Starting phenix.real_space_refine
on Sun Apr  5 15:38:59 2026 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/9u56_63864/04_2026/9u56_63864_neut.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/9u56_63864/04_2026/9u56_63864.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=2.91
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    model {
      file = "/net/cci-nas-00/data/ceres_data/9u56_63864/04_2026/9u56_63864_neut.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/9u56_63864/04_2026/9u56_63864_neut.cif"
    real_map_files = "/net/cci-nas-00/data/ceres_data/9u56_63864/04_2026/9u56_63864.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/9u56_63864/04_2026/9u56_63864.map"
  }
  resolution = 2.91
  write_initial_geo_file = False
  refinement {
    macro_cycles = 10
  }


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

Validating inputs
Origin is already at (0, 0, 0), no shifts will be applied
-------------------------------------------------------------------------------
Processing inputs
*****************
Set random seed
  Set to: 0
Set model cs if undefined
Decide on map wrapping
  Map wrapping is set to: False
Normalize map: mean=0, sd=1
  Input map: mean=   0.002 sd=   0.052
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      52      5.16       5
     C    7284      2.51       5
     N    1839      2.21       5
     O    1964      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

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

  Monomer Library directory:
    "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.1rc1-6017/lib/python3.9/site-packages/chem_data/mon_lib"
  Total number of atoms: 11139
  Number of models: 1
  Model: ""
    Number of chains: 2
    Chain: "A"
      Number of atoms: 10915
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 1379, 10915
          Classifications: {'peptide': 1379}
          Incomplete info: {'truncation_to_alanine': 1}
          Link IDs: {'PCIS': 1, 'PTRANS': 57, 'TRANS': 1320}
          Chain breaks: 2
          Unresolved non-hydrogen bonds: 6
          Unresolved non-hydrogen angles: 7
          Unresolved non-hydrogen dihedrals: 5
          Planarities with less than four sites: {'ARG:plan': 1}
          Unresolved non-hydrogen planarities: 5
    Chain: "A"
      Number of atoms: 224
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 8, 224
          Unusual residues: {'CLR': 8}
          Classifications: {'undetermined': 8}
          Link IDs: {None: 7}
  Time building chain proxies: 2.68, per 1000 atoms: 0.24
  Number of scatterers: 11139
  At special positions: 0
  Unit cell: (99, 110.25, 153.75, 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      52     16.00
     O    1964      8.00
     N    1839      7.00
     C    7284      6.00
    sf(0) = scattering factor at diffraction angle 0.

  Number of disulfides: simple=1, symmetry=0
    Simple disulfide: pdb=" SG  CYS A  10 " - pdb=" SG  CYS A  32 " 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: 0.64
  Conformation dependent library (CDL) restraints added in 519.3 milliseconds
  

  2746 Ramachandran restraints generated.
    1373 Oldfield, 0 Emsley, 1373 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  2572

  Finding SS restraints...
    Secondary structure from input PDB file:
      57 helices and 7 sheets defined
      69.3% alpha, 5.7% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 0.44
  Creating SS restraints...
    Processing helix  chain 'A' and resid 4 through 11
    Processing helix  chain 'A' and resid 29 through 60
    Processing helix  chain 'A' and resid 74 through 95
      removed outlier: 3.770A  pdb=" N   ALA A  78 " --> pdb=" O   ASN A  74 " (cutoff:3.500A)
      Proline residue:  A  88  - end of helix
    Processing helix  chain 'A' and resid 107 through 131
    Processing helix  chain 'A' and resid 140 through 163
    Processing helix  chain 'A' and resid 164 through 168
    Processing helix  chain 'A' and resid 169 through 193
    Processing helix  chain 'A' and resid 232 through 239
    Processing helix  chain 'A' and resid 242 through 252
    Processing helix  chain 'A' and resid 267 through 284
      removed outlier: 3.927A  pdb=" N   GLN A 284 " --> pdb=" O   ASP A 280 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 289 through 299
      removed outlier: 3.563A  pdb=" N   ALA A 293 " --> pdb=" O   TRP A 289 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 300 through 316
      removed outlier: 3.641A  pdb=" N   TRP A 308 " --> pdb=" O   TRP A 304 " (cutoff:3.500A)
      removed outlier: 3.643A  pdb=" N   GLY A 311 " --> pdb=" O   PHE A 307 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 317 through 332
      removed outlier: 3.762A  pdb=" N   LEU A 321 " --> pdb=" O   PHE A 317 " (cutoff:3.500A)
      removed outlier: 3.575A  pdb=" N   GLU A 332 " --> pdb=" O   LYS A 328 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 337 through 384
      removed outlier: 4.383A  pdb=" N   ILE A 341 " --> pdb=" O   TRP A 337 " (cutoff:3.500A)
      removed outlier: 3.529A  pdb=" N   ARG A 366 " --> pdb=" O   GLN A 362 " (cutoff:3.500A)
      removed outlier: 3.520A  pdb=" N   ALA A 374 " --> pdb=" O   ARG A 370 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 387 through 395
    Processing helix  chain 'A' and resid 397 through 405
      removed outlier: 3.747A  pdb=" N   THR A 405 " --> pdb=" O   ASN A 401 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 405 through 414
      removed outlier: 3.556A  pdb=" N   GLN A 411 " --> pdb=" O   ALA A 407 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 415 through 417
      No H-bonds generated for 'chain 'A' and resid 415 through 417'
    Processing helix  chain 'A' and resid 418 through 438
      Proline residue:  A 424  - end of helix
    Processing helix  chain 'A' and resid 439 through 449
      removed outlier: 3.762A  pdb=" N   LEU A 443 " --> pdb=" O   GLY A 439 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 451 through 483
      removed outlier: 3.528A  pdb=" N   LEU A 455 " --> pdb=" O   LEU A 451 " (cutoff:3.500A)
      removed outlier: 4.547A  pdb=" N   THR A 457 " --> pdb=" O   PHE A 453 " (cutoff:3.500A)
      removed outlier: 4.435A  pdb=" N   VAL A 458 " --> pdb=" O   PRO A 454 " (cutoff:3.500A)
      removed outlier: 4.332A  pdb=" N   ILE A 459 " --> pdb=" O   LEU A 455 " (cutoff:3.500A)
      removed outlier: 4.739A  pdb=" N   ILE A 460 " --> pdb=" O   GLN A 456 " (cutoff:3.500A)
      removed outlier: 3.557A  pdb=" N   ARG A 473 " --> pdb=" O   GLU A 469 " (cutoff:3.500A)
      removed outlier: 5.330A  pdb=" N   LYS A 476 " --> pdb=" O   GLN A 472 " (cutoff:3.500A)
      removed outlier: 3.538A  pdb=" N   GLU A 483 " --> pdb=" O   GLY A 479 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 487 through 495
    Processing helix  chain 'A' and resid 500 through 547
      removed outlier: 3.863A  pdb=" N   VAL A 504 " --> pdb=" O   PHE A 500 " (cutoff:3.500A)
      removed outlier: 3.659A  pdb=" N   GLN A 505 " --> pdb=" O   GLN A 501 " (cutoff:3.500A)
      Proline residue:  A 533  - end of helix
      removed outlier: 3.575A  pdb=" N   LEU A 547 " --> pdb=" O   VAL A 543 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 552 through 594
      removed outlier: 4.194A  pdb=" N   PHE A 568 " --> pdb=" O   ALA A 564 " (cutoff:3.500A)
      Proline residue:  A 569  - end of helix
      removed outlier: 3.737A  pdb=" N   LEU A 573 " --> pdb=" O   PRO A 569 " (cutoff:3.500A)
      Proline residue:  A 574  - end of helix
    Processing helix  chain 'A' and resid 654 through 664
    Processing helix  chain 'A' and resid 693 through 699
    Processing helix  chain 'A' and resid 705 through 716
    Processing helix  chain 'A' and resid 717 through 725
      removed outlier: 4.332A  pdb=" N   ASP A 721 " --> pdb=" O   SER A 717 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 727 through 731
      removed outlier: 3.796A  pdb=" N   LEU A 730 " --> pdb=" O   GLY A 727 " (cutoff:3.500A)
      removed outlier: 3.740A  pdb=" N   THR A 731 " --> pdb=" O   GLY A 728 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'A' and resid 727 through 731'
    Processing helix  chain 'A' and resid 741 through 757
      removed outlier: 3.550A  pdb=" N   ASN A 757 " --> pdb=" O   ALA A 753 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 771 through 782
    Processing helix  chain 'A' and resid 801 through 805
    Processing helix  chain 'A' and resid 821 through 829
    Processing helix  chain 'A' and resid 829 through 836
    Processing helix  chain 'A' and resid 904 through 916
      removed outlier: 3.677A  pdb=" N   LEU A 908 " --> pdb=" O   SER A 904 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 917 through 946
      removed outlier: 4.213A  pdb=" N   VAL A 921 " --> pdb=" O   GLY A 917 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 955 through 1001
      removed outlier: 3.885A  pdb=" N   TYR A 959 " --> pdb=" O   GLY A 955 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 1004 through 1011
      removed outlier: 3.802A  pdb=" N   PHE A1008 " --> pdb=" O   PRO A1004 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 1012 through 1030
      removed outlier: 3.834A  pdb=" N   ILE A1016 " --> pdb=" O   PRO A1012 " (cutoff:3.500A)
      removed outlier: 3.833A  pdb=" N   ASP A1023 " --> pdb=" O   ARG A1019 " (cutoff:3.500A)
      removed outlier: 4.331A  pdb=" N   LEU A1024 " --> pdb=" O   PHE A1020 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 1030 through 1056
    Processing helix  chain 'A' and resid 1056 through 1104
      removed outlier: 3.737A  pdb=" N   LEU A1060 " --> pdb=" O   SER A1056 " (cutoff:3.500A)
      Proline residue:  A1065  - end of helix
      removed outlier: 4.076A  pdb=" N   THR A1080 " --> pdb=" O   TYR A1076 " (cutoff:3.500A)
      removed outlier: 4.044A  pdb=" N   GLU A1083 " --> pdb=" O   ASN A1079 " (cutoff:3.500A)
      removed outlier: 4.484A  pdb=" N   SER A1093 " --> pdb=" O   SER A1089 " (cutoff:3.500A)
      Proline residue:  A1094  - end of helix
      removed outlier: 4.547A  pdb=" N   PHE A1099 " --> pdb=" O   VAL A1095 " (cutoff:3.500A)
      removed outlier: 5.030A  pdb=" N   GLY A1100 " --> pdb=" O   TYR A1096 " (cutoff:3.500A)
      removed outlier: 4.273A  pdb=" N   GLU A1101 " --> pdb=" O   ALA A1097 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 1105 through 1113
      removed outlier: 3.627A  pdb=" N   ILE A1109 " --> pdb=" O   GLY A1105 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 1117 through 1166
      removed outlier: 4.304A  pdb=" N   PHE A1132 " --> pdb=" O   ASN A1128 " (cutoff:3.500A)
      removed outlier: 4.067A  pdb=" N   ASN A1166 " --> pdb=" O   ALA A1162 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 1175 through 1187
    Processing helix  chain 'A' and resid 1188 through 1218
      removed outlier: 4.165A  pdb=" N   LEU A1192 " --> pdb=" O   ASN A1188 " (cutoff:3.500A)
      removed outlier: 4.379A  pdb=" N   SER A1201 " --> pdb=" O   LEU A1197 " (cutoff:3.500A)
      removed outlier: 3.921A  pdb=" N   LEU A1202 " --> pdb=" O   ARG A1198 " (cutoff:3.500A)
      removed outlier: 4.468A  pdb=" N   ALA A1209 " --> pdb=" O   ASN A1205 " (cutoff:3.500A)
      removed outlier: 4.619A  pdb=" N   VAL A1210 " --> pdb=" O   SER A1206 " (cutoff:3.500A)
      removed outlier: 3.865A  pdb=" N   GLU A1211 " --> pdb=" O   LEU A1207 " (cutoff:3.500A)
      removed outlier: 3.655A  pdb=" N   TYR A1216 " --> pdb=" O   ARG A1212 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 1283 through 1290
      removed outlier: 4.218A  pdb=" N   ASN A1287 " --> pdb=" O   SER A1283 " (cutoff:3.500A)
      removed outlier: 3.607A  pdb=" N   ALA A1288 " --> pdb=" O   SER A1284 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 1306 through 1310
    Processing helix  chain 'A' and resid 1311 through 1317
    Processing helix  chain 'A' and resid 1333 through 1338
    Processing helix  chain 'A' and resid 1344 through 1355
      removed outlier: 3.534A  pdb=" N   LEU A1352 " --> pdb=" O   LEU A1348 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 1357 through 1364
      removed outlier: 3.667A  pdb=" N   ARG A1363 " --> pdb=" O   ASP A1359 " (cutoff:3.500A)
      removed outlier: 3.763A  pdb=" N   ASN A1364 " --> pdb=" O   THR A1360 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 1366 through 1369
      removed outlier: 3.616A  pdb=" N   ASP A1369 " --> pdb=" O   LEU A1366 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'A' and resid 1366 through 1369'
    Processing helix  chain 'A' and resid 1373 through 1377
    Processing helix  chain 'A' and resid 1380 through 1396
      removed outlier: 3.727A  pdb=" N   ALA A1392 " --> pdb=" O   SER A1388 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 1410 through 1425
      removed outlier: 3.637A  pdb=" N   THR A1420 " --> pdb=" O   LEU A1416 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 1436 through 1440
      removed outlier: 3.743A  pdb=" N   THR A1439 " --> pdb=" O   ARG A1436 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 1459 through 1464
    Processing sheet with id=AA1, first strand: chain 'A' and resid 135 through 136
      removed outlier: 3.603A  pdb=" N   TYR A 135 " --> pdb=" O   PHE A  66 " (cutoff:3.500A)
    Processing sheet with id=AA2, first strand: chain 'A' and resid 632 through 639
      removed outlier: 5.419A  pdb=" N   GLY A 619 " --> pdb=" O   ASN A 634 " (cutoff:3.500A)
      removed outlier: 6.190A  pdb=" N   ASN A 636 " --> pdb=" O   ARG A 617 " (cutoff:3.500A)
      removed outlier: 6.739A  pdb=" N   ARG A 617 " --> pdb=" O   ASN A 636 " (cutoff:3.500A)
      removed outlier: 7.043A  pdb=" N   ASP A 638 " --> pdb=" O   SER A 615 " (cutoff:3.500A)
      removed outlier: 6.785A  pdb=" N   SER A 615 " --> pdb=" O   ASP A 638 " (cutoff:3.500A)
    Processing sheet with id=AA3, first strand: chain 'A' and resid 645 through 648
      removed outlier: 6.740A  pdb=" N   HIS A 812 " --> pdb=" O   VAL A 816 " (cutoff:3.500A)
      removed outlier: 5.410A  pdb=" N   VAL A 816 " --> pdb=" O   HIS A 812 " (cutoff:3.500A)
    Processing sheet with id=AA4, first strand: chain 'A' and resid 680 through 683
      removed outlier: 6.083A  pdb=" N   TYR A 761 " --> pdb=" O   VAL A 793 " (cutoff:3.500A)
    Processing sheet with id=AA5, first strand: chain 'A' and resid 1262 through 1265
      removed outlier: 5.292A  pdb=" N   VAL A1262 " --> pdb=" O   ASP A1246 " (cutoff:3.500A)
      removed outlier: 3.760A  pdb=" N   ASP A1246 " --> pdb=" O   VAL A1262 " (cutoff:3.500A)
      removed outlier: 3.574A  pdb=" N   LYS A1243 " --> pdb=" O   LEU A1301 " (cutoff:3.500A)
      removed outlier: 3.629A  pdb=" N   LEU A1301 " --> pdb=" O   LYS A1243 " (cutoff:3.500A)
      removed outlier: 3.607A  pdb=" N   GLU A1245 " --> pdb=" O   ARG A1299 " (cutoff:3.500A)
      removed outlier: 3.717A  pdb=" N   ARG A1299 " --> pdb=" O   GLU A1245 " (cutoff:3.500A)
      removed outlier: 4.405A  pdb=" N   VAL A1247 " --> pdb=" O   LYS A1297 " (cutoff:3.500A)
      removed outlier: 7.017A  pdb=" N   LYS A1297 " --> pdb=" O   VAL A1247 " (cutoff:3.500A)
    Processing sheet with id=AA6, first strand: chain 'A' and resid 1319 through 1322
      removed outlier: 3.535A  pdb=" N   LEU A1449 " --> pdb=" O   VAL A1275 " (cutoff:3.500A)
      removed outlier: 6.696A  pdb=" N   ILE A1446 " --> pdb=" O   PHE A1457 " (cutoff:3.500A)
      removed outlier: 4.387A  pdb=" N   PHE A1457 " --> pdb=" O   ILE A1446 " (cutoff:3.500A)
      removed outlier: 7.096A  pdb=" N   VAL A1448 " --> pdb=" O   GLN A1455 " (cutoff:3.500A)
    Processing sheet with id=AA7, first strand: chain 'A' and resid 1331 through 1332
      removed outlier: 4.290A  pdb=" N   GLY A1331 " --> pdb=" O   VAL A1372 " (cutoff:3.500A)

