Starting phenix.real_space_refine
on Mon Aug 25 07:10:21 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/7mvu_24056/08_2025/7mvu_24056.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/7mvu_24056/08_2025/7mvu_24056.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=3.77
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/cci-nas-00/data/ceres_data/7mvu_24056/08_2025/7mvu_24056.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/7mvu_24056/08_2025/7mvu_24056.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/7mvu_24056/08_2025/7mvu_24056.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/7mvu_24056/08_2025/7mvu_24056.cif"
  }
  resolution = 3.77
  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=  -0.001 sd=   0.025
Set stop_for_unknowns flag
  Set to: True
Assert model is a single copy model
Assert all atoms have isotropic ADPs
Construct map_model_manager
Extract box with map and model
Check model and map are aligned
Set scattering table
  Set to: electron
  Number of scattering types: 5
    Type Number    sf(0)   Gaussians
     S      66      5.16       5
     C    8190      2.51       5
     N    2169      2.21       5
     O    2379      1.98       5
     H   12841      0.53       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 14 residue(s): 0.01s

  Monomer Library directory:
    "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/chem_data/mon_lib"
  Total number of atoms: 25645
  Number of models: 1
  Model: ""
    Number of chains: 2
    Chain: "A"
      Number of atoms: 24654
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 1541, 24654
          Classifications: {'peptide': 1541}
          Link IDs: {'PTRANS': 58, 'TRANS': 1482}
          Chain breaks: 16
    Chain: "B"
      Number of atoms: 991
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 63, 991
          Classifications: {'peptide': 63}
          Link IDs: {'TRANS': 62}
  Time building chain proxies: 5.10, per 1000 atoms: 0.20
  Number of scatterers: 25645
  At special positions: 0
  Unit cell: (86.736, 118.428, 195.156, 90, 90, 90)
  Space group: P 1 (No. 1)
  Number of sites at special positions: 0
  Number of scattering types: 5
    Type Number    sf(0)
     S      66     16.00
     O    2379      8.00
     N    2169      7.00
     C    8190      6.00
     H   12841      1.00
    sf(0) = scattering factor at diffraction angle 0.

  Number of disulfides: simple=0, symmetry=0

  Automatic linking
    Parameters for automatic linking
      Linking & cutoffs
        Metal                : Auto  - 3.00
        Amino acid           : True  - 1.90
        Carbohydrate         : True  - 1.99
        Ligands              : True  - 1.99
        Small molecules      : False - 1.98
        Amino acid - RNA/DNA : False
      
  Number of custom bonds: simple=0, symmetry=0
  Time building additional restraints: 2.64
  Conformation dependent library (CDL) restraints added in 952.0 milliseconds
  
  Enol-peptide restraints added in 715.3 nanoseconds
  

  3136 Ramachandran restraints generated.
    1568 Oldfield, 0 Emsley, 1568 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  3076

  Finding SS restraints...
    Secondary structure from input PDB file:
      82 helices and 2 sheets defined
      77.2% alpha, 0.5% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 0.76
  Creating SS restraints...
    Processing helix  chain 'A' and resid 5 through 22
    Processing helix  chain 'A' and resid 27 through 38
      removed outlier: 3.830A  pdb=" N   GLU A  36 " --> pdb=" O   GLU A  32 " (cutoff:3.500A)
      removed outlier: 3.736A  pdb=" N   GLU A  37 " --> pdb=" O   THR A  33 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 38 through 44
      removed outlier: 3.887A  pdb=" N   ALA A  44 " --> pdb=" O   ASP A  40 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 52 through 62
    Processing helix  chain 'A' and resid 76 through 91
      removed outlier: 3.536A  pdb=" N   ASN A  81 " --> pdb=" O   GLU A  77 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 93 through 108
    Processing helix  chain 'A' and resid 108 through 114
      removed outlier: 4.245A  pdb=" N   THR A 112 " --> pdb=" O   GLY A 108 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 116 through 144
      removed outlier: 3.632A  pdb=" N   ARG A 129 " --> pdb=" O   PHE A 125 " (cutoff:3.500A)
      removed outlier: 3.676A  pdb=" N   MET A 136 " --> pdb=" O   LEU A 132 " (cutoff:3.500A)
      removed outlier: 3.527A  pdb=" N   ALA A 144 " --> pdb=" O   LEU A 140 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 149 through 164
    Processing helix  chain 'A' and resid 184 through 212
      removed outlier: 3.882A  pdb=" N   ARG A 188 " --> pdb=" O   LYS A 184 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 224 through 252
    Processing helix  chain 'A' and resid 256 through 269
      removed outlier: 3.502A  pdb=" N   PHE A 260 " --> pdb=" O   THR A 256 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 274 through 292
      removed outlier: 3.725A  pdb=" N   ILE A 278 " --> pdb=" O   ASP A 274 " (cutoff:3.500A)
      Proline residue:  A 282  - end of helix
    Processing helix  chain 'A' and resid 299 through 311
      removed outlier: 3.519A  pdb=" N   ARG A 305 " --> pdb=" O   GLN A 301 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 321 through 337
      removed outlier: 3.650A  pdb=" N   GLY A 325 " --> pdb=" O   LEU A 321 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 353 through 371
    Processing helix  chain 'A' and resid 371 through 384
      removed outlier: 3.604A  pdb=" N   LYS A 384 " --> pdb=" O   ALA A 380 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 390 through 394
      removed outlier: 3.881A  pdb=" N   LEU A 394 " --> pdb=" O   PRO A 391 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 415 through 437
      removed outlier: 3.986A  pdb=" N   GLN A 419 " --> pdb=" O   SER A 415 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 437 through 455
      removed outlier: 3.565A  pdb=" N   LEU A 441 " --> pdb=" O   LEU A 437 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 462 through 475
    Processing helix  chain 'A' and resid 478 through 483
    Processing helix  chain 'A' and resid 483 through 488
      removed outlier: 4.576A  pdb=" N   ASP A 488 " --> pdb=" O   SER A 484 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 491 through 500
    Processing helix  chain 'A' and resid 505 through 519
    Processing helix  chain 'A' and resid 522 through 534
    Processing helix  chain 'A' and resid 551 through 568
    Processing helix  chain 'A' and resid 592 through 613
    Processing helix  chain 'A' and resid 614 through 621
      removed outlier: 3.534A  pdb=" N   ILE A 621 " --> pdb=" O   ARG A 617 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 627 through 637
    Processing helix  chain 'A' and resid 641 through 656
      removed outlier: 3.909A  pdb=" N   ARG A 645 " --> pdb=" O   PRO A 641 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 660 through 677
      removed outlier: 3.734A  pdb=" N   ASN A 677 " --> pdb=" O   ALA A 673 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 700 through 714
      removed outlier: 3.790A  pdb=" N   GLU A 706 " --> pdb=" O   GLN A 702 " (cutoff:3.500A)
      removed outlier: 3.570A  pdb=" N   THR A 714 " --> pdb=" O   ARG A 710 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 716 through 730
    Processing helix  chain 'A' and resid 758 through 772
      removed outlier: 3.647A  pdb=" N   VAL A 762 " --> pdb=" O   ILE A 758 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 778 through 799
      removed outlier: 3.596A  pdb=" N   THR A 799 " --> pdb=" O   VAL A 795 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 802 through 812
    Processing helix  chain 'A' and resid 820 through 831
    Processing helix  chain 'A' and resid 832 through 841
    Processing helix  chain 'A' and resid 842 through 854
      removed outlier: 3.632A  pdb=" N   ILE A 846 " --> pdb=" O   ASN A 842 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 856 through 863
      removed outlier: 3.887A  pdb=" N   LEU A 860 " --> pdb=" O   ASP A 856 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 867 through 894
      removed outlier: 5.136A  pdb=" N   GLU A 888 " --> pdb=" O   LEU A 884 " (cutoff:3.500A)
      removed outlier: 4.858A  pdb=" N   THR A 889 " --> pdb=" O   GLU A 885 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 894 through 905
    Processing helix  chain 'A' and resid 928 through 937
      removed outlier: 4.073A  pdb=" N   VAL A 932 " --> pdb=" O   LEU A 928 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 938 through 941
      removed outlier: 4.159A  pdb=" N   GLY A 941 " --> pdb=" O   CYS A 938 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'A' and resid 938 through 941'
    Processing helix  chain 'A' and resid 942 through 959
    Processing helix  chain 'A' and resid 960 through 967
    Processing helix  chain 'A' and resid 978 through 983
    Processing helix  chain 'A' and resid 987 through 1002
    Processing helix  chain 'A' and resid 1012 through 1031
    Processing helix  chain 'A' and resid 1037 through 1044
      removed outlier: 3.683A  pdb=" N   GLN A1041 " --> pdb=" O   THR A1037 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 1065 through 1076
    Processing helix  chain 'A' and resid 1088 through 1107
    Processing helix  chain 'A' and resid 1108 through 1110
      No H-bonds generated for 'chain 'A' and resid 1108 through 1110'
    Processing helix  chain 'A' and resid 1111 through 1120
    Processing helix  chain 'A' and resid 1122 through 1131
    Processing helix  chain 'A' and resid 1148 through 1153
      removed outlier: 4.201A  pdb=" N   LEU A1152 " --> pdb=" O   CYS A1148 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 1154 through 1183
      removed outlier: 3.688A  pdb=" N   ALA A1158 " --> pdb=" O   ASP A1154 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 1185 through 1198
      removed outlier: 4.130A  pdb=" N   LYS A1189 " --> pdb=" O   ILE A1185 " (cutoff:3.500A)
      removed outlier: 3.813A  pdb=" N   ARG A1190 " --> pdb=" O   PRO A1186 " (cutoff:3.500A)
      removed outlier: 4.771A  pdb=" N   GLN A1191 " --> pdb=" O   SER A1187 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 1212 through 1217
    Processing helix  chain 'A' and resid 1257 through 1276
      removed outlier: 4.196A  pdb=" N   ALA A1261 " --> pdb=" O   ASP A1257 " (cutoff:3.500A)
      removed outlier: 3.628A  pdb=" N   ILE A1264 " --> pdb=" O   LYS A1260 " (cutoff:3.500A)
      removed outlier: 3.567A  pdb=" N   GLN A1276 " --> pdb=" O   TYR A1272 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 1278 through 1326
      removed outlier: 3.751A  pdb=" N   PHE A1282 " --> pdb=" O   ALA A1278 " (cutoff:3.500A)
      removed outlier: 4.370A  pdb=" N   GLU A1284 " --> pdb=" O   PRO A1280 " (cutoff:3.500A)
      removed outlier: 4.437A  pdb=" N   THR A1285 " --> pdb=" O   GLU A1281 " (cutoff:3.500A)
      removed outlier: 4.199A  pdb=" N   GLU A1295 " --> pdb=" O   LYS A1291 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 1335 through 1353
      Proline residue:  A1348  - end of helix
    Processing helix  chain 'A' and resid 1359 through 1374
      removed outlier: 3.920A  pdb=" N   GLU A1363 " --> pdb=" O   ASP A1359 " (cutoff:3.500A)
      removed outlier: 3.829A  pdb=" N   VAL A1367 " --> pdb=" O   GLU A1363 " (cutoff:3.500A)
      removed outlier: 3.823A  pdb=" N   ALA A1368 " --> pdb=" O   LEU A1364 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 1389 through 1413
      removed outlier: 3.705A  pdb=" N   GLN A1405 " --> pdb=" O   PHE A1401 " (cutoff:3.500A)
      removed outlier: 4.055A  pdb=" N   LEU A1406 " --> pdb=" O   GLN A1402 " (cutoff:3.500A)
      removed outlier: 3.558A  pdb=" N   CYS A1407 " --> pdb=" O   LEU A1403 " (cutoff:3.500A)
      removed outlier: 3.552A  pdb=" N   LEU A1408 " --> pdb=" O   PHE A1404 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 1417 through 1435
      removed outlier: 3.523A  pdb=" N   ALA A1434 " --> pdb=" O   ARG A1430 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 1455 through 1472
      removed outlier: 3.778A  pdb=" N   TYR A1471 " --> pdb=" O   ALA A1467 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 1472 through 1482
      removed outlier: 3.770A  pdb=" N   LEU A1476 " --> pdb=" O   GLY A1472 " (cutoff:3.500A)
      removed outlier: 3.863A  pdb=" N   VAL A1478 " --> pdb=" O   ARG A1474 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 1488 through 1508
      removed outlier: 3.929A  pdb=" N   THR A1492 " --> pdb=" O   THR A1488 " (cutoff:3.500A)
      removed outlier: 3.500A  pdb=" N   SER A1508 " --> pdb=" O   THR A1504 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 1520 through 1529
      removed outlier: 3.728A  pdb=" N   ASP A1524 " --> pdb=" O   CYS A1520 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 1530 through 1538
      removed outlier: 3.720A  pdb=" N   VAL A1534 " --> pdb=" O   ASN A1530 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 1541 through 1546
      removed outlier: 3.641A  pdb=" N   GLU A1545 " --> pdb=" O   GLU A1541 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 1570 through 1587
      removed outlier: 3.582A  pdb=" N   CYS A1587 " --> pdb=" O   LEU A1583 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 1589 through 1599
      removed outlier: 3.657A  pdb=" N   ALA A1593 " --> pdb=" O   THR A1589 " (cutoff:3.500A)
      removed outlier: 4.306A  pdb=" N   LYS A1594 " --> pdb=" O   ARG A1590 " (cutoff:3.500A)
      removed outlier: 3.943A  pdb=" N   TYR A1595 " --> pdb=" O   GLN A1591 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 1603 through 1608
      removed outlier: 3.722A  pdb=" N   GLN A1607 " --> pdb=" O   ARG A1603 " (cutoff:3.500A)
      removed outlier: 3.820A  pdb=" N   SER A1608 " --> pdb=" O   ALA A1604 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'A' and resid 1603 through 1608'
    Processing helix  chain 'A' and resid 1630 through 1654
      removed outlier: 4.444A  pdb=" N   ARG A1653 " --> pdb=" O   ALA A1649 " (cutoff:3.500A)
      removed outlier: 4.037A  pdb=" N   GLY A1654 " --> pdb=" O   VAL A1650 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 1657 through 1668
    Processing helix  chain 'A' and resid 1670 through 1680
      removed outlier: 3.533A  pdb=" N   VAL A1675 " --> pdb=" O   LEU A1671 " (cutoff:3.500A)
      removed outlier: 3.635A  pdb=" N   ASN A1679 " --> pdb=" O   VAL A1675 " (cutoff:3.500A)
      removed outlier: 3.854A  pdb=" N   ALA A1680 " --> pdb=" O   LEU A1676 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 1710 through 1734
    Processing helix  chain 'A' and resid 1734 through 1739
      removed outlier: 3.993A  pdb=" N   TYR A1738 " --> pdb=" O   GLY A1734 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 247 through 284
      removed outlier: 3.599A  pdb=" N   SER B 253 " --> pdb=" O   ASP B 249 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 289 through 299
      removed outlier: 4.130A  pdb=" N   TYR B 295 " --> pdb=" O   ARG B 291 " (cutoff:3.500A)
    Processing sheet with id=AA1, first strand: chain 'A' and resid 65 through 68
    Processing sheet with id=AA2, first strand: chain 'A' and resid 1199 through 1200

