Starting phenix.real_space_refine
on Sat Aug 23 10:21:49 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/8rq3_19431/08_2025/8rq3_19431.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/8rq3_19431/08_2025/8rq3_19431.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=3.21
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    model {
      file = "/net/cci-nas-00/data/ceres_data/8rq3_19431/08_2025/8rq3_19431.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/8rq3_19431/08_2025/8rq3_19431.cif"
    real_map_files = "/net/cci-nas-00/data/ceres_data/8rq3_19431/08_2025/8rq3_19431.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/8rq3_19431/08_2025/8rq3_19431.map"
  }
  resolution = 3.21
  write_initial_geo_file = False
  refinement {
    macro_cycles = 10
  }


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

Validating inputs
Origin is already at (0, 0, 0), no shifts will be applied
-------------------------------------------------------------------------------
Processing inputs
*****************
Set random seed
  Set to: 0
Set model cs if undefined
Decide on map wrapping
  Map wrapping is set to: False
Normalize map: mean=0, sd=1
  Input map: mean=   0.000 sd=   0.017
Set stop_for_unknowns flag
  Set to: True
Assert model is a single copy model
Assert all atoms have isotropic ADPs
Construct map_model_manager
Extract box with map and model
Check model and map are aligned
Set scattering table
  Set to: electron
  Number of scattering types: 4
    Type Number    sf(0)   Gaussians
     S      50      5.16       5
     C    7362      2.51       5
     N    1923      2.21       5
     O    2040      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 50 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: 11375
  Number of models: 1
  Model: ""
    Number of chains: 1
    Chain: "A"
      Number of atoms: 11375
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 1432, 11375
          Classifications: {'peptide': 1432}
          Link IDs: {'PTRANS': 42, 'TRANS': 1389}
          Chain breaks: 3
  Time building chain proxies: 2.28, per 1000 atoms: 0.20
  Number of scatterers: 11375
  At special positions: 0
  Unit cell: (105.78, 135.45, 148.995, 90, 90, 90)
  Space group: P 1 (No. 1)
  Number of sites at special positions: 0
  Number of scattering types: 4
    Type Number    sf(0)
     S      50     16.00
     O    2040      8.00
     N    1923      7.00
     C    7362      6.00
    sf(0) = scattering factor at diffraction angle 0.

  Number of disulfides: simple=1, symmetry=0
    Simple disulfide: pdb=" SG  CYS A   5 " - pdb=" SG  CYS A  25 " distance=2.03

  Automatic linking
    Parameters for automatic linking
      Linking & cutoffs
        Metal                : Auto  - 3.00
        Amino acid           : True  - 1.90
        Carbohydrate         : True  - 1.99
        Ligands              : True  - 1.99
        Small molecules      : False - 1.98
        Amino acid - RNA/DNA : False
      
  Number of custom bonds: simple=0, symmetry=0
  Time building additional restraints: 1.02
  Conformation dependent library (CDL) restraints added in 592.1 milliseconds
  
  Enol-peptide restraints added in 715.3 nanoseconds
  

  2848 Ramachandran restraints generated.
    1424 Oldfield, 0 Emsley, 1424 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  2698