    690 hydrogen bonds defined for protein.
    2031 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: 2.26

  Time building geometry restraints manager: 0.90 seconds

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

  Histogram of bond lengths:
        1.17 -     1.30: 1744
        1.30 -     1.43: 2908
        1.43 -     1.56: 6666
        1.56 -     1.69: 0
        1.69 -     1.82: 90
  Bond restraints: 11408
  Sorted by residual:
  bond pdb=" C   ALA A1176 "
       pdb=" O   ALA A1176 "
    ideal  model  delta    sigma   weight residual
    1.236  1.169  0.068 1.18e-02 7.18e+03 3.28e+01
  bond pdb=" C   ALA A1102 "
       pdb=" O   ALA A1102 "
    ideal  model  delta    sigma   weight residual
    1.236  1.179  0.057 1.15e-02 7.56e+03 2.47e+01
  bond pdb=" N   PHE A1099 "
       pdb=" CA  PHE A1099 "
    ideal  model  delta    sigma   weight residual
    1.459  1.506 -0.047 1.19e-02 7.06e+03 1.53e+01
  bond pdb=" N   PHE A 394 "
       pdb=" CA  PHE A 394 "
    ideal  model  delta    sigma   weight residual
    1.456  1.505 -0.050 1.35e-02 5.49e+03 1.35e+01
  bond pdb=" CA  ALA A1176 "
       pdb=" CB  ALA A1176 "
    ideal  model  delta    sigma   weight residual
    1.529  1.473  0.057 1.58e-02 4.01e+03 1.29e+01
  ... (remaining 11403 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     2.93: 15358
        2.93 -     5.86: 153
        5.86 -     8.78: 24
        8.78 -    11.71: 7
       11.71 -    14.64: 1
  Bond angle restraints: 15543
  Sorted by residual:
  angle pdb=" CA  ALA A1102 "
        pdb=" C   ALA A1102 "
        pdb=" O   ALA A1102 "
      ideal   model   delta    sigma   weight residual
     120.90  111.12    9.78 1.07e+00 8.73e-01 8.36e+01
  angle pdb=" C   PHE A 394 "
        pdb=" CA  PHE A 394 "
        pdb=" CB  PHE A 394 "
      ideal   model   delta    sigma   weight residual
     109.65   95.01   14.64 1.74e+00 3.30e-01 7.08e+01
  angle pdb=" N   GLU A1101 "
        pdb=" CA  GLU A1101 "
        pdb=" C   GLU A1101 "
      ideal   model   delta    sigma   weight residual
     111.07  103.29    7.78 1.07e+00 8.73e-01 5.28e+01
  angle pdb=" C   TRP A 496 "
        pdb=" CA  TRP A 496 "
        pdb=" CB  TRP A 496 "
      ideal   model   delta    sigma   weight residual
     112.03  101.48   10.55 1.56e+00 4.11e-01 4.57e+01
  angle pdb=" C   GLU A1101 "
        pdb=" CA  GLU A1101 "
        pdb=" CB  GLU A1101 "
      ideal   model   delta    sigma   weight residual
     110.88  100.48   10.40 1.57e+00 4.06e-01 4.39e+01
  ... (remaining 15538 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    24.42: 6565
       24.42 -    48.83: 502
       48.83 -    73.25: 80
       73.25 -    97.67: 8
       97.67 -   122.08: 3
  Dihedral angle restraints: 7158
    sinusoidal: 3166
      harmonic: 3992
  Sorted by residual:
  dihedral pdb=" C   PHE A 394 "
           pdb=" N   PHE A 394 "
           pdb=" CA  PHE A 394 "
           pdb=" CB  PHE A 394 "
      ideal   model   delta  harmonic     sigma   weight residual
    -122.60 -106.40  -16.20     0      2.50e+00 1.60e-01 4.20e+01
  dihedral pdb=" C   TRP A 496 "
           pdb=" N   TRP A 496 "
           pdb=" CA  TRP A 496 "
           pdb=" CB  TRP A 496 "
      ideal   model   delta  harmonic     sigma   weight residual
    -122.60 -107.89  -14.71     0      2.50e+00 1.60e-01 3.46e+01
  dihedral pdb=" CD  ARG A1110 "
           pdb=" NE  ARG A1110 "
           pdb=" CZ  ARG A1110 "
           pdb=" NH1 ARG A1110 "
      ideal   model   delta sinusoidal    sigma   weight residual
       0.00  -48.19   48.19     1      1.00e+01 1.00e-02 3.20e+01
  ... (remaining 7155 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.084: 1690
       0.084 -    0.168: 107
       0.168 -    0.251: 6
       0.251 -    0.335: 1
       0.335 -    0.419: 2
  Chirality restraints: 1806
  Sorted by residual:
  chirality pdb=" CA  TRP A 496 "
            pdb=" N   TRP A 496 "
            pdb=" C   TRP A 496 "
            pdb=" CB  TRP A 496 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.93   -0.42 2.00e-01 2.50e+01 4.39e+00
  chirality pdb=" CB  VAL A 164 "
            pdb=" CA  VAL A 164 "
            pdb=" CG1 VAL A 164 "
            pdb=" CG2 VAL A 164 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.63   -2.29   -0.34 2.00e-01 2.50e+01 2.89e+00
  chirality pdb=" CA  PHE A 394 "
            pdb=" N   PHE A 394 "
            pdb=" C   PHE A 394 "
            pdb=" CB  PHE A 394 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.84   -0.33 2.00e-01 2.50e+01 2.76e+00
  ... (remaining 1803 not shown)