    840 hydrogen bonds defined for protein.
    2502 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: 6.78

  Time building geometry restraints manager: 3.61 seconds

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

  Histogram of bond lengths:
        0.84 -     1.03: 12809
        1.03 -     1.23: 32
        1.23 -     1.42: 5384
        1.42 -     1.62: 7561
        1.62 -     1.81: 100
  Bond restraints: 25886
  Sorted by residual:
  bond pdb=" N   PRO A1186 "
       pdb=" CD  PRO A1186 "
    ideal  model  delta    sigma   weight residual
    1.473  1.427  0.046 1.40e-02 5.10e+03 1.06e+01
  bond pdb=" N   MET A   1 "
       pdb=" CA  MET A   1 "
    ideal  model  delta    sigma   weight residual
    1.458  1.490 -0.032 1.90e-02 2.77e+03 2.80e+00
  bond pdb=" N   MET A   1 "
       pdb=" H   MET A   1 "
    ideal  model  delta    sigma   weight residual
    0.860  0.890 -0.030 2.00e-02 2.50e+03 2.30e+00
  bond pdb=" CA  GLY A 757 "
       pdb=" C   GLY A 757 "
    ideal  model  delta    sigma   weight residual
    1.514  1.531 -0.017 1.41e-02 5.03e+03 1.43e+00
  bond pdb=" N   GLY A 757 "
       pdb=" CA  GLY A 757 "
    ideal  model  delta    sigma   weight residual
    1.449  1.465 -0.016 1.45e-02 4.76e+03 1.18e+00
  ... (remaining 25881 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     7.02: 46851
        7.02 -    14.03: 0
       14.03 -    21.05: 0
       21.05 -    28.06: 0
       28.06 -    35.08: 3
  Bond angle restraints: 46854
  Sorted by residual:
  angle pdb=" C   SER A1187 "
        pdb=" CA  SER A1187 "
        pdb=" HA  SER A1187 "
      ideal   model   delta    sigma   weight residual
     109.00   73.92   35.08 3.00e+00 1.11e-01 1.37e+02
  angle pdb=" N   SER A1187 "
        pdb=" CA  SER A1187 "
        pdb=" HA  SER A1187 "
      ideal   model   delta    sigma   weight residual
     110.00   75.50   34.50 3.00e+00 1.11e-01 1.32e+02
  angle pdb=" CB  SER A1187 "
        pdb=" CA  SER A1187 "
        pdb=" HA  SER A1187 "
      ideal   model   delta    sigma   weight residual
     109.00   74.86   34.14 3.00e+00 1.11e-01 1.29e+02
  angle pdb=" N   LYS A 978 "
        pdb=" CA  LYS A 978 "
        pdb=" C   LYS A 978 "
      ideal   model   delta    sigma   weight residual
     114.56  110.92    3.64 1.27e+00 6.20e-01 8.23e+00
  angle pdb=" N   LEU A1283 "
        pdb=" CA  LEU A1283 "
        pdb=" C   LEU A1283 "
      ideal   model   delta    sigma   weight residual
     111.02  107.89    3.13 1.22e+00 6.72e-01 6.58e+00
  ... (remaining 46849 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    12.12: 11355
       12.12 -    24.24: 515
       24.24 -    36.36: 99
       36.36 -    48.48: 49
       48.48 -    60.60: 61
  Dihedral angle restraints: 12079
    sinusoidal: 6584
      harmonic: 5495
  Sorted by residual:
  dihedral pdb=" C   SER A1187 "
           pdb=" N   SER A1187 "
           pdb=" CA  SER A1187 "
           pdb=" CB  SER A1187 "
      ideal   model   delta  harmonic     sigma   weight residual
    -122.60 -131.33    8.73     0      2.50e+00 1.60e-01 1.22e+01
  dihedral pdb=" N   SER A1187 "
           pdb=" C   SER A1187 "
           pdb=" CA  SER A1187 "
           pdb=" CB  SER A1187 "
      ideal   model   delta  harmonic     sigma   weight residual
     122.80  130.62   -7.82     0      2.50e+00 1.60e-01 9.78e+00
  dihedral pdb=" N   LEU B 279 "
           pdb=" CA  LEU B 279 "
           pdb=" CB  LEU B 279 "
           pdb=" CG  LEU B 279 "
      ideal   model   delta sinusoidal    sigma   weight residual
     -60.00  -98.85   38.85     3      1.50e+01 4.44e-03 6.86e+00
  ... (remaining 12076 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.067: 1907
       0.067 -    0.135: 120
       0.135 -    0.202: 1
       0.202 -    0.269: 0
       0.269 -    0.337: 1
  Chirality restraints: 2029
  Sorted by residual:
  chirality pdb=" CA  SER A1187 "
            pdb=" N   SER A1187 "
            pdb=" C   SER A1187 "
            pdb=" CB  SER A1187 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.17    0.34 2.00e-01 2.50e+01 2.83e+00
  chirality pdb=" CA  ILE A 167 "
            pdb=" N   ILE A 167 "
            pdb=" C   ILE A 167 "
            pdb=" CB  ILE A 167 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.43    2.57   -0.14 2.00e-01 2.50e+01 4.63e-01
  chirality pdb=" CA  ILE A 404 "
            pdb=" N   ILE A 404 "
            pdb=" C   ILE A 404 "
            pdb=" CB  ILE A 404 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.43    2.56   -0.13 2.00e-01 2.50e+01 4.23e-01
  ... (remaining 2026 not shown)

