry    : bond        0.00285 (10517)
  covalent geometry    : angle       0.56632 (14182)
  hydrogen bonds       : bond        0.03589 (  522)
  hydrogen bonds       : angle       4.11975 ( 1491)

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

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

  2534 Ramachandran restraints generated.
    1267 Oldfield, 0 Emsley, 1267 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2534 Ramachandran restraints generated.
    1267 Oldfield, 0 Emsley, 1267 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  101 residues out of total 1140 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 91
  time to evaluate  : 0.245 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  246 MET cc_start: 0.9149 (mmm) cc_final: 0.8779 (mmm)
REVERT: A  355 MET cc_start: 0.9582 (mmm) cc_final: 0.8889 (mmm)
REVERT: A  427 ASP cc_start: 0.8845 (t0) cc_final: 0.8549 (m-30)
REVERT: A  622 GLU cc_start: 0.9480 (tm-30) cc_final: 0.9064 (tm-30)
REVERT: A  674 ILE cc_start: 0.9443 (mm) cc_final: 0.9140 (mm)
REVERT: A  691 MET cc_start: 0.9135 (tpp) cc_final: 0.8799 (mpp)
REVERT: A  769 GLU cc_start: 0.8970 (tp30) cc_final: 0.8480 (tp30)
REVERT: A  804 MET cc_start: 0.9014 (tpp) cc_final: 0.8725 (tpp)
REVERT: A  912 MET cc_start: 0.8402 (mmt) cc_final: 0.8165 (mmt)
REVERT: A 1032 MET cc_start: 0.8948 (mpp) cc_final: 0.8638 (mpp)
REVERT: A 1085 MET cc_start: 0.8778 (mpp) cc_final: 0.8156 (mpp)
REVERT: A 1120 MET cc_start: 0.9427 (mtp) cc_final: 0.9130 (mtp)
REVERT: A 1186 MET cc_start: 0.8610 (tmm) cc_final: 0.7993 (tmm)
REVERT: A 1223 GLU cc_start: 0.9520 (pt0) cc_final: 0.9255 (pt0)
REVERT: A 1227 ASN cc_start: 0.9457 (m110) cc_final: 0.9203 (m110)
REVERT: A 1459 TYR cc_start: 0.9241 (m-80) cc_final: 0.8984 (m-80)
REVERT: A 1465 PHE cc_start: 0.8770 (p90) cc_final: 0.8487 (t80)
  outliers start: 10
  outliers final: 6
  residues processed: 99
  average time/residue: 0.0839
  time to fit residues: 11.9561
Evaluate side-chains
  87 residues out of total 1140 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 6
    poor density    : 81
  time to evaluate  : 0.287 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  519 LEU
Chi-restraints excluded: chain A residue  538 VAL
Chi-restraints excluded: chain A residue  870 VAL
Chi-restraints excluded: chain A residue 1026 MET
Chi-restraints excluded: chain A residue 1076 THR
Chi-restraints excluded: chain A residue 1512 VAL
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 128
   random chunks:
   chunk 62 optimal weight:    2.9990
   chunk 97 optimal weight:    0.8980
   chunk 35 optimal weight:    1.9990
   chunk 14 optimal weight:    4.9990
   chunk 50 optimal weight:    0.0770
   chunk 48 optimal weight:    1.9990
   chunk 51 optimal weight:    8.9990
   chunk 118 optimal weight:    3.9990
   chunk 103 optimal weight:    1.9990
   chunk 15 optimal weight:    3.9990
   chunk 81 optimal weight:    0.9990
   overall best weight:    1.1944

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3073 r_free = 0.3073 target = 0.052287 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 34)----------------|
| r_work = 0.2662 r_free = 0.2662 target = 0.037851 restraints weight = 49460.825|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 27)----------------|
| r_work = 0.2704 r_free = 0.2704 target = 0.039327 restraints weight = 26353.085|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 36)----------------|
| r_work = 0.2734 r_free = 0.2734 target = 0.040371 restraints weight = 17406.618|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 36)----------------|
| r_work = 0.2756 r_free = 0.2756 target = 0.041102 restraints weight = 13027.810|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 29)----------------|
| r_work = 0.2770 r_free = 0.2770 target = 0.041595 restraints weight = 10613.989|
|-----------------------------------------------------------------------------|
r_work (final): 0.2749
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8604
moved from start:          0.2088

