Starting phenix.real_space_refine
on Sun Apr  5 15:36:14 2026 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/9u58_63866/04_2026/9u58_63866_neut.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/9u58_63866/04_2026/9u58_63866.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=3.36
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    model {
      file = "/net/cci-nas-00/data/ceres_data/9u58_63866/04_2026/9u58_63866_neut.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/9u58_63866/04_2026/9u58_63866_neut.cif"
    real_map_files = "/net/cci-nas-00/data/ceres_data/9u58_63866/04_2026/9u58_63866.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/9u58_63866/04_2026/9u58_63866.map"
  }
  resolution = 3.36
  write_initial_geo_file = False
  refinement {
    macro_cycles = 10
  }


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

Validating inputs
Origin is already at (0, 0, 0), no shifts will be applied
-------------------------------------------------------------------------------
Processing inputs
*****************
Set random seed
  Set to: 0
Set model cs if undefined
Decide on map wrapping
  Map wrapping is set to: False
Normalize map: mean=0, sd=1
  Input map: mean=   0.001 sd=   0.037
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      53      5.16       5
     C    7275      2.51       5
     N    1847      2.21       5
     O    1969      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

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

  Monomer Library directory:
    "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.1rc1-6017/lib/python3.9/site-packages/chem_data/mon_lib"
  Total number of atoms: 11144
  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: 229
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 8, 229
          Unusual residues: {'CLR': 7}
          Classifications: {'peptide': 1, 'undetermined': 7}
          Link IDs: {None: 7}
  Time building chain proxies: 2.56, per 1000 atoms: 0.23
  Number of scatterers: 11144
  At special positions: 0
  Unit cell: (82.88, 97.68, 150.96, 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      53     16.00
     O    1969      8.00
     N    1847      7.00
     C    7275      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: 0.99
  Conformation dependent library (CDL) restraints added in 494.9 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:  2574

  Finding SS restraints...
    Secondary structure from input PDB file:
      63 helices and 6 sheets defined
      67.9% alpha, 3.1% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 0.41
  Creating SS restraints...
    Processing helix  chain 'A' and resid 5 through 11
    Processing helix  chain 'A' and resid 17 through 22
    Processing helix  chain 'A' and resid 29 through 59
    Processing helix  chain 'A' and resid 75 through 94
      removed outlier: 3.950A  pdb=" N   LEU A  79 " --> pdb=" O   TYR A  75 " (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 164
      removed outlier: 3.919A  pdb=" N   VAL A 164 " --> pdb=" O   LEU A 160 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 165 through 168
    Processing helix  chain 'A' and resid 169 through 192
    Processing helix  chain 'A' and resid 226 through 231
      removed outlier: 4.279A  pdb=" N   LYS A 229 " --> pdb=" O   CYS A 226 " (cutoff:3.500A)
      removed outlier: 3.858A  pdb=" N   ALA A 231 " --> pdb=" O   GLU A 228 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 233 through 238
    Processing helix  chain 'A' and resid 239 through 241
      No H-bonds generated for 'chain 'A' and resid 239 through 241'
    Processing helix  chain 'A' and resid 242 through 252
      removed outlier: 3.733A  pdb=" N   MET A 246 " --> pdb=" O   MET A 242 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 267 through 284
      removed outlier: 3.813A  pdb=" N   GLN A 284 " --> pdb=" O   ASP A 280 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 289 through 299
      removed outlier: 3.801A  pdb=" N   ALA A 293 " --> pdb=" O   TRP A 289 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 300 through 316
      removed outlier: 4.466A  pdb=" N   TRP A 308 " --> pdb=" O   TRP A 304 " (cutoff:3.500A)
      removed outlier: 4.155A  pdb=" N   GLY A 311 " --> pdb=" O   PHE A 307 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 317 through 332
      removed outlier: 3.778A  pdb=" N   LEU A 321 " --> pdb=" O   PHE A 317 " (cutoff:3.500A)
      removed outlier: 3.791A  pdb=" N   LEU A 322 " --> pdb=" O   VAL A 318 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 335 through 337
      No H-bonds generated for 'chain 'A' and resid 335 through 337'
    Processing helix  chain 'A' and resid 338 through 384
    Processing helix  chain 'A' and resid 387 through 396
    Processing helix  chain 'A' and resid 398 through 404
    Processing helix  chain 'A' and resid 405 through 416
      removed outlier: 4.051A  pdb=" N   GLN A 415 " --> pdb=" O   GLN A 411 " (cutoff:3.500A)
      removed outlier: 4.217A  pdb=" N   SER A 416 " --> pdb=" O   GLN A 412 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 418 through 438
      Proline residue:  A 424  - end of helix
    Processing helix  chain 'A' and resid 440 through 451
      removed outlier: 4.452A  pdb=" N   LEU A 451 " --> pdb=" O   LEU A 447 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 453 through 483
      removed outlier: 3.513A  pdb=" N   THR A 457 " --> pdb=" O   PHE A 453 " (cutoff:3.500A)
      removed outlier: 3.731A  pdb=" N   VAL A 458 " --> pdb=" O   PRO A 454 " (cutoff:3.500A)
      removed outlier: 4.133A  pdb=" N   ILE A 459 " --> pdb=" O   LEU A 455 " (cutoff:3.500A)
      removed outlier: 4.083A  pdb=" N   ILE A 460 " --> pdb=" O   GLN A 456 " (cutoff:3.500A)
      removed outlier: 3.642A  pdb=" N   GLU A 469 " --> pdb=" O   LYS A 465 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 487 through 495
      removed outlier: 4.274A  pdb=" N   CYS A 493 " --> pdb=" O   ASP A 489 " (cutoff:3.500A)
      removed outlier: 3.507A  pdb=" N   ALA A 495 " --> pdb=" O   VAL A 491 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 497 through 547
      removed outlier: 4.453A  pdb=" N   LYS A 503 " --> pdb=" O   SER A 499 " (cutoff:3.500A)
      removed outlier: 3.551A  pdb=" N   VAL A 504 " --> pdb=" O   PHE A 500 " (cutoff:3.500A)
      removed outlier: 5.182A  pdb=" N   THR A 506 " --> pdb=" O   SER A 502 " (cutoff:3.500A)
      removed outlier: 4.135A  pdb=" N   LEU A 524 " --> pdb=" O   LEU A 520 " (cutoff:3.500A)
      removed outlier: 3.782A  pdb=" N   ASN A 525 " --> pdb=" O   LEU A 521 " (cutoff:3.500A)
      removed outlier: 3.941A  pdb=" N   MET A 526 " --> pdb=" O   GLY A 522 " (cutoff:3.500A)
      removed outlier: 3.851A  pdb=" N   ILE A 528 " --> pdb=" O   LEU A 524 " (cutoff:3.500A)
      Proline residue:  A 533  - end of helix
      removed outlier: 3.512A  pdb=" N   LEU A 547 " --> pdb=" O   VAL A 543 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 552 through 566
    Processing helix  chain 'A' and resid 566 through 594
      removed outlier: 4.146A  pdb=" N   LEU A 570 " --> pdb=" O   LEU A 566 " (cutoff:3.500A)
      removed outlier: 3.536A  pdb=" N   PHE A 571 " --> pdb=" O   ARG A 567 " (cutoff:3.500A)
      Proline residue:  A 574  - end of helix
    Processing helix  chain 'A' and resid 654 through 663
    Processing helix  chain 'A' and resid 693 through 698
    Processing helix  chain 'A' and resid 705 through 716
      removed outlier: 3.654A  pdb=" N   THR A 716 " --> pdb=" O   ALA A 712 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 717 through 725
      removed outlier: 3.894A  pdb=" N   ASP A 721 " --> pdb=" O   SER A 717 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 727 through 731