  Planarity restraints: 3782
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   GLU A 759 "   -0.024 5.00e-02 4.00e+02   3.71e-02 2.20e+00
        pdb=" N   PRO A 760 "    0.064 5.00e-02 4.00e+02
        pdb=" CA  PRO A 760 "   -0.019 5.00e-02 4.00e+02
        pdb=" CD  PRO A 760 "   -0.021 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  LEU A1307 "   -0.005 2.00e-02 2.50e+03   1.00e-02 1.00e+00
        pdb=" C   LEU A1307 "    0.017 2.00e-02 2.50e+03
        pdb=" O   LEU A1307 "   -0.006 2.00e-02 2.50e+03
        pdb=" N   THR A1308 "   -0.006 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  ILE A1294 "    0.005 2.00e-02 2.50e+03   9.54e-03 9.10e-01
        pdb=" C   ILE A1294 "   -0.016 2.00e-02 2.50e+03
        pdb=" O   ILE A1294 "    0.006 2.00e-02 2.50e+03
        pdb=" N   GLU A1295 "    0.005 2.00e-02 2.50e+03
  ... (remaining 3779 not shown)

  Histogram of nonbonded interaction distances:
        1.62 -     2.21: 1271
        2.21 -     2.81: 54868
        2.81 -     3.41: 68510
        3.41 -     4.00: 83955
        4.00 -     4.60: 135333
  Nonbonded interactions: 343937
  Sorted by model distance:
  nonbonded pdb=" HA  SER A1187 "
            pdb=" HB3 SER A1187 "
     model   vdw
     1.618 1.952
  nonbonded pdb=" OE1 GLN A 460 "
            pdb=" H   GLN A 460 "
     model   vdw
     1.650 2.450
  nonbonded pdb=" OE1 GLU A1013 "
            pdb=" H   GLU A1013 "
     model   vdw
     1.653 2.450
  nonbonded pdb=" O   SER A 421 "
            pdb=" HD1 HIS A 425 "
     model   vdw
     1.661 2.450
  nonbonded pdb=" OE1 GLN A 702 "
            pdb=" H   GLN A 702 "
     model   vdw
     1.662 2.450
  ... (remaining 343932 not shown)

  NOTE: a complete listing of the restraints can be obtained by requesting
        output of .geo file.
Find NCS groups from input model
Time spend for trying shortcut: 0.00
========== WARNING! ============

  No NCS relation were found !!!

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

Found NCS groups:
  found none.
Set up NCS constraints
  No NCS constraints will be used in refinement.
Set refine NCS operators
Adjust number of macro_cycles
  Number of macro_cycles: 10
Reset NCS operators
Extract rigid body selections
Check and reset occupancies
  Occupancies: min=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:             0.810
  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:             0.170
  Extract box with map and model:          0.370
  Check model and map are aligned:         0.080
  Set scattering table:                    0.070
  Process input model:                     27.690
  Find NCS groups from input model:        0.110
  Set up NCS constraints:                  0.040
  Set refine NCS operators:                0.000
  Adjust number of macro_cycles:           0.000
  Reset NCS operators:                     0.000
  Extract rigid body selections:           0.000
  Check and reset occupancies:             0.010
  Load rotamer database and sin/cos tables:1.900
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   31.250
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7555
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      :  0.002   0.046  13045  Z= 0.088
  Angle     :  0.363   5.941  17658  Z= 0.209
  Chirality :  0.032   0.337   2029
  Planarity :  0.002   0.037   2254
  Dihedral  :  6.378  60.596   4824
  Min Nonbonded Distance : 2.187

Molprobity Statistics.
  All-atom Clashscore : 3.51
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.15 %
    Favored  : 98.85 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  0.72 %
    Favored  : 99.28 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -0.33 (0.21), residues: 1568
  helix:  0.62 (0.15), residues: 1154
  sheet:  None (None), residues: 0
  loop : -2.59 (0.27), residues: 414

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.001   0.000   ARG A1430 
 TYR   0.009   0.001   TYR A1089 
 PHE   0.005   0.000   PHE A 745 
 TRP   0.004   0.000   TRP A1296 
 HIS   0.001   0.000   HIS A1068 

Details of bonding type rmsd
  covalent geometry    : bond        0.00153 (13045)
  covalent geometry    : angle       0.36333 (17658)
  hydrogen bonds       : bond        0.11117 (  840)
  hydrogen bonds       : angle       4.72338 ( 2502)

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

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

  3136 Ramachandran restraints generated.
    1568 Oldfield, 0 Emsley, 1568 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3136 Ramachandran restraints generated.
    1568 Oldfield, 0 Emsley, 1568 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  312 residues out of total 1393 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 312
  time to evaluate  : 0.704 
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: symmetry clash
   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: symmetry clash
   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: symmetry clash
   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: symmetry clash
   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: symmetry clash
   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: symmetry clash
   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: symmetry clash
   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  191 GLU cc_start: 0.9104 (tt0) cc_final: 0.8645 (tp30)
REVERT: A  471 ILE cc_start: 0.8770 (mt) cc_final: 0.8445 (mt)
REVERT: A  675 MET cc_start: 0.7012 (mmm) cc_final: 0.5909 (mmm)
REVERT: A 1173 ILE cc_start: 0.9086 (mt) cc_final: 0.8789 (tp)
REVERT: A 1369 LYS cc_start: 0.8446 (tttt) cc_final: 0.8091 (tppt)
REVERT: A 1636 TYR cc_start: 0.9147 (m-80) cc_final: 0.8818 (m-10)
REVERT: A 1727 MET cc_start: 0.7813 (ttp) cc_final: 0.7373 (tpt)
REVERT: B  290 GLN cc_start: 0.8858 (tt0) cc_final: 0.8369 (tm-30)
  outliers start: 0
  outliers final: 0
  residues processed: 312
  average time/residue: 0.3543
  time to fit residues: 148.9539
Evaluate side-chains
  188 residues out of total 1393 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 188
  time to evaluate  : 0.699 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 160
   random chunks:
   chunk 98 optimal weight:    4.9990
   chunk 107 optimal weight:    4.9990
   chunk 10 optimal weight:    3.9990
   chunk 66 optimal weight:    5.9990
   chunk 130 optimal weight:    4.9990
   chunk 124 optimal weight:    4.9990
   chunk 103 optimal weight:    0.9980
   chunk 77 optimal weight:    0.9990
   chunk 122 optimal weight:    4.9990
   chunk 91 optimal weight:    0.9980
   chunk 149 optimal weight:    9.9990
   overall best weight:    2.3986

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

Flipped N/Q/H residues before XYZ refinement:
A  38 GLN
A 642 HIS
A 677 ASN
** A1135 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
A1660 GLN

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3859 r_free = 0.3859 target = 0.072028 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 40)----------------|
| r_work = 0.3438 r_free = 0.3438 target = 0.053843 restraints weight = 218838.752|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 36)----------------|
| r_work = 0.3493 r_free = 0.3493 target = 0.056465 restraints weight = 123946.453|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 38)----------------|
| r_work = 0.3532 r_free = 0.3532 target = 0.058275 restraints weight = 81831.281|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 44)----------------|
| r_work = 0.3559 r_free = 0.3559 target = 0.059537 restraints weight = 60153.378|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 35)----------------|
| r_work = 0.3579 r_free = 0.3579 target = 0.060417 restraints weight = 47899.983|
|-----------------------------------------------------------------------------|
r_work (final): 0.3565
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8159
moved from start:          0.3126