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.032  10517  Z= 0.107
  Angle     :  0.569  10.666  14182  Z= 0.283
  Chirality :  0.039   0.256   1553
  Planarity :  0.004   0.043   1803
  Dihedral  :  3.865  17.132   1385
  Min Nonbonded Distance : 2.519

Molprobity Statistics.
  All-atom Clashscore : 6.76
  Ramachandran Plot:
    Outliers :  0.08 %
    Allowed  :  3.87 %
    Favored  : 96.05 %
  Rotamer:
    Outliers :  0.96 %
    Allowed  : 10.79 %
    Favored  : 88.25 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 1.82 %
    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:  1.22 (0.25), residues: 1267
  helix:  1.87 (0.20), residues: 650
  sheet: -0.05 (0.52), residues: 104
  loop : -0.35 (0.29), residues: 513

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG A1297 
 TYR   0.010   0.001   TYR A 648 
 PHE   0.013   0.001   PHE A1265 
 TRP   0.009   0.001   TRP A 359 
 HIS   0.002   0.001   HIS A 818 

Details of bonding type rmsd
  covalent geometry    : bond        0.00239 (10517)
  covalent geometry    : angle       0.56862 (14182)
  hydrogen bonds       : bond        0.03439 (  522)
  hydrogen bonds       : angle       4.04300 ( 1491)

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

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

  2534 Ramachandran restraints generated.
    1267 Oldfield, 0 Emsley, 1267 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2534 Ramachandran restraints generated.
    1267 Oldfield, 0 Emsley, 1267 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  99 residues out of total 1140 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 88
  time to evaluate  : 0.342 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  355 MET cc_start: 0.9548 (mmm) cc_final: 0.8808 (mmm)
REVERT: A  427 ASP cc_start: 0.8676 (t0) cc_final: 0.8397 (m-30)
REVERT: A  622 GLU cc_start: 0.9422 (tm-30) cc_final: 0.8968 (tm-30)
REVERT: A  674 ILE cc_start: 0.9449 (mm) cc_final: 0.9133 (mm)
REVERT: A  691 MET cc_start: 0.9090 (tpp) cc_final: 0.8786 (mpp)
REVERT: A  769 GLU cc_start: 0.8960 (tp30) cc_final: 0.8475 (tp30)
REVERT: A  804 MET cc_start: 0.9023 (tpp) cc_final: 0.8752 (tpp)
REVERT: A  931 MET cc_start: 0.8191 (ppp) cc_final: 0.7857 (ppp)
REVERT: A 1032 MET cc_start: 0.8965 (mpp) cc_final: 0.8629 (mpp)
REVERT: A 1034 MET cc_start: 0.9299 (mtm) cc_final: 0.8868 (mpp)
REVERT: A 1085 MET cc_start: 0.8773 (mpp) cc_final: 0.8098 (mpp)
REVERT: A 1120 MET cc_start: 0.9359 (mtp) cc_final: 0.9076 (mtp)
REVERT: A 1186 MET cc_start: 0.8673 (tmm) cc_final: 0.8091 (tmm)
REVERT: A 1223 GLU cc_start: 0.9513 (pt0) cc_final: 0.9229 (pt0)
REVERT: A 1227 ASN cc_start: 0.9431 (m110) cc_final: 0.9170 (m110)
REVERT: A 1459 TYR cc_start: 0.9170 (m-80) cc_final: 0.8942 (m-80)
REVERT: A 1465 PHE cc_start: 0.8759 (p90) cc_final: 0.8439 (t80)
  outliers start: 11
  outliers final: 6
  residues processed: 96
  average time/residue: 0.0820
  time to fit residues: 11.4451
Evaluate side-chains
  84 residues out of total 1140 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 6
    poor density    : 78
  time to evaluate  : 0.692 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  519 LEU
Chi-restraints excluded: chain A residue  538 VAL
Chi-restraints excluded: chain A residue  870 VAL
Chi-restraints excluded: chain A residue 1026 MET
Chi-restraints excluded: chain A residue 1076 THR
Chi-restraints excluded: chain A residue 1512 VAL
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 128
   random chunks:
   chunk 3 optimal weight:    5.9990
   chunk 100 optimal weight:    0.0670
   chunk 86 optimal weight:    0.0170
   chunk 20 optimal weight:    1.9990
   chunk 84 optimal weight:   10.0000
   chunk 53 optimal weight:    4.9990
   chunk 88 optimal weight:    5.9990
   chunk 30 optimal weight:    6.9990
   chunk 34 optimal weight:    2.9990
   chunk 115 optimal weight:    5.9990
   chunk 28 optimal weight:    6.9990
   overall best weight:    2.0162