  Finding SS restraints...
    Secondary structure from input PDB file:
      61 helices and 7 sheets defined
      69.9% alpha, 7.1% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 0.58
  Creating SS restraints...
    Processing helix  chain 'A' and resid 1 through 6
      removed outlier: 3.719A  pdb=" N   CYS A   5 " --> pdb=" O   ASP A   2 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 23 through 51
      removed outlier: 4.599A  pdb=" N   VAL A  32 " --> pdb=" O   GLN A  28 " (cutoff:3.500A)
      Proline residue:  A  35  - end of helix
      removed outlier: 3.678A  pdb=" N   LEU A  42 " --> pdb=" O   PHE A  38 " (cutoff:3.500A)
      Proline residue:  A  44  - end of helix
    Processing helix  chain 'A' and resid 61 through 90
    Processing helix  chain 'A' and resid 100 through 118
      removed outlier: 3.705A  pdb=" N   HIS A 118 " --> pdb=" O   LEU A 114 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 119 through 123
    Processing helix  chain 'A' and resid 128 through 155
      removed outlier: 3.666A  pdb=" N   VAL A 143 " --> pdb=" O   VAL A 139 " (cutoff:3.500A)
      removed outlier: 4.882A  pdb=" N   PHE A 144 " --> pdb=" O   LEU A 140 " (cutoff:3.500A)
      removed outlier: 4.436A  pdb=" N   GLN A 145 " --> pdb=" O   CYS A 141 " (cutoff:3.500A)
      removed outlier: 3.510A  pdb=" N   LYS A 155 " --> pdb=" O   ARG A 151 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 160 through 183
      removed outlier: 3.539A  pdb=" N   SER A 164 " --> pdb=" O   ASN A 160 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 192 through 196
    Processing helix  chain 'A' and resid 198 through 204
    Processing helix  chain 'A' and resid 208 through 218
      removed outlier: 3.832A  pdb=" N   LEU A 213 " --> pdb=" O   ASP A 209 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 233 through 265
      removed outlier: 4.806A  pdb=" N   LYS A 247 " --> pdb=" O   ALA A 243 " (cutoff:3.500A)
      removed outlier: 4.529A  pdb=" N   ASP A 248 " --> pdb=" O   ALA A 244 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 305 through 332
      removed outlier: 6.643A  pdb=" N   VAL A 316 " --> pdb=" O   LYS A 312 " (cutoff:3.500A)
      removed outlier: 6.629A  pdb=" N   VAL A 317 " --> pdb=" O   THR A 313 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 334 through 348
    Processing helix  chain 'A' and resid 353 through 401
      removed outlier: 3.997A  pdb=" N   TYR A 357 " --> pdb=" O   VAL A 353 " (cutoff:3.500A)
      removed outlier: 3.520A  pdb=" N   ILE A 358 " --> pdb=" O   TRP A 354 " (cutoff:3.500A)
      removed outlier: 6.052A  pdb=" N   CYS A 359 " --> pdb=" O   PHE A 355 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 404 through 409
    Processing helix  chain 'A' and resid 412 through 422
    Processing helix  chain 'A' and resid 422 through 433
    Processing helix  chain 'A' and resid 435 through 456
      removed outlier: 4.546A  pdb=" N   VAL A 441 " --> pdb=" O   VAL A 437 " (cutoff:3.500A)
      removed outlier: 3.980A  pdb=" N   GLU A 454 " --> pdb=" O   PHE A 450 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 458 through 504
      removed outlier: 4.116A  pdb=" N   GLY A 462 " --> pdb=" O   SER A 458 " (cutoff:3.500A)
      removed outlier: 4.086A  pdb=" N   ILE A 470 " --> pdb=" O   MET A 466 " (cutoff:3.500A)
      Proline residue:  A 471  - end of helix
    Processing helix  chain 'A' and resid 504 through 511
    Processing helix  chain 'A' and resid 513 through 564
      Proline residue:  A 550  - end of helix
    Processing helix  chain 'A' and resid 571 through 586
    Processing helix  chain 'A' and resid 587 through 613
      Proline residue:  A 593  - end of helix
      removed outlier: 3.808A  pdb=" N   VAL A 604 " --> pdb=" O   LEU A 600 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 672 through 682
      removed outlier: 3.507A  pdb=" N   GLY A 682 " --> pdb=" O   SER A 678 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 711 through 717
    Processing helix  chain 'A' and resid 722 through 733
    Processing helix  chain 'A' and resid 735 through 742
    Processing helix  chain 'A' and resid 758 through 774
      removed outlier: 3.772A  pdb=" N   ASP A 774 " --> pdb=" O   ALA A 770 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 788 through 800
    Processing helix  chain 'A' and resid 820 through 824
    Processing helix  chain 'A' and resid 840 through 847
    Processing helix  chain 'A' and resid 849 through 858
      removed outlier: 3.727A  pdb=" N   ARG A 853 " --> pdb=" O   GLY A 849 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 859 through 861
      No H-bonds generated for 'chain 'A' and resid 859 through 861'
    Processing helix  chain 'A' and resid 900 through 912
      removed outlier: 3.603A  pdb=" N   LEU A 905 " --> pdb=" O   ARG A 901 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 959 through 971
      removed outlier: 4.098A  pdb=" N   TYR A 963 " --> pdb=" O   LYS A 959 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 972 through 998
      removed outlier: 3.686A  pdb=" N   ASN A 985 " --> pdb=" O   PHE A 981 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 999 through 1004
      removed outlier: 3.645A  pdb=" N   ASP A1002 " --> pdb=" O   TRP A 999 " (cutoff:3.500A)
      removed outlier: 3.559A  pdb=" N   SER A1003 " --> pdb=" O   THR A1000 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 1008 through 1011
      removed outlier: 3.829A  pdb=" N   ASN A1011 " --> pdb=" O   GLY A1008 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'A' and resid 1008 through 1011'
    Processing helix  chain 'A' and resid 1012 through 1061
    Processing helix  chain 'A' and resid 1064 through 1071
      removed outlier: 3.851A  pdb=" N   PHE A1068 " --> pdb=" O   PRO A1064 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 1072 through 1082
      removed outlier: 3.558A  pdb=" N   ILE A1076 " --> pdb=" O   PRO A1072 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 1083 through 1089
    Processing helix  chain 'A' and resid 1089 through 1116
      removed outlier: 3.895A  pdb=" N   GLN A1093 " --> pdb=" O   ASP A1089 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 1117 through 1121
    Processing helix  chain 'A' and resid 1122 through 1165
      removed outlier: 3.794A  pdb=" N   LEU A1126 " --> pdb=" O   ILE A1122 " (cutoff:3.500A)
      removed outlier: 3.911A  pdb=" N   GLN A1143 " --> pdb=" O   ALA A1139 " (cutoff:3.500A)
      removed outlier: 3.870A  pdb=" N   SER A1153 " --> pdb=" O   SER A1149 " (cutoff:3.500A)
      Proline residue:  A1154  - end of helix
    Processing helix  chain 'A' and resid 1165 through 1173
    Processing helix  chain 'A' and resid 1174 through 1225
      removed outlier: 3.580A  pdb=" N   PHE A1178 " --> pdb=" O   HIS A1174 " (cutoff:3.500A)
      removed outlier: 3.866A  pdb=" N   CYS A1192 " --> pdb=" O   ILE A1188 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 1230 through 1242
      removed outlier: 3.631A  pdb=" N   VAL A1234 " --> pdb=" O   THR A1230 " (cutoff:3.500A)
      removed outlier: 4.213A  pdb=" N   ASN A1240 " --> pdb=" O   PHE A1236 " (cutoff:3.500A)
      removed outlier: 3.690A  pdb=" N   LEU A1242 " --> pdb=" O   LEU A1238 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 1244 through 1262
    Processing helix  chain 'A' and resid 1262 through 1273
      removed outlier: 3.543A  pdb=" N   ASN A1273 " --> pdb=" O   SER A1269 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 1335 through 1343
      removed outlier: 4.037A  pdb=" N   LEU A1339 " --> pdb=" O   GLY A1335 " (cutoff:3.500A)
      removed outlier: 4.188A  pdb=" N   THR A1340 " --> pdb=" O   LYS A1336 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 1362 through 1364
      No H-bonds generated for 'chain 'A' and resid 1362 through 1364'
    Processing helix  chain 'A' and resid 1365 through 1372
      removed outlier: 3.971A  pdb=" N   ARG A1372 " --> pdb=" O   ASP A1368 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 1387 through 1392
    Processing helix  chain 'A' and resid 1398 through 1409
    Processing helix  chain 'A' and resid 1411 through 1416
    Processing helix  chain 'A' and resid 1434 through 1450
    Processing helix  chain 'A' and resid 1464 through 1479
    Processing helix  chain 'A' and resid 1490 through 1494
      removed outlier: 3.827A  pdb=" N   THR A1493 " --> pdb=" O   ARG A1490 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 1513 through 1519
      removed outlier: 4.120A  pdb=" N   SER A1519 " --> pdb=" O   GLU A1515 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 1522 through 1528
    Processing sheet with id=AA1, first strand: chain 'A' and resid 623 through 626
      removed outlier: 5.892A  pdb=" N   ARG A 624 " --> pdb=" O   ILE A 693 " (cutoff:3.500A)
      removed outlier: 7.159A  pdb=" N   ASN A 686 " --> pdb=" O   PHE A 640 " (cutoff:3.500A)
      removed outlier: 6.868A  pdb=" N   PHE A 640 " --> pdb=" O   ASN A 686 " (cutoff:3.500A)
      removed outlier: 6.504A  pdb=" N   HIS A 688 " --> pdb=" O   ALA A 638 " (cutoff:3.500A)
      removed outlier: 4.248A  pdb=" N   ALA A 638 " --> pdb=" O   HIS A 688 " (cutoff:3.500A)
      removed outlier: 5.232A  pdb=" N   VAL A 653 " --> pdb=" O   GLU A 637 " (cutoff:3.500A)
      removed outlier: 4.146A  pdb=" N   SER A 639 " --> pdb=" O   GLN A 651 " (cutoff:3.500A)
      removed outlier: 6.915A  pdb=" N   GLN A 651 " --> pdb=" O   SER A 639 " (cutoff:3.500A)
    Processing sheet with id=AA2, first strand: chain 'A' and resid 697 through 700
      removed outlier: 6.578A  pdb=" N   ALA A 698 " --> pdb=" O   ILE A 779 " (cutoff:3.500A)
      removed outlier: 6.234A  pdb=" N   VAL A 663 " --> pdb=" O   PHE A 813 " (cutoff:3.500A)
      removed outlier: 6.411A  pdb=" N   ALA A 664 " --> pdb=" O   VAL A 828 " (cutoff:3.500A)
      removed outlier: 7.799A  pdb=" N   LEU A 830 " --> pdb=" O   ALA A 664 " (cutoff:3.500A)
      removed outlier: 6.633A  pdb=" N   VAL A 666 " --> pdb=" O   LEU A 830 " (cutoff:3.500A)
      removed outlier: 6.748A  pdb=" N   ILE A 827 " --> pdb=" O   LYS A 838 " (cutoff:3.500A)
      removed outlier: 4.456A  pdb=" N   LYS A 838 " --> pdb=" O   ILE A 827 " (cutoff:3.500A)
      removed outlier: 7.041A  pdb=" N   VAL A 829 " --> pdb=" O   LEU A 836 " (cutoff:3.500A)
    Processing sheet with id=AA3, first strand: chain 'A' and resid 709 through 710
    Processing sheet with id=AA4, first strand: chain 'A' and resid 1313 through 1316
      removed outlier: 5.918A  pdb=" N   LYS A1314 " --> pdb=" O   VAL A1303 " (cutoff:3.500A)
      removed outlier: 7.807A  pdb=" N   VAL A1303 " --> pdb=" O   LYS A1314 " (cutoff:3.500A)
    Processing sheet with id=AA5, first strand: chain 'A' and resid 1313 through 1316
      removed outlier: 5.918A  pdb=" N   LYS A1314 " --> pdb=" O   VAL A1303 " (cutoff:3.500A)
      removed outlier: 7.807A  pdb=" N   VAL A1303 " --> pdb=" O   LYS A1314 " (cutoff:3.500A)
      removed outlier: 5.420A  pdb=" N   PHE A1298 " --> pdb=" O   ILE A1355 " (cutoff:3.500A)
      removed outlier: 6.461A  pdb=" N   ILE A1355 " --> pdb=" O   PHE A1298 " (cutoff:3.500A)
      removed outlier: 5.259A  pdb=" N   ASN A1300 " --> pdb=" O   GLN A1353 " (cutoff:3.500A)
      removed outlier: 5.071A  pdb=" N   GLN A1353 " --> pdb=" O   ASN A1300 " (cutoff:3.500A)
    Processing sheet with id=AA6, first strand: chain 'A' and resid 1375 through 1376
      removed outlier: 6.273A  pdb=" N   ILE A1376 " --> pdb=" O   ASP A1457 " (cutoff:3.500A)
      removed outlier: 6.194A  pdb=" N   LEU A1454 " --> pdb=" O   ILE A1485 " (cutoff:3.500A)
      removed outlier: 7.565A  pdb=" N   ILE A1487 " --> pdb=" O   LEU A1454 " (cutoff:3.500A)
      removed outlier: 6.912A  pdb=" N   LEU A1456 " --> pdb=" O   ILE A1487 " (cutoff:3.500A)
      removed outlier: 6.241A  pdb=" N   LYS A1325 " --> pdb=" O   LYS A1499 " (cutoff:3.500A)
      removed outlier: 7.532A  pdb=" N   MET A1501 " --> pdb=" O   LYS A1325 " (cutoff:3.500A)
      removed outlier: 6.492A  pdb=" N   GLY A1327 " --> pdb=" O   MET A1501 " (cutoff:3.500A)
      removed outlier: 7.677A  pdb=" N   LEU A1503 " --> pdb=" O   GLY A1327 " (cutoff:3.500A)
      removed outlier: 5.877A  pdb=" N   VAL A1329 " --> pdb=" O   LEU A1503 " (cutoff:3.500A)
    Processing sheet with id=AA7, first strand: chain 'A' and resid 1385 through 1386

    736 hydrogen bonds defined for protein.
    2151 hydrogen bond angles defined for protein.
    Restraints generated for nucleic acids:
      0 hydrogen bonds
      0 hydrogen bond angles
      0 basepair planarities
      0 basepair parallelities
      0 stacking parallelities
  Total time for adding SS restraints: 2.10