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.064  13045  Z= 0.187
  Angle     :  0.539   6.749  17658  Z= 0.289
  Chirality :  0.035   0.341   2029
  Planarity :  0.004   0.039   2254
  Dihedral  :  2.465  11.900   1716
  Min Nonbonded Distance : 2.211

Molprobity Statistics.
  All-atom Clashscore : 6.24
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.81 %
    Favored  : 97.19 %
  Rotamer:
    Outliers :  1.15 %
    Allowed  :  7.47 %
    Favored  : 91.39 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  1.24 (0.22), residues: 1568
  helix:  1.77 (0.16), residues: 1162
  sheet:  None (None), residues: 0
  loop : -2.08 (0.29), residues: 406

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.000   ARG A1430 
 TYR   0.016   0.001   TYR A1431 
 PHE   0.016   0.001   PHE A1067 
 TRP   0.008   0.001   TRP A 552 
 HIS   0.005   0.001   HIS A1255 

Details of bonding type rmsd
  covalent geometry    : bond        0.00376 (13045)
  covalent geometry    : angle       0.53940 (17658)
  hydrogen bonds       : bond        0.03157 (  840)
  hydrogen bonds       : angle       3.78691 ( 2502)

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

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

  3136 Ramachandran restraints generated.
    1568 Oldfield, 0 Emsley, 1568 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3136 Ramachandran restraints generated.
    1568 Oldfield, 0 Emsley, 1568 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  196 residues out of total 1393 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 180
  time to evaluate  : 0.728 
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: symmetry clash
   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: symmetry clash
   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: symmetry clash
   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: symmetry clash
   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: symmetry clash
   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: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  191 GLU cc_start: 0.9557 (tt0) cc_final: 0.9042 (tp30)
REVERT: A  462 MET cc_start: 0.8493 (mmm) cc_final: 0.8260 (mmm)
REVERT: A  467 PHE cc_start: 0.9332 (t80) cc_final: 0.9067 (t80)
REVERT: A  598 MET cc_start: 0.9168 (ttp) cc_final: 0.8673 (tmm)
REVERT: A 1127 MET cc_start: 0.8920 (mmm) cc_final: 0.8678 (mmm)
REVERT: A 1190 ARG cc_start: 0.9447 (ttm170) cc_final: 0.9164 (tpp-160)
REVERT: A 1324 MET cc_start: 0.9418 (mtm) cc_final: 0.9209 (mtm)
REVERT: A 1636 TYR cc_start: 0.9528 (m-80) cc_final: 0.9184 (m-10)
REVERT: A 1727 MET cc_start: 0.8087 (ttp) cc_final: 0.7532 (tpt)
REVERT: B  247 ASP cc_start: 0.8390 (t70) cc_final: 0.7987 (t70)
  outliers start: 16
  outliers final: 14
  residues processed: 188
  average time/residue: 0.3818
  time to fit residues: 96.7118
Evaluate side-chains
  173 residues out of total 1393 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 159
  time to evaluate  : 0.719 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  599 LEU
Chi-restraints excluded: chain A residue  655 LEU
Chi-restraints excluded: chain A residue  665 ASP
Chi-restraints excluded: chain A residue  672 GLU
Chi-restraints excluded: chain A residue  849 LEU
Chi-restraints excluded: chain A residue  879 VAL
Chi-restraints excluded: chain A residue  986 ASN
Chi-restraints excluded: chain A residue 1468 ILE
Chi-restraints excluded: chain A residue 1477 ASN
Chi-restraints excluded: chain A residue 1583 LEU
Chi-restraints excluded: chain A residue 1674 HIS
Chi-restraints excluded: chain B residue  245 GLU
Chi-restraints excluded: chain B residue  250 THR
Chi-restraints excluded: chain B residue  255 LEU
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 160
   random chunks:
   chunk 49 optimal weight:    7.9990
   chunk 85 optimal weight:    2.9990
   chunk 103 optimal weight:    5.9990
   chunk 58 optimal weight:    5.9990
   chunk 70 optimal weight:    3.9990
   chunk 10 optimal weight:    9.9990
   chunk 60 optimal weight:    6.9990
   chunk 142 optimal weight:    6.9990
   chunk 80 optimal weight:    3.9990
   chunk 94 optimal weight:    3.9990
   chunk 110 optimal weight:    0.0570
   overall best weight:    3.0106

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

Flipped N/Q/H residues before XYZ refinement:
A 238 GLN
A 254 HIS
** A 363 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A1135 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
A1221 ASN
B 282 ASN

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3740 r_free = 0.3740 target = 0.066400 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 43)----------------|
| r_work = 0.3308 r_free = 0.3308 target = 0.048584 restraints weight = 225214.721|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 46)----------------|
| r_work = 0.3363 r_free = 0.3363 target = 0.051012 restraints weight = 124797.358|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 38)----------------|
| r_work = 0.3402 r_free = 0.3402 target = 0.052676 restraints weight = 82126.776|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 41)----------------|
| r_work = 0.3430 r_free = 0.3430 target = 0.053837 restraints weight = 60712.354|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 29)----------------|
| r_work = 0.3448 r_free = 0.3448 target = 0.054584 restraints weight = 48681.240|
|-----------------------------------------------------------------------------|
r_work (final): 0.3429
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8300
moved from start:          0.4547

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.072  13045  Z= 0.225
  Angle     :  0.577   7.313  17658  Z= 0.311
  Chirality :  0.035   0.351   2029
  Planarity :  0.004   0.052   2254
  Dihedral  :  2.860  14.030   1716
  Min Nonbonded Distance : 2.280

Molprobity Statistics.
  All-atom Clashscore : 7.95
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.25 %
    Favored  : 96.75 %
  Rotamer:
    Outliers :  1.72 %
    Allowed  :  8.04 %
    Favored  : 90.24 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  1.28 (0.21), residues: 1568
  helix:  1.75 (0.15), residues: 1170
  sheet:  None (None), residues: 0
  loop : -1.96 (0.28), residues: 398

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.001   ARG A1259 
 TYR   0.016   0.002   TYR B 251 
 PHE   0.030   0.001   PHE A1404 
 TRP   0.016   0.001   TRP B 287 
 HIS   0.012   0.001   HIS A 239 

Details of bonding type rmsd
  covalent geometry    : bond        0.00450 (13045)
  covalent geometry    : angle       0.57684 (17658)
  hydrogen bonds       : bond        0.03129 (  840)
  hydrogen bonds       : angle       3.95569 ( 2502)

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

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

  3136 Ramachandran restraints generated.
    1568 Oldfield, 0 Emsley, 1568 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3136 Ramachandran restraints generated.
    1568 Oldfield, 0 Emsley, 1568 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  180 residues out of total 1393 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 24
    poor density    : 156
  time to evaluate  : 0.693 
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: symmetry clash
   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: symmetry clash
   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: symmetry clash
   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: symmetry clash
   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: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  190 MET cc_start: 0.9608 (mmp) cc_final: 0.9196 (mmm)
REVERT: A  191 GLU cc_start: 0.9506 (tt0) cc_final: 0.9072 (tp30)
REVERT: A  462 MET cc_start: 0.8362 (mmm) cc_final: 0.8107 (mmm)
REVERT: A  598 MET cc_start: 0.9114 (ttp) cc_final: 0.8477 (tmm)
REVERT: A  837 MET cc_start: 0.9064 (mmm) cc_final: 0.8778 (mmm)
REVERT: A 1086 MET cc_start: 0.8178 (mmt) cc_final: 0.7495 (mtm)
REVERT: A 1431 TYR cc_start: 0.9367 (t80) cc_final: 0.9157 (t80)
REVERT: A 1495 MET cc_start: 0.8571 (mtm) cc_final: 0.8281 (ptm)
REVERT: A 1636 TYR cc_start: 0.9612 (m-80) cc_final: 0.9221 (m-10)
REVERT: B  247 ASP cc_start: 0.8661 (t70) cc_final: 0.8298 (t70)
  outliers start: 24
  outliers final: 16
  residues processed: 170
  average time/residue: 0.3589
  time to fit residues: 82.5805
Evaluate side-chains
  157 residues out of total 1393 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 141
  time to evaluate  : 0.736 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   36 GLU
Chi-restraints excluded: chain A residue  154 GLU
Chi-restraints excluded: chain A residue  240 GLU
Chi-restraints excluded: chain A residue  283 VAL
Chi-restraints excluded: chain A residue  418 LEU
Chi-restraints excluded: chain A residue  665 ASP
Chi-restraints excluded: chain A residue  672 GLU
Chi-restraints excluded: chain A residue  849 LEU
Chi-restraints excluded: chain A residue  879 VAL
Chi-restraints excluded: chain A residue  986 ASN
Chi-restraints excluded: chain A residue 1271 GLU
Chi-restraints excluded: chain A residue 1468 ILE
Chi-restraints excluded: chain A residue 1477 ASN
Chi-restraints excluded: chain A residue 1497 LEU
Chi-restraints excluded: chain A residue 1674 HIS
Chi-restraints excluded: chain B residue  245 GLU
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 160
   random chunks:
   chunk 117 optimal weight:    7.9990
   chunk 1 optimal weight:   10.0000
   chunk 98 optimal weight:    1.9990
   chunk 55 optimal weight:    5.9990
   chunk 13 optimal weight:    0.8980
   chunk 138 optimal weight:    0.0970
   chunk 78 optimal weight:    4.9990
   chunk 14 optimal weight:    1.9990
   chunk 34 optimal weight:    0.8980
   chunk 44 optimal weight:    3.9990
   chunk 36 optimal weight:    0.0770
   overall best weight:    0.7938