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3067 r_free = 0.3067 target = 0.051912 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 38)----------------|
| r_work = 0.2652 r_free = 0.2652 target = 0.037509 restraints weight = 48422.783|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 35)----------------|
| r_work = 0.2696 r_free = 0.2696 target = 0.038931 restraints weight = 26071.644|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 35)----------------|
| r_work = 0.2726 r_free = 0.2726 target = 0.039959 restraints weight = 17338.610|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 37)----------------|
| r_work = 0.2747 r_free = 0.2747 target = 0.040660 restraints weight = 13059.664|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 28)----------------|
| r_work = 0.2760 r_free = 0.2760 target = 0.041126 restraints weight = 10714.962|
|-----------------------------------------------------------------------------|
r_work (final): 0.2735
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8626
moved from start:          0.2162

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.042  10517  Z= 0.131
  Angle     :  0.577  10.416  14182  Z= 0.288
  Chirality :  0.039   0.249   1553
  Planarity :  0.004   0.042   1803
  Dihedral  :  3.874  17.403   1385
  Min Nonbonded Distance : 2.514

Molprobity Statistics.
  All-atom Clashscore : 7.15
  Ramachandran Plot:
    Outliers :  0.08 %
    Allowed  :  4.10 %
    Favored  : 95.82 %
  Rotamer:
    Outliers :  0.70 %
    Allowed  : 11.14 %
    Favored  : 88.16 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 1.82 %
    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:  1.22 (0.25), residues: 1267
  helix:  1.89 (0.21), residues: 652
  sheet: -0.05 (0.52), residues: 104
  loop : -0.38 (0.29), residues: 511

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG A1297 
 TYR   0.010   0.001   TYR A 648 
 PHE   0.013   0.001   PHE A1265 
 TRP   0.008   0.001   TRP A 359 
 HIS   0.003   0.001   HIS A 486 

Details of bonding type rmsd
  covalent geometry    : bond        0.00295 (10517)
  covalent geometry    : angle       0.57693 (14182)
  hydrogen bonds       : bond        0.03518 (  522)
  hydrogen bonds       : angle       4.05802 ( 1491)