  Time building geometry restraints manager: 1.37 seconds

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

  Histogram of bond lengths:
        1.22 -     1.33: 3416
        1.33 -     1.45: 1705
        1.45 -     1.57: 6409
        1.57 -     1.69: 0
        1.69 -     1.81: 80
  Bond restraints: 11610
  Sorted by residual:
  bond pdb=" CG  LEU A  74 "
       pdb=" CD2 LEU A  74 "
    ideal  model  delta    sigma   weight residual
    1.521  1.440  0.081 3.30e-02 9.18e+02 6.02e+00
  bond pdb=" CG1 ILE A1042 "
       pdb=" CD1 ILE A1042 "
    ideal  model  delta    sigma   weight residual
    1.513  1.425  0.088 3.90e-02 6.57e+02 5.14e+00
  bond pdb=" CB  ILE A 203 "
       pdb=" CG2 ILE A 203 "
    ideal  model  delta    sigma   weight residual
    1.521  1.450  0.071 3.30e-02 9.18e+02 4.58e+00
  bond pdb=" CG1 ILE A 318 "
       pdb=" CD1 ILE A 318 "
    ideal  model  delta    sigma   weight residual
    1.513  1.436  0.077 3.90e-02 6.57e+02 3.85e+00
  bond pdb=" CB  VAL A 212 "
       pdb=" CG1 VAL A 212 "
    ideal  model  delta    sigma   weight residual
    1.521  1.457  0.064 3.30e-02 9.18e+02 3.77e+00
  ... (remaining 11605 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     1.82: 15127
        1.82 -     3.63: 514
        3.63 -     5.45: 70
        5.45 -     7.27: 21
        7.27 -     9.08: 6
  Bond angle restraints: 15738
  Sorted by residual:
  angle pdb=" C   ARG A 918 "
        pdb=" N   ARG A 919 "
        pdb=" CA  ARG A 919 "
      ideal   model   delta    sigma   weight residual
     122.05  115.35    6.70 1.48e+00 4.57e-01 2.05e+01
  angle pdb=" N   GLN A1134 "
        pdb=" CA  GLN A1134 "
        pdb=" CB  GLN A1134 "
      ideal   model   delta    sigma   weight residual
     110.16  115.26   -5.10 1.48e+00 4.57e-01 1.19e+01
  angle pdb=" N   GLY A 920 "
        pdb=" CA  GLY A 920 "
        pdb=" C   GLY A 920 "
      ideal   model   delta    sigma   weight residual
     113.18  105.62    7.56 2.37e+00 1.78e-01 1.02e+01
  angle pdb=" C   ARG A1438 "
        pdb=" N   GLN A1439 "
        pdb=" CA  GLN A1439 "
      ideal   model   delta    sigma   weight residual
     120.72  115.63    5.09 1.67e+00 3.59e-01 9.31e+00
  angle pdb=" C   ASN A1299 "
        pdb=" N   ASN A1300 "
        pdb=" CA  ASN A1300 "
      ideal   model   delta    sigma   weight residual
     121.54  127.14   -5.60 1.91e+00 2.74e-01 8.59e+00
  ... (remaining 15733 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    17.76: 6159
       17.76 -    35.52: 636
       35.52 -    53.28: 103
       53.28 -    71.04: 19
       71.04 -    88.80: 10
  Dihedral angle restraints: 6927
    sinusoidal: 2761
      harmonic: 4166
  Sorted by residual:
  dihedral pdb=" CA  THR A 815 "
           pdb=" C   THR A 815 "
           pdb=" N   HIS A 816 "
           pdb=" CA  HIS A 816 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  160.08   19.92     0      5.00e+00 4.00e-02 1.59e+01
  dihedral pdb=" CA  SER A 189 "
           pdb=" C   SER A 189 "
           pdb=" N   THR A 190 "
           pdb=" CA  THR A 190 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00 -161.14  -18.86     0      5.00e+00 4.00e-02 1.42e+01
  dihedral pdb=" CA  GLY A 356 "
           pdb=" C   GLY A 356 "
           pdb=" N   TYR A 357 "
           pdb=" CA  TYR A 357 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  161.78   18.22     0      5.00e+00 4.00e-02 1.33e+01
  ... (remaining 6924 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.038: 1057
       0.038 -    0.076: 579
       0.076 -    0.114: 147
       0.114 -    0.152: 52
       0.152 -    0.190: 7
  Chirality restraints: 1842
  Sorted by residual:
  chirality pdb=" CA  GLU A 514 "
            pdb=" N   GLU A 514 "
            pdb=" C   GLU A 514 "
            pdb=" CB  GLU A 514 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.32    0.19 2.00e-01 2.50e+01 9.07e-01
  chirality pdb=" CA  ARG A 919 "
            pdb=" N   ARG A 919 "
            pdb=" C   ARG A 919 "
            pdb=" CB  ARG A 919 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.34    0.17 2.00e-01 2.50e+01 7.06e-01
  chirality pdb=" CB  ILE A 307 "
            pdb=" CA  ILE A 307 "
            pdb=" CG1 ILE A 307 "
            pdb=" CG2 ILE A 307 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.64    2.48    0.16 2.00e-01 2.50e+01 6.75e-01
  ... (remaining 1839 not shown)

  Planarity restraints: 1949
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CB  PHE A  63 "    0.023 2.00e-02 2.50e+03   2.21e-02 8.55e+00
        pdb=" CG  PHE A  63 "   -0.051 2.00e-02 2.50e+03
        pdb=" CD1 PHE A  63 "    0.011 2.00e-02 2.50e+03
        pdb=" CD2 PHE A  63 "    0.007 2.00e-02 2.50e+03
        pdb=" CE1 PHE A  63 "    0.001 2.00e-02 2.50e+03
        pdb=" CE2 PHE A  63 "    0.005 2.00e-02 2.50e+03
        pdb=" CZ  PHE A  63 "    0.003 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  ARG A 919 "    0.011 2.00e-02 2.50e+03   2.32e-02 5.36e+00
        pdb=" C   ARG A 919 "   -0.040 2.00e-02 2.50e+03
        pdb=" O   ARG A 919 "    0.015 2.00e-02 2.50e+03
        pdb=" N   GLY A 920 "    0.013 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   ILE A1124 "    0.036 5.00e-02 4.00e+02   5.45e-02 4.75e+00
        pdb=" N   PRO A1125 "   -0.094 5.00e-02 4.00e+02
        pdb=" CA  PRO A1125 "    0.027 5.00e-02 4.00e+02
        pdb=" CD  PRO A1125 "    0.031 5.00e-02 4.00e+02
  ... (remaining 1946 not shown)

  Histogram of nonbonded interaction distances:
        2.15 -     2.70: 346
        2.70 -     3.25: 12090
        3.25 -     3.80: 18368
        3.80 -     4.35: 22873
        4.35 -     4.90: 38974
  Nonbonded interactions: 92651
  Sorted by model distance:
  nonbonded pdb=" N   VAL A 958 "
            pdb=" OE1 GLU A1259 "
     model   vdw
     2.149 3.120
  nonbonded pdb=" OG  SER A1049 "
            pdb=" OD1 ASP A1088 "
     model   vdw
     2.206 3.040
  nonbonded pdb=" NE2 GLN A 661 "
            pdb=" OD1 ASP A 825 "
     model   vdw
     2.208 3.120
  nonbonded pdb=" O   THR A1317 "
            pdb=" OH  TYR A1511 "
     model   vdw
     2.225 3.040
  nonbonded pdb=" OD1 ASN A 405 "
            pdb=" NH2 ARG A 408 "
     model   vdw
     2.249 3.120
  ... (remaining 92646 not shown)

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

  No NCS relation were found !!!

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

Found NCS groups:
  found none.
Set up NCS constraints
  No NCS constraints will be used in refinement.
Set refine NCS operators
Adjust number of macro_cycles
  Number of macro_cycles: 10
Reset NCS operators
Extract rigid body selections
Check and reset occupancies
  Occupancies: min=1.00 max=1.00 mean=1.00
Load rotamer database and sin/cos tables
Set ADP refinement strategy
  ADPs will be refined as individual isotropic
Make a string to write initial .geo file
Internal consistency checks
Time:
  Set random seed:                         0.000
  Set model cs if undefined:               0.000
  Decide on map wrapping:                  0.000
  Normalize map: mean=0, sd=1:             5.220
  Set stop_for_unknowns flag:              0.000
  Assert model is a single copy model:     0.000
  Assert all atoms have isotropic ADPs:    0.000
  Construct map_model_manager:             0.010
  Extract box with map and model:          0.270
  Check model and map are aligned:         0.040
  Set scattering table:                    0.030
  Process input model:                     11.870
  Find NCS groups from input model:        0.050
  Set up NCS constraints:                  0.020
  Set refine NCS operators:                0.000
  Adjust number of macro_cycles:           0.000
  Reset NCS operators:                     0.000
  Extract rigid body selections:           0.000
  Check and reset occupancies:             0.000
  Load rotamer database and sin/cos tables:1.360
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   18.870
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8051
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      :  0.009   0.088  11611  Z= 0.367
  Angle     :  0.806   9.084  15740  Z= 0.437
  Chirality :  0.050   0.190   1842
  Planarity :  0.005   0.054   1949
  Dihedral  : 14.581  88.798   4226
  Min Nonbonded Distance : 2.149

Molprobity Statistics.
  All-atom Clashscore : 9.58
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.18 %
    Favored  : 93.82 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  0.47 %
    Favored  : 99.53 %
  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: -0.39 (0.22), residues: 1424
  helix:  0.51 (0.17), residues: 924
  sheet: -1.24 (0.65), residues: 66
  loop : -1.66 (0.29), residues: 434

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.010   0.001   ARG A 811 
 TYR   0.032   0.002   TYR A  48 
 PHE   0.051   0.003   PHE A  63 
 TRP   0.025   0.002   TRP A  45 
 HIS   0.007   0.001   HIS A1367 

Details of bonding type rmsd
  covalent geometry    : bond        0.00922 (11610)
  covalent geometry    : angle       0.80606 (15738)
  SS BOND              : bond        0.00183 (    1)
  SS BOND              : angle       0.39313 (    2)
  hydrogen bonds       : bond        0.13735 (  734)
  hydrogen bonds       : angle       5.86255 ( 2151)