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

Flipped N/Q/H residues before XYZ refinement:
A1135 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3763 r_free = 0.3763 target = 0.067517 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 38)----------------|
| r_work = 0.3336 r_free = 0.3336 target = 0.049583 restraints weight = 219701.727|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 26)----------------|
| r_work = 0.3391 r_free = 0.3391 target = 0.052115 restraints weight = 121054.331|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 36)----------------|
| r_work = 0.3430 r_free = 0.3430 target = 0.053829 restraints weight = 79006.240|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 31)----------------|
| r_work = 0.3457 r_free = 0.3457 target = 0.055027 restraints weight = 58109.685|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 39)----------------|
| r_work = 0.3476 r_free = 0.3476 target = 0.055846 restraints weight = 46430.699|
|-----------------------------------------------------------------------------|
r_work (final): 0.3454
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8260
moved from start:          0.4802

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.025  13045  Z= 0.103
  Angle     :  0.490   7.252  17658  Z= 0.249
  Chirality :  0.034   0.343   2029
  Planarity :  0.003   0.035   2254
  Dihedral  :  2.687  13.299   1716
  Min Nonbonded Distance : 2.258

Molprobity Statistics.
  All-atom Clashscore : 6.00
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.74 %
    Favored  : 97.26 %
  Rotamer:
    Outliers :  1.15 %
    Allowed  :  9.19 %
    Favored  : 89.66 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  2.06 (0.22), residues: 1568
  helix:  2.32 (0.15), residues: 1171
  sheet:  None (None), residues: 0
  loop : -1.70 (0.29), residues: 397

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARG A 305 
 TYR   0.019   0.001   TYR B 251 
 PHE   0.018   0.001   PHE A1404 
 TRP   0.007   0.001   TRP B 287 
 HIS   0.006   0.001   HIS A 239 

Details of bonding type rmsd
  covalent geometry    : bond        0.00219 (13045)
  covalent geometry    : angle       0.48996 (17658)
  hydrogen bonds       : bond        0.02672 (  840)
  hydrogen bonds       : angle       3.51393 ( 2502)

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

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

  3136 Ramachandran restraints generated.
    1568 Oldfield, 0 Emsley, 1568 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3136 Ramachandran restraints generated.
    1568 Oldfield, 0 Emsley, 1568 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  170 residues out of total 1393 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 154
  time to evaluate  : 0.701 
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: symmetry clash
   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: symmetry clash
   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: symmetry clash
   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: symmetry clash
   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: symmetry clash
   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: symmetry clash
   revert: symmetry clash
REVERT: A  191 GLU cc_start: 0.9554 (tt0) cc_final: 0.9010 (tp30)
REVERT: A  462 MET cc_start: 0.8177 (mmm) cc_final: 0.7972 (mmm)
REVERT: A  598 MET cc_start: 0.9261 (ttp) cc_final: 0.8664 (tmm)
REVERT: A  837 MET cc_start: 0.9035 (mmm) cc_final: 0.8721 (mmm)
REVERT: A 1101 LEU cc_start: 0.9698 (OUTLIER) cc_final: 0.9497 (mt)
REVERT: A 1315 GLN cc_start: 0.9393 (tt0) cc_final: 0.8385 (tp-100)
REVERT: A 1372 LEU cc_start: 0.9614 (tp) cc_final: 0.9371 (tp)
REVERT: A 1636 TYR cc_start: 0.9524 (m-80) cc_final: 0.9173 (m-10)
REVERT: A 1727 MET cc_start: 0.8259 (ttp) cc_final: 0.7859 (tpp)
REVERT: B  247 ASP cc_start: 0.8679 (t70) cc_final: 0.8300 (t70)
  outliers start: 16
  outliers final: 11
  residues processed: 163
  average time/residue: 0.3389
  time to fit residues: 75.7142
Evaluate side-chains
  155 residues out of total 1393 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 143
  time to evaluate  : 0.847 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  240 GLU
Chi-restraints excluded: chain A residue  418 LEU
Chi-restraints excluded: chain A residue  599 LEU
Chi-restraints excluded: chain A residue  672 GLU
Chi-restraints excluded: chain A residue  879 VAL
Chi-restraints excluded: chain A residue 1101 LEU
Chi-restraints excluded: chain A residue 1271 GLU
Chi-restraints excluded: chain A residue 1468 ILE
Chi-restraints excluded: chain A residue 1477 ASN
Chi-restraints excluded: chain A residue 1583 LEU
Chi-restraints excluded: chain A residue 1674 HIS
Chi-restraints excluded: chain B residue  245 GLU
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 160
   random chunks:
   chunk 14 optimal weight:    9.9990
   chunk 155 optimal weight:    5.9990
   chunk 96 optimal weight:    8.9990
   chunk 22 optimal weight:    5.9990
   chunk 60 optimal weight:    0.9980
   chunk 123 optimal weight:    4.9990
   chunk 75 optimal weight:    2.9990
   chunk 74 optimal weight:    1.9990
   chunk 86 optimal weight:    5.9990
   chunk 143 optimal weight:    8.9990
   chunk 94 optimal weight:    4.9990
   overall best weight:    3.1988

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

Flipped N/Q/H residues before XYZ refinement:
** A 363 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
A1574 GLN
A1607 GLN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3651 r_free = 0.3651 target = 0.061988 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 44)----------------|
| r_work = 0.3205 r_free = 0.3205 target = 0.044755 restraints weight = 230651.819|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 25)----------------|
| r_work = 0.3260 r_free = 0.3260 target = 0.047046 restraints weight = 124911.609|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 46)----------------|
| r_work = 0.3298 r_free = 0.3298 target = 0.048605 restraints weight = 81778.497|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 34)----------------|
| r_work = 0.3324 r_free = 0.3324 target = 0.049670 restraints weight = 60541.435|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 37)----------------|
| r_work = 0.3342 r_free = 0.3342 target = 0.050406 restraints weight = 48884.593|
|-----------------------------------------------------------------------------|
r_work (final): 0.3324
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8390
moved from start:          0.5787

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.098  13045  Z= 0.239
  Angle     :  0.581   6.500  17658  Z= 0.322
  Chirality :  0.035   0.335   2029
  Planarity :  0.004   0.053   2254
  Dihedral  :  3.125  13.863   1716
  Min Nonbonded Distance : 2.284

Molprobity Statistics.
  All-atom Clashscore : 9.55
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.34 %
    Favored  : 95.66 %
  Rotamer:
    Outliers :  1.36 %
    Allowed  :  9.48 %
    Favored  : 89.16 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  1.43 (0.21), residues: 1568
  helix:  1.79 (0.15), residues: 1181
  sheet:  None (None), residues: 0
  loop : -1.75 (0.29), residues: 387

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.018   0.001   ARG B 270 
 TYR   0.019   0.002   TYR B 251 
 PHE   0.015   0.002   PHE A1404 
 TRP   0.009   0.001   TRP A1373 
 HIS   0.007   0.001   HIS A1068 

Details of bonding type rmsd
  covalent geometry    : bond        0.00456 (13045)
  covalent geometry    : angle       0.58096 (17658)
  hydrogen bonds       : bond        0.03178 (  840)
  hydrogen bonds       : angle       4.02403 ( 2502)

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

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

  3136 Ramachandran restraints generated.
    1568 Oldfield, 0 Emsley, 1568 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3136 Ramachandran restraints generated.
    1568 Oldfield, 0 Emsley, 1568 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  159 residues out of total 1393 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 19
    poor density    : 140
  time to evaluate  : 0.697 
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: symmetry clash
   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: symmetry clash
   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: symmetry clash
   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: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  191 GLU cc_start: 0.9642 (tt0) cc_final: 0.9108 (tp30)
REVERT: A  515 MET cc_start: 0.9191 (ttp) cc_final: 0.8921 (ttp)
REVERT: A  598 MET cc_start: 0.9205 (ttp) cc_final: 0.8541 (tmm)
REVERT: A  599 LEU cc_start: 0.9625 (OUTLIER) cc_final: 0.9369 (mm)
REVERT: A  837 MET cc_start: 0.9148 (mmm) cc_final: 0.8821 (mmm)
REVERT: A 1001 MET cc_start: 0.9570 (mmm) cc_final: 0.9360 (mmm)
REVERT: A 1282 PHE cc_start: 0.7907 (t80) cc_final: 0.7660 (t80)
REVERT: A 1636 TYR cc_start: 0.9588 (m-80) cc_final: 0.9175 (m-10)
REVERT: B  247 ASP cc_start: 0.8765 (t70) cc_final: 0.8394 (p0)
REVERT: B  273 ARG cc_start: 0.9614 (ptm160) cc_final: 0.9098 (ttp80)
  outliers start: 19
  outliers final: 16
  residues processed: 152
  average time/residue: 0.3088
  time to fit residues: 65.7575
Evaluate side-chains
  148 residues out of total 1393 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 17
    poor density    : 131
  time to evaluate  : 0.733 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   36 GLU
Chi-restraints excluded: chain A residue  240 GLU
Chi-restraints excluded: chain A residue  283 VAL
Chi-restraints excluded: chain A residue  418 LEU
Chi-restraints excluded: chain A residue  599 LEU
Chi-restraints excluded: chain A residue  665 ASP
Chi-restraints excluded: chain A residue  672 GLU
Chi-restraints excluded: chain A residue  879 VAL
Chi-restraints excluded: chain A residue  986 ASN
Chi-restraints excluded: chain A residue 1271 GLU
Chi-restraints excluded: chain A residue 1468 ILE
Chi-restraints excluded: chain A residue 1477 ASN
Chi-restraints excluded: chain A residue 1497 LEU
Chi-restraints excluded: chain A residue 1574 GLN
Chi-restraints excluded: chain A residue 1583 LEU
Chi-restraints excluded: chain A residue 1674 HIS
Chi-restraints excluded: chain B residue  245 GLU
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 160
   random chunks:
   chunk 145 optimal weight:   10.0000
   chunk 18 optimal weight:    0.2980
   chunk 83 optimal weight:    2.9990
   chunk 35 optimal weight:    3.9990
   chunk 36 optimal weight:    0.4980
   chunk 71 optimal weight:    1.9990
   chunk 115 optimal weight:    0.0470
   chunk 122 optimal weight:    3.9990
   chunk 113 optimal weight:    0.7980
   chunk 143 optimal weight:    6.9990
   chunk 128 optimal weight:    6.9990
   overall best weight:    0.7280