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

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

  2534 Ramachandran restraints generated.
    1267 Oldfield, 0 Emsley, 1267 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2534 Ramachandran restraints generated.
    1267 Oldfield, 0 Emsley, 1267 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  91 residues out of total 1140 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 8
    poor density    : 83
  time to evaluate  : 0.442 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  246 MET cc_start: 0.9111 (mmm) cc_final: 0.8670 (mmm)
REVERT: A  355 MET cc_start: 0.9563 (mmm) cc_final: 0.8819 (mmm)
REVERT: A  427 ASP cc_start: 0.8749 (t0) cc_final: 0.8476 (m-30)
REVERT: A  622 GLU cc_start: 0.9450 (tm-30) cc_final: 0.8980 (tm-30)
REVERT: A  674 ILE cc_start: 0.9453 (mm) cc_final: 0.9141 (mm)
REVERT: A  691 MET cc_start: 0.9119 (tpp) cc_final: 0.8754 (mpp)
REVERT: A  769 GLU cc_start: 0.8998 (tp30) cc_final: 0.8523 (tp30)
REVERT: A  804 MET cc_start: 0.9029 (tpp) cc_final: 0.8748 (tpp)
REVERT: A  926 ARG cc_start: 0.9414 (mtt90) cc_final: 0.9058 (mmt180)
REVERT: A  931 MET cc_start: 0.8233 (ppp) cc_final: 0.7920 (ppp)
REVERT: A 1032 MET cc_start: 0.8954 (mpp) cc_final: 0.8536 (mpp)
REVERT: A 1034 MET cc_start: 0.9289 (mtm) cc_final: 0.8802 (mpp)
REVERT: A 1085 MET cc_start: 0.8751 (mpp) cc_final: 0.8144 (mpp)
REVERT: A 1120 MET cc_start: 0.9376 (mtp) cc_final: 0.9088 (mtp)
REVERT: A 1186 MET cc_start: 0.8672 (tmm) cc_final: 0.8153 (tmm)
REVERT: A 1223 GLU cc_start: 0.9510 (pt0) cc_final: 0.9232 (pt0)
REVERT: A 1227 ASN cc_start: 0.9441 (m110) cc_final: 0.9181 (m110)
REVERT: A 1402 LYS cc_start: 0.9526 (mtpt) cc_final: 0.9259 (mmtm)
  outliers start: 8
  outliers final: 7
  residues processed: 89
  average time/residue: 0.0794
  time to fit residues: 10.4062
Evaluate side-chains
  87 residues out of total 1140 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 7
    poor density    : 80
  time to evaluate  : 0.361 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  519 LEU
Chi-restraints excluded: chain A residue  538 VAL
Chi-restraints excluded: chain A residue  870 VAL
Chi-restraints excluded: chain A residue 1026 MET
Chi-restraints excluded: chain A residue 1056 MET
Chi-restraints excluded: chain A residue 1076 THR
Chi-restraints excluded: chain A residue 1512 VAL
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 128
   random chunks:
   chunk 113 optimal weight:   20.0000
   chunk 17 optimal weight:    5.9990
   chunk 3 optimal weight:    5.9990
   chunk 26 optimal weight:    4.9990
   chunk 16 optimal weight:    4.9990
   chunk 76 optimal weight:    0.4980
   chunk 45 optimal weight:    1.9990
   chunk 13 optimal weight:   10.0000
   chunk 127 optimal weight:    0.9990
   chunk 36 optimal weight:    4.9990
   chunk 5 optimal weight:    6.9990
   overall best weight:    2.6988

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3028 r_free = 0.3028 target = 0.051471 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 32)----------------|
| r_work = 0.2602 r_free = 0.2602 target = 0.036771 restraints weight = 49765.567|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 33)----------------|
| r_work = 0.2644 r_free = 0.2644 target = 0.038222 restraints weight = 26673.043|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 36)----------------|
| r_work = 0.2675 r_free = 0.2675 target = 0.039223 restraints weight = 17790.905|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 25)----------------|
| r_work = 0.2695 r_free = 0.2695 target = 0.039908 restraints weight = 13462.692|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 32)----------------|
| r_work = 0.2706 r_free = 0.2706 target = 0.040321 restraints weight = 11122.095|
|-----------------------------------------------------------------------------|
r_work (final): 0.2692
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8593
moved from start:          0.2212

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.044  10517  Z= 0.158
  Angle     :  0.594  11.550  14182  Z= 0.297
  Chirality :  0.040   0.271   1553
  Planarity :  0.004   0.041   1803
  Dihedral  :  3.927  17.711   1385
  Min Nonbonded Distance : 2.508

Molprobity Statistics.
  All-atom Clashscore : 7.63
  Ramachandran Plot:
    Outliers :  0.16 %
    Allowed  :  4.18 %
    Favored  : 95.66 %
  Rotamer:
    Outliers :  0.70 %
    Allowed  : 11.58 %
    Favored  : 87.72 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 1.82 %
    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:  1.25 (0.25), residues: 1267
  helix:  1.90 (0.21), residues: 651
  sheet: -0.00 (0.52), residues: 104
  loop : -0.35 (0.29), residues: 512

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG A1297 
 TYR   0.018   0.001   TYR A1459 
 PHE   0.014   0.001   PHE A1265 
 TRP   0.007   0.001   TRP A 359 
 HIS   0.003   0.001   HIS A 486 

Details of bonding type rmsd
  covalent geometry    : bond        0.00353 (10517)
  covalent geometry    : angle       0.59439 (14182)
  hydrogen bonds       : bond        0.03628 (  522)
  hydrogen bonds       : angle       4.14609 ( 1491)