  Planarity restraints: 1910
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CD  ARG A1110 "    0.823 9.50e-02 1.11e+02   3.69e-01 8.26e+01
        pdb=" NE  ARG A1110 "   -0.049 2.00e-02 2.50e+03
        pdb=" CZ  ARG A1110 "   -0.009 2.00e-02 2.50e+03
        pdb=" NH1 ARG A1110 "   -0.002 2.00e-02 2.50e+03
        pdb=" NH2 ARG A1110 "    0.024 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  ALA A1097 "    0.040 2.00e-02 2.50e+03   7.57e-02 5.73e+01
        pdb=" C   ALA A1097 "   -0.131 2.00e-02 2.50e+03
        pdb=" O   ALA A1097 "    0.047 2.00e-02 2.50e+03
        pdb=" N   GLN A1098 "    0.044 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  LYS A 393 "    0.028 2.00e-02 2.50e+03   5.43e-02 2.94e+01
        pdb=" C   LYS A 393 "   -0.094 2.00e-02 2.50e+03
        pdb=" O   LYS A 393 "    0.034 2.00e-02 2.50e+03
        pdb=" N   PHE A 394 "    0.031 2.00e-02 2.50e+03
  ... (remaining 1907 not shown)

  Histogram of nonbonded interaction distances:
        2.23 -     2.76: 1862
        2.76 -     3.30: 10420
        3.30 -     3.83: 17820
        3.83 -     4.37: 19743
        4.37 -     4.90: 35244
  Nonbonded interactions: 85089
  Sorted by model distance:
  nonbonded pdb=" OE2 GLU A 665 "
            pdb=" NH1 ARG A1110 "
     model   vdw
     2.231 3.120
  nonbonded pdb=" NZ  LYS A1243 "
            pdb=" OD1 ASP A1304 "
     model   vdw
     2.234 3.120
  nonbonded pdb=" OD2 ASP A 266 "
            pdb=" OH  TYR A 369 "
     model   vdw
     2.306 3.040
  nonbonded pdb=" O   ALA A 554 "
            pdb=" OG1 THR A 558 "
     model   vdw
     2.309 3.040
  nonbonded pdb=" OD2 ASP A 154 "
            pdb=" NE2 GLN A 183 "
     model   vdw
     2.313 3.120
  ... (remaining 85084 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:             5.820
  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:             0.020
  Extract box with map and model:          0.190
  Check model and map are aligned:         0.040
  Set scattering table:                    0.030
  Process input model:                     11.640
  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:7.470
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   25.280
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8167
moved from start:          0.0000

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.068  11409  Z= 0.263
  Angle     :  0.725  14.639  15545  Z= 0.457
  Chirality :  0.043   0.419   1806
  Planarity :  0.010   0.369   1910
  Dihedral  : 16.321 122.084   4583
  Min Nonbonded Distance : 2.231

Molprobity Statistics.
  All-atom Clashscore : 6.55
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.91 %
    Favored  : 97.09 %
  Rotamer:
    Outliers :  3.02 %
    Allowed  : 16.35 %
    Favored  : 80.64 %
  Cbeta Deviations :  0.23 %
  Peptide Plane:
    Cis-proline     : 1.72 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  1.64 (0.23), residues: 1373
  helix:  2.05 (0.18), residues: 886
  sheet:  0.93 (0.63), residues: 75
  loop : -1.06 (0.29), residues: 412

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.008   0.000   ARG A 391 
 TYR   0.017   0.001   TYR A 369 
 PHE   0.017   0.001   PHE A 394 
 TRP   0.020   0.001   TRP A1142 
 HIS   0.002   0.000   HIS A 954 

Details of bonding type rmsd
  covalent geometry    : bond        0.00403 (11408)
  covalent geometry    : angle       0.72526 (15543)
  SS BOND              : bond        0.00111 (    1)
  SS BOND              : angle       0.30447 (    2)
  hydrogen bonds       : bond        0.16472 (  690)
  hydrogen bonds       : angle       5.61196 ( 2031)

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

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

  2746 Ramachandran restraints generated.
    1373 Oldfield, 0 Emsley, 1373 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2746 Ramachandran restraints generated.
    1373 Oldfield, 0 Emsley, 1373 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  131 residues out of total 1194 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 36
    poor density    : 95
  time to evaluate  : 0.438 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  134 ILE cc_start: 0.6756 (OUTLIER) cc_final: 0.6384 (mt)
REVERT: A  166 GLU cc_start: 0.7956 (OUTLIER) cc_final: 0.7609 (pm20)
REVERT: A  394 PHE cc_start: 0.7801 (OUTLIER) cc_final: 0.7293 (t80)
REVERT: A  399 ILE cc_start: 0.6926 (OUTLIER) cc_final: 0.6629 (mm)
REVERT: A  401 ASN cc_start: 0.6600 (OUTLIER) cc_final: 0.6239 (m-40)
REVERT: A  497 GLU cc_start: 0.7926 (OUTLIER) cc_final: 0.7724 (mp0)
REVERT: A  572 MET cc_start: 0.6849 (mmm) cc_final: 0.6255 (mmt)
REVERT: A  699 LEU cc_start: 0.7278 (OUTLIER) cc_final: 0.7053 (tm)
REVERT: A 1131 ARG cc_start: 0.8690 (OUTLIER) cc_final: 0.8404 (mtm180)
REVERT: A 1271 LYS cc_start: 0.6880 (mttt) cc_final: 0.6667 (mppt)
REVERT: A 1350 GLU cc_start: 0.7360 (tp30) cc_final: 0.7127 (tp30)
  outliers start: 36
  outliers final: 18
  residues processed: 126
  average time/residue: 0.5069
  time to fit residues: 69.9032
Evaluate side-chains
  113 residues out of total 1194 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 26
    poor density    : 87
  time to evaluate  : 0.387 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  134 ILE
Chi-restraints excluded: chain A residue  166 GLU
Chi-restraints excluded: chain A residue  394 PHE
Chi-restraints excluded: chain A residue  399 ILE
Chi-restraints excluded: chain A residue  401 ASN
Chi-restraints excluded: chain A residue  402 LEU
Chi-restraints excluded: chain A residue  403 MET
Chi-restraints excluded: chain A residue  406 ASP
Chi-restraints excluded: chain A residue  447 LEU
Chi-restraints excluded: chain A residue  489 ASP
Chi-restraints excluded: chain A residue  497 GLU
Chi-restraints excluded: chain A residue  546 LEU
Chi-restraints excluded: chain A residue  694 VAL
Chi-restraints excluded: chain A residue  699 LEU
Chi-restraints excluded: chain A residue  903 VAL
Chi-restraints excluded: chain A residue 1000 ILE
Chi-restraints excluded: chain A residue 1057 THR
Chi-restraints excluded: chain A residue 1106 LEU
Chi-restraints excluded: chain A residue 1107 SER
Chi-restraints excluded: chain A residue 1108 THR
Chi-restraints excluded: chain A residue 1115 TYR
Chi-restraints excluded: chain A residue 1131 ARG
Chi-restraints excluded: chain A residue 1148 GLU
Chi-restraints excluded: chain A residue 1173 GLN
Chi-restraints excluded: chain A residue 1295 VAL
Chi-restraints excluded: chain A residue 1399 ILE
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 137
   random chunks:
   chunk 98 optimal weight:    1.9990
   chunk 107 optimal weight:    2.9990
   chunk 10 optimal weight:    1.9990
   chunk 66 optimal weight:    0.9980
   chunk 130 optimal weight:    7.9990
   chunk 124 optimal weight:    0.9990
   chunk 103 optimal weight:    1.9990
   chunk 77 optimal weight:    0.8980
   chunk 122 optimal weight:    5.9990
   chunk 91 optimal weight:    0.9990
   chunk 55 optimal weight:    4.9990
   overall best weight:    1.1786

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

Flipped N/Q/H residues before XYZ refinement:
A1383 GLN
A1455 GLN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4395 r_free = 0.4395 target = 0.216465 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 40)----------------|
| r_work = 0.3573 r_free = 0.3573 target = 0.133671 restraints weight = 12543.124|
|-----------------------------------------------------------------------------|
r_work (start): 0.3464 rms_B_bonded: 3.05
r_work: 0.3149 rms_B_bonded: 3.48 restraints_weight: 0.5000
r_work (final): 0.3149
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8123
moved from start:          0.0984

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.033  11409  Z= 0.174
  Angle     :  0.573   8.744  15545  Z= 0.300
  Chirality :  0.041   0.180   1806
  Planarity :  0.004   0.050   1910
  Dihedral  :  9.648  69.703   2070
  Min Nonbonded Distance : 2.598

Molprobity Statistics.
  All-atom Clashscore : 5.00
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.84 %
    Favored  : 97.16 %
  Rotamer:
    Outliers :  4.02 %
    Allowed  : 14.84 %
    Favored  : 81.14 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 1.72 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  1.70 (0.23), residues: 1373
  helix:  1.95 (0.17), residues: 901
  sheet:  1.10 (0.63), residues: 74
  loop : -0.81 (0.30), residues: 398

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.000   ARG A1019 
 TYR   0.019   0.002   TYR A 369 
 PHE   0.023   0.002   PHE A1034 
 TRP   0.018   0.001   TRP A1142 
 HIS   0.003   0.001   HIS A1356 

Details of bonding type rmsd
  covalent geometry    : bond        0.00366 (11408)
  covalent geometry    : angle       0.57320 (15543)
  SS BOND              : bond        0.00323 (    1)
  SS BOND              : angle       0.96202 (    2)
  hydrogen bonds       : bond        0.08712 (  690)
  hydrogen bonds       : angle       4.56095 ( 2031)