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

Flipped N/Q/H residues before XYZ refinement:
** A 363 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3684 r_free = 0.3684 target = 0.063530 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 37)----------------|
| r_work = 0.3248 r_free = 0.3248 target = 0.046084 restraints weight = 223394.767|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 38)----------------|
| r_work = 0.3305 r_free = 0.3305 target = 0.048520 restraints weight = 119917.098|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 38)----------------|
| r_work = 0.3343 r_free = 0.3343 target = 0.050162 restraints weight = 77539.755|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 26)----------------|
| r_work = 0.3369 r_free = 0.3369 target = 0.051257 restraints weight = 56922.304|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 34)----------------|
| r_work = 0.3388 r_free = 0.3388 target = 0.052072 restraints weight = 45692.205|
|-----------------------------------------------------------------------------|
r_work (final): 0.3369
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8332
moved from start:          0.5873

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.045  13045  Z= 0.101
  Angle     :  0.504   6.705  17658  Z= 0.255
  Chirality :  0.034   0.342   2029
  Planarity :  0.003   0.041   2254
  Dihedral  :  2.902  13.973   1716
  Min Nonbonded Distance : 2.330

Molprobity Statistics.
  All-atom Clashscore : 6.71
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.74 %
    Favored  : 97.26 %
  Rotamer:
    Outliers :  1.08 %
    Allowed  : 10.91 %
    Favored  : 88.01 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  2.26 (0.22), residues: 1568
  helix:  2.40 (0.15), residues: 1178
  sheet:  None (None), residues: 0
  loop : -1.45 (0.30), residues: 390

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.007   0.000   ARG A 900 
 TYR   0.019   0.001   TYR B 251 
 PHE   0.019   0.001   PHE A1404 
 TRP   0.007   0.001   TRP B 287 
 HIS   0.006   0.001   HIS A 239 

Details of bonding type rmsd
  covalent geometry    : bond        0.00225 (13045)
  covalent geometry    : angle       0.50379 (17658)
  hydrogen bonds       : bond        0.02701 (  840)
  hydrogen bonds       : angle       3.51312 ( 2502)

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

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

  3136 Ramachandran restraints generated.
    1568 Oldfield, 0 Emsley, 1568 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3136 Ramachandran restraints generated.
    1568 Oldfield, 0 Emsley, 1568 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  155 residues out of total 1393 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 15
    poor density    : 140
  time to evaluate  : 0.822 
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: symmetry clash
   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: symmetry clash
   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: symmetry clash
   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: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  191 GLU cc_start: 0.9626 (tt0) cc_final: 0.9063 (tp30)
REVERT: A  515 MET cc_start: 0.9202 (ttp) cc_final: 0.8876 (ttp)
REVERT: A  598 MET cc_start: 0.9233 (ttp) cc_final: 0.8531 (tmm)
REVERT: A  728 THR cc_start: 0.9297 (m) cc_final: 0.9092 (t)
REVERT: A  837 MET cc_start: 0.9167 (mmm) cc_final: 0.8850 (mmm)
REVERT: A 1086 MET cc_start: 0.8119 (mmt) cc_final: 0.7674 (mtm)
REVERT: A 1101 LEU cc_start: 0.9688 (OUTLIER) cc_final: 0.9085 (mt)
REVERT: A 1282 PHE cc_start: 0.7898 (t80) cc_final: 0.7588 (t80)
REVERT: A 1315 GLN cc_start: 0.9412 (tt0) cc_final: 0.8427 (tp-100)
REVERT: A 1541 GLU cc_start: 0.9137 (OUTLIER) cc_final: 0.8846 (mp0)
REVERT: B  247 ASP cc_start: 0.8641 (t70) cc_final: 0.8349 (t70)
REVERT: B  258 LYS cc_start: 0.9482 (ttpp) cc_final: 0.9279 (ptpp)
REVERT: B  273 ARG cc_start: 0.9607 (ptm160) cc_final: 0.9071 (ttp-110)
  outliers start: 15
  outliers final: 12
  residues processed: 149
  average time/residue: 0.3180
  time to fit residues: 67.4695
Evaluate side-chains
  150 residues out of total 1393 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 136
  time to evaluate  : 0.705 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  240 GLU
Chi-restraints excluded: chain A residue  418 LEU
Chi-restraints excluded: chain A residue  599 LEU
Chi-restraints excluded: chain A residue  672 GLU
Chi-restraints excluded: chain A residue  879 VAL
Chi-restraints excluded: chain A residue 1101 LEU
Chi-restraints excluded: chain A residue 1271 GLU
Chi-restraints excluded: chain A residue 1468 ILE
Chi-restraints excluded: chain A residue 1477 ASN
Chi-restraints excluded: chain A residue 1497 LEU
Chi-restraints excluded: chain A residue 1541 GLU
Chi-restraints excluded: chain A residue 1583 LEU
Chi-restraints excluded: chain A residue 1674 HIS
Chi-restraints excluded: chain B residue  245 GLU
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 160
   random chunks:
   chunk 106 optimal weight:    7.9990
   chunk 33 optimal weight:    5.9990
   chunk 82 optimal weight:    0.6980
   chunk 88 optimal weight:    0.9990
   chunk 56 optimal weight:    4.9990
   chunk 103 optimal weight:    0.8980
   chunk 38 optimal weight:    0.0670
   chunk 105 optimal weight:    0.9980
   chunk 53 optimal weight:    0.9980
   chunk 49 optimal weight:    7.9990
   chunk 97 optimal weight:   10.0000
   overall best weight:    0.7318

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

Flipped N/Q/H residues before XYZ refinement:
** A 363 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
A1607 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3682 r_free = 0.3682 target = 0.063351 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 40)----------------|
| r_work = 0.3253 r_free = 0.3253 target = 0.046077 restraints weight = 219948.255|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 44)----------------|
| r_work = 0.3309 r_free = 0.3309 target = 0.048477 restraints weight = 117954.356|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 30)----------------|
| r_work = 0.3348 r_free = 0.3348 target = 0.050117 restraints weight = 76382.835|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 52)----------------|
| r_work = 0.3374 r_free = 0.3374 target = 0.051239 restraints weight = 55867.069|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 37)----------------|
| r_work = 0.3392 r_free = 0.3392 target = 0.052024 restraints weight = 44708.005|
|-----------------------------------------------------------------------------|
r_work (final): 0.3369
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8330
moved from start:          0.5978

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.032  13045  Z= 0.096
  Angle     :  0.493   7.196  17658  Z= 0.250
  Chirality :  0.034   0.341   2029
  Planarity :  0.003   0.034   2254
  Dihedral  :  2.789  13.356   1716
  Min Nonbonded Distance : 2.339

Molprobity Statistics.
  All-atom Clashscore : 6.32
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.51 %
    Favored  : 96.49 %
  Rotamer:
    Outliers :  1.08 %
    Allowed  : 11.20 %
    Favored  : 87.72 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  2.57 (0.22), residues: 1568
  helix:  2.63 (0.15), residues: 1174
  sheet:  None (None), residues: 0
  loop : -1.30 (0.30), residues: 394

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.006   0.000   ARG B 270 
 TYR   0.016   0.001   TYR B 251 
 PHE   0.011   0.001   PHE B 278 
 TRP   0.008   0.001   TRP A1105 
 HIS   0.005   0.001   HIS A 239 

Details of bonding type rmsd
  covalent geometry    : bond        0.00212 (13045)
  covalent geometry    : angle       0.49328 (17658)
  hydrogen bonds       : bond        0.02605 (  840)
  hydrogen bonds       : angle       3.43355 ( 2502)