      removed outlier: 3.817A  pdb=" N   LEU A 730 " --> pdb=" O   GLY A 727 " (cutoff:3.500A)
      removed outlier: 3.525A  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 734 through 738
      removed outlier: 3.891A  pdb=" N   VAL A 738 " --> pdb=" O   GLU A 735 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 741 through 757
    Processing helix  chain 'A' and resid 765 through 770
      removed outlier: 3.883A  pdb=" N   SER A 768 " --> pdb=" O   ASP A 765 " (cutoff:3.500A)
      removed outlier: 4.113A  pdb=" N   ALA A 769 " --> pdb=" O   PRO A 766 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 771 through 782
      removed outlier: 3.573A  pdb=" N   GLY A 775 " --> pdb=" O   ASP A 771 " (cutoff:3.500A)
    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
      removed outlier: 3.759A  pdb=" N   MET A 836 " --> pdb=" O   PHE A 832 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 904 through 916
      removed outlier: 3.575A  pdb=" N   GLY A 916 " --> pdb=" O   GLN A 912 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 918 through 947
      removed outlier: 3.571A  pdb=" N   LEU A 924 " --> pdb=" O   VAL A 920 " (cutoff:3.500A)
      removed outlier: 3.797A  pdb=" N   ASP A 947 " --> pdb=" O   SER A 943 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 957 through 966
      removed outlier: 3.747A  pdb=" N   ILE A 962 " --> pdb=" O   PHE A 958 " (cutoff:3.500A)
      removed outlier: 3.524A  pdb=" N   TYR A 963 " --> pdb=" O   TYR A 959 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 986 through 1001
      removed outlier: 3.962A  pdb=" N   LYS A 990 " --> pdb=" O   LEU A 986 " (cutoff:3.500A)
      removed outlier: 4.499A  pdb=" N   LEU A 992 " --> pdb=" O   ALA A 988 " (cutoff:3.500A)
      removed outlier: 3.680A  pdb=" N   ASP A 994 " --> pdb=" O   LYS A 990 " (cutoff:3.500A)
      removed outlier: 4.174A  pdb=" N   ASN A 995 " --> pdb=" O   LYS A 991 " (cutoff:3.500A)
      removed outlier: 4.209A  pdb=" N   MET A 996 " --> pdb=" O   LEU A 992 " (cutoff:3.500A)
      removed outlier: 3.687A  pdb=" N   ILE A1000 " --> pdb=" O   MET A 996 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 1004 through 1011
      removed outlier: 4.000A  pdb=" N   PHE A1008 " --> pdb=" O   PRO A1004 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 1012 through 1030
      removed outlier: 3.912A  pdb=" N   ILE A1016 " --> pdb=" O   PRO A1012 " (cutoff:3.500A)
      removed outlier: 4.524A  pdb=" N   ASP A1023 " --> pdb=" O   ARG A1019 " (cutoff:3.500A)
      removed outlier: 4.417A  pdb=" N   LEU A1024 " --> pdb=" O   PHE A1020 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 1030 through 1056
      removed outlier: 3.918A  pdb=" N   PHE A1038 " --> pdb=" O   PHE A1034 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 1056 through 1092
      removed outlier: 3.848A  pdb=" N   LEU A1060 " --> pdb=" O   SER A1056 " (cutoff:3.500A)
      Proline residue:  A1065  - end of helix
      removed outlier: 4.944A  pdb=" N   THR A1080 " --> pdb=" O   TYR A1076 " (cutoff:3.500A)
      removed outlier: 3.973A  pdb=" N   GLU A1083 " --> pdb=" O   ASN A1079 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 1093 through 1112
      removed outlier: 4.541A  pdb=" N   PHE A1099 " --> pdb=" O   VAL A1095 " (cutoff:3.500A)
      removed outlier: 4.459A  pdb=" N   GLY A1100 " --> pdb=" O   TYR A1096 " (cutoff:3.500A)
      removed outlier: 5.586A  pdb=" N   SER A1107 " --> pdb=" O   LEU A1103 " (cutoff:3.500A)
      removed outlier: 5.940A  pdb=" N   THR A1108 " --> pdb=" O   ASN A1104 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 1114 through 1165
      removed outlier: 4.117A  pdb=" N   MET A1118 " --> pdb=" O   ALA A1114 " (cutoff:3.500A)
      removed outlier: 4.612A  pdb=" N   PHE A1132 " --> pdb=" O   ASN A1128 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 1177 through 1185
    Processing helix  chain 'A' and resid 1194 through 1199
    Processing helix  chain 'A' and resid 1199 through 1218
      removed outlier: 4.767A  pdb=" N   ALA A1209 " --> pdb=" O   ASN A1205 " (cutoff:3.500A)
      removed outlier: 4.839A  pdb=" N   VAL A1210 " --> pdb=" O   SER A1206 " (cutoff:3.500A)
      removed outlier: 3.984A  pdb=" N   GLU A1211 " --> pdb=" O   LEU A1207 " (cutoff:3.500A)
      removed outlier: 3.704A  pdb=" N   TYR A1216 " --> pdb=" O   ARG A1212 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 1282 through 1290
      removed outlier: 4.091A  pdb=" N   LEU A1286 " --> pdb=" O   LYS A1282 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 1306 through 1310
    Processing helix  chain 'A' and resid 1311 through 1317
      removed outlier: 3.727A  pdb=" N   ARG A1316 " --> pdb=" O   LEU A1312 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 1333 through 1338
    Processing helix  chain 'A' and resid 1344 through 1355
      removed outlier: 3.747A  pdb=" N   ALA A1355 " --> pdb=" O   SER A1351 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 1357 through 1364
      removed outlier: 3.831A  pdb=" N   ARG A1363 " --> pdb=" O   ASP A1359 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 1366 through 1369
      removed outlier: 4.227A  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 1380 through 1396
      removed outlier: 3.530A  pdb=" N   ARG A1384 " --> pdb=" O   SER A1380 " (cutoff:3.500A)
      removed outlier: 3.727A  pdb=" N   SER A1390 " --> pdb=" O   LEU A1386 " (cutoff:3.500A)
      removed outlier: 3.522A  pdb=" N   ARG A1391 " --> pdb=" O   LEU A1387 " (cutoff:3.500A)
      removed outlier: 3.712A  pdb=" N   ALA A1392 " --> pdb=" O   SER A1388 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 1410 through 1425
      removed outlier: 3.985A  pdb=" N   THR A1420 " --> pdb=" O   LEU A1416 " (cutoff:3.500A)
      removed outlier: 3.728A  pdb=" N   PHE A1425 " --> pdb=" O   ILE A1421 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 1436 through 1440
    Processing sheet with id=AA1, first strand: chain 'A' and resid 638 through 639
      removed outlier: 3.613A  pdb=" N   ARG A 617 " --> pdb=" O   ILE A 673 " (cutoff:3.500A)
    Processing sheet with id=AA2, first strand: chain 'A' and resid 619 through 621
      removed outlier: 5.646A  pdb=" N   GLY A 619 " --> pdb=" O   ASN A 634 " (cutoff:3.500A)
    Processing sheet with id=AA3, first strand: chain 'A' and resid 760 through 762
      removed outlier: 6.926A  pdb=" N   TYR A 761 " --> pdb=" O   VAL A 793 " (cutoff:3.500A)
  No H-bonds generated for sheet with id=AA3
    Processing sheet with id=AA4, first strand: chain 'A' and resid 1259 through 1265
      removed outlier: 6.131A  pdb=" N   HIS A1260 " --> pdb=" O   LEU A1249 " (cutoff:3.500A)
      removed outlier: 7.685A  pdb=" N   LEU A1249 " --> pdb=" O   HIS A1260 " (cutoff:3.500A)
      removed outlier: 7.167A  pdb=" N   PHE A1264 " --> pdb=" O   GLU A1245 " (cutoff:3.500A)
      removed outlier: 5.453A  pdb=" N   GLU A1245 " --> pdb=" O   PHE A1264 " (cutoff:3.500A)
      removed outlier: 3.567A  pdb=" N   ARG A1299 " --> pdb=" O   GLU A1245 " (cutoff:3.500A)
      removed outlier: 4.170A  pdb=" N   VAL A1247 " --> pdb=" O   LYS A1297 " (cutoff:3.500A)
      removed outlier: 6.770A  pdb=" N   LYS A1297 " --> pdb=" O   VAL A1247 " (cutoff:3.500A)
    Processing sheet with id=AA5, first strand: chain 'A' and resid 1274 through 1276
      removed outlier: 4.192A  pdb=" N   GLU A1456 " --> pdb=" O   VAL A1448 " (cutoff:3.500A)
    Processing sheet with id=AA6, first strand: chain 'A' and resid 1331 through 1332
      removed outlier: 3.909A  pdb=" N   GLY A1331 " --> pdb=" O   VAL A1372 " (cutoff:3.500A)