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

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

  2534 Ramachandran restraints generated.
    1267 Oldfield, 0 Emsley, 1267 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2534 Ramachandran restraints generated.
    1267 Oldfield, 0 Emsley, 1267 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  92 residues out of total 1140 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 8
    poor density    : 84
  time to evaluate  : 0.440 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  246 MET cc_start: 0.9111 (mmm) cc_final: 0.8666 (mmm)
REVERT: A  355 MET cc_start: 0.9609 (mmm) cc_final: 0.8809 (mmm)
REVERT: A  427 ASP cc_start: 0.8872 (t0) cc_final: 0.8586 (m-30)
REVERT: A  622 GLU cc_start: 0.9507 (tm-30) cc_final: 0.9043 (tm-30)
REVERT: A  674 ILE cc_start: 0.9463 (mm) cc_final: 0.9133 (mm)
REVERT: A  691 MET cc_start: 0.9165 (tpp) cc_final: 0.8695 (tpp)
REVERT: A  769 GLU cc_start: 0.9053 (tp30) cc_final: 0.8439 (tm-30)
REVERT: A  804 MET cc_start: 0.9017 (tpp) cc_final: 0.8733 (tpp)
REVERT: A  931 MET cc_start: 0.8199 (ppp) cc_final: 0.7919 (ppp)
REVERT: A 1032 MET cc_start: 0.8945 (mpp) cc_final: 0.8432 (mpp)
REVERT: A 1034 MET cc_start: 0.9297 (mtm) cc_final: 0.8780 (mpp)
REVERT: A 1085 MET cc_start: 0.8748 (mpp) cc_final: 0.8114 (mpp)
REVERT: A 1120 MET cc_start: 0.9402 (mtp) cc_final: 0.9075 (mtp)
REVERT: A 1186 MET cc_start: 0.8627 (tmm) cc_final: 0.7979 (tmm)
REVERT: A 1223 GLU cc_start: 0.9511 (pt0) cc_final: 0.9253 (pt0)
REVERT: A 1227 ASN cc_start: 0.9460 (m110) cc_final: 0.9210 (m110)
REVERT: A 1317 MET cc_start: 0.7199 (tmm) cc_final: 0.6919 (tmm)
  outliers start: 8
  outliers final: 5
  residues processed: 91
  average time/residue: 0.0899
  time to fit residues: 12.0774
Evaluate side-chains
  86 residues out of total 1140 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 5
    poor density    : 81
  time to evaluate  : 0.305 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  519 LEU
Chi-restraints excluded: chain A residue  538 VAL
Chi-restraints excluded: chain A residue  870 VAL
Chi-restraints excluded: chain A residue 1056 MET
Chi-restraints excluded: chain A residue 1512 VAL
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 128
   random chunks:
   chunk 51 optimal weight:    8.9990
   chunk 103 optimal weight:    3.9990
   chunk 58 optimal weight:    1.9990
   chunk 110 optimal weight:    7.9990
   chunk 20 optimal weight:    0.7980
   chunk 116 optimal weight:    0.7980
   chunk 4 optimal weight:    0.7980
   chunk 41 optimal weight:    4.9990
   chunk 29 optimal weight:    9.9990
   chunk 46 optimal weight:    9.9990
   chunk 0 optimal weight:   10.0000
   overall best weight:    1.6784

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

Flipped N/Q/H residues before XYZ refinement:
A1090 HIS

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3042 r_free = 0.3042 target = 0.051961 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 36)----------------|
| r_work = 0.2624 r_free = 0.2624 target = 0.037367 restraints weight = 48291.319|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 22)----------------|
| r_work = 0.2667 r_free = 0.2667 target = 0.038833 restraints weight = 25864.429|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 22)----------------|
| r_work = 0.2697 r_free = 0.2697 target = 0.039832 restraints weight = 17249.057|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 36)----------------|
| r_work = 0.2718 r_free = 0.2718 target = 0.040542 restraints weight = 13049.156|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 28)----------------|
| r_work = 0.2732 r_free = 0.2732 target = 0.041033 restraints weight = 10726.046|
|-----------------------------------------------------------------------------|
r_work (final): 0.2715
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8572
moved from start:          0.2319

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.039  10517  Z= 0.122
  Angle     :  0.605  12.644  14182  Z= 0.296
  Chirality :  0.040   0.289   1553
  Planarity :  0.004   0.042   1803
  Dihedral  :  3.893  17.454   1385
  Min Nonbonded Distance : 2.516