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

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

  3136 Ramachandran restraints generated.
    1568 Oldfield, 0 Emsley, 1568 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3136 Ramachandran restraints generated.
    1568 Oldfield, 0 Emsley, 1568 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  157 residues out of total 1393 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 15
    poor density    : 142
  time to evaluate  : 0.789 
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: symmetry clash
   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: symmetry clash
   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: symmetry clash
   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: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  191 GLU cc_start: 0.9620 (tt0) cc_final: 0.9057 (tp30)
REVERT: A  515 MET cc_start: 0.9210 (ttp) cc_final: 0.8893 (ttp)
REVERT: A  598 MET cc_start: 0.9227 (ttp) cc_final: 0.8552 (tmm)
REVERT: A  837 MET cc_start: 0.9210 (mmm) cc_final: 0.8831 (mmm)
REVERT: A  951 LYS cc_start: 0.9414 (tppt) cc_final: 0.9135 (tppt)
REVERT: A 1086 MET cc_start: 0.8157 (mmt) cc_final: 0.7681 (mtm)
REVERT: A 1282 PHE cc_start: 0.7882 (t80) cc_final: 0.7522 (t80)
REVERT: A 1315 GLN cc_start: 0.9461 (tt0) cc_final: 0.8479 (tp-100)
REVERT: B  247 ASP cc_start: 0.8613 (t70) cc_final: 0.8320 (t70)
REVERT: B  273 ARG cc_start: 0.9620 (ptm160) cc_final: 0.9087 (ttp-110)
  outliers start: 15
  outliers final: 14
  residues processed: 150
  average time/residue: 0.3221
  time to fit residues: 67.4756
Evaluate side-chains
  143 residues out of total 1393 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 129
  time to evaluate  : 0.690 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  240 GLU
Chi-restraints excluded: chain A residue  418 LEU
Chi-restraints excluded: chain A residue  599 LEU
Chi-restraints excluded: chain A residue  672 GLU
Chi-restraints excluded: chain A residue  879 VAL
Chi-restraints excluded: chain A residue 1101 LEU
Chi-restraints excluded: chain A residue 1271 GLU
Chi-restraints excluded: chain A residue 1468 ILE
Chi-restraints excluded: chain A residue 1477 ASN
Chi-restraints excluded: chain A residue 1497 LEU
Chi-restraints excluded: chain A residue 1574 GLN
Chi-restraints excluded: chain A residue 1583 LEU
Chi-restraints excluded: chain A residue 1674 HIS
Chi-restraints excluded: chain B residue  245 GLU
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 160
   random chunks:
   chunk 119 optimal weight:    2.9990
   chunk 20 optimal weight:    8.9990
   chunk 68 optimal weight:    2.9990
   chunk 103 optimal weight:    4.9990
   chunk 81 optimal weight:    4.9990
   chunk 18 optimal weight:    0.6980
   chunk 144 optimal weight:    4.9990
   chunk 57 optimal weight:    1.9990
   chunk 0 optimal weight:    9.9990
   chunk 75 optimal weight:    2.9990
   chunk 62 optimal weight:    0.4980
   overall best weight:    1.8386

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

Flipped N/Q/H residues before XYZ refinement:
A 363 GLN
A 531 ASN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3640 r_free = 0.3640 target = 0.061404 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 36)----------------|
| r_work = 0.3204 r_free = 0.3204 target = 0.044357 restraints weight = 227584.267|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 30)----------------|
| r_work = 0.3260 r_free = 0.3260 target = 0.046676 restraints weight = 121314.925|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 35)----------------|
| r_work = 0.3298 r_free = 0.3298 target = 0.048251 restraints weight = 78423.078|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 24)----------------|
| r_work = 0.3324 r_free = 0.3324 target = 0.049307 restraints weight = 57559.843|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 33)----------------|
| r_work = 0.3343 r_free = 0.3343 target = 0.050083 restraints weight = 46218.682|
|-----------------------------------------------------------------------------|
r_work (final): 0.3324
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8384
moved from start:          0.6377

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.051  13045  Z= 0.149
  Angle     :  0.516   7.032  17658  Z= 0.270
  Chirality :  0.034   0.336   2029
  Planarity :  0.003   0.035   2254
  Dihedral  :  2.883  13.914   1716
  Min Nonbonded Distance : 2.322

Molprobity Statistics.
  All-atom Clashscore : 6.59
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.76 %
    Favored  : 96.24 %
  Rotamer:
    Outliers :  1.15 %
    Allowed  : 11.06 %
    Favored  : 87.80 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  2.46 (0.22), residues: 1568
  helix:  2.50 (0.15), residues: 1181
  sheet:  None (None), residues: 0
  loop : -1.30 (0.30), residues: 387

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARG A1430 
 TYR   0.010   0.001   TYR B 251 
 PHE   0.009   0.001   PHE A1067 
 TRP   0.005   0.001   TRP A1226 
 HIS   0.005   0.001   HIS A 239 

Details of bonding type rmsd
  covalent geometry    : bond        0.00302 (13045)
  covalent geometry    : angle       0.51555 (17658)
  hydrogen bonds       : bond        0.02737 (  840)
  hydrogen bonds       : angle       3.64188 ( 2502)

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

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

  3136 Ramachandran restraints generated.
    1568 Oldfield, 0 Emsley, 1568 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3136 Ramachandran restraints generated.
    1568 Oldfield, 0 Emsley, 1568 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  146 residues out of total 1393 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 130
  time to evaluate  : 0.646 
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: symmetry clash
   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: symmetry clash
   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: symmetry clash
   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  191 GLU cc_start: 0.9620 (tt0) cc_final: 0.9087 (tp30)
REVERT: A  280 LEU cc_start: 0.9544 (mm) cc_final: 0.9312 (pp)
REVERT: A  515 MET cc_start: 0.9230 (ttp) cc_final: 0.8908 (ttp)
REVERT: A  837 MET cc_start: 0.9260 (mmm) cc_final: 0.8899 (mmm)
REVERT: A  951 LYS cc_start: 0.9475 (tppt) cc_final: 0.9207 (tppt)
REVERT: A 1282 PHE cc_start: 0.8129 (t80) cc_final: 0.7793 (t80)
REVERT: B  247 ASP cc_start: 0.8653 (t70) cc_final: 0.8382 (t70)
REVERT: B  273 ARG cc_start: 0.9618 (ptm160) cc_final: 0.9319 (ptm160)
  outliers start: 16
  outliers final: 13
  residues processed: 139
  average time/residue: 0.3242
  time to fit residues: 62.9976
Evaluate side-chains
  141 residues out of total 1393 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 128
  time to evaluate  : 0.712 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   36 GLU
Chi-restraints excluded: chain A residue  240 GLU
Chi-restraints excluded: chain A residue  418 LEU
Chi-restraints excluded: chain A residue  532 PHE
Chi-restraints excluded: chain A residue  672 GLU
Chi-restraints excluded: chain A residue  879 VAL
Chi-restraints excluded: chain A residue 1271 GLU
Chi-restraints excluded: chain A residue 1468 ILE
Chi-restraints excluded: chain A residue 1477 ASN
Chi-restraints excluded: chain A residue 1497 LEU
Chi-restraints excluded: chain A residue 1583 LEU
Chi-restraints excluded: chain A residue 1674 HIS
Chi-restraints excluded: chain B residue  245 GLU
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 160
   random chunks:
   chunk 37 optimal weight:    3.9990
   chunk 72 optimal weight:    3.9990
   chunk 120 optimal weight:    7.9990
   chunk 11 optimal weight:    0.9980
   chunk 147 optimal weight:    9.9990
   chunk 31 optimal weight:    4.9990
   chunk 106 optimal weight:    0.0570
   chunk 17 optimal weight:    5.9990
   chunk 158 optimal weight:    2.9990
   chunk 86 optimal weight:    5.9990
   chunk 102 optimal weight:    3.9990
   overall best weight:    2.4104

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

Flipped N/Q/H residues before XYZ refinement:
A 771 ASN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3590 r_free = 0.3590 target = 0.059107 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 36)----------------|
| r_work = 0.3150 r_free = 0.3150 target = 0.042439 restraints weight = 233392.026|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 39)----------------|
| r_work = 0.3206 r_free = 0.3206 target = 0.044697 restraints weight = 122935.141|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 40)----------------|
| r_work = 0.3244 r_free = 0.3244 target = 0.046220 restraints weight = 79042.603|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 25)----------------|
| r_work = 0.3271 r_free = 0.3271 target = 0.047258 restraints weight = 58006.864|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 42)----------------|
| r_work = 0.3290 r_free = 0.3290 target = 0.047991 restraints weight = 46596.910|
|-----------------------------------------------------------------------------|
r_work (final): 0.3271
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8424
moved from start:          0.6980

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.059  13045  Z= 0.182
  Angle     :  0.561   7.194  17658  Z= 0.298
  Chirality :  0.035   0.346   2029
  Planarity :  0.004   0.053   2254
  Dihedral  :  3.100  14.162   1716
  Min Nonbonded Distance : 2.332

Molprobity Statistics.
  All-atom Clashscore : 8.15
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.27 %
    Favored  : 95.73 %
  Rotamer:
    Outliers :  1.29 %
    Allowed  : 11.20 %
    Favored  : 87.51 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  2.22 (0.22), residues: 1568
  helix:  2.29 (0.15), residues: 1189
  sheet:  None (None), residues: 0
  loop : -1.32 (0.31), residues: 379

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.001   ARG A 669 
 TYR   0.012   0.001   TYR B 251 
 PHE   0.010   0.001   PHE A 766 
 TRP   0.047   0.002   TRP A 748 
 HIS   0.006   0.001   HIS A 239 

Details of bonding type rmsd
  covalent geometry    : bond        0.00359 (13045)
  covalent geometry    : angle       0.56148 (17658)
  hydrogen bonds       : bond        0.02943 (  840)
  hydrogen bonds       : angle       3.84214 ( 2502)