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

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

  2746 Ramachandran restraints generated.
    1373 Oldfield, 0 Emsley, 1373 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2746 Ramachandran restraints generated.
    1373 Oldfield, 0 Emsley, 1373 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  143 residues out of total 1194 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 48
    poor density    : 95
  time to evaluate  : 0.421 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  166 GLU cc_start: 0.7410 (OUTLIER) cc_final: 0.7127 (pm20)
REVERT: A  572 MET cc_start: 0.6704 (mmm) cc_final: 0.6117 (mmt)
REVERT: A  699 LEU cc_start: 0.7311 (OUTLIER) cc_final: 0.7110 (tm)
REVERT: A 1131 ARG cc_start: 0.8707 (OUTLIER) cc_final: 0.8341 (mtp180)
REVERT: A 1208 ASN cc_start: 0.7190 (m-40) cc_final: 0.6684 (m-40)
REVERT: A 1211 GLU cc_start: 0.8031 (OUTLIER) cc_final: 0.7412 (pt0)
REVERT: A 1309 LYS cc_start: 0.8197 (OUTLIER) cc_final: 0.7731 (mtmm)
REVERT: A 1350 GLU cc_start: 0.7802 (tp30) cc_final: 0.7584 (tp30)
  outliers start: 48
  outliers final: 22
  residues processed: 132
  average time/residue: 0.5071
  time to fit residues: 73.1418
Evaluate side-chains
  116 residues out of total 1194 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 27
    poor density    : 89
  time to evaluate  : 0.389 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   49 LEU
Chi-restraints excluded: chain A residue   58 LEU
Chi-restraints excluded: chain A residue   63 VAL
Chi-restraints excluded: chain A residue   94 MET
Chi-restraints excluded: chain A residue  166 GLU
Chi-restraints excluded: chain A residue  364 VAL
Chi-restraints excluded: chain A residue  403 MET
Chi-restraints excluded: chain A residue  404 THR
Chi-restraints excluded: chain A residue  440 VAL
Chi-restraints excluded: chain A residue  450 VAL
Chi-restraints excluded: chain A residue  453 PHE
Chi-restraints excluded: chain A residue  489 ASP
Chi-restraints excluded: chain A residue  534 VAL
Chi-restraints excluded: chain A residue  546 LEU
Chi-restraints excluded: chain A residue  699 LEU
Chi-restraints excluded: chain A residue 1000 ILE
Chi-restraints excluded: chain A residue 1063 ILE
Chi-restraints excluded: chain A residue 1107 SER
Chi-restraints excluded: chain A residue 1108 THR
Chi-restraints excluded: chain A residue 1115 TYR
Chi-restraints excluded: chain A residue 1131 ARG
Chi-restraints excluded: chain A residue 1148 GLU
Chi-restraints excluded: chain A residue 1211 GLU
Chi-restraints excluded: chain A residue 1309 LYS
Chi-restraints excluded: chain A residue 1321 ILE
Chi-restraints excluded: chain A residue 1327 VAL
Chi-restraints excluded: chain A residue 1399 ILE
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 137
   random chunks:
   chunk 68 optimal weight:    1.9990
   chunk 20 optimal weight:    3.9990
   chunk 106 optimal weight:    2.9990
   chunk 82 optimal weight:    2.9990
   chunk 74 optimal weight:    0.0020
   chunk 80 optimal weight:    4.9990
   chunk 29 optimal weight:    1.9990
   chunk 61 optimal weight:   10.0000
   chunk 48 optimal weight:    0.5980
   chunk 103 optimal weight:    2.9990
   chunk 104 optimal weight:    0.5980
   overall best weight:    1.0392

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

Flipped N/Q/H residues before XYZ refinement:
A 295 ASN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4395 r_free = 0.4395 target = 0.216507 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 54)----------------|
| r_work = 0.3588 r_free = 0.3588 target = 0.134558 restraints weight = 12675.795|
|-----------------------------------------------------------------------------|
r_work (start): 0.3475 rms_B_bonded: 3.00
r_work: 0.3190 rms_B_bonded: 3.13 restraints_weight: 0.5000
r_work: 0.3046 rms_B_bonded: 4.81 restraints_weight: 0.2500
r_work (final): 0.3046
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8225
moved from start:          0.1212

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.037  11409  Z= 0.158
  Angle     :  0.528   6.217  15545  Z= 0.277
  Chirality :  0.040   0.169   1806
  Planarity :  0.004   0.048   1910
  Dihedral  :  8.293  58.972   2044
  Min Nonbonded Distance : 2.604

Molprobity Statistics.
  All-atom Clashscore : 4.51
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.55 %
    Favored  : 97.45 %
  Rotamer:
    Outliers :  4.11 %
    Allowed  : 15.93 %
    Favored  : 79.97 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 1.72 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  1.84 (0.23), residues: 1373
  helix:  2.05 (0.17), residues: 901
  sheet:  1.13 (0.63), residues: 79
  loop : -0.76 (0.30), residues: 393

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG A1131 
 TYR   0.017   0.001   TYR A 369 
 PHE   0.022   0.001   PHE A1034 
 TRP   0.018   0.001   TRP A1142 
 HIS   0.003   0.001   HIS A1356 

Details of bonding type rmsd
  covalent geometry    : bond        0.00326 (11408)
  covalent geometry    : angle       0.52771 (15543)
  SS BOND              : bond        0.00281 (    1)
  SS BOND              : angle       0.92386 (    2)
  hydrogen bonds       : bond        0.08463 (  690)
  hydrogen bonds       : angle       4.36173 ( 2031)

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

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

  2746 Ramachandran restraints generated.
    1373 Oldfield, 0 Emsley, 1373 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2746 Ramachandran restraints generated.
    1373 Oldfield, 0 Emsley, 1373 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  144 residues out of total 1194 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 49
    poor density    : 95
  time to evaluate  : 0.384 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  166 GLU cc_start: 0.7480 (OUTLIER) cc_final: 0.7209 (pm20)
REVERT: A  338 MET cc_start: 0.8455 (OUTLIER) cc_final: 0.8238 (mmt)
REVERT: A  570 LEU cc_start: 0.7788 (OUTLIER) cc_final: 0.7496 (mp)
REVERT: A  572 MET cc_start: 0.6751 (mmm) cc_final: 0.6164 (mmt)
REVERT: A  699 LEU cc_start: 0.7402 (OUTLIER) cc_final: 0.7167 (tm)
REVERT: A 1028 ASP cc_start: 0.7498 (m-30) cc_final: 0.7174 (m-30)
REVERT: A 1131 ARG cc_start: 0.8775 (OUTLIER) cc_final: 0.8414 (mtm180)
REVERT: A 1168 ARG cc_start: 0.8648 (OUTLIER) cc_final: 0.8328 (ttp-110)
REVERT: A 1208 ASN cc_start: 0.7295 (m-40) cc_final: 0.6781 (m-40)
REVERT: A 1211 GLU cc_start: 0.8167 (OUTLIER) cc_final: 0.7590 (pt0)
REVERT: A 1309 LYS cc_start: 0.8144 (OUTLIER) cc_final: 0.7698 (mtmm)
  outliers start: 49
  outliers final: 22
  residues processed: 135
  average time/residue: 0.4934
  time to fit residues: 73.1701
Evaluate side-chains
  120 residues out of total 1194 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 30
    poor density    : 90
  time to evaluate  : 0.403 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   58 LEU
Chi-restraints excluded: chain A residue   63 VAL
Chi-restraints excluded: chain A residue   74 ASN
Chi-restraints excluded: chain A residue  166 GLU
Chi-restraints excluded: chain A residue  260 TRP
Chi-restraints excluded: chain A residue  338 MET
Chi-restraints excluded: chain A residue  364 VAL
Chi-restraints excluded: chain A residue  403 MET
Chi-restraints excluded: chain A residue  440 VAL
Chi-restraints excluded: chain A residue  450 VAL
Chi-restraints excluded: chain A residue  453 PHE
Chi-restraints excluded: chain A residue  489 ASP
Chi-restraints excluded: chain A residue  546 LEU
Chi-restraints excluded: chain A residue  570 LEU
Chi-restraints excluded: chain A residue  694 VAL
Chi-restraints excluded: chain A residue  699 LEU
Chi-restraints excluded: chain A residue  903 VAL
Chi-restraints excluded: chain A residue 1000 ILE
Chi-restraints excluded: chain A residue 1024 LEU
Chi-restraints excluded: chain A residue 1063 ILE
Chi-restraints excluded: chain A residue 1108 THR
Chi-restraints excluded: chain A residue 1115 TYR
Chi-restraints excluded: chain A residue 1131 ARG
Chi-restraints excluded: chain A residue 1148 GLU
Chi-restraints excluded: chain A residue 1168 ARG
Chi-restraints excluded: chain A residue 1211 GLU
Chi-restraints excluded: chain A residue 1309 LYS
Chi-restraints excluded: chain A residue 1321 ILE
Chi-restraints excluded: chain A residue 1327 VAL
Chi-restraints excluded: chain A residue 1399 ILE
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 137
   random chunks:
   chunk 122 optimal weight:    0.9980
   chunk 116 optimal weight:    9.9990
   chunk 68 optimal weight:    7.9990
   chunk 67 optimal weight:    3.9990
   chunk 89 optimal weight:    0.7980
   chunk 66 optimal weight:    0.6980
   chunk 15 optimal weight:    0.6980
   chunk 91 optimal weight:    2.9990
   chunk 126 optimal weight:    6.9990
   chunk 79 optimal weight:    1.9990
   chunk 130 optimal weight:    0.9980
   overall best weight:    0.8380

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

Flipped N/Q/H residues before XYZ refinement:
A 295 ASN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4389 r_free = 0.4389 target = 0.216218 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 41)----------------|
| r_work = 0.3582 r_free = 0.3582 target = 0.133989 restraints weight = 12664.258|
|-----------------------------------------------------------------------------|
r_work (start): 0.3472 rms_B_bonded: 3.02
r_work: 0.3176 rms_B_bonded: 3.33 restraints_weight: 0.5000
r_work (final): 0.3176
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8097
moved from start:          0.1354

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.033  11409  Z= 0.147
  Angle     :  0.514   7.859  15545  Z= 0.271
  Chirality :  0.040   0.173   1806
  Planarity :  0.004   0.047   1910
  Dihedral  :  7.947  58.505   2043
  Min Nonbonded Distance : 2.577

Molprobity Statistics.
  All-atom Clashscore : 4.42
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.84 %
    Favored  : 97.16 %
  Rotamer:
    Outliers :  4.53 %
    Allowed  : 15.76 %
    Favored  : 79.72 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 1.72 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  1.89 (0.23), residues: 1373
  helix:  2.06 (0.17), residues: 914
  sheet:  1.17 (0.63), residues: 79
  loop : -0.74 (0.31), residues: 380

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG A1131 
 TYR   0.017   0.001   TYR A 369 
 PHE   0.023   0.001   PHE A1034 
 TRP   0.018   0.001   TRP A1142 
 HIS   0.002   0.001   HIS A 193 