    620 hydrogen bonds defined for protein.
    1815 hydrogen bond angles defined for protein.
    Restraints generated for nucleic acids:
      0 hydrogen bonds
      0 hydrogen bond angles
      0 basepair planarities
      0 basepair parallelities
      0 stacking parallelities
  Total time for adding SS restraints: 1.91

  Time building geometry restraints manager: 1.25 seconds

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

  Histogram of bond lengths:
        1.18 -     1.31: 1760
        1.31 -     1.43: 2995
        1.43 -     1.56: 6560
        1.56 -     1.69: 3
        1.69 -     1.81: 92
  Bond restraints: 11410
  Sorted by residual:
  bond pdb=" C6  ATA A1501 "
       pdb=" N11 ATA A1501 "
    ideal  model  delta    sigma   weight residual
    1.340  1.454 -0.114 2.00e-02 2.50e+03 3.23e+01
  bond pdb=" C   ATA A1501 "
       pdb=" ND  ATA A1501 "
    ideal  model  delta    sigma   weight residual
    1.332  1.436 -0.104 2.00e-02 2.50e+03 2.69e+01
  bond pdb=" CA  SER A 499 "
       pdb=" C   SER A 499 "
    ideal  model  delta    sigma   weight residual
    1.522  1.451  0.071 1.38e-02 5.25e+03 2.65e+01
  bond pdb=" C4  ATA A1501 "
       pdb=" N7  ATA A1501 "
    ideal  model  delta    sigma   weight residual
    1.342  1.443 -0.101 2.00e-02 2.50e+03 2.54e+01
  bond pdb=" N   ATA A1501 "
       pdb=" C'  ATA A1501 "
    ideal  model  delta    sigma   weight residual
    1.348  1.443 -0.095 2.00e-02 2.50e+03 2.24e+01
  ... (remaining 11405 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     3.33: 15161
        3.33 -     6.66: 322
        6.66 -    10.00: 46
       10.00 -    13.33: 4
       13.33 -    16.66: 5
  Bond angle restraints: 15538
  Sorted by residual:
  angle pdb=" CA  PRO A1339 "
        pdb=" N   PRO A1339 "
        pdb=" CD  PRO A1339 "
      ideal   model   delta    sigma   weight residual
     112.00   96.16   15.84 1.40e+00 5.10e-01 1.28e+02
  angle pdb=" N   PRO A1225 "
        pdb=" CA  PRO A1225 "
        pdb=" CB  PRO A1225 "
      ideal   model   delta    sigma   weight residual
     103.25   96.33    6.92 1.05e+00 9.07e-01 4.34e+01
  angle pdb=" C   GLU A 166 "
        pdb=" N   TYR A 167 "
        pdb=" CA  TYR A 167 "
      ideal   model   delta    sigma   weight residual
     123.17  114.08    9.09 1.49e+00 4.50e-01 3.72e+01
  angle pdb=" N   LYS A 503 "
        pdb=" CA  LYS A 503 "
        pdb=" C   LYS A 503 "
      ideal   model   delta    sigma   weight residual
     114.62  108.20    6.42 1.14e+00 7.69e-01 3.17e+01
  angle pdb=" C2  ATA A1501 "
        pdb=" N1  ATA A1501 "
        pdb=" C6  ATA A1501 "
      ideal   model   delta    sigma   weight residual
     113.99  130.65  -16.66 3.00e+00 1.11e-01 3.08e+01
  ... (remaining 15533 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    24.42: 6622
       24.42 -    48.83: 415
       48.83 -    73.24: 70
       73.24 -    97.66: 11
       97.66 -   122.07: 3
  Dihedral angle restraints: 7121
    sinusoidal: 3127
      harmonic: 3994
  Sorted by residual:
  dihedral pdb=" CD  ARG A  53 "
           pdb=" NE  ARG A  53 "
           pdb=" CZ  ARG A  53 "
           pdb=" NH1 ARG A  53 "
      ideal   model   delta sinusoidal    sigma   weight residual
       0.00  -47.84   47.84     1      1.00e+01 1.00e-02 3.16e+01
  dihedral pdb=" CA  THR A 255 "
           pdb=" C   THR A 255 "
           pdb=" N   GLU A 256 "
           pdb=" CA  GLU A 256 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  154.66   25.34     0      5.00e+00 4.00e-02 2.57e+01
  dihedral pdb=" CA  SER A 967 "
           pdb=" C   SER A 967 "
           pdb=" N   PHE A 968 "
           pdb=" CA  PHE A 968 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  155.96   24.04     0      5.00e+00 4.00e-02 2.31e+01
  ... (remaining 7118 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.065: 1307
       0.065 -    0.130: 422
       0.130 -    0.194: 61
       0.194 -    0.259: 7
       0.259 -    0.324: 3
  Chirality restraints: 1800
  Sorted by residual:
  chirality pdb=" CB  ILE A1433 "
            pdb=" CA  ILE A1433 "
            pdb=" CG1 ILE A1433 "
            pdb=" CG2 ILE A1433 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.64    2.32    0.32 2.00e-01 2.50e+01 2.62e+00
  chirality pdb=" CG  LEU A1051 "
            pdb=" CB  LEU A1051 "
            pdb=" CD1 LEU A1051 "
            pdb=" CD2 LEU A1051 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.59   -2.31   -0.28 2.00e-01 2.50e+01 1.92e+00
  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    2.23    0.28 2.00e-01 2.50e+01 1.91e+00
  ... (remaining 1797 not shown)

  Planarity restraints: 1915
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CD  ARG A  53 "    0.815 9.50e-02 1.11e+02   3.65e-01 8.11e+01
        pdb=" NE  ARG A  53 "   -0.048 2.00e-02 2.50e+03
        pdb=" CZ  ARG A  53 "   -0.010 2.00e-02 2.50e+03
        pdb=" NH1 ARG A  53 "   -0.002 2.00e-02 2.50e+03
        pdb=" NH2 ARG A  53 "    0.024 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CB  TRP A 265 "    0.056 2.00e-02 2.50e+03   5.45e-02 7.42e+01
        pdb=" CG  TRP A 265 "   -0.140 2.00e-02 2.50e+03
        pdb=" CD1 TRP A 265 "    0.080 2.00e-02 2.50e+03
        pdb=" CD2 TRP A 265 "   -0.007 2.00e-02 2.50e+03
        pdb=" NE1 TRP A 265 "   -0.015 2.00e-02 2.50e+03
        pdb=" CE2 TRP A 265 "   -0.004 2.00e-02 2.50e+03
        pdb=" CE3 TRP A 265 "    0.007 2.00e-02 2.50e+03
        pdb=" CZ2 TRP A 265 "    0.004 2.00e-02 2.50e+03
        pdb=" CZ3 TRP A 265 "    0.008 2.00e-02 2.50e+03
        pdb=" CH2 TRP A 265 "    0.011 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   ASP A1338 "    0.110 5.00e-02 4.00e+02   1.53e-01 3.74e+01
        pdb=" N   PRO A1339 "   -0.264 5.00e-02 4.00e+02
        pdb=" CA  PRO A1339 "    0.075 5.00e-02 4.00e+02
        pdb=" CD  PRO A1339 "    0.078 5.00e-02 4.00e+02
  ... (remaining 1912 not shown)

  Histogram of nonbonded interaction distances:
        2.20 -     2.74: 1651
        2.74 -     3.28: 11313
        3.28 -     3.82: 17579
        3.82 -     4.36: 20529
        4.36 -     4.90: 34780
  Nonbonded interactions: 85852
  Sorted by model distance:
  nonbonded pdb=" O   ARG A1436 "
            pdb=" OG1 THR A1439 "
     model   vdw
     2.198 3.040
  nonbonded pdb=" O   LEU A  39 "
            pdb=" NE2 GLN A  43 "
     model   vdw
     2.198 3.120
  nonbonded pdb=" O   ARG A1422 "
            pdb=" NZ  LYS A1426 "
     model   vdw
     2.201 3.120
  nonbonded pdb=" O   PHE A 968 "
            pdb=" N   VAL A 971 "
     model   vdw
     2.205 3.120
  nonbonded pdb=" OD2 ASP A 721 "
            pdb=" NH1 ARG A 747 "
     model   vdw
     2.210 3.120
  ... (remaining 85847 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:             3.960
  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:          0.200
  Check model and map are aligned:         0.030
  Set scattering table:                    0.030
  Process input model:                     11.220
  Find NCS groups from input model:        0.050
  Set up NCS constraints:                  0.020
  Set refine NCS operators:                0.000
  Adjust number of macro_cycles:           0.000
  Reset NCS operators:                     0.000
  Extract rigid body selections:           0.000
  Check and reset occupancies:             0.000
  Load rotamer database and sin/cos tables:1.340
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   16.870
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8208
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      :  0.014   0.121  11411  Z= 0.605
  Angle     :  1.220  16.661  15540  Z= 0.664
  Chirality :  0.062   0.324   1800
  Planarity :  0.011   0.365   1915
  Dihedral  : 15.563 122.075   4544
  Min Nonbonded Distance : 2.198

Molprobity Statistics.
  All-atom Clashscore : 15.67
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  8.30 %
    Favored  : 91.70 %
  Rotamer:
    Outliers :  1.51 %
    Allowed  :  1.34 %
    Favored  : 97.15 %
  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: -2.23 (0.21), residues: 1373
  helix: -1.17 (0.16), residues: 861
  sheet: -1.33 (0.66), residues: 65
  loop : -1.82 (0.27), residues: 447

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.017   0.001   ARG A 370 
 TYR   0.060   0.004   TYR A1185 
 PHE   0.029   0.003   PHE A 425 
 TRP   0.140   0.005   TRP A 265 
 HIS   0.006   0.001   HIS A 193 

Details of bonding type rmsd
  covalent geometry    : bond        0.01421 (11410)
  covalent geometry    : angle       1.22010 (15538)
  SS BOND              : bond        0.00229 (    1)
  SS BOND              : angle       1.30931 (    2)
  hydrogen bonds       : bond        0.18093 (  620)
  hydrogen bonds       : angle       6.96347 ( 1815)

*********************** 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
  152 residues out of total 1194 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 18
    poor density    : 134
  time to evaluate  : 0.402 
Fit side-chains
   revert: symmetry clash
REVERT: A   87 GLU cc_start: 0.8144 (tm-30) cc_final: 0.7911 (tm-30)
REVERT: A  112 PHE cc_start: 0.8353 (m-80) cc_final: 0.8090 (m-80)
REVERT: A  133 LYS cc_start: 0.7743 (ptmt) cc_final: 0.7409 (mmmt)
REVERT: A  382 LYS cc_start: 0.8077 (OUTLIER) cc_final: 0.7678 (mmmt)
REVERT: A 1185 TYR cc_start: 0.8156 (m-10) cc_final: 0.7796 (m-10)
REVERT: A 1250 ARG cc_start: 0.8021 (mtp180) cc_final: 0.7461 (mtp180)
REVERT: A 1418 GLN cc_start: 0.8792 (tp-100) cc_final: 0.8536 (tp-100)
  outliers start: 18
  outliers final: 12
  residues processed: 149
  average time/residue: 0.1031
  time to fit residues: 22.3371
Evaluate side-chains
  126 residues out of total 1194 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 113
  time to evaluate  : 0.411 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   53 ARG
Chi-restraints excluded: chain A residue  163 SER
Chi-restraints excluded: chain A residue  165 LYS
Chi-restraints excluded: chain A residue  166 GLU
Chi-restraints excluded: chain A residue  382 LYS
Chi-restraints excluded: chain A residue  398 LYS
Chi-restraints excluded: chain A residue  399 ILE
Chi-restraints excluded: chain A residue  531 SER
Chi-restraints excluded: chain A residue  532 ILE
Chi-restraints excluded: chain A residue 1189 ILE
Chi-restraints excluded: chain A residue 1190 THR
Chi-restraints excluded: chain A residue 1193 LEU
Chi-restraints excluded: chain A residue 1194 THR
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 137
   random chunks:
   chunk 98 optimal weight:    0.7980
   chunk 107 optimal weight:    0.9990
   chunk 10 optimal weight:    6.9990
   chunk 66 optimal weight:    5.9990
   chunk 130 optimal weight:    3.9990
   chunk 124 optimal weight:    0.9980
   chunk 103 optimal weight:    0.7980
   chunk 77 optimal weight:    5.9990
   chunk 122 optimal weight:    0.9980
   chunk 91 optimal weight:    0.8980
   chunk 55 optimal weight:    1.9990
   overall best weight:    0.8980