Molprobity Statistics.
  All-atom Clashscore : 7.53
  Ramachandran Plot:
    Outliers :  0.08 %
    Allowed  :  4.26 %
    Favored  : 95.66 %
  Rotamer:
    Outliers :  0.53 %
    Allowed  : 11.75 %
    Favored  : 87.72 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 1.82 %
    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:  1.26 (0.25), residues: 1267
  helix:  1.90 (0.21), residues: 651
  sheet:  0.15 (0.52), residues: 104
  loop : -0.36 (0.29), residues: 512

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.009   0.000   ARG A 926 
 TYR   0.009   0.001   TYR A 777 
 PHE   0.022   0.001   PHE A1546 
 TRP   0.008   0.001   TRP A 359 
 HIS   0.004   0.001   HIS A 922 

Details of bonding type rmsd
  covalent geometry    : bond        0.00276 (10517)
  covalent geometry    : angle       0.60465 (14182)
  hydrogen bonds       : bond        0.03508 (  522)
  hydrogen bonds       : angle       4.06193 ( 1491)

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

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

  2534 Ramachandran restraints generated.
    1267 Oldfield, 0 Emsley, 1267 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2534 Ramachandran restraints generated.
    1267 Oldfield, 0 Emsley, 1267 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  89 residues out of total 1140 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 6
    poor density    : 83
  time to evaluate  : 0.384 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  246 MET cc_start: 0.9121 (mmm) cc_final: 0.8666 (mmm)
REVERT: A  355 MET cc_start: 0.9596 (mmm) cc_final: 0.8797 (mmm)
REVERT: A  427 ASP cc_start: 0.8852 (t0) cc_final: 0.8566 (m-30)
REVERT: A  622 GLU cc_start: 0.9491 (tm-30) cc_final: 0.9038 (tm-30)
REVERT: A  674 ILE cc_start: 0.9427 (mm) cc_final: 0.9122 (mm)
REVERT: A  691 MET cc_start: 0.9130 (tpp) cc_final: 0.8751 (mpp)
REVERT: A  769 GLU cc_start: 0.9061 (tp30) cc_final: 0.8462 (tm-30)
REVERT: A  804 MET cc_start: 0.9019 (tpp) cc_final: 0.8732 (tpp)
REVERT: A  912 MET cc_start: 0.8378 (mmt) cc_final: 0.8167 (mmt)
REVERT: A 1032 MET cc_start: 0.8980 (mpp) cc_final: 0.8467 (mpp)
REVERT: A 1034 MET cc_start: 0.9267 (mtm) cc_final: 0.8679 (mpp)
REVERT: A 1056 MET cc_start: 0.9605 (OUTLIER) cc_final: 0.9031 (mmm)
REVERT: A 1085 MET cc_start: 0.8733 (mpp) cc_final: 0.8109 (mpp)
REVERT: A 1120 MET cc_start: 0.9389 (mtp) cc_final: 0.9064 (mtp)
REVERT: A 1186 MET cc_start: 0.8675 (tmm) cc_final: 0.7984 (tmm)
REVERT: A 1223 GLU cc_start: 0.9512 (pt0) cc_final: 0.9250 (pt0)
REVERT: A 1227 ASN cc_start: 0.9436 (m110) cc_final: 0.9185 (m110)
REVERT: A 1317 MET cc_start: 0.7120 (tmm) cc_final: 0.6849 (tmm)
REVERT: A 1402 LYS cc_start: 0.9512 (mtpt) cc_final: 0.9275 (mmtm)
  outliers start: 6
  outliers final: 5
  residues processed: 88
  average time/residue: 0.0994
  time to fit residues: 12.8373
Evaluate side-chains
  88 residues out of total 1140 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 6
    poor density    : 82
  time to evaluate  : 0.341 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  519 LEU
Chi-restraints excluded: chain A residue  538 VAL
Chi-restraints excluded: chain A residue  870 VAL
Chi-restraints excluded: chain A residue 1056 MET
Chi-restraints excluded: chain A residue 1090 HIS
Chi-restraints excluded: chain A residue 1512 VAL
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 128
   random chunks:
   chunk 94 optimal weight:    0.9990
   chunk 1 optimal weight:    0.4980
   chunk 98 optimal weight:    2.9990
   chunk 75 optimal weight:    1.9990
   chunk 34 optimal weight:    2.9990
   chunk 92 optimal weight:    3.9990
   chunk 124 optimal weight:    8.9990
   chunk 69 optimal weight:    0.9980
   chunk 36 optimal weight:    1.9990
   chunk 33 optimal weight:    3.9990
   chunk 15 optimal weight:    6.9990
   overall best weight:    1.2986