Details of bonding type rmsd
  covalent geometry    : bond        0.00293 (11408)
  covalent geometry    : angle       0.51377 (15543)
  SS BOND              : bond        0.00254 (    1)
  SS BOND              : angle       0.75792 (    2)
  hydrogen bonds       : bond        0.08043 (  690)
  hydrogen bonds       : angle       4.28426 ( 2031)

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

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

  2746 Ramachandran restraints generated.
    1373 Oldfield, 0 Emsley, 1373 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2746 Ramachandran restraints generated.
    1373 Oldfield, 0 Emsley, 1373 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  147 residues out of total 1194 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 54
    poor density    : 93
  time to evaluate  : 0.425 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  166 GLU cc_start: 0.7406 (OUTLIER) cc_final: 0.7141 (pm20)
REVERT: A  338 MET cc_start: 0.8173 (OUTLIER) cc_final: 0.7967 (mmt)
REVERT: A  570 LEU cc_start: 0.7797 (OUTLIER) cc_final: 0.7531 (mp)
REVERT: A  572 MET cc_start: 0.6799 (mmm) cc_final: 0.6169 (mmt)
REVERT: A  699 LEU cc_start: 0.7331 (OUTLIER) cc_final: 0.7103 (tm)
REVERT: A 1028 ASP cc_start: 0.7256 (m-30) cc_final: 0.6901 (m-30)
REVERT: A 1131 ARG cc_start: 0.8657 (OUTLIER) cc_final: 0.8391 (mtm180)
REVERT: A 1168 ARG cc_start: 0.8567 (OUTLIER) cc_final: 0.8238 (ttp-110)
REVERT: A 1208 ASN cc_start: 0.7176 (m-40) cc_final: 0.6663 (m-40)
REVERT: A 1211 GLU cc_start: 0.8020 (OUTLIER) cc_final: 0.7431 (pt0)
REVERT: A 1309 LYS cc_start: 0.8134 (OUTLIER) cc_final: 0.7691 (mtmm)
  outliers start: 54
  outliers final: 26
  residues processed: 137
  average time/residue: 0.5184
  time to fit residues: 77.7191
Evaluate side-chains
  124 residues out of total 1194 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 34
    poor density    : 90
  time to evaluate  : 0.398 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   58 LEU
Chi-restraints excluded: chain A residue   63 VAL
Chi-restraints excluded: chain A residue  166 GLU
Chi-restraints excluded: chain A residue  194 LEU
Chi-restraints excluded: chain A residue  232 ASN
Chi-restraints excluded: chain A residue  260 TRP
Chi-restraints excluded: chain A residue  338 MET
Chi-restraints excluded: chain A residue  364 VAL
Chi-restraints excluded: chain A residue  376 ILE
Chi-restraints excluded: chain A residue  403 MET
Chi-restraints excluded: chain A residue  440 VAL
Chi-restraints excluded: chain A residue  450 VAL
Chi-restraints excluded: chain A residue  489 ASP
Chi-restraints excluded: chain A residue  546 LEU
Chi-restraints excluded: chain A residue  570 LEU
Chi-restraints excluded: chain A residue  694 VAL
Chi-restraints excluded: chain A residue  699 LEU
Chi-restraints excluded: chain A residue  903 VAL
Chi-restraints excluded: chain A residue 1000 ILE
Chi-restraints excluded: chain A residue 1024 LEU
Chi-restraints excluded: chain A residue 1057 THR
Chi-restraints excluded: chain A residue 1063 ILE
Chi-restraints excluded: chain A residue 1108 THR
Chi-restraints excluded: chain A residue 1115 TYR
Chi-restraints excluded: chain A residue 1131 ARG
Chi-restraints excluded: chain A residue 1148 GLU
Chi-restraints excluded: chain A residue 1164 MET
Chi-restraints excluded: chain A residue 1168 ARG
Chi-restraints excluded: chain A residue 1211 GLU
Chi-restraints excluded: chain A residue 1309 LYS
Chi-restraints excluded: chain A residue 1321 ILE
Chi-restraints excluded: chain A residue 1327 VAL
Chi-restraints excluded: chain A residue 1332 THR
Chi-restraints excluded: chain A residue 1399 ILE
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 137
   random chunks:
   chunk 24 optimal weight:    0.7980
   chunk 122 optimal weight:    4.9990
   chunk 116 optimal weight:    7.9990
   chunk 107 optimal weight:    2.9990
   chunk 0 optimal weight:    6.9990
   chunk 96 optimal weight:    2.9990
   chunk 60 optimal weight:    3.9990
   chunk 85 optimal weight:    0.9990
   chunk 2 optimal weight:    0.9980
   chunk 74 optimal weight:    7.9990
   chunk 128 optimal weight:    8.9990
   overall best weight:    1.7586

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

Flipped N/Q/H residues before XYZ refinement:
** A 295 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4342 r_free = 0.4342 target = 0.210822 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 50)----------------|
| r_work = 0.3529 r_free = 0.3529 target = 0.129578 restraints weight = 12608.094|
|-----------------------------------------------------------------------------|
r_work (start): 0.3407 rms_B_bonded: 2.68
r_work: 0.3116 rms_B_bonded: 3.05 restraints_weight: 0.5000
r_work: 0.2974 rms_B_bonded: 4.65 restraints_weight: 0.2500
r_work (final): 0.2974
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8287
moved from start:          0.1813

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.043  11409  Z= 0.208
  Angle     :  0.592   7.431  15545  Z= 0.310
  Chirality :  0.042   0.169   1806
  Planarity :  0.004   0.048   1910
  Dihedral  :  8.195  59.449   2043
  Min Nonbonded Distance : 2.566

Molprobity Statistics.
  All-atom Clashscore : 5.22
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.91 %
    Favored  : 97.09 %
  Rotamer:
    Outliers :  4.78 %
    Allowed  : 15.76 %
    Favored  : 79.46 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 1.72 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  1.60 (0.23), residues: 1373
  helix:  1.81 (0.17), residues: 906
  sheet:  0.95 (0.66), residues: 70
  loop : -0.64 (0.30), residues: 397

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG A1124 
 TYR   0.020   0.002   TYR A 369 
 PHE   0.027   0.002   PHE A1034 
 TRP   0.018   0.002   TRP A1142 
 HIS   0.006   0.001   HIS A 800 

Details of bonding type rmsd
  covalent geometry    : bond        0.00471 (11408)
  covalent geometry    : angle       0.59223 (15543)
  SS BOND              : bond        0.00274 (    1)
  SS BOND              : angle       1.10460 (    2)
  hydrogen bonds       : bond        0.10048 (  690)
  hydrogen bonds       : angle       4.41190 ( 2031)

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

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

  2746 Ramachandran restraints generated.
    1373 Oldfield, 0 Emsley, 1373 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2746 Ramachandran restraints generated.
    1373 Oldfield, 0 Emsley, 1373 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  146 residues out of total 1194 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 57
    poor density    : 89
  time to evaluate  : 0.399 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  136 ILE cc_start: 0.7893 (mp) cc_final: 0.7443 (OUTLIER)
REVERT: A  166 GLU cc_start: 0.7587 (OUTLIER) cc_final: 0.7362 (pm20)
REVERT: A  192 MET cc_start: 0.6448 (mmm) cc_final: 0.6163 (tpp)
REVERT: A  572 MET cc_start: 0.6907 (mmm) cc_final: 0.6211 (mmt)
REVERT: A 1131 ARG cc_start: 0.8803 (OUTLIER) cc_final: 0.8396 (mtm180)
REVERT: A 1168 ARG cc_start: 0.8764 (OUTLIER) cc_final: 0.8477 (ttp-110)
REVERT: A 1208 ASN cc_start: 0.7288 (m-40) cc_final: 0.6776 (m-40)
REVERT: A 1211 GLU cc_start: 0.8165 (OUTLIER) cc_final: 0.7573 (pt0)
REVERT: A 1309 LYS cc_start: 0.8146 (OUTLIER) cc_final: 0.7689 (mtmm)
REVERT: A 1409 VAL cc_start: 0.4128 (OUTLIER) cc_final: 0.3800 (m)
  outliers start: 57
  outliers final: 31
  residues processed: 138
  average time/residue: 0.4812
  time to fit residues: 73.0229
Evaluate side-chains
  125 residues out of total 1194 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 36
    poor density    : 89
  time to evaluate  : 0.415 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   49 LEU
Chi-restraints excluded: chain A residue   58 LEU
Chi-restraints excluded: chain A residue   63 VAL
Chi-restraints excluded: chain A residue  134 ILE
Chi-restraints excluded: chain A residue  166 GLU
Chi-restraints excluded: chain A residue  194 LEU
Chi-restraints excluded: chain A residue  232 ASN
Chi-restraints excluded: chain A residue  260 TRP
Chi-restraints excluded: chain A residue  298 LEU
Chi-restraints excluded: chain A residue  364 VAL
Chi-restraints excluded: chain A residue  403 MET
Chi-restraints excluded: chain A residue  440 VAL
Chi-restraints excluded: chain A residue  450 VAL
Chi-restraints excluded: chain A residue  489 ASP
Chi-restraints excluded: chain A residue  534 VAL
Chi-restraints excluded: chain A residue  546 LEU
Chi-restraints excluded: chain A residue  694 VAL
Chi-restraints excluded: chain A residue  800 HIS
Chi-restraints excluded: chain A residue  903 VAL
Chi-restraints excluded: chain A residue  971 VAL
Chi-restraints excluded: chain A residue 1000 ILE
Chi-restraints excluded: chain A residue 1024 LEU
Chi-restraints excluded: chain A residue 1063 ILE
Chi-restraints excluded: chain A residue 1090 ILE
Chi-restraints excluded: chain A residue 1108 THR
Chi-restraints excluded: chain A residue 1115 TYR
Chi-restraints excluded: chain A residue 1131 ARG
Chi-restraints excluded: chain A residue 1148 GLU
Chi-restraints excluded: chain A residue 1168 ARG
Chi-restraints excluded: chain A residue 1211 GLU
Chi-restraints excluded: chain A residue 1309 LYS
Chi-restraints excluded: chain A residue 1321 ILE
Chi-restraints excluded: chain A residue 1327 VAL
Chi-restraints excluded: chain A residue 1332 THR
Chi-restraints excluded: chain A residue 1399 ILE
Chi-restraints excluded: chain A residue 1409 VAL
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 137
   random chunks:
   chunk 76 optimal weight:    7.9990
   chunk 5 optimal weight:    5.9990
   chunk 71 optimal weight:    0.7980
   chunk 38 optimal weight:    0.8980
   chunk 16 optimal weight:    0.9990
   chunk 107 optimal weight:    1.9990
   chunk 2 optimal weight:    0.9980
   chunk 81 optimal weight:    7.9990
   chunk 117 optimal weight:    9.9990
   chunk 94 optimal weight:    2.9990
   chunk 133 optimal weight:    8.9990
   overall best weight:    1.1384