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

Flipped N/Q/H residues before XYZ refinement:
A  43 GLN
A1079 ASN
** A1383 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4205 r_free = 0.4205 target = 0.192490 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 55)----------------|
| r_work = 0.3651 r_free = 0.3651 target = 0.138699 restraints weight = 13870.844|
|-----------------------------------------------------------------------------|
r_work (start): 0.3625 rms_B_bonded: 1.89
r_work: 0.3264 rms_B_bonded: 2.79 restraints_weight: 0.5000
r_work: 0.3136 rms_B_bonded: 4.50 restraints_weight: 0.2500
r_work (final): 0.3136
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8288
moved from start:          0.1358

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.078  11411  Z= 0.177
  Angle     :  0.724  11.036  15540  Z= 0.362
  Chirality :  0.045   0.244   1800
  Planarity :  0.005   0.072   1915
  Dihedral  : 10.319  64.481   2009
  Min Nonbonded Distance : 2.520

Molprobity Statistics.
  All-atom Clashscore : 9.30
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.44 %
    Favored  : 95.56 %
  Rotamer:
    Outliers :  1.42 %
    Allowed  :  7.54 %
    Favored  : 91.03 %
  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: -1.04 (0.22), residues: 1373
  helix: -0.16 (0.17), residues: 879
  sheet: -0.64 (0.69), residues: 65
  loop : -1.62 (0.29), residues: 429

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.001   ARG A 140 
 TYR   0.028   0.002   TYR A 369 
 PHE   0.014   0.002   PHE A 352 
 TRP   0.034   0.002   TRP A 265 
 HIS   0.003   0.001   HIS A 277 

Details of bonding type rmsd
  covalent geometry    : bond        0.00386 (11410)
  covalent geometry    : angle       0.72401 (15538)
  SS BOND              : bond        0.00347 (    1)
  SS BOND              : angle       0.69576 (    2)
  hydrogen bonds       : bond        0.08147 (  620)
  hydrogen bonds       : angle       5.20979 ( 1815)

*********************** 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
  150 residues out of total 1194 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 17
    poor density    : 133
  time to evaluate  : 0.424 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  698 ILE cc_start: 0.8199 (mt) cc_final: 0.7967 (mm)
REVERT: A  750 MET cc_start: 0.8509 (mpp) cc_final: 0.8046 (mpp)
REVERT: A 1087 MET cc_start: 0.8058 (ttm) cc_final: 0.7806 (mtt)
REVERT: A 1185 TYR cc_start: 0.8274 (m-10) cc_final: 0.8050 (m-10)
REVERT: A 1250 ARG cc_start: 0.8175 (mtp180) cc_final: 0.7730 (mtp180)
REVERT: A 1418 GLN cc_start: 0.8819 (tp-100) cc_final: 0.8577 (tp-100)
  outliers start: 17
  outliers final: 15
  residues processed: 145
  average time/residue: 0.1041
  time to fit residues: 21.7474
Evaluate side-chains
  135 residues out of total 1194 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 15
    poor density    : 120
  time to evaluate  : 0.289 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   48 VAL
Chi-restraints excluded: chain A residue   50 CYS
Chi-restraints excluded: chain A residue   53 ARG
Chi-restraints excluded: chain A residue  166 GLU
Chi-restraints excluded: chain A residue  367 VAL
Chi-restraints excluded: chain A residue  382 LYS
Chi-restraints excluded: chain A residue  402 LEU
Chi-restraints excluded: chain A residue  528 ILE
Chi-restraints excluded: chain A residue  686 VAL
Chi-restraints excluded: chain A residue  902 VAL
Chi-restraints excluded: chain A residue  912 GLN
Chi-restraints excluded: chain A residue 1001 LEU
Chi-restraints excluded: chain A residue 1068 VAL
Chi-restraints excluded: chain A residue 1194 THR
Chi-restraints excluded: chain A residue 1429 THR
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 137
   random chunks:
   chunk 82 optimal weight:    2.9990
   chunk 74 optimal weight:    2.9990
   chunk 80 optimal weight:    7.9990
   chunk 29 optimal weight:    0.7980
   chunk 61 optimal weight:   10.0000
   chunk 48 optimal weight:    0.9990
   chunk 103 optimal weight:    3.9990
   chunk 104 optimal weight:    0.5980
   chunk 36 optimal weight:    3.9990
   chunk 19 optimal weight:    7.9990
   chunk 57 optimal weight:    3.9990
   overall best weight:    1.6786

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

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

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4209 r_free = 0.4209 target = 0.191269 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 75)----------------|
| r_work = 0.3662 r_free = 0.3662 target = 0.138186 restraints weight = 13658.252|
|-----------------------------------------------------------------------------|
r_work (start): 0.3643 rms_B_bonded: 2.03
r_work: 0.3260 rms_B_bonded: 2.95 restraints_weight: 0.5000
r_work: 0.3126 rms_B_bonded: 4.90 restraints_weight: 0.2500
r_work (final): 0.3126
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8349
moved from start:          0.1622

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.057  11411  Z= 0.213
  Angle     :  0.703  12.170  15540  Z= 0.348
  Chirality :  0.045   0.212   1800
  Planarity :  0.005   0.059   1915
  Dihedral  :  9.546  59.834   1990
  Min Nonbonded Distance : 2.512

Molprobity Statistics.
  All-atom Clashscore : 8.45
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.81 %
    Favored  : 95.19 %
  Rotamer:
    Outliers :  2.10 %
    Allowed  : 12.82 %
    Favored  : 85.08 %
  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: -0.66 (0.23), residues: 1373
  helix:  0.14 (0.17), residues: 882
  sheet: -0.40 (0.68), residues: 65
  loop : -1.50 (0.30), residues: 426

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARG A 370 
 TYR   0.033   0.002   TYR A 369 
 PHE   0.021   0.002   PHE A1070 
 TRP   0.028   0.002   TRP A 265 
 HIS   0.002   0.001   HIS A1260 

Details of bonding type rmsd
  covalent geometry    : bond        0.00500 (11410)
  covalent geometry    : angle       0.70340 (15538)
  SS BOND              : bond        0.00215 (    1)
  SS BOND              : angle       0.55425 (    2)
  hydrogen bonds       : bond        0.08171 (  620)
  hydrogen bonds       : angle       5.00661 ( 1815)

*********************** 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
  154 residues out of total 1194 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 25
    poor density    : 129
  time to evaluate  : 0.397 
Fit side-chains
   revert: symmetry clash
REVERT: A  102 ASP cc_start: 0.8042 (p0) cc_final: 0.7777 (p0)
REVERT: A  367 VAL cc_start: 0.8792 (OUTLIER) cc_final: 0.8338 (t)
REVERT: A  382 LYS cc_start: 0.8593 (OUTLIER) cc_final: 0.7684 (mmmt)
REVERT: A  750 MET cc_start: 0.8610 (mpp) cc_final: 0.8088 (mpp)
REVERT: A 1087 MET cc_start: 0.8133 (ttm) cc_final: 0.7877 (mtt)
REVERT: A 1185 TYR cc_start: 0.8357 (m-10) cc_final: 0.8099 (m-10)
REVERT: A 1250 ARG cc_start: 0.8231 (mtp180) cc_final: 0.7869 (mtp180)
REVERT: A 1418 GLN cc_start: 0.8814 (tp-100) cc_final: 0.8531 (tp-100)
  outliers start: 25
  outliers final: 17
  residues processed: 149
  average time/residue: 0.1003
  time to fit residues: 21.8844
Evaluate side-chains
  137 residues out of total 1194 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 19
    poor density    : 118
  time to evaluate  : 0.394 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   47 LEU
Chi-restraints excluded: chain A residue   48 VAL
Chi-restraints excluded: chain A residue  166 GLU
Chi-restraints excluded: chain A residue  260 TRP
Chi-restraints excluded: chain A residue  310 ILE
Chi-restraints excluded: chain A residue  367 VAL
Chi-restraints excluded: chain A residue  369 TYR
Chi-restraints excluded: chain A residue  382 LYS
Chi-restraints excluded: chain A residue  402 LEU
Chi-restraints excluded: chain A residue  490 THR
Chi-restraints excluded: chain A residue  528 ILE
Chi-restraints excluded: chain A residue  686 VAL
Chi-restraints excluded: chain A residue  912 GLN
Chi-restraints excluded: chain A residue  919 TRP
Chi-restraints excluded: chain A residue 1001 LEU
Chi-restraints excluded: chain A residue 1068 VAL
Chi-restraints excluded: chain A residue 1194 THR
Chi-restraints excluded: chain A residue 1383 GLN
Chi-restraints excluded: chain A residue 1429 THR
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 137
   random chunks:
   chunk 126 optimal weight:    6.9990
   chunk 79 optimal weight:    9.9990
   chunk 130 optimal weight:    7.9990
   chunk 71 optimal weight:    9.9990
   chunk 60 optimal weight:    7.9990
   chunk 122 optimal weight:    6.9990
   chunk 37 optimal weight:    0.8980
   chunk 18 optimal weight:    0.8980
   chunk 64 optimal weight:    0.0970
   chunk 131 optimal weight:    2.9990
   chunk 31 optimal weight:    0.9980
   overall best weight:    1.1780