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

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

  2848 Ramachandran restraints generated.
    1424 Oldfield, 0 Emsley, 1424 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2848 Ramachandran restraints generated.
    1424 Oldfield, 0 Emsley, 1424 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  127 residues out of total 1268 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 127
  time to evaluate  : 0.452 
Fit side-chains
REVERT: A   52 ARG cc_start: 0.7498 (ptp-170) cc_final: 0.7184 (ptp-170)
REVERT: A  763 GLN cc_start: 0.7642 (mt0) cc_final: 0.7429 (tt0)
REVERT: A  806 LEU cc_start: 0.7692 (mp) cc_final: 0.7168 (mp)
REVERT: A  811 ARG cc_start: 0.7097 (ptt180) cc_final: 0.6716 (ptt180)
REVERT: A 1280 TRP cc_start: 0.8122 (m-10) cc_final: 0.7724 (m-10)
  outliers start: 0
  outliers final: 0
  residues processed: 127
  average time/residue: 0.1018
  time to fit residues: 18.6758
Evaluate side-chains
  107 residues out of total 1268 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 107
  time to evaluate  : 0.412 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 143
   random chunks:
   chunk 98 optimal weight:    0.5980
   chunk 107 optimal weight:    2.9990
   chunk 10 optimal weight:    3.9990
   chunk 66 optimal weight:    3.9990
   chunk 130 optimal weight:   10.0000
   chunk 124 optimal weight:    0.5980
   chunk 103 optimal weight:    0.6980
   chunk 77 optimal weight:    3.9990
   chunk 122 optimal weight:    5.9990
   chunk 91 optimal weight:    1.9990
   chunk 55 optimal weight:    0.5980
   overall best weight:    0.8982

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

Flipped N/Q/H residues before XYZ refinement:
A  28 GLN
A 145 GLN
** A 418 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 993 ASN
A1059 ASN
** A1367 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4155 r_free = 0.4155 target = 0.194536 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 68)----------------|
| r_work = 0.3303 r_free = 0.3303 target = 0.113197 restraints weight = 12492.815|
|-----------------------------------------------------------------------------|
r_work (start): 0.3081 rms_B_bonded: 2.13
r_work: 0.2942 rms_B_bonded: 2.62 restraints_weight: 0.5000
r_work: 0.2796 rms_B_bonded: 4.03 restraints_weight: 0.2500
r_work (final): 0.2796
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7581
moved from start:          0.1107

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.052  11611  Z= 0.155
  Angle     :  0.578   8.173  15740  Z= 0.302
  Chirality :  0.042   0.149   1842
  Planarity :  0.004   0.045   1949
  Dihedral  :  4.327  22.745   1541
  Min Nonbonded Distance : 2.475

Molprobity Statistics.
  All-atom Clashscore : 7.24
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.49 %
    Favored  : 95.51 %
  Rotamer:
    Outliers :  0.79 %
    Allowed  :  7.73 %
    Favored  : 91.48 %
  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:  0.45 (0.23), residues: 1424
  helix:  1.26 (0.17), residues: 944
  sheet: -0.99 (0.63), residues: 67
  loop : -1.72 (0.29), residues: 413

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.000   ARG A 811 
 TYR   0.020   0.001   TYR A  48 
 PHE   0.025   0.002   PHE A1236 
 TRP   0.015   0.001   TRP A1202 
 HIS   0.004   0.001   HIS A 794 

Details of bonding type rmsd
  covalent geometry    : bond        0.00366 (11610)
  covalent geometry    : angle       0.57833 (15738)
  SS BOND              : bond        0.00203 (    1)
  SS BOND              : angle       0.89161 (    2)
  hydrogen bonds       : bond        0.05287 (  734)
  hydrogen bonds       : angle       4.33847 ( 2151)

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

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

  2848 Ramachandran restraints generated.
    1424 Oldfield, 0 Emsley, 1424 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2848 Ramachandran restraints generated.
    1424 Oldfield, 0 Emsley, 1424 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  132 residues out of total 1268 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 122
  time to evaluate  : 0.389 
Fit side-chains
REVERT: A    1 MET cc_start: 0.6486 (mmm) cc_final: 0.5102 (ppp)
REVERT: A   52 ARG cc_start: 0.6914 (ptp-170) cc_final: 0.6583 (ptp-170)
REVERT: A  203 ILE cc_start: 0.8053 (mm) cc_final: 0.7219 (pt)
REVERT: A  500 GLU cc_start: 0.7141 (tp30) cc_final: 0.6619 (pt0)
REVERT: A  634 LYS cc_start: 0.6359 (OUTLIER) cc_final: 0.6120 (ttpp)
  outliers start: 10
  outliers final: 3
  residues processed: 126
  average time/residue: 0.0940
  time to fit residues: 17.4239
Evaluate side-chains
  112 residues out of total 1268 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 4
    poor density    : 108
  time to evaluate  : 0.308 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  209 ASP
Chi-restraints excluded: chain A residue  245 MET
Chi-restraints excluded: chain A residue  634 LYS
Chi-restraints excluded: chain A residue 1369 LEU
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 143
   random chunks:
   chunk 20 optimal weight:    0.7980
   chunk 78 optimal weight:    2.9990
   chunk 66 optimal weight:    4.9990
   chunk 81 optimal weight:   20.0000
   chunk 109 optimal weight:    0.9990
   chunk 107 optimal weight:    0.9980
   chunk 34 optimal weight:    1.9990
   chunk 135 optimal weight:   10.0000
   chunk 29 optimal weight:    0.7980
   chunk 106 optimal weight:    1.9990
   chunk 115 optimal weight:    1.9990
   overall best weight:    1.1184

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

Flipped N/Q/H residues before XYZ refinement:
A  28 GLN
A 986 ASN
** A1367 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4154 r_free = 0.4154 target = 0.194666 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 34)----------------|
| r_work = 0.3479 r_free = 0.3479 target = 0.125679 restraints weight = 12589.049|
|-----------------------------------------------------------------------------|
r_work (start): 0.3271 rms_B_bonded: 2.27
r_work: 0.2969 rms_B_bonded: 2.64 restraints_weight: 0.5000
r_work: 0.2824 rms_B_bonded: 4.06 restraints_weight: 0.2500
r_work (final): 0.2824
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7679
moved from start:          0.1405

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.043  11611  Z= 0.164
  Angle     :  0.555   8.125  15740  Z= 0.288
  Chirality :  0.041   0.142   1842
  Planarity :  0.004   0.045   1949
  Dihedral  :  4.107  20.585   1541
  Min Nonbonded Distance : 2.525

Molprobity Statistics.
  All-atom Clashscore : 6.55
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.63 %
    Favored  : 95.37 %
  Rotamer:
    Outliers :  1.58 %
    Allowed  : 11.67 %
    Favored  : 86.75 %
  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:  0.85 (0.23), residues: 1424
  helix:  1.57 (0.17), residues: 936
  sheet: -0.66 (0.63), residues: 67
  loop : -1.56 (0.29), residues: 421

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARG A 811 
 TYR   0.017   0.001   TYR A  48 
 PHE   0.022   0.002   PHE A1236 
 TRP   0.014   0.001   TRP A1202 
 HIS   0.004   0.001   HIS A1367 

Details of bonding type rmsd
  covalent geometry    : bond        0.00398 (11610)
  covalent geometry    : angle       0.55522 (15738)
  SS BOND              : bond        0.00105 (    1)
  SS BOND              : angle       0.51143 (    2)
  hydrogen bonds       : bond        0.05102 (  734)
  hydrogen bonds       : angle       4.08526 ( 2151)

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

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

  2848 Ramachandran restraints generated.
    1424 Oldfield, 0 Emsley, 1424 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2848 Ramachandran restraints generated.
    1424 Oldfield, 0 Emsley, 1424 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  136 residues out of total 1268 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 20
    poor density    : 116
  time to evaluate  : 0.384 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A    1 MET cc_start: 0.6510 (mmm) cc_final: 0.5253 (ppp)
REVERT: A   52 ARG cc_start: 0.6954 (ptp-170) cc_final: 0.6663 (ptp-170)
REVERT: A  137 LEU cc_start: 0.7260 (OUTLIER) cc_final: 0.7031 (mp)
REVERT: A  203 ILE cc_start: 0.8108 (mm) cc_final: 0.7286 (pt)
REVERT: A  300 ASP cc_start: 0.8421 (OUTLIER) cc_final: 0.8114 (t0)
REVERT: A  500 GLU cc_start: 0.7225 (tp30) cc_final: 0.6684 (tp30)
REVERT: A  634 LYS cc_start: 0.6407 (OUTLIER) cc_final: 0.6159 (ttpp)
REVERT: A  688 HIS cc_start: 0.7082 (t70) cc_final: 0.6558 (t70)
REVERT: A  763 GLN cc_start: 0.7570 (mm-40) cc_final: 0.7033 (tt0)
  outliers start: 20
  outliers final: 10
  residues processed: 131
  average time/residue: 0.1013
  time to fit residues: 19.1003
Evaluate side-chains
  121 residues out of total 1268 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 108
  time to evaluate  : 0.344 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   74 LEU
Chi-restraints excluded: chain A residue  107 LEU
Chi-restraints excluded: chain A residue  111 LEU
Chi-restraints excluded: chain A residue  137 LEU
Chi-restraints excluded: chain A residue  239 SER
Chi-restraints excluded: chain A residue  245 MET
Chi-restraints excluded: chain A residue  300 ASP
Chi-restraints excluded: chain A residue  459 ILE
Chi-restraints excluded: chain A residue  634 LYS
Chi-restraints excluded: chain A residue  993 ASN
Chi-restraints excluded: chain A residue 1282 THR
Chi-restraints excluded: chain A residue 1375 ILE
Chi-restraints excluded: chain A residue 1439 GLN
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 143
   random chunks:
   chunk 56 optimal weight:    1.9990
   chunk 93 optimal weight:    0.7980
   chunk 11 optimal weight:    0.8980
   chunk 88 optimal weight:    0.5980
   chunk 132 optimal weight:    3.9990
   chunk 138 optimal weight:    0.9980
   chunk 66 optimal weight:    1.9990
   chunk 45 optimal weight:    3.9990
   chunk 106 optimal weight:    2.9990
   chunk 55 optimal weight:    0.6980
   chunk 85 optimal weight:    0.0770
   overall best weight:    0.6138