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

Flipped N/Q/H residues before XYZ refinement:
** A 159 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4359 r_free = 0.4359 target = 0.212811 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 56)----------------|
| r_work = 0.3577 r_free = 0.3577 target = 0.133039 restraints weight = 12663.207|
|-----------------------------------------------------------------------------|
r_work (start): 0.3456 rms_B_bonded: 2.63
r_work: 0.3161 rms_B_bonded: 3.06 restraints_weight: 0.5000
r_work: 0.3021 rms_B_bonded: 4.70 restraints_weight: 0.2500
r_work (final): 0.3021
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8259
moved from start:          0.1802

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.034  11409  Z= 0.165
  Angle     :  0.538   6.302  15545  Z= 0.284
  Chirality :  0.040   0.172   1806
  Planarity :  0.004   0.047   1910
  Dihedral  :  7.871  59.695   2041
  Min Nonbonded Distance : 2.539

Molprobity Statistics.
  All-atom Clashscore : 4.56
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.91 %
    Favored  : 97.09 %
  Rotamer:
    Outliers :  3.94 %
    Allowed  : 16.85 %
    Favored  : 79.21 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 1.72 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  1.73 (0.23), residues: 1373
  helix:  1.94 (0.17), residues: 907
  sheet:  0.91 (0.66), residues: 71
  loop : -0.65 (0.31), residues: 395

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG A1117 
 TYR   0.017   0.001   TYR A 369 
 PHE   0.025   0.001   PHE A1034 
 TRP   0.019   0.001   TRP A1142 
 HIS   0.004   0.001   HIS A 193 

Details of bonding type rmsd
  covalent geometry    : bond        0.00343 (11408)
  covalent geometry    : angle       0.53822 (15543)
  SS BOND              : bond        0.00285 (    1)
  SS BOND              : angle       0.87948 (    2)
  hydrogen bonds       : bond        0.08869 (  690)
  hydrogen bonds       : angle       4.30868 ( 2031)

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

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

  2746 Ramachandran restraints generated.
    1373 Oldfield, 0 Emsley, 1373 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2746 Ramachandran restraints generated.
    1373 Oldfield, 0 Emsley, 1373 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  136 residues out of total 1194 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 47
    poor density    : 89
  time to evaluate  : 0.412 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  166 GLU cc_start: 0.7577 (OUTLIER) cc_final: 0.7314 (pm20)
REVERT: A  192 MET cc_start: 0.6447 (mmm) cc_final: 0.6151 (tpp)
REVERT: A  572 MET cc_start: 0.6906 (mmm) cc_final: 0.6191 (mmt)
REVERT: A 1131 ARG cc_start: 0.8752 (OUTLIER) cc_final: 0.8381 (mtm180)
REVERT: A 1168 ARG cc_start: 0.8697 (OUTLIER) cc_final: 0.8400 (ttp-110)
REVERT: A 1208 ASN cc_start: 0.7255 (m-40) cc_final: 0.6756 (m-40)
REVERT: A 1211 GLU cc_start: 0.8153 (OUTLIER) cc_final: 0.7582 (pt0)
REVERT: A 1309 LYS cc_start: 0.8150 (OUTLIER) cc_final: 0.7672 (mtmm)
  outliers start: 47
  outliers final: 27
  residues processed: 127
  average time/residue: 0.4895
  time to fit residues: 68.2759
Evaluate side-chains
  118 residues out of total 1194 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 32
    poor density    : 86
  time to evaluate  : 0.422 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   58 LEU
Chi-restraints excluded: chain A residue   63 VAL
Chi-restraints excluded: chain A residue  166 GLU
Chi-restraints excluded: chain A residue  194 LEU
Chi-restraints excluded: chain A residue  232 ASN
Chi-restraints excluded: chain A residue  260 TRP
Chi-restraints excluded: chain A residue  298 LEU
Chi-restraints excluded: chain A residue  364 VAL
Chi-restraints excluded: chain A residue  403 MET
Chi-restraints excluded: chain A residue  440 VAL
Chi-restraints excluded: chain A residue  450 VAL
Chi-restraints excluded: chain A residue  489 ASP
Chi-restraints excluded: chain A residue  534 VAL
Chi-restraints excluded: chain A residue  546 LEU
Chi-restraints excluded: chain A residue  694 VAL
Chi-restraints excluded: chain A residue  800 HIS
Chi-restraints excluded: chain A residue  903 VAL
Chi-restraints excluded: chain A residue 1000 ILE
Chi-restraints excluded: chain A residue 1057 THR
Chi-restraints excluded: chain A residue 1063 ILE
Chi-restraints excluded: chain A residue 1108 THR
Chi-restraints excluded: chain A residue 1115 TYR
Chi-restraints excluded: chain A residue 1131 ARG
Chi-restraints excluded: chain A residue 1148 GLU
Chi-restraints excluded: chain A residue 1168 ARG
Chi-restraints excluded: chain A residue 1183 LEU
Chi-restraints excluded: chain A residue 1211 GLU
Chi-restraints excluded: chain A residue 1309 LYS
Chi-restraints excluded: chain A residue 1321 ILE
Chi-restraints excluded: chain A residue 1327 VAL
Chi-restraints excluded: chain A residue 1332 THR
Chi-restraints excluded: chain A residue 1399 ILE
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 137
   random chunks:
   chunk 124 optimal weight:    6.9990
   chunk 27 optimal weight:    0.7980
   chunk 56 optimal weight:    2.9990
   chunk 54 optimal weight:    3.9990
   chunk 134 optimal weight:    0.7980
   chunk 2 optimal weight:    2.9990
   chunk 74 optimal weight:    0.0670
   chunk 108 optimal weight:    0.8980
   chunk 125 optimal weight:    4.9990
   chunk 87 optimal weight:    1.9990
   chunk 16 optimal weight:    2.9990
   overall best weight:    0.9120

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

Flipped N/Q/H residues before XYZ refinement:
** A 159 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4370 r_free = 0.4370 target = 0.214122 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 55)----------------|
| r_work = 0.3585 r_free = 0.3585 target = 0.134200 restraints weight = 12599.714|
|-----------------------------------------------------------------------------|
r_work (start): 0.3458 rms_B_bonded: 2.71
r_work: 0.3184 rms_B_bonded: 3.04 restraints_weight: 0.5000
r_work: 0.3042 rms_B_bonded: 4.68 restraints_weight: 0.2500
r_work (final): 0.3042
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8219
moved from start:          0.1816

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.036  11409  Z= 0.152
  Angle     :  0.519   5.586  15545  Z= 0.274
  Chirality :  0.040   0.173   1806
  Planarity :  0.004   0.047   1910
  Dihedral  :  7.568  58.803   2041
  Min Nonbonded Distance : 2.557

Molprobity Statistics.
  All-atom Clashscore : 4.73
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.91 %
    Favored  : 97.09 %
  Rotamer:
    Outliers :  3.60 %
    Allowed  : 17.60 %
    Favored  : 78.79 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 1.72 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  1.89 (0.23), residues: 1373
  helix:  2.06 (0.17), residues: 908
  sheet:  1.00 (0.66), residues: 71
  loop : -0.63 (0.31), residues: 394

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG A1117 
 TYR   0.017   0.001   TYR A 369 
 PHE   0.026   0.001   PHE A 112 
 TRP   0.019   0.001   TRP A1142 
 HIS   0.003   0.001   HIS A 193 

Details of bonding type rmsd
  covalent geometry    : bond        0.00307 (11408)
  covalent geometry    : angle       0.51902 (15543)
  SS BOND              : bond        0.00248 (    1)
  SS BOND              : angle       0.73458 (    2)
  hydrogen bonds       : bond        0.08257 (  690)
  hydrogen bonds       : angle       4.20943 ( 2031)

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

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

  2746 Ramachandran restraints generated.
    1373 Oldfield, 0 Emsley, 1373 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2746 Ramachandran restraints generated.
    1373 Oldfield, 0 Emsley, 1373 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  135 residues out of total 1194 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 43
    poor density    : 92
  time to evaluate  : 0.416 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  166 GLU cc_start: 0.7509 (OUTLIER) cc_final: 0.7288 (pm20)
REVERT: A  279 TRP cc_start: 0.8036 (t-100) cc_final: 0.7717 (t-100)
REVERT: A  570 LEU cc_start: 0.7775 (OUTLIER) cc_final: 0.7500 (mp)
REVERT: A  572 MET cc_start: 0.6829 (mmm) cc_final: 0.6527 (tpp)
REVERT: A 1168 ARG cc_start: 0.8647 (OUTLIER) cc_final: 0.8321 (ttp-110)
REVERT: A 1208 ASN cc_start: 0.7253 (m-40) cc_final: 0.6747 (m-40)
REVERT: A 1211 GLU cc_start: 0.8137 (OUTLIER) cc_final: 0.7575 (pt0)
REVERT: A 1309 LYS cc_start: 0.8139 (OUTLIER) cc_final: 0.7661 (mtmm)
REVERT: A 1409 VAL cc_start: 0.4220 (OUTLIER) cc_final: 0.3901 (m)
  outliers start: 43
  outliers final: 29
  residues processed: 129
  average time/residue: 0.4696
  time to fit residues: 66.7671
Evaluate side-chains
  125 residues out of total 1194 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 35
    poor density    : 90
  time to evaluate  : 0.483 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   58 LEU
Chi-restraints excluded: chain A residue   63 VAL
Chi-restraints excluded: chain A residue  166 GLU
Chi-restraints excluded: chain A residue  194 LEU
Chi-restraints excluded: chain A residue  232 ASN
Chi-restraints excluded: chain A residue  260 TRP
Chi-restraints excluded: chain A residue  298 LEU
Chi-restraints excluded: chain A residue  315 SER
Chi-restraints excluded: chain A residue  364 VAL
Chi-restraints excluded: chain A residue  403 MET
Chi-restraints excluded: chain A residue  440 VAL
Chi-restraints excluded: chain A residue  450 VAL
Chi-restraints excluded: chain A residue  475 ASP
Chi-restraints excluded: chain A residue  489 ASP
Chi-restraints excluded: chain A residue  534 VAL
Chi-restraints excluded: chain A residue  546 LEU
Chi-restraints excluded: chain A residue  570 LEU
Chi-restraints excluded: chain A residue  694 VAL
Chi-restraints excluded: chain A residue  800 HIS
Chi-restraints excluded: chain A residue  903 VAL
Chi-restraints excluded: chain A residue 1000 ILE
Chi-restraints excluded: chain A residue 1024 LEU
Chi-restraints excluded: chain A residue 1057 THR
Chi-restraints excluded: chain A residue 1063 ILE
Chi-restraints excluded: chain A residue 1108 THR
Chi-restraints excluded: chain A residue 1115 TYR
Chi-restraints excluded: chain A residue 1148 GLU
Chi-restraints excluded: chain A residue 1168 ARG
Chi-restraints excluded: chain A residue 1183 LEU
Chi-restraints excluded: chain A residue 1211 GLU
Chi-restraints excluded: chain A residue 1309 LYS
Chi-restraints excluded: chain A residue 1321 ILE
Chi-restraints excluded: chain A residue 1327 VAL
Chi-restraints excluded: chain A residue 1332 THR
Chi-restraints excluded: chain A residue 1409 VAL
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 137
   random chunks:
   chunk 44 optimal weight:    5.9990
   chunk 32 optimal weight:    2.9990
   chunk 98 optimal weight:    0.9990
   chunk 61 optimal weight:   20.0000
   chunk 91 optimal weight:    0.2980
   chunk 130 optimal weight:    9.9990
   chunk 40 optimal weight:    0.9990
   chunk 94 optimal weight:    2.9990
   chunk 113 optimal weight:    0.7980
   chunk 129 optimal weight:    5.9990
   chunk 14 optimal weight:    2.9990
   overall best weight:    1.2186