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

Flipped N/Q/H residues before XYZ refinement:
A1336 ASN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4229 r_free = 0.4229 target = 0.193429 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 45)----------------|
| r_work = 0.3693 r_free = 0.3693 target = 0.140897 restraints weight = 13753.925|
|-----------------------------------------------------------------------------|
r_work (start): 0.3672 rms_B_bonded: 2.09
r_work: 0.3285 rms_B_bonded: 3.01 restraints_weight: 0.5000
r_work: 0.3153 rms_B_bonded: 4.91 restraints_weight: 0.2500
r_work (final): 0.3153
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8308
moved from start:          0.1926

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.045  11411  Z= 0.168
  Angle     :  0.653  10.858  15540  Z= 0.321
  Chirality :  0.043   0.182   1800
  Planarity :  0.004   0.038   1915
  Dihedral  :  9.126  58.373   1986
  Min Nonbonded Distance : 2.536

Molprobity Statistics.
  All-atom Clashscore : 7.66
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.86 %
    Favored  : 96.14 %
  Rotamer:
    Outliers :  2.18 %
    Allowed  : 14.33 %
    Favored  : 83.49 %
  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: -0.33 (0.23), residues: 1373
  helix:  0.41 (0.18), residues: 884
  sheet: -0.27 (0.68), residues: 65
  loop : -1.40 (0.29), residues: 424

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG A  53 
 TYR   0.028   0.002   TYR A 369 
 PHE   0.020   0.001   PHE A 119 
 TRP   0.025   0.001   TRP A 496 
 HIS   0.002   0.001   HIS A 193 

Details of bonding type rmsd
  covalent geometry    : bond        0.00377 (11410)
  covalent geometry    : angle       0.65263 (15538)
  SS BOND              : bond        0.00233 (    1)
  SS BOND              : angle       0.42745 (    2)
  hydrogen bonds       : bond        0.07443 (  620)
  hydrogen bonds       : angle       4.78043 ( 1815)

*********************** 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
  155 residues out of total 1194 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 26
    poor density    : 129
  time to evaluate  : 0.448 
Fit side-chains
   revert: symmetry clash
REVERT: A  102 ASP cc_start: 0.8060 (p0) cc_final: 0.7794 (p0)
REVERT: A  367 VAL cc_start: 0.8767 (OUTLIER) cc_final: 0.8318 (t)
REVERT: A  382 LYS cc_start: 0.8564 (OUTLIER) cc_final: 0.7681 (mmmt)
REVERT: A  698 ILE cc_start: 0.8168 (mt) cc_final: 0.7918 (mm)
REVERT: A 1087 MET cc_start: 0.8077 (ttm) cc_final: 0.7854 (mtt)
REVERT: A 1185 TYR cc_start: 0.8327 (m-10) cc_final: 0.8065 (m-80)
REVERT: A 1250 ARG cc_start: 0.8234 (mtp180) cc_final: 0.8031 (mtp180)
REVERT: A 1385 GLN cc_start: 0.9093 (OUTLIER) cc_final: 0.8492 (mp10)
REVERT: A 1418 GLN cc_start: 0.8794 (tp-100) cc_final: 0.8273 (tp-100)
  outliers start: 26
  outliers final: 17
  residues processed: 150
  average time/residue: 0.0978
  time to fit residues: 21.7361
Evaluate side-chains
  137 residues out of total 1194 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 20
    poor density    : 117
  time to evaluate  : 0.404 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   30 THR
Chi-restraints excluded: chain A residue   47 LEU
Chi-restraints excluded: chain A residue   48 VAL
Chi-restraints excluded: chain A residue   50 CYS
Chi-restraints excluded: chain A residue  166 GLU
Chi-restraints excluded: chain A residue  310 ILE
Chi-restraints excluded: chain A residue  367 VAL
Chi-restraints excluded: chain A residue  382 LYS
Chi-restraints excluded: chain A residue  402 LEU
Chi-restraints excluded: chain A residue  528 ILE
Chi-restraints excluded: chain A residue  686 VAL
Chi-restraints excluded: chain A residue  902 VAL
Chi-restraints excluded: chain A residue  912 GLN
Chi-restraints excluded: chain A residue  919 TRP
Chi-restraints excluded: chain A residue 1001 LEU
Chi-restraints excluded: chain A residue 1068 VAL
Chi-restraints excluded: chain A residue 1190 THR
Chi-restraints excluded: chain A residue 1307 VAL
Chi-restraints excluded: chain A residue 1385 GLN
Chi-restraints excluded: chain A residue 1429 THR
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 137
   random chunks:
   chunk 105 optimal weight:    0.6980
   chunk 35 optimal weight:    0.8980
   chunk 38 optimal weight:    0.8980
   chunk 25 optimal weight:    0.0470
   chunk 7 optimal weight:   10.0000
   chunk 65 optimal weight:   10.0000
   chunk 80 optimal weight:    5.9990
   chunk 76 optimal weight:   10.0000
   chunk 5 optimal weight:   10.0000
   chunk 127 optimal weight:    0.9980
   chunk 53 optimal weight:    0.9980
   overall best weight:    0.7078

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4254 r_free = 0.4254 target = 0.196071 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 71)----------------|
| r_work = 0.3726 r_free = 0.3726 target = 0.143573 restraints weight = 13648.892|
|-----------------------------------------------------------------------------|
r_work (start): 0.3705 rms_B_bonded: 1.91
r_work: 0.3354 rms_B_bonded: 2.75 restraints_weight: 0.5000
r_work: 0.3221 rms_B_bonded: 4.56 restraints_weight: 0.2500
r_work (final): 0.3221
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8242
moved from start:          0.2278

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.046  11411  Z= 0.140
  Angle     :  0.603  10.243  15540  Z= 0.297
  Chirality :  0.041   0.158   1800
  Planarity :  0.004   0.036   1915
  Dihedral  :  8.739  59.432   1985
  Min Nonbonded Distance : 2.555

Molprobity Statistics.
  All-atom Clashscore : 7.04
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.86 %
    Favored  : 96.14 %
  Rotamer:
    Outliers :  2.35 %
    Allowed  : 16.18 %
    Favored  : 81.48 %
  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: -0.02 (0.23), residues: 1373
  helix:  0.66 (0.18), residues: 890
  sheet: -0.08 (0.67), residues: 65
  loop : -1.35 (0.30), residues: 418

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG A 906 
 TYR   0.022   0.001   TYR A 369 
 PHE   0.022   0.001   PHE A 119 
 TRP   0.021   0.001   TRP A 496 
 HIS   0.002   0.001   HIS A 954 

Details of bonding type rmsd
  covalent geometry    : bond        0.00292 (11410)
  covalent geometry    : angle       0.60292 (15538)
  SS BOND              : bond        0.00234 (    1)
  SS BOND              : angle       0.35227 (    2)
  hydrogen bonds       : bond        0.06562 (  620)
  hydrogen bonds       : angle       4.52891 ( 1815)

*********************** 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
  158 residues out of total 1194 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 28
    poor density    : 130
  time to evaluate  : 0.400 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  102 ASP cc_start: 0.8035 (p0) cc_final: 0.7794 (p0)
REVERT: A  431 LEU cc_start: 0.8541 (OUTLIER) cc_final: 0.8151 (mt)
REVERT: A  484 VAL cc_start: 0.8350 (t) cc_final: 0.8031 (p)
REVERT: A  698 ILE cc_start: 0.8129 (mt) cc_final: 0.7872 (mm)
REVERT: A  765 ASP cc_start: 0.8210 (t0) cc_final: 0.7870 (t70)
REVERT: A 1185 TYR cc_start: 0.8248 (m-10) cc_final: 0.7952 (m-80)
REVERT: A 1236 TRP cc_start: 0.7766 (t60) cc_final: 0.7488 (t60)
REVERT: A 1250 ARG cc_start: 0.8197 (mtp180) cc_final: 0.7960 (mtp180)
REVERT: A 1418 GLN cc_start: 0.8787 (tp-100) cc_final: 0.8515 (tp-100)
  outliers start: 28
  outliers final: 19
  residues processed: 153
  average time/residue: 0.1001
  time to fit residues: 22.4985
Evaluate side-chains
  143 residues out of total 1194 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 20
    poor density    : 123
  time to evaluate  : 0.398 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   17 VAL
Chi-restraints excluded: chain A residue   30 THR
Chi-restraints excluded: chain A residue   47 LEU
Chi-restraints excluded: chain A residue  166 GLU
Chi-restraints excluded: chain A residue  185 LEU
Chi-restraints excluded: chain A residue  260 TRP
Chi-restraints excluded: chain A residue  310 ILE
Chi-restraints excluded: chain A residue  369 TYR
Chi-restraints excluded: chain A residue  402 LEU
Chi-restraints excluded: chain A residue  431 LEU
Chi-restraints excluded: chain A residue  490 THR
Chi-restraints excluded: chain A residue  686 VAL
Chi-restraints excluded: chain A residue  690 PHE
Chi-restraints excluded: chain A residue  912 GLN
Chi-restraints excluded: chain A residue  999 SER
Chi-restraints excluded: chain A residue 1001 LEU
Chi-restraints excluded: chain A residue 1068 VAL
Chi-restraints excluded: chain A residue 1307 VAL
Chi-restraints excluded: chain A residue 1385 GLN
Chi-restraints excluded: chain A residue 1433 ILE
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 137
   random chunks:
   chunk 31 optimal weight:    0.7980
   chunk 132 optimal weight:    7.9990
   chunk 55 optimal weight:    1.9990
   chunk 30 optimal weight:    0.7980
   chunk 45 optimal weight:    1.9990
   chunk 41 optimal weight:    2.9990
   chunk 40 optimal weight:    0.6980
   chunk 22 optimal weight:    1.9990
   chunk 83 optimal weight:    3.9990
   chunk 102 optimal weight:    0.0980
   chunk 13 optimal weight:    7.9990
   overall best weight:    0.8782