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

Flipped N/Q/H residues before XYZ refinement:
A1090 HIS

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3052 r_free = 0.3052 target = 0.052396 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 35)----------------|
| r_work = 0.2634 r_free = 0.2634 target = 0.037716 restraints weight = 47903.618|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 37)----------------|
| r_work = 0.2677 r_free = 0.2677 target = 0.039195 restraints weight = 25767.071|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 43)----------------|
| r_work = 0.2707 r_free = 0.2707 target = 0.040197 restraints weight = 17210.333|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 32)----------------|
| r_work = 0.2728 r_free = 0.2728 target = 0.040890 restraints weight = 13070.107|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 34)----------------|
| r_work = 0.2741 r_free = 0.2741 target = 0.041372 restraints weight = 10770.514|
|-----------------------------------------------------------------------------|
r_work (final): 0.2723
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8568
moved from start:          0.2381

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.037  10517  Z= 0.115
  Angle     :  0.626  13.556  14182  Z= 0.303
  Chirality :  0.040   0.294   1553
  Planarity :  0.004   0.043   1803
  Dihedral  :  3.935  17.987   1385
  Min Nonbonded Distance : 2.520

Molprobity Statistics.
  All-atom Clashscore : 8.17
  Ramachandran Plot:
    Outliers :  0.08 %
    Allowed  :  4.42 %
    Favored  : 95.50 %
  Rotamer:
    Outliers :  0.44 %
    Allowed  : 11.93 %
    Favored  : 87.63 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 1.82 %
    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:  1.24 (0.25), residues: 1267
  helix:  1.87 (0.21), residues: 651
  sheet:  0.16 (0.53), residues: 104
  loop : -0.36 (0.29), residues: 512

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.008   0.000   ARG A 926 
 TYR   0.009   0.001   TYR A 777 
 PHE   0.021   0.001   PHE A1546 
 TRP   0.008   0.001   TRP A 359 
 HIS   0.009   0.001   HIS A1090 

Details of bonding type rmsd
  covalent geometry    : bond        0.00260 (10517)
  covalent geometry    : angle       0.62601 (14182)
  hydrogen bonds       : bond        0.03479 (  522)
  hydrogen bonds       : angle       4.09332 ( 1491)