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

Flipped N/Q/H residues before XYZ refinement:
A 328 HIS
A 986 ASN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4180 r_free = 0.4180 target = 0.197509 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 68)----------------|
| r_work = 0.3342 r_free = 0.3342 target = 0.116328 restraints weight = 12582.238|
|-----------------------------------------------------------------------------|
r_work (start): 0.3099 rms_B_bonded: 2.15
r_work: 0.2963 rms_B_bonded: 2.62 restraints_weight: 0.5000
r_work: 0.2818 rms_B_bonded: 4.04 restraints_weight: 0.2500
r_work (final): 0.2818
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7510
moved from start:          0.1838

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.029  11611  Z= 0.120
  Angle     :  0.508   8.062  15740  Z= 0.263
  Chirality :  0.040   0.139   1842
  Planarity :  0.003   0.044   1949
  Dihedral  :  3.859  22.318   1541
  Min Nonbonded Distance : 2.546

Molprobity Statistics.
  All-atom Clashscore : 5.81
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.49 %
    Favored  : 95.51 %
  Rotamer:
    Outliers :  2.05 %
    Allowed  : 13.64 %
    Favored  : 84.31 %
  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:  1.25 (0.23), residues: 1424
  helix:  1.91 (0.17), residues: 940
  sheet: -0.33 (0.64), residues: 67
  loop : -1.55 (0.29), residues: 417

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.000   ARG A1304 
 TYR   0.012   0.001   TYR A  48 
 PHE   0.017   0.001   PHE A1236 
 TRP   0.013   0.001   TRP A1202 
 HIS   0.002   0.001   HIS A 688 

Details of bonding type rmsd
  covalent geometry    : bond        0.00269 (11610)
  covalent geometry    : angle       0.50752 (15738)
  SS BOND              : bond        0.00110 (    1)
  SS BOND              : angle       0.51997 (    2)
  hydrogen bonds       : bond        0.04388 (  734)
  hydrogen bonds       : angle       3.81605 ( 2151)

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

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

  2848 Ramachandran restraints generated.
    1424 Oldfield, 0 Emsley, 1424 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2848 Ramachandran restraints generated.
    1424 Oldfield, 0 Emsley, 1424 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  147 residues out of total 1268 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 26
    poor density    : 121
  time to evaluate  : 0.438 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A    1 MET cc_start: 0.6462 (mmm) cc_final: 0.5379 (ppp)
REVERT: A  203 ILE cc_start: 0.8035 (mm) cc_final: 0.7223 (pt)
REVERT: A  300 ASP cc_start: 0.8365 (OUTLIER) cc_final: 0.8095 (t0)
REVERT: A  500 GLU cc_start: 0.7158 (tp30) cc_final: 0.6752 (tp30)
REVERT: A  634 LYS cc_start: 0.6335 (OUTLIER) cc_final: 0.6110 (ttpp)
REVERT: A  688 HIS cc_start: 0.7158 (t70) cc_final: 0.6723 (t70)
REVERT: A 1276 ASN cc_start: 0.8735 (m-40) cc_final: 0.8488 (m-40)
REVERT: A 1280 TRP cc_start: 0.7760 (m-10) cc_final: 0.7506 (m-10)
  outliers start: 26
  outliers final: 15
  residues processed: 139
  average time/residue: 0.0864
  time to fit residues: 17.7132
Evaluate side-chains
  125 residues out of total 1268 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 17
    poor density    : 108
  time to evaluate  : 0.257 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   63 PHE
Chi-restraints excluded: chain A residue   74 LEU
Chi-restraints excluded: chain A residue  111 LEU
Chi-restraints excluded: chain A residue  212 VAL
Chi-restraints excluded: chain A residue  239 SER
Chi-restraints excluded: chain A residue  300 ASP
Chi-restraints excluded: chain A residue  459 ILE
Chi-restraints excluded: chain A residue  634 LYS
Chi-restraints excluded: chain A residue  811 ARG
Chi-restraints excluded: chain A residue  986 ASN
Chi-restraints excluded: chain A residue  993 ASN
Chi-restraints excluded: chain A residue 1282 THR
Chi-restraints excluded: chain A residue 1293 HIS
Chi-restraints excluded: chain A residue 1361 VAL
Chi-restraints excluded: chain A residue 1369 LEU
Chi-restraints excluded: chain A residue 1375 ILE
Chi-restraints excluded: chain A residue 1439 GLN
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 143
   random chunks:
   chunk 9 optimal weight:    5.9990
   chunk 79 optimal weight:   10.0000
   chunk 68 optimal weight:    0.9980
   chunk 78 optimal weight:    0.0270
   chunk 66 optimal weight:    3.9990
   chunk 64 optimal weight:    1.9990
   chunk 127 optimal weight:    8.9990
   chunk 4 optimal weight:    0.8980
   chunk 50 optimal weight:    0.9990
   chunk 74 optimal weight:    0.8980
   chunk 49 optimal weight:    0.9980
   overall best weight:    0.7638

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

Flipped N/Q/H residues before XYZ refinement:
A 986 ASN
A1341 ASN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4182 r_free = 0.4182 target = 0.196680 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 56)----------------|
| r_work = 0.3348 r_free = 0.3348 target = 0.116081 restraints weight = 12555.358|
|-----------------------------------------------------------------------------|
r_work (start): 0.3120 rms_B_bonded: 2.16
r_work: 0.2985 rms_B_bonded: 2.63 restraints_weight: 0.5000
r_work: 0.2840 rms_B_bonded: 4.05 restraints_weight: 0.2500
r_work (final): 0.2840
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7591
moved from start:          0.1907

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.037  11611  Z= 0.131
  Angle     :  0.511   8.525  15740  Z= 0.263
  Chirality :  0.040   0.137   1842
  Planarity :  0.003   0.045   1949
  Dihedral  :  3.795  20.530   1541
  Min Nonbonded Distance : 2.560

Molprobity Statistics.
  All-atom Clashscore : 5.64
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.28 %
    Favored  : 95.72 %
  Rotamer:
    Outliers :  1.89 %
    Allowed  : 14.67 %
    Favored  : 83.44 %
  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:  1.42 (0.23), residues: 1424
  helix:  2.01 (0.17), residues: 941
  sheet: -0.05 (0.66), residues: 67
  loop : -1.45 (0.30), residues: 416

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG A1304 
 TYR   0.013   0.001   TYR A  48 
 PHE   0.017   0.001   PHE A1236 
 TRP   0.012   0.001   TRP A1202 
 HIS   0.003   0.001   HIS A1053 

Details of bonding type rmsd
  covalent geometry    : bond        0.00305 (11610)
  covalent geometry    : angle       0.51089 (15738)
  SS BOND              : bond        0.00120 (    1)
  SS BOND              : angle       0.49316 (    2)
  hydrogen bonds       : bond        0.04486 (  734)
  hydrogen bonds       : angle       3.78063 ( 2151)

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

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

  2848 Ramachandran restraints generated.
    1424 Oldfield, 0 Emsley, 1424 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2848 Ramachandran restraints generated.
    1424 Oldfield, 0 Emsley, 1424 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  137 residues out of total 1268 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 24
    poor density    : 113
  time to evaluate  : 0.322 
Fit side-chains
   revert: symmetry clash
REVERT: A    1 MET cc_start: 0.6499 (mmm) cc_final: 0.5481 (ppp)
REVERT: A   63 PHE cc_start: 0.7200 (OUTLIER) cc_final: 0.6080 (t80)
REVERT: A  203 ILE cc_start: 0.8071 (mm) cc_final: 0.7238 (pt)
REVERT: A  300 ASP cc_start: 0.8359 (OUTLIER) cc_final: 0.8112 (t0)
REVERT: A  500 GLU cc_start: 0.7239 (tp30) cc_final: 0.6766 (tp30)
REVERT: A  634 LYS cc_start: 0.6415 (OUTLIER) cc_final: 0.6187 (ttpp)
REVERT: A  688 HIS cc_start: 0.7192 (t70) cc_final: 0.6750 (t70)
REVERT: A  763 GLN cc_start: 0.7528 (mm-40) cc_final: 0.7130 (tt0)
REVERT: A 1276 ASN cc_start: 0.8768 (m-40) cc_final: 0.8513 (m-40)
REVERT: A 1280 TRP cc_start: 0.7660 (m-10) cc_final: 0.7455 (m-10)
  outliers start: 24
  outliers final: 17
  residues processed: 130
  average time/residue: 0.0853
  time to fit residues: 16.8221
Evaluate side-chains
  129 residues out of total 1268 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 20
    poor density    : 109
  time to evaluate  : 0.289 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   63 PHE
Chi-restraints excluded: chain A residue   74 LEU
Chi-restraints excluded: chain A residue   84 LEU
Chi-restraints excluded: chain A residue  111 LEU
Chi-restraints excluded: chain A residue  137 LEU
Chi-restraints excluded: chain A residue  212 VAL
Chi-restraints excluded: chain A residue  239 SER
Chi-restraints excluded: chain A residue  300 ASP
Chi-restraints excluded: chain A residue  459 ILE
Chi-restraints excluded: chain A residue  634 LYS
Chi-restraints excluded: chain A residue  811 ARG
Chi-restraints excluded: chain A residue  993 ASN
Chi-restraints excluded: chain A residue 1282 THR
Chi-restraints excluded: chain A residue 1293 HIS
Chi-restraints excluded: chain A residue 1339 LEU
Chi-restraints excluded: chain A residue 1341 ASN
Chi-restraints excluded: chain A residue 1361 VAL
Chi-restraints excluded: chain A residue 1369 LEU
Chi-restraints excluded: chain A residue 1375 ILE
Chi-restraints excluded: chain A residue 1439 GLN
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 143
   random chunks:
   chunk 22 optimal weight:    3.9990
   chunk 13 optimal weight:    0.6980
   chunk 116 optimal weight:    0.8980
   chunk 52 optimal weight:    0.1980
   chunk 130 optimal weight:    1.9990
   chunk 36 optimal weight:    0.7980
   chunk 42 optimal weight:    0.5980
   chunk 10 optimal weight:    0.7980
   chunk 106 optimal weight:    0.9990
   chunk 3 optimal weight:    1.9990
   chunk 0 optimal weight:   10.0000
   overall best weight:    0.6180