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4262 r_free = 0.4262 target = 0.196927 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 71)----------------|
| r_work = 0.3725 r_free = 0.3725 target = 0.143593 restraints weight = 13771.944|
|-----------------------------------------------------------------------------|
r_work (start): 0.3689 rms_B_bonded: 1.97
r_work: 0.3331 rms_B_bonded: 2.84 restraints_weight: 0.5000
r_work: 0.3202 rms_B_bonded: 4.62 restraints_weight: 0.2500
r_work (final): 0.3202
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8255
moved from start:          0.2454

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.039  11411  Z= 0.144
  Angle     :  0.612  10.191  15540  Z= 0.297
  Chirality :  0.041   0.159   1800
  Planarity :  0.004   0.034   1915
  Dihedral  :  8.503  58.822   1981
  Min Nonbonded Distance : 2.550

Molprobity Statistics.
  All-atom Clashscore : 6.99
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.57 %
    Favored  : 96.43 %
  Rotamer:
    Outliers :  2.85 %
    Allowed  : 16.85 %
    Favored  : 80.30 %
  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:  0.19 (0.23), residues: 1373
  helix:  0.81 (0.18), residues: 885
  sheet:  0.18 (0.66), residues: 67
  loop : -1.24 (0.30), residues: 421

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.000   ARG A  65 
 TYR   0.024   0.001   TYR A 369 
 PHE   0.022   0.001   PHE A 119 
 TRP   0.020   0.001   TRP A 121 
 HIS   0.001   0.001   HIS A 954 

Details of bonding type rmsd
  covalent geometry    : bond        0.00312 (11410)
  covalent geometry    : angle       0.61171 (15538)
  SS BOND              : bond        0.00209 (    1)
  SS BOND              : angle       0.32528 (    2)
  hydrogen bonds       : bond        0.06577 (  620)
  hydrogen bonds       : angle       4.44303 ( 1815)

*********************** 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
  162 residues out of total 1194 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 34
    poor density    : 128
  time to evaluate  : 0.416 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  102 ASP cc_start: 0.8132 (p0) cc_final: 0.7895 (p0)
REVERT: A  357 GLU cc_start: 0.8698 (OUTLIER) cc_final: 0.8226 (tt0)
REVERT: A  431 LEU cc_start: 0.8563 (OUTLIER) cc_final: 0.8170 (mt)
REVERT: A  484 VAL cc_start: 0.8132 (t) cc_final: 0.7887 (p)
REVERT: A  765 ASP cc_start: 0.8192 (t0) cc_final: 0.7844 (t70)
REVERT: A 1185 TYR cc_start: 0.8297 (m-10) cc_final: 0.8015 (m-80)
REVERT: A 1190 THR cc_start: 0.9211 (OUTLIER) cc_final: 0.9001 (m)
REVERT: A 1250 ARG cc_start: 0.8208 (mtp180) cc_final: 0.7964 (mtp180)
  outliers start: 34
  outliers final: 25
  residues processed: 158
  average time/residue: 0.0982
  time to fit residues: 22.9290
Evaluate side-chains
  151 residues out of total 1194 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 28
    poor density    : 123
  time to evaluate  : 0.408 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   17 VAL
Chi-restraints excluded: chain A residue   30 THR
Chi-restraints excluded: chain A residue   47 LEU
Chi-restraints excluded: chain A residue  166 GLU
Chi-restraints excluded: chain A residue  185 LEU
Chi-restraints excluded: chain A residue  260 TRP
Chi-restraints excluded: chain A residue  310 ILE
Chi-restraints excluded: chain A residue  357 GLU
Chi-restraints excluded: chain A residue  367 VAL
Chi-restraints excluded: chain A residue  369 TYR
Chi-restraints excluded: chain A residue  402 LEU
Chi-restraints excluded: chain A residue  431 LEU
Chi-restraints excluded: chain A residue  490 THR
Chi-restraints excluded: chain A residue  512 LEU
Chi-restraints excluded: chain A residue  686 VAL
Chi-restraints excluded: chain A residue  690 PHE
Chi-restraints excluded: chain A residue  771 ASP
Chi-restraints excluded: chain A residue  999 SER
Chi-restraints excluded: chain A residue 1001 LEU
Chi-restraints excluded: chain A residue 1068 VAL
Chi-restraints excluded: chain A residue 1182 LEU
Chi-restraints excluded: chain A residue 1190 THR
Chi-restraints excluded: chain A residue 1293 VAL
Chi-restraints excluded: chain A residue 1307 VAL
Chi-restraints excluded: chain A residue 1338 ASP
Chi-restraints excluded: chain A residue 1385 GLN
Chi-restraints excluded: chain A residue 1429 THR
Chi-restraints excluded: chain A residue 1433 ILE
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 137
   random chunks:
   chunk 18 optimal weight:    0.8980
   chunk 70 optimal weight:   10.0000
   chunk 121 optimal weight:   10.0000
   chunk 80 optimal weight:    8.9990
   chunk 36 optimal weight:    2.9990
   chunk 104 optimal weight:    0.7980
   chunk 130 optimal weight:    6.9990
   chunk 59 optimal weight:    8.9990
   chunk 132 optimal weight:    8.9990
   chunk 93 optimal weight:    2.9990
   chunk 91 optimal weight:    1.9990
   overall best weight:    1.9386

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

Flipped N/Q/H residues before XYZ refinement:
A 777 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4210 r_free = 0.4210 target = 0.191547 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 51)----------------|
| r_work = 0.3679 r_free = 0.3679 target = 0.139756 restraints weight = 13688.758|
|-----------------------------------------------------------------------------|
r_work (start): 0.3660 rms_B_bonded: 1.94
r_work: 0.3272 rms_B_bonded: 2.78 restraints_weight: 0.5000
r_work: 0.3138 rms_B_bonded: 4.61 restraints_weight: 0.2500
r_work (final): 0.3138
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8342
moved from start:          0.2285

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.058  11411  Z= 0.221
  Angle     :  0.689  11.087  15540  Z= 0.337
  Chirality :  0.044   0.166   1800
  Planarity :  0.004   0.037   1915
  Dihedral  :  8.744  59.291   1981
  Min Nonbonded Distance : 2.517

Molprobity Statistics.
  All-atom Clashscore : 7.79
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.93 %
    Favored  : 96.07 %
  Rotamer:
    Outliers :  3.60 %
    Allowed  : 16.85 %
    Favored  : 79.55 %
  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: -0.05 (0.23), residues: 1373
  helix:  0.58 (0.18), residues: 886
  sheet:  0.19 (0.66), residues: 67
  loop : -1.24 (0.30), residues: 420

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARG A 906 
 TYR   0.035   0.002   TYR A 369 
 PHE   0.022   0.002   PHE A1070 
 TRP   0.024   0.002   TRP A 496 
 HIS   0.002   0.001   HIS A 418 

Details of bonding type rmsd
  covalent geometry    : bond        0.00531 (11410)
  covalent geometry    : angle       0.68917 (15538)
  SS BOND              : bond        0.00180 (    1)
  SS BOND              : angle       0.50641 (    2)
  hydrogen bonds       : bond        0.07875 (  620)
  hydrogen bonds       : angle       4.67143 ( 1815)