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

Flipped N/Q/H residues before XYZ refinement:
** A 159 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4358 r_free = 0.4358 target = 0.212822 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 52)----------------|
| r_work = 0.3572 r_free = 0.3572 target = 0.132817 restraints weight = 12557.641|
|-----------------------------------------------------------------------------|
r_work (start): 0.3454 rms_B_bonded: 2.51
r_work: 0.3152 rms_B_bonded: 3.11 restraints_weight: 0.5000
r_work: 0.3009 rms_B_bonded: 4.80 restraints_weight: 0.2500
r_work (final): 0.3009
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8264
moved from start:          0.1937

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.044  11409  Z= 0.169
  Angle     :  0.551  10.024  15545  Z= 0.288
  Chirality :  0.040   0.173   1806
  Planarity :  0.004   0.046   1910
  Dihedral  :  7.537  59.754   2035
  Min Nonbonded Distance : 2.515

Molprobity Statistics.
  All-atom Clashscore : 4.47
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.84 %
    Favored  : 97.16 %
  Rotamer:
    Outliers :  3.94 %
    Allowed  : 17.52 %
    Favored  : 78.54 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 1.72 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  1.82 (0.23), residues: 1373
  helix:  2.00 (0.17), residues: 907
  sheet:  0.93 (0.65), residues: 71
  loop : -0.62 (0.31), residues: 395

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG A 599 
 TYR   0.019   0.001   TYR A 369 
 PHE   0.027   0.002   PHE A1034 
 TRP   0.018   0.001   TRP A1142 
 HIS   0.004   0.001   HIS A 193 

Details of bonding type rmsd
  covalent geometry    : bond        0.00364 (11408)
  covalent geometry    : angle       0.55065 (15543)
  SS BOND              : bond        0.00256 (    1)
  SS BOND              : angle       0.80904 (    2)
  hydrogen bonds       : bond        0.08816 (  690)
  hydrogen bonds       : angle       4.23092 ( 2031)

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

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

  2746 Ramachandran restraints generated.
    1373 Oldfield, 0 Emsley, 1373 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2746 Ramachandran restraints generated.
    1373 Oldfield, 0 Emsley, 1373 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  142 residues out of total 1194 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 47
    poor density    : 95
  time to evaluate  : 0.409 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   93 ILE cc_start: 0.7606 (pt) cc_final: 0.7290 (pp)
REVERT: A   94 MET cc_start: 0.7231 (mmm) cc_final: 0.6603 (tpt)
REVERT: A  136 ILE cc_start: 0.7939 (mp) cc_final: 0.7461 (OUTLIER)
REVERT: A  192 MET cc_start: 0.6398 (mmm) cc_final: 0.6015 (tpp)
REVERT: A  279 TRP cc_start: 0.8075 (t-100) cc_final: 0.7781 (t-100)
REVERT: A  338 MET cc_start: 0.8549 (OUTLIER) cc_final: 0.8338 (mmt)
REVERT: A  570 LEU cc_start: 0.7797 (OUTLIER) cc_final: 0.7516 (mp)
REVERT: A  572 MET cc_start: 0.6867 (mmm) cc_final: 0.6127 (mmt)
REVERT: A 1168 ARG cc_start: 0.8689 (OUTLIER) cc_final: 0.8384 (ttp-110)
REVERT: A 1208 ASN cc_start: 0.7246 (m-40) cc_final: 0.6744 (m-40)
REVERT: A 1211 GLU cc_start: 0.8163 (OUTLIER) cc_final: 0.7581 (pt0)
REVERT: A 1309 LYS cc_start: 0.8148 (OUTLIER) cc_final: 0.7663 (mtmm)
REVERT: A 1317 LYS cc_start: 0.7823 (OUTLIER) cc_final: 0.7576 (tptp)
  outliers start: 47
  outliers final: 33
  residues processed: 133
  average time/residue: 0.4924
  time to fit residues: 72.1761
Evaluate side-chains
  132 residues out of total 1194 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 38
    poor density    : 94
  time to evaluate  : 0.391 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   58 LEU
Chi-restraints excluded: chain A residue   63 VAL
Chi-restraints excluded: chain A residue  194 LEU
Chi-restraints excluded: chain A residue  232 ASN
Chi-restraints excluded: chain A residue  260 TRP
Chi-restraints excluded: chain A residue  298 LEU
Chi-restraints excluded: chain A residue  315 SER
Chi-restraints excluded: chain A residue  338 MET
Chi-restraints excluded: chain A residue  364 VAL
Chi-restraints excluded: chain A residue  385 ARG
Chi-restraints excluded: chain A residue  399 ILE
Chi-restraints excluded: chain A residue  403 MET
Chi-restraints excluded: chain A residue  440 VAL
Chi-restraints excluded: chain A residue  450 VAL
Chi-restraints excluded: chain A residue  481 MET
Chi-restraints excluded: chain A residue  489 ASP
Chi-restraints excluded: chain A residue  534 VAL
Chi-restraints excluded: chain A residue  546 LEU
Chi-restraints excluded: chain A residue  570 LEU
Chi-restraints excluded: chain A residue  694 VAL
Chi-restraints excluded: chain A residue  800 HIS
Chi-restraints excluded: chain A residue  903 VAL
Chi-restraints excluded: chain A residue 1000 ILE
Chi-restraints excluded: chain A residue 1024 LEU
Chi-restraints excluded: chain A residue 1057 THR
Chi-restraints excluded: chain A residue 1063 ILE
Chi-restraints excluded: chain A residue 1108 THR
Chi-restraints excluded: chain A residue 1115 TYR
Chi-restraints excluded: chain A residue 1148 GLU
Chi-restraints excluded: chain A residue 1168 ARG
Chi-restraints excluded: chain A residue 1183 LEU
Chi-restraints excluded: chain A residue 1211 GLU
Chi-restraints excluded: chain A residue 1309 LYS
Chi-restraints excluded: chain A residue 1317 LYS
Chi-restraints excluded: chain A residue 1321 ILE
Chi-restraints excluded: chain A residue 1327 VAL
Chi-restraints excluded: chain A residue 1332 THR
Chi-restraints excluded: chain A residue 1399 ILE
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 137
   random chunks:
   chunk 1 optimal weight:    2.9990
   chunk 61 optimal weight:    2.9990
   chunk 31 optimal weight:    0.9990
   chunk 13 optimal weight:    0.6980
   chunk 25 optimal weight:    0.8980
   chunk 109 optimal weight:    1.9990
   chunk 60 optimal weight:    8.9990
   chunk 8 optimal weight:    1.9990
   chunk 70 optimal weight:    0.5980
   chunk 12 optimal weight:    5.9990
   chunk 121 optimal weight:   10.0000
   overall best weight:    1.0384

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

Flipped N/Q/H residues before XYZ refinement:
** A 159 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4375 r_free = 0.4375 target = 0.214739 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 41)----------------|
| r_work = 0.3558 r_free = 0.3558 target = 0.132109 restraints weight = 12463.114|
|-----------------------------------------------------------------------------|
r_work (start): 0.3442 rms_B_bonded: 3.00
r_work: 0.3157 rms_B_bonded: 3.22 restraints_weight: 0.5000
r_work: 0.3013 rms_B_bonded: 4.98 restraints_weight: 0.2500
r_work (final): 0.3013
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8230
moved from start:          0.1963

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.039  11409  Z= 0.157
  Angle     :  0.537   9.379  15545  Z= 0.281
  Chirality :  0.040   0.174   1806
  Planarity :  0.004   0.046   1910
  Dihedral  :  7.293  58.125   2032
  Min Nonbonded Distance : 2.520

Molprobity Statistics.
  All-atom Clashscore : 4.73
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.84 %
    Favored  : 97.16 %
  Rotamer:
    Outliers :  3.77 %
    Allowed  : 17.77 %
    Favored  : 78.46 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 1.72 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  1.91 (0.23), residues: 1373
  helix:  2.06 (0.17), residues: 909
  sheet:  0.87 (0.66), residues: 71
  loop : -0.56 (0.31), residues: 393

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG A 599 
 TYR   0.017   0.001   TYR A 369 
 PHE   0.026   0.001   PHE A1034 
 TRP   0.019   0.001   TRP A1142 
 HIS   0.003   0.001   HIS A 954 

Details of bonding type rmsd
  covalent geometry    : bond        0.00327 (11408)
  covalent geometry    : angle       0.53667 (15543)
  SS BOND              : bond        0.00258 (    1)
  SS BOND              : angle       0.73778 (    2)
  hydrogen bonds       : bond        0.08383 (  690)
  hydrogen bonds       : angle       4.17689 ( 2031)