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

Flipped N/Q/H residues before XYZ refinement:
A 986 ASN
A1185 GLN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4191 r_free = 0.4191 target = 0.197434 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 72)----------------|
| r_work = 0.3372 r_free = 0.3372 target = 0.117685 restraints weight = 12519.415|
|-----------------------------------------------------------------------------|
r_work (start): 0.3145 rms_B_bonded: 2.09
r_work: 0.3012 rms_B_bonded: 2.55 restraints_weight: 0.5000
r_work: 0.2867 rms_B_bonded: 3.96 restraints_weight: 0.2500
r_work (final): 0.2867
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7501
moved from start:          0.2071

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.032  11611  Z= 0.120
  Angle     :  0.497   8.706  15740  Z= 0.256
  Chirality :  0.040   0.137   1842
  Planarity :  0.003   0.045   1949
  Dihedral  :  3.720  21.338   1541
  Min Nonbonded Distance : 2.569

Molprobity Statistics.
  All-atom Clashscore : 5.81
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.14 %
    Favored  : 95.86 %
  Rotamer:
    Outliers :  2.13 %
    Allowed  : 15.54 %
    Favored  : 82.33 %
  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:  1.60 (0.23), residues: 1424
  helix:  2.17 (0.17), residues: 940
  sheet: -0.08 (0.65), residues: 67
  loop : -1.41 (0.30), residues: 417

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARG A1304 
 TYR   0.013   0.001   TYR A  48 
 PHE   0.015   0.001   PHE A1236 
 TRP   0.012   0.001   TRP A1202 
 HIS   0.003   0.001   HIS A 688 

Details of bonding type rmsd
  covalent geometry    : bond        0.00271 (11610)
  covalent geometry    : angle       0.49738 (15738)
  SS BOND              : bond        0.00126 (    1)
  SS BOND              : angle       0.48541 (    2)
  hydrogen bonds       : bond        0.04317 (  734)
  hydrogen bonds       : angle       3.68673 ( 2151)

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

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

  2848 Ramachandran restraints generated.
    1424 Oldfield, 0 Emsley, 1424 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2848 Ramachandran restraints generated.
    1424 Oldfield, 0 Emsley, 1424 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  147 residues out of total 1268 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 27
    poor density    : 120
  time to evaluate  : 0.333 
Fit side-chains
   revert: symmetry clash
REVERT: A    1 MET cc_start: 0.6445 (mmm) cc_final: 0.5514 (ppp)
REVERT: A   63 PHE cc_start: 0.7121 (OUTLIER) cc_final: 0.6074 (t80)
REVERT: A  203 ILE cc_start: 0.8011 (mm) cc_final: 0.7178 (pt)
REVERT: A  300 ASP cc_start: 0.8343 (OUTLIER) cc_final: 0.8103 (t0)
REVERT: A  500 GLU cc_start: 0.7149 (tp30) cc_final: 0.6706 (tp30)
REVERT: A  763 GLN cc_start: 0.7482 (mm-40) cc_final: 0.7053 (tt0)
REVERT: A  826 GLU cc_start: 0.6740 (tm-30) cc_final: 0.6406 (tm-30)
REVERT: A 1276 ASN cc_start: 0.8745 (m-40) cc_final: 0.8495 (m-40)
REVERT: A 1280 TRP cc_start: 0.7620 (m-10) cc_final: 0.7384 (m-10)
REVERT: A 1501 MET cc_start: 0.4868 (mmp) cc_final: 0.3438 (ttt)
  outliers start: 27
  outliers final: 15
  residues processed: 140
  average time/residue: 0.0942
  time to fit residues: 19.9884
Evaluate side-chains
  131 residues out of total 1268 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 17
    poor density    : 114
  time to evaluate  : 0.445 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   63 PHE
Chi-restraints excluded: chain A residue   74 LEU
Chi-restraints excluded: chain A residue   84 LEU
Chi-restraints excluded: chain A residue  111 LEU
Chi-restraints excluded: chain A residue  137 LEU
Chi-restraints excluded: chain A residue  212 VAL
Chi-restraints excluded: chain A residue  239 SER
Chi-restraints excluded: chain A residue  300 ASP
Chi-restraints excluded: chain A residue  370 GLN
Chi-restraints excluded: chain A residue  459 ILE
Chi-restraints excluded: chain A residue  986 ASN
Chi-restraints excluded: chain A residue  993 ASN
Chi-restraints excluded: chain A residue 1282 THR
Chi-restraints excluded: chain A residue 1293 HIS
Chi-restraints excluded: chain A residue 1361 VAL
Chi-restraints excluded: chain A residue 1375 ILE
Chi-restraints excluded: chain A residue 1439 GLN
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 143
   random chunks:
   chunk 6 optimal weight:    0.6980
   chunk 98 optimal weight:    1.9990
   chunk 106 optimal weight:    0.3980
   chunk 9 optimal weight:    8.9990
   chunk 5 optimal weight:    6.9990
   chunk 123 optimal weight:    8.9990
   chunk 140 optimal weight:    7.9990
   chunk 110 optimal weight:    0.9990
   chunk 130 optimal weight:    2.9990
   chunk 132 optimal weight:   10.0000
   chunk 82 optimal weight:    8.9990
   overall best weight:    1.4186

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

Flipped N/Q/H residues before XYZ refinement:
A 688 HIS
A 986 ASN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4158 r_free = 0.4158 target = 0.193876 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 34)----------------|
| r_work = 0.3498 r_free = 0.3498 target = 0.125401 restraints weight = 12591.035|
|-----------------------------------------------------------------------------|
r_work (start): 0.3397 rms_B_bonded: 2.20
r_work: 0.3113 rms_B_bonded: 2.68 restraints_weight: 0.5000
r_work: 0.2968 rms_B_bonded: 4.15 restraints_weight: 0.2500
r_work (final): 0.2968
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7905
moved from start:          0.1871

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.054  11611  Z= 0.187
  Angle     :  0.556   9.295  15740  Z= 0.285
  Chirality :  0.042   0.135   1842
  Planarity :  0.004   0.044   1949
  Dihedral  :  3.867  20.029   1541
  Min Nonbonded Distance : 2.555

Molprobity Statistics.
  All-atom Clashscore : 6.24
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.35 %
    Favored  : 95.65 %
  Rotamer:
    Outliers :  1.97 %
    Allowed  : 16.64 %
    Favored  : 81.39 %
  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:  1.38 (0.23), residues: 1424
  helix:  1.93 (0.17), residues: 942
  sheet: -0.02 (0.67), residues: 67
  loop : -1.35 (0.30), residues: 415

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.000   ARG A1304 
 TYR   0.021   0.001   TYR A  48 
 PHE   0.023   0.002   PHE A1236 
 TRP   0.011   0.001   TRP A1202 
 HIS   0.003   0.001   HIS A 688 

Details of bonding type rmsd
  covalent geometry    : bond        0.00464 (11610)
  covalent geometry    : angle       0.55594 (15738)
  SS BOND              : bond        0.00136 (    1)
  SS BOND              : angle       0.48086 (    2)
  hydrogen bonds       : bond        0.05115 (  734)
  hydrogen bonds       : angle       3.86340 ( 2151)