*********************** 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
  167 residues out of total 1194 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 43
    poor density    : 124
  time to evaluate  : 0.406 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  102 ASP cc_start: 0.8182 (p0) cc_final: 0.7949 (p0)
REVERT: A  367 VAL cc_start: 0.8690 (OUTLIER) cc_final: 0.8175 (t)
REVERT: A  484 VAL cc_start: 0.8309 (t) cc_final: 0.8065 (p)
REVERT: A  750 MET cc_start: 0.8576 (mpp) cc_final: 0.8167 (mpp)
REVERT: A  765 ASP cc_start: 0.8233 (t0) cc_final: 0.7879 (t70)
REVERT: A 1185 TYR cc_start: 0.8405 (m-10) cc_final: 0.8155 (m-80)
REVERT: A 1250 ARG cc_start: 0.8249 (mtp180) cc_final: 0.7996 (mtp180)
REVERT: A 1418 GLN cc_start: 0.8764 (tp-100) cc_final: 0.8274 (tp-100)
  outliers start: 43
  outliers final: 32
  residues processed: 158
  average time/residue: 0.0919
  time to fit residues: 21.8472
Evaluate side-chains
  151 residues out of total 1194 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 33
    poor density    : 118
  time to evaluate  : 0.378 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   17 VAL
Chi-restraints excluded: chain A residue   30 THR
Chi-restraints excluded: chain A residue   47 LEU
Chi-restraints excluded: chain A residue   48 VAL
Chi-restraints excluded: chain A residue   50 CYS
Chi-restraints excluded: chain A residue  161 VAL
Chi-restraints excluded: chain A residue  166 GLU
Chi-restraints excluded: chain A residue  232 ASN
Chi-restraints excluded: chain A residue  260 TRP
Chi-restraints excluded: chain A residue  270 THR
Chi-restraints excluded: chain A residue  310 ILE
Chi-restraints excluded: chain A residue  357 GLU
Chi-restraints excluded: chain A residue  367 VAL
Chi-restraints excluded: chain A residue  369 TYR
Chi-restraints excluded: chain A residue  402 LEU
Chi-restraints excluded: chain A residue  485 LEU
Chi-restraints excluded: chain A residue  490 THR
Chi-restraints excluded: chain A residue  686 VAL
Chi-restraints excluded: chain A residue  690 PHE
Chi-restraints excluded: chain A residue  771 ASP
Chi-restraints excluded: chain A residue  974 THR
Chi-restraints excluded: chain A residue  999 SER
Chi-restraints excluded: chain A residue 1001 LEU
Chi-restraints excluded: chain A residue 1068 VAL
Chi-restraints excluded: chain A residue 1108 THR
Chi-restraints excluded: chain A residue 1182 LEU
Chi-restraints excluded: chain A residue 1190 THR
Chi-restraints excluded: chain A residue 1293 VAL
Chi-restraints excluded: chain A residue 1307 VAL
Chi-restraints excluded: chain A residue 1338 ASP
Chi-restraints excluded: chain A residue 1385 GLN
Chi-restraints excluded: chain A residue 1429 THR
Chi-restraints excluded: chain A residue 1433 ILE
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 137
   random chunks:
   chunk 0 optimal weight:   10.0000
   chunk 111 optimal weight:    0.9990
   chunk 64 optimal weight:    8.9990
   chunk 56 optimal weight:    0.7980
   chunk 8 optimal weight:    4.9990
   chunk 32 optimal weight:    0.9980
   chunk 65 optimal weight:    4.9990
   chunk 26 optimal weight:    0.7980
   chunk 44 optimal weight:    0.7980
   chunk 133 optimal weight:    0.9990
   chunk 22 optimal weight:    0.6980
   overall best weight:    0.8180

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4246 r_free = 0.4246 target = 0.195222 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 59)----------------|
| r_work = 0.3711 r_free = 0.3711 target = 0.142335 restraints weight = 13719.268|
|-----------------------------------------------------------------------------|
r_work (start): 0.3684 rms_B_bonded: 1.87
r_work: 0.3332 rms_B_bonded: 2.70 restraints_weight: 0.5000
r_work: 0.3206 rms_B_bonded: 4.37 restraints_weight: 0.2500
r_work (final): 0.3206
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8251
moved from start:          0.2570

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.039  11411  Z= 0.141
  Angle     :  0.609  11.576  15540  Z= 0.296
  Chirality :  0.041   0.152   1800
  Planarity :  0.004   0.039   1915
  Dihedral  :  8.374  59.802   1981
  Min Nonbonded Distance : 2.553

Molprobity Statistics.
  All-atom Clashscore : 7.66
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.50 %
    Favored  : 96.50 %
  Rotamer:
    Outliers :  2.68 %
    Allowed  : 17.85 %
    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:  0.26 (0.23), residues: 1373
  helix:  0.81 (0.18), residues: 886
  sheet:  0.46 (0.64), residues: 67
  loop : -1.15 (0.30), residues: 420

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARG A1422 
 TYR   0.023   0.001   TYR A 369 
 PHE   0.020   0.001   PHE A 119 
 TRP   0.022   0.001   TRP A 496 
 HIS   0.002   0.000   HIS A 954 

Details of bonding type rmsd
  covalent geometry    : bond        0.00301 (11410)
  covalent geometry    : angle       0.60880 (15538)
  SS BOND              : bond        0.00225 (    1)
  SS BOND              : angle       0.37350 (    2)
  hydrogen bonds       : bond        0.06666 (  620)
  hydrogen bonds       : angle       4.42763 ( 1815)

*********************** 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
  155 residues out of total 1194 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 32
    poor density    : 123
  time to evaluate  : 0.393 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  102 ASP cc_start: 0.8150 (p0) cc_final: 0.7904 (p0)
REVERT: A  357 GLU cc_start: 0.8689 (OUTLIER) cc_final: 0.8136 (tt0)
REVERT: A  484 VAL cc_start: 0.8100 (t) cc_final: 0.7872 (p)
REVERT: A  488 MET cc_start: 0.8860 (mmm) cc_final: 0.8573 (mmm)
REVERT: A  765 ASP cc_start: 0.8140 (t0) cc_final: 0.7777 (t70)
REVERT: A  923 MET cc_start: 0.7209 (mmm) cc_final: 0.6939 (mmm)
REVERT: A 1185 TYR cc_start: 0.8329 (m-10) cc_final: 0.8045 (m-80)
REVERT: A 1250 ARG cc_start: 0.8265 (mtp180) cc_final: 0.7982 (mtp180)
  outliers start: 32
  outliers final: 28
  residues processed: 150
  average time/residue: 0.0918
  time to fit residues: 20.8483
Evaluate side-chains
  147 residues out of total 1194 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 29
    poor density    : 118
  time to evaluate  : 0.391 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   17 VAL
Chi-restraints excluded: chain A residue   30 THR
Chi-restraints excluded: chain A residue   47 LEU
Chi-restraints excluded: chain A residue   50 CYS
Chi-restraints excluded: chain A residue  161 VAL
Chi-restraints excluded: chain A residue  166 GLU
Chi-restraints excluded: chain A residue  185 LEU
Chi-restraints excluded: chain A residue  260 TRP
Chi-restraints excluded: chain A residue  310 ILE
Chi-restraints excluded: chain A residue  357 GLU
Chi-restraints excluded: chain A residue  367 VAL
Chi-restraints excluded: chain A residue  369 TYR
Chi-restraints excluded: chain A residue  402 LEU
Chi-restraints excluded: chain A residue  485 LEU
Chi-restraints excluded: chain A residue  490 THR
Chi-restraints excluded: chain A residue  512 LEU
Chi-restraints excluded: chain A residue  686 VAL
Chi-restraints excluded: chain A residue  690 PHE
Chi-restraints excluded: chain A residue  771 ASP
Chi-restraints excluded: chain A residue  974 THR
Chi-restraints excluded: chain A residue 1001 LEU
Chi-restraints excluded: chain A residue 1068 VAL
Chi-restraints excluded: chain A residue 1182 LEU
Chi-restraints excluded: chain A residue 1293 VAL
Chi-restraints excluded: chain A residue 1307 VAL
Chi-restraints excluded: chain A residue 1338 ASP
Chi-restraints excluded: chain A residue 1385 GLN
Chi-restraints excluded: chain A residue 1429 THR
Chi-restraints excluded: chain A residue 1433 ILE
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 137
   random chunks:
   chunk 51 optimal weight:    0.7980
   chunk 31 optimal weight:    1.9990
   chunk 74 optimal weight:    0.5980
   chunk 66 optimal weight:    8.9990
   chunk 2 optimal weight:    3.9990
   chunk 37 optimal weight:    4.9990
   chunk 65 optimal weight:    3.9990
   chunk 105 optimal weight:    1.9990
   chunk 69 optimal weight:    6.9990
   chunk 54 optimal weight:    0.6980
   chunk 126 optimal weight:    5.9990
   overall best weight:    1.2184

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4247 r_free = 0.4247 target = 0.195482 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 77)----------------|
| r_work = 0.3705 r_free = 0.3705 target = 0.142009 restraints weight = 13639.179|
|-----------------------------------------------------------------------------|
r_work (start): 0.3672 rms_B_bonded: 2.02
r_work: 0.3296 rms_B_bonded: 2.98 restraints_weight: 0.5000
r_work: 0.3161 rms_B_bonded: 4.91 restraints_weight: 0.2500
r_work (final): 0.3161
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8305
moved from start:          0.2573

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.045  11411  Z= 0.163
  Angle     :  0.622  12.359  15540  Z= 0.303
  Chirality :  0.042   0.155   1800
  Planarity :  0.004   0.039   1915
  Dihedral  :  8.369  59.704   1981
  Min Nonbonded Distance : 2.541

Molprobity Statistics.
  All-atom Clashscore : 7.17
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.79 %
    Favored  : 96.21 %
  Rotamer:
    Outliers :  3.10 %
    Allowed  : 17.85 %
    Favored  : 79.04 %
  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:  0.30 (0.23), residues: 1373
  helix:  0.83 (0.18), residues: 888
  sheet:  0.52 (0.62), residues: 67
  loop : -1.10 (0.30), residues: 418