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

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

  3136 Ramachandran restraints generated.
    1568 Oldfield, 0 Emsley, 1568 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3136 Ramachandran restraints generated.
    1568 Oldfield, 0 Emsley, 1568 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  148 residues out of total 1393 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 18
    poor density    : 130
  time to evaluate  : 0.726 
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: symmetry clash
   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: symmetry clash
   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: symmetry clash
   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: symmetry clash
REVERT: A  191 GLU cc_start: 0.9621 (tt0) cc_final: 0.9140 (tp30)
REVERT: A  515 MET cc_start: 0.9304 (ttp) cc_final: 0.8986 (ttp)
REVERT: A  837 MET cc_start: 0.9296 (mmm) cc_final: 0.8907 (mmm)
REVERT: A  951 LYS cc_start: 0.9489 (tppt) cc_final: 0.9209 (tppt)
REVERT: A 1282 PHE cc_start: 0.8203 (t80) cc_final: 0.7848 (t80)
REVERT: A 1506 ARG cc_start: 0.9000 (tpt-90) cc_final: 0.8356 (ttm-80)
REVERT: A 1541 GLU cc_start: 0.9356 (OUTLIER) cc_final: 0.9113 (mp0)
REVERT: B  273 ARG cc_start: 0.9653 (ptm160) cc_final: 0.9378 (ptm160)
  outliers start: 18
  outliers final: 14
  residues processed: 141
  average time/residue: 0.3160
  time to fit residues: 62.4923
Evaluate side-chains
  140 residues out of total 1393 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 15
    poor density    : 125
  time to evaluate  : 0.714 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   36 GLU
Chi-restraints excluded: chain A residue  240 GLU
Chi-restraints excluded: chain A residue  418 LEU
Chi-restraints excluded: chain A residue  532 PHE
Chi-restraints excluded: chain A residue  665 ASP
Chi-restraints excluded: chain A residue  672 GLU
Chi-restraints excluded: chain A residue  879 VAL
Chi-restraints excluded: chain A residue 1271 GLU
Chi-restraints excluded: chain A residue 1468 ILE
Chi-restraints excluded: chain A residue 1477 ASN
Chi-restraints excluded: chain A residue 1497 LEU
Chi-restraints excluded: chain A residue 1541 GLU
Chi-restraints excluded: chain A residue 1583 LEU
Chi-restraints excluded: chain A residue 1674 HIS
Chi-restraints excluded: chain B residue  245 GLU
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 160
   random chunks:
   chunk 159 optimal weight:    0.8980
   chunk 131 optimal weight:    0.9980
   chunk 107 optimal weight:    0.1980
   chunk 71 optimal weight:    1.9990
   chunk 46 optimal weight:    0.7980
   chunk 29 optimal weight:    3.9990
   chunk 94 optimal weight:    3.9990
   chunk 152 optimal weight:    0.4980
   chunk 138 optimal weight:    4.9990
   chunk 135 optimal weight:    1.9990
   chunk 79 optimal weight:    0.8980
   overall best weight:    0.6580

-------------------------------------------------------------------------------
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 = 0.3620 r_free = 0.3620 target = 0.060415 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 42)----------------|
| r_work = 0.3181 r_free = 0.3181 target = 0.043434 restraints weight = 225404.573|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 38)----------------|
| r_work = 0.3239 r_free = 0.3239 target = 0.045779 restraints weight = 118106.066|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 38)----------------|
| r_work = 0.3279 r_free = 0.3279 target = 0.047375 restraints weight = 75674.467|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 32)----------------|
| r_work = 0.3306 r_free = 0.3306 target = 0.048463 restraints weight = 55117.754|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 42)----------------|
| r_work = 0.3324 r_free = 0.3324 target = 0.049201 restraints weight = 44117.974|
|-----------------------------------------------------------------------------|
r_work (final): 0.3305
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8382
moved from start:          0.6970

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.036  13045  Z= 0.098
  Angle     :  0.525   7.219  17658  Z= 0.265
  Chirality :  0.035   0.339   2029
  Planarity :  0.003   0.033   2254
  Dihedral  :  2.974  13.886   1716
  Min Nonbonded Distance : 2.330

Molprobity Statistics.
  All-atom Clashscore : 6.94
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.12 %
    Favored  : 96.88 %
  Rotamer:
    Outliers :  0.86 %
    Allowed  : 11.70 %
    Favored  : 87.44 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  2.68 (0.22), residues: 1568
  helix:  2.63 (0.15), residues: 1187
  sheet:  None (None), residues: 0
  loop : -1.11 (0.31), residues: 381

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.000   ARG B 270 
 TYR   0.012   0.001   TYR A1089 
 PHE   0.011   0.001   PHE A1067 
 TRP   0.029   0.001   TRP A 748 
 HIS   0.005   0.001   HIS A 247 

Details of bonding type rmsd
  covalent geometry    : bond        0.00219 (13045)
  covalent geometry    : angle       0.52525 (17658)
  hydrogen bonds       : bond        0.02708 (  840)
  hydrogen bonds       : angle       3.48658 ( 2502)

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

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

  3136 Ramachandran restraints generated.
    1568 Oldfield, 0 Emsley, 1568 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3136 Ramachandran restraints generated.
    1568 Oldfield, 0 Emsley, 1568 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  144 residues out of total 1393 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 132
  time to evaluate  : 0.732 
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: symmetry clash
   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: symmetry clash
   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: symmetry clash
   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  191 GLU cc_start: 0.9586 (tt0) cc_final: 0.9150 (tp30)
REVERT: A  515 MET cc_start: 0.9292 (ttp) cc_final: 0.8947 (ttp)
REVERT: A  837 MET cc_start: 0.9250 (mmm) cc_final: 0.8896 (mmm)
REVERT: A  951 LYS cc_start: 0.9484 (tppt) cc_final: 0.9196 (tppt)
REVERT: A 1282 PHE cc_start: 0.8139 (t80) cc_final: 0.7774 (t80)
REVERT: A 1506 ARG cc_start: 0.9084 (tpt-90) cc_final: 0.8480 (ttm-80)
REVERT: A 1541 GLU cc_start: 0.9340 (OUTLIER) cc_final: 0.9097 (mp0)
  outliers start: 12
  outliers final: 11
  residues processed: 138
  average time/residue: 0.3189
  time to fit residues: 62.6498
Evaluate side-chains
  144 residues out of total 1393 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 132
  time to evaluate  : 0.699 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  240 GLU
Chi-restraints excluded: chain A residue  418 LEU
Chi-restraints excluded: chain A residue  532 PHE
Chi-restraints excluded: chain A residue  672 GLU
Chi-restraints excluded: chain A residue  879 VAL
Chi-restraints excluded: chain A residue 1271 GLU
Chi-restraints excluded: chain A residue 1468 ILE
Chi-restraints excluded: chain A residue 1477 ASN
Chi-restraints excluded: chain A residue 1541 GLU
Chi-restraints excluded: chain A residue 1583 LEU
Chi-restraints excluded: chain A residue 1674 HIS
Chi-restraints excluded: chain B residue  245 GLU
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 160
   random chunks:
   chunk 28 optimal weight:    4.9990
   chunk 50 optimal weight:    4.9990
   chunk 45 optimal weight:    0.8980
   chunk 102 optimal weight:    4.9990
   chunk 128 optimal weight:    4.9990
   chunk 55 optimal weight:    0.7980
   chunk 68 optimal weight:    1.9990
   chunk 108 optimal weight:    4.9990
   chunk 107 optimal weight:    2.9990
   chunk 5 optimal weight:   10.0000
   chunk 144 optimal weight:    0.0770
   overall best weight:    1.3542

-------------------------------------------------------------------------------
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 = 0.3600 r_free = 0.3600 target = 0.059559 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 31)----------------|
| r_work = 0.3162 r_free = 0.3162 target = 0.042782 restraints weight = 226851.397|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 32)----------------|
| r_work = 0.3219 r_free = 0.3219 target = 0.045075 restraints weight = 119652.544|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 34)----------------|
| r_work = 0.3259 r_free = 0.3259 target = 0.046639 restraints weight = 76828.696|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 36)----------------|
| r_work = 0.3285 r_free = 0.3285 target = 0.047702 restraints weight = 56001.600|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 35)----------------|
| r_work = 0.3303 r_free = 0.3303 target = 0.048433 restraints weight = 44888.095|
|-----------------------------------------------------------------------------|
r_work (final): 0.3287
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8400
moved from start:          0.7128

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.047  13045  Z= 0.125
  Angle     :  0.536   9.817  17658  Z= 0.274
  Chirality :  0.034   0.338   2029
  Planarity :  0.003   0.050   2254
  Dihedral  :  2.944  13.856   1716
  Min Nonbonded Distance : 2.319

Molprobity Statistics.
  All-atom Clashscore : 7.41
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.38 %
    Favored  : 96.62 %
  Rotamer:
    Outliers :  0.86 %
    Allowed  : 11.99 %
    Favored  : 87.15 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  2.69 (0.22), residues: 1568
  helix:  2.61 (0.15), residues: 1188
  sheet:  None (None), residues: 0
  loop : -1.04 (0.32), residues: 380

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.000   ARG B 270 
 TYR   0.012   0.001   TYR B 251 
 PHE   0.009   0.001   PHE A1067 
 TRP   0.028   0.001   TRP A 748 
 HIS   0.004   0.001   HIS A 239 

Details of bonding type rmsd
  covalent geometry    : bond        0.00262 (13045)
  covalent geometry    : angle       0.53589 (17658)
  hydrogen bonds       : bond        0.02713 (  840)
  hydrogen bonds       : angle       3.60843 ( 2502)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 4707.40 seconds
wall clock time: 81 minutes 11.88 seconds (4871.88 seconds total)