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

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

  2848 Ramachandran restraints generated.
    1424 Oldfield, 0 Emsley, 1424 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2848 Ramachandran restraints generated.
    1424 Oldfield, 0 Emsley, 1424 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  137 residues out of total 1268 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 25
    poor density    : 112
  time to evaluate  : 0.415 
Fit side-chains
   revert: symmetry clash
REVERT: A   63 PHE cc_start: 0.7591 (OUTLIER) cc_final: 0.6578 (t80)
REVERT: A   74 LEU cc_start: 0.7217 (OUTLIER) cc_final: 0.6890 (mt)
REVERT: A  203 ILE cc_start: 0.8230 (mm) cc_final: 0.7386 (pt)
REVERT: A  300 ASP cc_start: 0.8380 (OUTLIER) cc_final: 0.8150 (t0)
REVERT: A  500 GLU cc_start: 0.7471 (tp30) cc_final: 0.7038 (tp30)
REVERT: A  688 HIS cc_start: 0.7286 (t-90) cc_final: 0.6920 (t70)
REVERT: A  763 GLN cc_start: 0.7747 (mm-40) cc_final: 0.7294 (tt0)
REVERT: A 1280 TRP cc_start: 0.7915 (m-10) cc_final: 0.7532 (m-10)
REVERT: A 1501 MET cc_start: 0.5034 (mmp) cc_final: 0.3637 (ttt)
  outliers start: 25
  outliers final: 16
  residues processed: 128
  average time/residue: 0.0832
  time to fit residues: 15.8464
Evaluate side-chains
  129 residues out of total 1268 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 19
    poor density    : 110
  time to evaluate  : 0.259 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   63 PHE
Chi-restraints excluded: chain A residue   74 LEU
Chi-restraints excluded: chain A residue   84 LEU
Chi-restraints excluded: chain A residue  111 LEU
Chi-restraints excluded: chain A residue  212 VAL
Chi-restraints excluded: chain A residue  239 SER
Chi-restraints excluded: chain A residue  245 MET
Chi-restraints excluded: chain A residue  300 ASP
Chi-restraints excluded: chain A residue  370 GLN
Chi-restraints excluded: chain A residue  459 ILE
Chi-restraints excluded: chain A residue  811 ARG
Chi-restraints excluded: chain A residue  986 ASN
Chi-restraints excluded: chain A residue 1232 ASP
Chi-restraints excluded: chain A residue 1282 THR
Chi-restraints excluded: chain A residue 1293 HIS
Chi-restraints excluded: chain A residue 1339 LEU
Chi-restraints excluded: chain A residue 1361 VAL
Chi-restraints excluded: chain A residue 1375 ILE
Chi-restraints excluded: chain A residue 1439 GLN
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 143
   random chunks:
   chunk 15 optimal weight:    0.9980
   chunk 96 optimal weight:    0.6980
   chunk 39 optimal weight:    1.9990
   chunk 17 optimal weight:    1.9990
   chunk 109 optimal weight:    0.6980
   chunk 44 optimal weight:    0.6980
   chunk 57 optimal weight:    0.9980
   chunk 60 optimal weight:    5.9990
   chunk 125 optimal weight:   10.0000
   chunk 88 optimal weight:    0.5980
   chunk 54 optimal weight:    0.7980
   overall best weight:    0.6980

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

Flipped N/Q/H residues before XYZ refinement:
A 986 ASN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4184 r_free = 0.4184 target = 0.196827 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 36)----------------|
| r_work = 0.3494 r_free = 0.3494 target = 0.126522 restraints weight = 12641.577|
|-----------------------------------------------------------------------------|
r_work (start): 0.3360 rms_B_bonded: 2.89
r_work: 0.3071 rms_B_bonded: 2.83 restraints_weight: 0.5000
r_work: 0.2924 rms_B_bonded: 4.37 restraints_weight: 0.2500
r_work (final): 0.2924
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7709
moved from start:          0.2122

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.040  11611  Z= 0.127
  Angle     :  0.515   8.817  15740  Z= 0.263
  Chirality :  0.040   0.144   1842
  Planarity :  0.003   0.043   1949
  Dihedral  :  3.727  21.484   1541
  Min Nonbonded Distance : 2.565

Molprobity Statistics.
  All-atom Clashscore : 5.85
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.21 %
    Favored  : 95.79 %
  Rotamer:
    Outliers :  1.50 %
    Allowed  : 17.27 %
    Favored  : 81.23 %
  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:  1.66 (0.23), residues: 1424
  helix:  2.18 (0.17), residues: 939
  sheet: -0.01 (0.66), residues: 67
  loop : -1.29 (0.30), residues: 418

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.006   0.000   ARG A1304 
 TYR   0.018   0.001   TYR A  48 
 PHE   0.016   0.001   PHE A 813 
 TRP   0.014   0.001   TRP A1202 
 HIS   0.002   0.001   HIS A1053 

Details of bonding type rmsd
  covalent geometry    : bond        0.00293 (11610)
  covalent geometry    : angle       0.51465 (15738)
  SS BOND              : bond        0.00138 (    1)
  SS BOND              : angle       0.51166 (    2)
  hydrogen bonds       : bond        0.04453 (  734)
  hydrogen bonds       : angle       3.69255 ( 2151)

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

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

  2848 Ramachandran restraints generated.
    1424 Oldfield, 0 Emsley, 1424 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2848 Ramachandran restraints generated.
    1424 Oldfield, 0 Emsley, 1424 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  131 residues out of total 1268 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 19
    poor density    : 112
  time to evaluate  : 0.455 
Fit side-chains
   revert: symmetry clash
REVERT: A   63 PHE cc_start: 0.7356 (OUTLIER) cc_final: 0.6280 (t80)
REVERT: A  203 ILE cc_start: 0.8130 (mm) cc_final: 0.7324 (pt)
REVERT: A  500 GLU cc_start: 0.7337 (tp30) cc_final: 0.6878 (tp30)
REVERT: A  634 LYS cc_start: 0.6533 (OUTLIER) cc_final: 0.6257 (ttpp)
REVERT: A  680 MET cc_start: 0.8105 (ttm) cc_final: 0.7788 (ttm)
REVERT: A  688 HIS cc_start: 0.7393 (t-90) cc_final: 0.7087 (t70)
REVERT: A  763 GLN cc_start: 0.7585 (mm-40) cc_final: 0.7162 (tt0)
REVERT: A 1276 ASN cc_start: 0.8827 (m-40) cc_final: 0.8582 (m-40)
REVERT: A 1280 TRP cc_start: 0.7761 (m-10) cc_final: 0.7405 (m-10)
REVERT: A 1501 MET cc_start: 0.4946 (mmp) cc_final: 0.3521 (ttt)
  outliers start: 19
  outliers final: 12
  residues processed: 125
  average time/residue: 0.1045
  time to fit residues: 19.4219
Evaluate side-chains
  120 residues out of total 1268 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 106
  time to evaluate  : 0.420 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   63 PHE
Chi-restraints excluded: chain A residue   74 LEU
Chi-restraints excluded: chain A residue   84 LEU
Chi-restraints excluded: chain A residue  111 LEU
Chi-restraints excluded: chain A residue  212 VAL
Chi-restraints excluded: chain A residue  239 SER
Chi-restraints excluded: chain A residue  370 GLN
Chi-restraints excluded: chain A residue  459 ILE
Chi-restraints excluded: chain A residue  634 LYS
Chi-restraints excluded: chain A residue 1282 THR
Chi-restraints excluded: chain A residue 1293 HIS
Chi-restraints excluded: chain A residue 1361 VAL
Chi-restraints excluded: chain A residue 1375 ILE
Chi-restraints excluded: chain A residue 1439 GLN
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 143
   random chunks:
   chunk 37 optimal weight:    2.9990
   chunk 126 optimal weight:    0.8980
   chunk 99 optimal weight:    0.9990
   chunk 67 optimal weight:    0.2980
   chunk 34 optimal weight:    0.9980
   chunk 128 optimal weight:    0.1980
   chunk 6 optimal weight:    0.7980
   chunk 81 optimal weight:    5.9990
   chunk 29 optimal weight:    0.9990
   chunk 47 optimal weight:    0.9990
   chunk 54 optimal weight:    0.7980
   overall best weight:    0.5980

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

Flipped N/Q/H residues before XYZ refinement:
A 986 ASN
** A1240 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4185 r_free = 0.4185 target = 0.196759 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 45)----------------|
| r_work = 0.3448 r_free = 0.3448 target = 0.123106 restraints weight = 12429.923|
|-----------------------------------------------------------------------------|
r_work (start): 0.3252 rms_B_bonded: 2.60
r_work: 0.2993 rms_B_bonded: 2.91 restraints_weight: 0.5000
r_work: 0.2848 rms_B_bonded: 4.50 restraints_weight: 0.2500
r_work (final): 0.2848
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7607
moved from start:          0.2272

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.037  11611  Z= 0.120
  Angle     :  0.516   8.996  15740  Z= 0.263
  Chirality :  0.039   0.138   1842
  Planarity :  0.003   0.042   1949
  Dihedral  :  3.643  20.318   1541
  Min Nonbonded Distance : 2.531

Molprobity Statistics.
  All-atom Clashscore : 5.59
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.00 %
    Favored  : 96.00 %
  Rotamer:
    Outliers :  1.50 %
    Allowed  : 17.27 %
    Favored  : 81.23 %
  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:  1.79 (0.23), residues: 1424
  helix:  2.29 (0.17), residues: 941
  sheet: -0.01 (0.67), residues: 67
  loop : -1.29 (0.30), residues: 416

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.007   0.000   ARG A1304 
 TYR   0.016   0.001   TYR A  48 
 PHE   0.014   0.001   PHE A1236 
 TRP   0.013   0.001   TRP A1202 
 HIS   0.003   0.001   HIS A1053 

Details of bonding type rmsd
  covalent geometry    : bond        0.00275 (11610)
  covalent geometry    : angle       0.51629 (15738)
  SS BOND              : bond        0.00133 (    1)
  SS BOND              : angle       0.47656 (    2)
  hydrogen bonds       : bond        0.04268 (  734)
  hydrogen bonds       : angle       3.63045 ( 2151)