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

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

  2534 Ramachandran restraints generated.
    1267 Oldfield, 0 Emsley, 1267 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2534 Ramachandran restraints generated.
    1267 Oldfield, 0 Emsley, 1267 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  88 residues out of total 1140 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 5
    poor density    : 83
  time to evaluate  : 0.437 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  246 MET cc_start: 0.9116 (mmm) cc_final: 0.8660 (mmm)
REVERT: A  355 MET cc_start: 0.9586 (mmm) cc_final: 0.8796 (mmm)
REVERT: A  427 ASP cc_start: 0.8830 (t0) cc_final: 0.8535 (m-30)
REVERT: A  622 GLU cc_start: 0.9475 (tm-30) cc_final: 0.9013 (tm-30)
REVERT: A  674 ILE cc_start: 0.9406 (mm) cc_final: 0.9097 (mm)
REVERT: A  691 MET cc_start: 0.9117 (tpp) cc_final: 0.8740 (mpp)
REVERT: A  769 GLU cc_start: 0.9066 (tp30) cc_final: 0.8465 (tm-30)
REVERT: A  804 MET cc_start: 0.9042 (tpp) cc_final: 0.8771 (tpp)
REVERT: A 1032 MET cc_start: 0.8981 (mpp) cc_final: 0.8446 (mpp)
REVERT: A 1034 MET cc_start: 0.9247 (mtm) cc_final: 0.8624 (mpp)
REVERT: A 1056 MET cc_start: 0.9605 (mmp) cc_final: 0.9030 (mmm)
REVERT: A 1085 MET cc_start: 0.8726 (mpp) cc_final: 0.8078 (mpp)
REVERT: A 1120 MET cc_start: 0.9378 (mtp) cc_final: 0.9046 (mtp)
REVERT: A 1186 MET cc_start: 0.8678 (tmm) cc_final: 0.8164 (tmm)
REVERT: A 1223 GLU cc_start: 0.9513 (pt0) cc_final: 0.9249 (pt0)
REVERT: A 1227 ASN cc_start: 0.9425 (m110) cc_final: 0.9182 (m110)
REVERT: A 1317 MET cc_start: 0.7124 (tmm) cc_final: 0.6855 (tmm)
REVERT: A 1402 LYS cc_start: 0.9509 (mtpt) cc_final: 0.9270 (mmtm)
  outliers start: 5
  outliers final: 5
  residues processed: 88
  average time/residue: 0.1024
  time to fit residues: 13.1079
Evaluate side-chains
  87 residues out of total 1140 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 5
    poor density    : 82
  time to evaluate  : 0.438 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  519 LEU
Chi-restraints excluded: chain A residue  538 VAL
Chi-restraints excluded: chain A residue  870 VAL
Chi-restraints excluded: chain A residue 1090 HIS
Chi-restraints excluded: chain A residue 1512 VAL
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 128
   random chunks:
   chunk 56 optimal weight:    1.9990
   chunk 67 optimal weight:    9.9990
   chunk 116 optimal weight:    8.9990
   chunk 101 optimal weight:    4.9990
   chunk 72 optimal weight:    1.9990
   chunk 113 optimal weight:   20.0000
   chunk 62 optimal weight:    0.0470
   chunk 14 optimal weight:    0.8980
   chunk 9 optimal weight:    0.0970
   chunk 36 optimal weight:    0.7980
   chunk 25 optimal weight:    1.9990
   overall best weight:    0.7678

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

Flipped N/Q/H residues before XYZ refinement:
A1090 HIS

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3069 r_free = 0.3069 target = 0.052999 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 33)----------------|
| r_work = 0.2653 r_free = 0.2653 target = 0.038275 restraints weight = 48391.512|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 32)----------------|
| r_work = 0.2697 r_free = 0.2697 target = 0.039781 restraints weight = 25875.378|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 36)----------------|
| r_work = 0.2728 r_free = 0.2728 target = 0.040812 restraints weight = 17224.280|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 28)----------------|
| r_work = 0.2747 r_free = 0.2747 target = 0.041513 restraints weight = 12999.362|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 30)----------------|
| r_work = 0.2763 r_free = 0.2763 target = 0.042043 restraints weight = 10736.271|
|-----------------------------------------------------------------------------|
r_work (final): 0.2726
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8522
moved from start:          0.2481

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.036  10517  Z= 0.105
  Angle     :  0.623  13.565  14182  Z= 0.300
  Chirality :  0.040   0.277   1553
  Planarity :  0.004   0.043   1803
  Dihedral  :  3.907  18.951   1385
  Min Nonbonded Distance : 2.525

Molprobity Statistics.
  All-atom Clashscore : 7.34
  Ramachandran Plot:
    Outliers :  0.08 %
    Allowed  :  4.18 %
    Favored  : 95.74 %
  Rotamer:
    Outliers :  0.70 %
    Allowed  : 11.84 %
    Favored  : 87.46 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 1.82 %
    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:  1.23 (0.25), residues: 1267
  helix:  1.83 (0.21), residues: 651
  sheet:  0.14 (0.53), residues: 104
  loop : -0.31 (0.29), residues: 512

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.008   0.000   ARG A 926 
 TYR   0.010   0.001   TYR A 777 
 PHE   0.021   0.001   PHE A1546 
 TRP   0.008   0.001   TRP A 359 
 HIS   0.008   0.001   HIS A1090 

Details of bonding type rmsd
  covalent geometry    : bond        0.00235 (10517)
  covalent geometry    : angle       0.62324 (14182)
  hydrogen bonds       : bond        0.03419 (  522)
  hydrogen bonds       : angle       4.03224 ( 1491)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 1353.25 seconds
wall clock time: 24 minutes 21.40 seconds (1461.40 seconds total)