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

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

  2746 Ramachandran restraints generated.
    1373 Oldfield, 0 Emsley, 1373 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2746 Ramachandran restraints generated.
    1373 Oldfield, 0 Emsley, 1373 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  136 residues out of total 1194 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 45
    poor density    : 91
  time to evaluate  : 0.427 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  136 ILE cc_start: 0.7877 (mp) cc_final: 0.7427 (OUTLIER)
REVERT: A  192 MET cc_start: 0.6402 (mmm) cc_final: 0.6060 (tpp)
REVERT: A  279 TRP cc_start: 0.8034 (t-100) cc_final: 0.7751 (t-100)
REVERT: A  338 MET cc_start: 0.8487 (OUTLIER) cc_final: 0.8283 (mmt)
REVERT: A  399 ILE cc_start: 0.7368 (OUTLIER) cc_final: 0.6813 (mp)
REVERT: A  570 LEU cc_start: 0.7758 (OUTLIER) cc_final: 0.7484 (mp)
REVERT: A  572 MET cc_start: 0.6817 (mmm) cc_final: 0.6517 (tpp)
REVERT: A 1168 ARG cc_start: 0.8665 (OUTLIER) cc_final: 0.8346 (ttp-110)
REVERT: A 1208 ASN cc_start: 0.7210 (m-40) cc_final: 0.6712 (m-40)
REVERT: A 1211 GLU cc_start: 0.8151 (OUTLIER) cc_final: 0.7589 (pt0)
REVERT: A 1309 LYS cc_start: 0.8126 (OUTLIER) cc_final: 0.7635 (mtmm)
REVERT: A 1317 LYS cc_start: 0.7785 (OUTLIER) cc_final: 0.7546 (tptp)
  outliers start: 45
  outliers final: 31
  residues processed: 128
  average time/residue: 0.5015
  time to fit residues: 70.4578
Evaluate side-chains
  128 residues out of total 1194 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 37
    poor density    : 91
  time to evaluate  : 0.424 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   58 LEU
Chi-restraints excluded: chain A residue   63 VAL
Chi-restraints excluded: chain A residue  232 ASN
Chi-restraints excluded: chain A residue  260 TRP
Chi-restraints excluded: chain A residue  298 LEU
Chi-restraints excluded: chain A residue  315 SER
Chi-restraints excluded: chain A residue  338 MET
Chi-restraints excluded: chain A residue  364 VAL
Chi-restraints excluded: chain A residue  385 ARG
Chi-restraints excluded: chain A residue  399 ILE
Chi-restraints excluded: chain A residue  440 VAL
Chi-restraints excluded: chain A residue  450 VAL
Chi-restraints excluded: chain A residue  489 ASP
Chi-restraints excluded: chain A residue  534 VAL
Chi-restraints excluded: chain A residue  546 LEU
Chi-restraints excluded: chain A residue  570 LEU
Chi-restraints excluded: chain A residue  694 VAL
Chi-restraints excluded: chain A residue  800 HIS
Chi-restraints excluded: chain A residue  903 VAL
Chi-restraints excluded: chain A residue  971 VAL
Chi-restraints excluded: chain A residue 1000 ILE
Chi-restraints excluded: chain A residue 1024 LEU
Chi-restraints excluded: chain A residue 1057 THR
Chi-restraints excluded: chain A residue 1063 ILE
Chi-restraints excluded: chain A residue 1108 THR
Chi-restraints excluded: chain A residue 1115 TYR
Chi-restraints excluded: chain A residue 1148 GLU
Chi-restraints excluded: chain A residue 1164 MET
Chi-restraints excluded: chain A residue 1168 ARG
Chi-restraints excluded: chain A residue 1183 LEU
Chi-restraints excluded: chain A residue 1211 GLU
Chi-restraints excluded: chain A residue 1309 LYS
Chi-restraints excluded: chain A residue 1317 LYS
Chi-restraints excluded: chain A residue 1321 ILE
Chi-restraints excluded: chain A residue 1327 VAL
Chi-restraints excluded: chain A residue 1332 THR
Chi-restraints excluded: chain A residue 1399 ILE
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 137
   random chunks:
   chunk 10 optimal weight:    0.1980
   chunk 19 optimal weight:    5.9990
   chunk 130 optimal weight:   20.0000
   chunk 59 optimal weight:    7.9990
   chunk 88 optimal weight:    1.9990
   chunk 81 optimal weight:    3.9990
   chunk 36 optimal weight:    4.9990
   chunk 115 optimal weight:    9.9990
   chunk 60 optimal weight:    9.9990
   chunk 45 optimal weight:    3.9990
   chunk 50 optimal weight:    0.9990
   overall best weight:    2.2388

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

Flipped N/Q/H residues before XYZ refinement:
** A 159 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 954 HIS
A1287 ASN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4337 r_free = 0.4337 target = 0.210380 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 47)----------------|
| r_work = 0.3486 r_free = 0.3486 target = 0.127032 restraints weight = 12469.508|
|-----------------------------------------------------------------------------|
r_work (start): 0.3366 rms_B_bonded: 2.85
r_work: 0.3081 rms_B_bonded: 3.15 restraints_weight: 0.5000
r_work: 0.2936 rms_B_bonded: 4.83 restraints_weight: 0.2500
r_work (final): 0.2936
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8288
moved from start:          0.2303

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.006   0.052  11409  Z= 0.241
  Angle     :  0.641   9.229  15545  Z= 0.333
  Chirality :  0.044   0.185   1806
  Planarity :  0.004   0.047   1910
  Dihedral  :  7.581  57.395   2029
  Min Nonbonded Distance : 2.456

Molprobity Statistics.
  All-atom Clashscore : 5.09
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.13 %
    Favored  : 96.87 %
  Rotamer:
    Outliers :  3.19 %
    Allowed  : 18.44 %
    Favored  : 78.37 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 1.72 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  1.46 (0.23), residues: 1373
  helix:  1.67 (0.17), residues: 907
  sheet:  0.80 (0.63), residues: 76
  loop : -0.62 (0.31), residues: 390

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.000   ARG A1117 
 TYR   0.018   0.002   TYR A 369 
 PHE   0.030   0.002   PHE A1034 
 TRP   0.016   0.002   TRP A1142 
 HIS   0.005   0.001   HIS A 954 

Details of bonding type rmsd
  covalent geometry    : bond        0.00570 (11408)
  covalent geometry    : angle       0.64082 (15543)
  SS BOND              : bond        0.00269 (    1)
  SS BOND              : angle       1.17568 (    2)
  hydrogen bonds       : bond        0.10537 (  690)
  hydrogen bonds       : angle       4.38455 ( 2031)

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

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

  2746 Ramachandran restraints generated.
    1373 Oldfield, 0 Emsley, 1373 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2746 Ramachandran restraints generated.
    1373 Oldfield, 0 Emsley, 1373 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  131 residues out of total 1194 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 38
    poor density    : 93
  time to evaluate  : 0.414 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  136 ILE cc_start: 0.7818 (mp) cc_final: 0.7384 (OUTLIER)
REVERT: A  192 MET cc_start: 0.6414 (mmm) cc_final: 0.6034 (tpp)
REVERT: A  572 MET cc_start: 0.6922 (mmm) cc_final: 0.6513 (tpp)
REVERT: A 1024 LEU cc_start: 0.7515 (OUTLIER) cc_final: 0.7157 (mp)
REVERT: A 1168 ARG cc_start: 0.8755 (OUTLIER) cc_final: 0.8462 (ttp-110)
REVERT: A 1208 ASN cc_start: 0.7295 (m-40) cc_final: 0.6748 (m-40)
REVERT: A 1211 GLU cc_start: 0.8147 (OUTLIER) cc_final: 0.7579 (pt0)
REVERT: A 1309 LYS cc_start: 0.8106 (OUTLIER) cc_final: 0.7627 (mtmm)
  outliers start: 38
  outliers final: 28
  residues processed: 125
  average time/residue: 0.4941
  time to fit residues: 67.8992
Evaluate side-chains
  122 residues out of total 1194 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 31
    poor density    : 91
  time to evaluate  : 0.435 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   58 LEU
Chi-restraints excluded: chain A residue   63 VAL
Chi-restraints excluded: chain A residue  232 ASN
Chi-restraints excluded: chain A residue  260 TRP
Chi-restraints excluded: chain A residue  298 LEU
Chi-restraints excluded: chain A residue  315 SER
Chi-restraints excluded: chain A residue  364 VAL
Chi-restraints excluded: chain A residue  385 ARG
Chi-restraints excluded: chain A residue  399 ILE
Chi-restraints excluded: chain A residue  440 VAL
Chi-restraints excluded: chain A residue  450 VAL
Chi-restraints excluded: chain A residue  489 ASP
Chi-restraints excluded: chain A residue  534 VAL
Chi-restraints excluded: chain A residue  546 LEU
Chi-restraints excluded: chain A residue  694 VAL
Chi-restraints excluded: chain A residue  903 VAL
Chi-restraints excluded: chain A residue  971 VAL
Chi-restraints excluded: chain A residue 1000 ILE
Chi-restraints excluded: chain A residue 1024 LEU
Chi-restraints excluded: chain A residue 1063 ILE
Chi-restraints excluded: chain A residue 1108 THR
Chi-restraints excluded: chain A residue 1115 TYR
Chi-restraints excluded: chain A residue 1148 GLU
Chi-restraints excluded: chain A residue 1168 ARG
Chi-restraints excluded: chain A residue 1183 LEU
Chi-restraints excluded: chain A residue 1211 GLU
Chi-restraints excluded: chain A residue 1309 LYS
Chi-restraints excluded: chain A residue 1321 ILE
Chi-restraints excluded: chain A residue 1327 VAL
Chi-restraints excluded: chain A residue 1332 THR
Chi-restraints excluded: chain A residue 1399 ILE
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 137
   random chunks:
   chunk 17 optimal weight:    1.9990
   chunk 61 optimal weight:   10.0000
   chunk 114 optimal weight:    0.9990
   chunk 20 optimal weight:    0.7980
   chunk 97 optimal weight:    0.3980
   chunk 116 optimal weight:    7.9990
   chunk 37 optimal weight:    3.9990
   chunk 18 optimal weight:    0.8980
   chunk 40 optimal weight:    0.8980
   chunk 8 optimal weight:    0.9980
   chunk 101 optimal weight:    1.9990
   overall best weight:    0.7980

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

Flipped N/Q/H residues before XYZ refinement:
** A 159 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4366 r_free = 0.4366 target = 0.213573 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 46)----------------|
| r_work = 0.3591 r_free = 0.3591 target = 0.134007 restraints weight = 12603.768|
|-----------------------------------------------------------------------------|
r_work (start): 0.3478 rms_B_bonded: 2.40
r_work: 0.3164 rms_B_bonded: 3.18 restraints_weight: 0.5000
r_work: 0.3022 rms_B_bonded: 4.90 restraints_weight: 0.2500
r_work (final): 0.3022
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8258
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   0.043  11409  Z= 0.151
  Angle     :  0.539   8.952  15545  Z= 0.284
  Chirality :  0.040   0.173   1806
  Planarity :  0.004   0.046   1910
  Dihedral  :  7.149  56.982   2029
  Min Nonbonded Distance : 2.486

Molprobity Statistics.
  All-atom Clashscore : 5.00
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.84 %
    Favored  : 97.16 %
  Rotamer:
    Outliers :  2.85 %
    Allowed  : 19.11 %
    Favored  : 78.04 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 1.72 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  1.87 (0.23), residues: 1373
  helix:  2.02 (0.17), residues: 908
  sheet:  0.97 (0.64), residues: 76
  loop : -0.58 (0.31), residues: 389

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG A 599 
 TYR   0.016   0.001   TYR A 369 
 PHE   0.025   0.001   PHE A1034 
 TRP   0.021   0.001   TRP A1142 
 HIS   0.003   0.001   HIS A 193 

Details of bonding type rmsd
  covalent geometry    : bond        0.00295 (11408)
  covalent geometry    : angle       0.53922 (15543)
  SS BOND              : bond        0.00285 (    1)
  SS BOND              : angle       0.73314 (    2)
  hydrogen bonds       : bond        0.08344 (  690)
  hydrogen bonds       : angle       4.21430 ( 2031)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 5014.64 seconds
wall clock time: 85 minutes 43.43 seconds (5143.43 seconds total)