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

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

  2848 Ramachandran restraints generated.
    1424 Oldfield, 0 Emsley, 1424 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2848 Ramachandran restraints generated.
    1424 Oldfield, 0 Emsley, 1424 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  133 residues out of total 1268 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 19
    poor density    : 114
  time to evaluate  : 0.423 
Fit side-chains
   revert: symmetry clash
REVERT: A   63 PHE cc_start: 0.7252 (OUTLIER) cc_final: 0.6248 (t80)
REVERT: A  203 ILE cc_start: 0.8084 (mm) cc_final: 0.7258 (pt)
REVERT: A  500 GLU cc_start: 0.7264 (tp30) cc_final: 0.6832 (tp30)
REVERT: A  631 LYS cc_start: 0.6384 (mmpt) cc_final: 0.6122 (mmtt)
REVERT: A  680 MET cc_start: 0.8180 (ttm) cc_final: 0.7885 (ttm)
REVERT: A  688 HIS cc_start: 0.7406 (OUTLIER) cc_final: 0.7076 (t70)
REVERT: A  763 GLN cc_start: 0.7581 (mm-40) cc_final: 0.7170 (tt0)
REVERT: A 1276 ASN cc_start: 0.8830 (m-40) cc_final: 0.8584 (m-40)
REVERT: A 1280 TRP cc_start: 0.7741 (m-10) cc_final: 0.7388 (m-10)
REVERT: A 1501 MET cc_start: 0.4950 (mmp) cc_final: 0.3527 (ttt)
  outliers start: 19
  outliers final: 13
  residues processed: 127
  average time/residue: 0.1031
  time to fit residues: 19.2909
Evaluate side-chains
  126 residues out of total 1268 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 15
    poor density    : 111
  time to evaluate  : 0.340 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   63 PHE
Chi-restraints excluded: chain A residue   74 LEU
Chi-restraints excluded: chain A residue   84 LEU
Chi-restraints excluded: chain A residue  111 LEU
Chi-restraints excluded: chain A residue  212 VAL
Chi-restraints excluded: chain A residue  239 SER
Chi-restraints excluded: chain A residue  370 GLN
Chi-restraints excluded: chain A residue  688 HIS
Chi-restraints excluded: chain A residue  811 ARG
Chi-restraints excluded: chain A residue 1232 ASP
Chi-restraints excluded: chain A residue 1282 THR
Chi-restraints excluded: chain A residue 1293 HIS
Chi-restraints excluded: chain A residue 1361 VAL
Chi-restraints excluded: chain A residue 1375 ILE
Chi-restraints excluded: chain A residue 1439 GLN
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 143
   random chunks:
   chunk 66 optimal weight:    6.9990
   chunk 77 optimal weight:    0.0050
   chunk 28 optimal weight:    0.7980
   chunk 8 optimal weight:    0.6980
   chunk 47 optimal weight:    0.9990
   chunk 121 optimal weight:    7.9990
   chunk 53 optimal weight:    0.9980
   chunk 93 optimal weight:    0.9980
   chunk 9 optimal weight:    0.3980
   chunk 103 optimal weight:    0.7980
   chunk 39 optimal weight:    2.9990
   overall best weight:    0.5394

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

Flipped N/Q/H residues before XYZ refinement:
A  28 GLN
A 986 ASN
** A1240 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4186 r_free = 0.4186 target = 0.197021 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 45)----------------|
| r_work = 0.3447 r_free = 0.3447 target = 0.123179 restraints weight = 12558.459|
|-----------------------------------------------------------------------------|
r_work (start): 0.3296 rms_B_bonded: 2.63
r_work: 0.3044 rms_B_bonded: 2.89 restraints_weight: 0.5000
r_work: 0.2899 rms_B_bonded: 4.48 restraints_weight: 0.2500
r_work (final): 0.2899
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7608
moved from start:          0.2431

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.036  11611  Z= 0.116
  Angle     :  0.510   8.854  15740  Z= 0.259
  Chirality :  0.039   0.144   1842
  Planarity :  0.003   0.040   1949
  Dihedral  :  3.567  21.302   1541
  Min Nonbonded Distance : 2.526

Molprobity Statistics.
  All-atom Clashscore : 5.64
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.14 %
    Favored  : 95.86 %
  Rotamer:
    Outliers :  1.50 %
    Allowed  : 17.19 %
    Favored  : 81.31 %
  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:  1.89 (0.23), residues: 1424
  helix:  2.37 (0.17), residues: 942
  sheet:  0.01 (0.67), residues: 67
  loop : -1.26 (0.30), residues: 415

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.008   0.000   ARG A1304 
 TYR   0.014   0.001   TYR A  48 
 PHE   0.019   0.001   PHE A 813 
 TRP   0.013   0.001   TRP A1202 
 HIS   0.002   0.001   HIS A1053 

Details of bonding type rmsd
  covalent geometry    : bond        0.00262 (11610)
  covalent geometry    : angle       0.51021 (15738)
  SS BOND              : bond        0.00093 (    1)
  SS BOND              : angle       0.40595 (    2)
  hydrogen bonds       : bond        0.04113 (  734)
  hydrogen bonds       : angle       3.56617 ( 2151)

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

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

  2848 Ramachandran restraints generated.
    1424 Oldfield, 0 Emsley, 1424 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2848 Ramachandran restraints generated.
    1424 Oldfield, 0 Emsley, 1424 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  134 residues out of total 1268 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 19
    poor density    : 115
  time to evaluate  : 0.358 
Fit side-chains
   revert: symmetry clash
REVERT: A   52 ARG cc_start: 0.6906 (ptp-170) cc_final: 0.6695 (mtt180)
REVERT: A   63 PHE cc_start: 0.7243 (OUTLIER) cc_final: 0.6256 (t80)
REVERT: A  203 ILE cc_start: 0.8090 (mm) cc_final: 0.7264 (pt)
REVERT: A  500 GLU cc_start: 0.7229 (tp30) cc_final: 0.6853 (tp30)
REVERT: A  680 MET cc_start: 0.8197 (ttm) cc_final: 0.7916 (ttm)
REVERT: A  688 HIS cc_start: 0.7487 (OUTLIER) cc_final: 0.7163 (t70)
REVERT: A  763 GLN cc_start: 0.7557 (mm-40) cc_final: 0.7142 (tt0)
REVERT: A  797 ASN cc_start: 0.8292 (m110) cc_final: 0.7927 (m-40)
REVERT: A 1276 ASN cc_start: 0.8883 (m-40) cc_final: 0.8651 (m-40)
REVERT: A 1280 TRP cc_start: 0.7725 (m-10) cc_final: 0.7430 (m-10)
REVERT: A 1501 MET cc_start: 0.4988 (mmp) cc_final: 0.3591 (ttt)
  outliers start: 19
  outliers final: 12
  residues processed: 127
  average time/residue: 0.0895
  time to fit residues: 17.0642
Evaluate side-chains
  124 residues out of total 1268 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 110
  time to evaluate  : 0.257 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   63 PHE
Chi-restraints excluded: chain A residue   84 LEU
Chi-restraints excluded: chain A residue  111 LEU
Chi-restraints excluded: chain A residue  212 VAL
Chi-restraints excluded: chain A residue  239 SER
Chi-restraints excluded: chain A residue  370 GLN
Chi-restraints excluded: chain A residue  688 HIS
Chi-restraints excluded: chain A residue  811 ARG
Chi-restraints excluded: chain A residue  986 ASN
Chi-restraints excluded: chain A residue 1293 HIS
Chi-restraints excluded: chain A residue 1339 LEU
Chi-restraints excluded: chain A residue 1361 VAL
Chi-restraints excluded: chain A residue 1375 ILE
Chi-restraints excluded: chain A residue 1439 GLN
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 143
   random chunks:
   chunk 19 optimal weight:    0.5980
   chunk 141 optimal weight:    0.9980
   chunk 31 optimal weight:    0.8980
   chunk 134 optimal weight:    0.8980
   chunk 95 optimal weight:    0.5980
   chunk 92 optimal weight:    0.8980
   chunk 25 optimal weight:    7.9990
   chunk 9 optimal weight:    6.9990
   chunk 85 optimal weight:    5.9990
   chunk 124 optimal weight:    1.9990
   chunk 11 optimal weight:    2.9990
   overall best weight:    0.7780

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

Flipped N/Q/H residues before XYZ refinement:
A 539 GLN
A 986 ASN
** A1240 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4183 r_free = 0.4183 target = 0.196485 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 40)----------------|
| r_work = 0.3442 r_free = 0.3442 target = 0.122640 restraints weight = 12527.744|
|-----------------------------------------------------------------------------|
r_work (start): 0.3370 rms_B_bonded: 2.62
r_work: 0.3119 rms_B_bonded: 2.97 restraints_weight: 0.5000
r_work: 0.2975 rms_B_bonded: 4.60 restraints_weight: 0.2500
r_work (final): 0.2975
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8010
moved from start:          0.2381

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.039  11611  Z= 0.131
  Angle     :  0.522   8.973  15740  Z= 0.266
  Chirality :  0.040   0.142   1842
  Planarity :  0.003   0.041   1949
  Dihedral  :  3.573  19.368   1541
  Min Nonbonded Distance : 2.525

Molprobity Statistics.
  All-atom Clashscore : 5.68
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.86 %
    Favored  : 96.14 %
  Rotamer:
    Outliers :  1.26 %
    Allowed  : 17.35 %
    Favored  : 81.39 %
  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:  1.84 (0.23), residues: 1424
  helix:  2.34 (0.17), residues: 942
  sheet: -0.01 (0.66), residues: 67
  loop : -1.27 (0.30), residues: 415

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.007   0.000   ARG A1304 
 TYR   0.017   0.001   TYR A  48 
 PHE   0.018   0.001   PHE A1236 
 TRP   0.012   0.001   TRP A1202 
 HIS   0.003   0.001   HIS A1053 

Details of bonding type rmsd
  covalent geometry    : bond        0.00312 (11610)
  covalent geometry    : angle       0.52151 (15738)
  SS BOND              : bond        0.00154 (    1)
  SS BOND              : angle       0.48632 (    2)
  hydrogen bonds       : bond        0.04321 (  734)
  hydrogen bonds       : angle       3.59549 ( 2151)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 3430.40 seconds
wall clock time: 59 minutes 20.42 seconds (3560.42 seconds total)