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARG A1422 
 TYR   0.027   0.001   TYR A 369 
 PHE   0.020   0.001   PHE A 119 
 TRP   0.021   0.001   TRP A 121 
 HIS   0.001   0.000   HIS A 193 

Details of bonding type rmsd
  covalent geometry    : bond        0.00372 (11410)
  covalent geometry    : angle       0.62209 (15538)
  SS BOND              : bond        0.00186 (    1)
  SS BOND              : angle       0.39275 (    2)
  hydrogen bonds       : bond        0.06970 (  620)
  hydrogen bonds       : angle       4.45521 ( 1815)

*********************** 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
  157 residues out of total 1194 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 37
    poor density    : 120
  time to evaluate  : 0.410 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  102 ASP cc_start: 0.8182 (p0) cc_final: 0.7950 (p0)
REVERT: A  357 GLU cc_start: 0.8734 (OUTLIER) cc_final: 0.8292 (tt0)
REVERT: A  367 VAL cc_start: 0.8683 (OUTLIER) cc_final: 0.8184 (t)
REVERT: A  484 VAL cc_start: 0.8154 (t) cc_final: 0.7862 (p)
REVERT: A  488 MET cc_start: 0.8867 (mmm) cc_final: 0.8649 (tpt)
REVERT: A  599 ARG cc_start: 0.5269 (ptm160) cc_final: 0.4734 (ptt180)
REVERT: A  765 ASP cc_start: 0.8174 (t0) cc_final: 0.7805 (t70)
REVERT: A 1185 TYR cc_start: 0.8418 (m-10) cc_final: 0.8137 (m-80)
REVERT: A 1250 ARG cc_start: 0.8275 (mtp180) cc_final: 0.7989 (mtp180)
  outliers start: 37
  outliers final: 31
  residues processed: 153
  average time/residue: 0.0892
  time to fit residues: 20.8240
Evaluate side-chains
  151 residues out of total 1194 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 33
    poor density    : 118
  time to evaluate  : 0.412 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   17 VAL
Chi-restraints excluded: chain A residue   30 THR
Chi-restraints excluded: chain A residue   47 LEU
Chi-restraints excluded: chain A residue   50 CYS
Chi-restraints excluded: chain A residue  161 VAL
Chi-restraints excluded: chain A residue  166 GLU
Chi-restraints excluded: chain A residue  232 ASN
Chi-restraints excluded: chain A residue  260 TRP
Chi-restraints excluded: chain A residue  270 THR
Chi-restraints excluded: chain A residue  310 ILE
Chi-restraints excluded: chain A residue  357 GLU
Chi-restraints excluded: chain A residue  367 VAL
Chi-restraints excluded: chain A residue  369 TYR
Chi-restraints excluded: chain A residue  402 LEU
Chi-restraints excluded: chain A residue  485 LEU
Chi-restraints excluded: chain A residue  490 THR
Chi-restraints excluded: chain A residue  512 LEU
Chi-restraints excluded: chain A residue  645 VAL
Chi-restraints excluded: chain A residue  686 VAL
Chi-restraints excluded: chain A residue  690 PHE
Chi-restraints excluded: chain A residue  771 ASP
Chi-restraints excluded: chain A residue  971 VAL
Chi-restraints excluded: chain A residue  974 THR
Chi-restraints excluded: chain A residue 1001 LEU
Chi-restraints excluded: chain A residue 1068 VAL
Chi-restraints excluded: chain A residue 1108 THR
Chi-restraints excluded: chain A residue 1182 LEU
Chi-restraints excluded: chain A residue 1190 THR
Chi-restraints excluded: chain A residue 1293 VAL
Chi-restraints excluded: chain A residue 1307 VAL
Chi-restraints excluded: chain A residue 1385 GLN
Chi-restraints excluded: chain A residue 1429 THR
Chi-restraints excluded: chain A residue 1433 ILE
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 137
   random chunks:
   chunk 5 optimal weight:    8.9990
   chunk 26 optimal weight:    0.0050
   chunk 14 optimal weight:    2.9990
   chunk 45 optimal weight:    0.8980
   chunk 11 optimal weight:    4.9990
   chunk 70 optimal weight:    6.9990
   chunk 85 optimal weight:    0.9990
   chunk 130 optimal weight:    3.9990
   chunk 18 optimal weight:    0.8980
   chunk 27 optimal weight:    0.0980
   chunk 79 optimal weight:    0.9980
   overall best weight:    0.5794

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4282 r_free = 0.4282 target = 0.199018 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 31)----------------|
| r_work = 0.3803 r_free = 0.3803 target = 0.151246 restraints weight = 13657.872|
|-----------------------------------------------------------------------------|
r_work (start): 0.3780 rms_B_bonded: 2.19
r_work: 0.3346 rms_B_bonded: 3.05 restraints_weight: 0.5000
r_work (final): 0.3346
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8108
moved from start:          0.2853

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.037  11411  Z= 0.127
  Angle     :  0.587  13.169  15540  Z= 0.284
  Chirality :  0.040   0.148   1800
  Planarity :  0.004   0.039   1915
  Dihedral  :  8.050  57.697   1981
  Min Nonbonded Distance : 2.503

Molprobity Statistics.
  All-atom Clashscore : 6.99
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.28 %
    Favored  : 96.72 %
  Rotamer:
    Outliers :  2.10 %
    Allowed  : 18.69 %
    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:  0.58 (0.23), residues: 1373
  helix:  1.07 (0.18), residues: 887
  sheet:  0.65 (0.61), residues: 67
  loop : -1.06 (0.31), residues: 419

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARG A1422 
 TYR   0.019   0.001   TYR A 369 
 PHE   0.021   0.001   PHE A 119 
 TRP   0.023   0.001   TRP A 121 
 HIS   0.002   0.000   HIS A 954 

Details of bonding type rmsd
  covalent geometry    : bond        0.00260 (11410)
  covalent geometry    : angle       0.58662 (15538)
  SS BOND              : bond        0.00212 (    1)
  SS BOND              : angle       0.31044 (    2)
  hydrogen bonds       : bond        0.06041 (  620)
  hydrogen bonds       : angle       4.27855 ( 1815)

********************** 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
  153 residues out of total 1194 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 25
    poor density    : 128
  time to evaluate  : 0.423 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   22 VAL cc_start: 0.9153 (t) cc_final: 0.8786 (m)
REVERT: A   55 TRP cc_start: 0.7517 (t-100) cc_final: 0.6684 (t60)
REVERT: A  102 ASP cc_start: 0.7970 (p0) cc_final: 0.7737 (p0)
REVERT: A  357 GLU cc_start: 0.8490 (OUTLIER) cc_final: 0.7999 (tt0)
REVERT: A  488 MET cc_start: 0.8836 (mmm) cc_final: 0.8605 (mmm)
REVERT: A  599 ARG cc_start: 0.5131 (ptm160) cc_final: 0.4844 (ptt180)
REVERT: A  923 MET cc_start: 0.6654 (mmm) cc_final: 0.6448 (mmm)
REVERT: A 1087 MET cc_start: 0.7726 (tpp) cc_final: 0.7349 (mtt)
REVERT: A 1185 TYR cc_start: 0.8145 (m-10) cc_final: 0.7842 (m-80)
REVERT: A 1236 TRP cc_start: 0.7665 (t60) cc_final: 0.7377 (t60)
REVERT: A 1250 ARG cc_start: 0.8277 (mtp180) cc_final: 0.8024 (mtp180)
REVERT: A 1418 GLN cc_start: 0.8643 (tp-100) cc_final: 0.8264 (tp-100)
  outliers start: 25
  outliers final: 23
  residues processed: 151
  average time/residue: 0.0984
  time to fit residues: 21.9622
Evaluate side-chains
  146 residues out of total 1194 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 24
    poor density    : 122
  time to evaluate  : 0.403 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   17 VAL
Chi-restraints excluded: chain A residue   30 THR
Chi-restraints excluded: chain A residue   47 LEU
Chi-restraints excluded: chain A residue  166 GLU
Chi-restraints excluded: chain A residue  185 LEU
Chi-restraints excluded: chain A residue  260 TRP
Chi-restraints excluded: chain A residue  270 THR
Chi-restraints excluded: chain A residue  310 ILE
Chi-restraints excluded: chain A residue  357 GLU
Chi-restraints excluded: chain A residue  367 VAL
Chi-restraints excluded: chain A residue  490 THR
Chi-restraints excluded: chain A residue  512 LEU
Chi-restraints excluded: chain A residue  645 VAL
Chi-restraints excluded: chain A residue  686 VAL
Chi-restraints excluded: chain A residue  690 PHE
Chi-restraints excluded: chain A residue  771 ASP
Chi-restraints excluded: chain A residue  971 VAL
Chi-restraints excluded: chain A residue 1108 THR
Chi-restraints excluded: chain A residue 1182 LEU
Chi-restraints excluded: chain A residue 1293 VAL
Chi-restraints excluded: chain A residue 1307 VAL
Chi-restraints excluded: chain A residue 1385 GLN
Chi-restraints excluded: chain A residue 1429 THR
Chi-restraints excluded: chain A residue 1433 ILE
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 137
   random chunks:
   chunk 126 optimal weight:    4.9990
   chunk 48 optimal weight:    1.9990
   chunk 105 optimal weight:    0.5980
   chunk 70 optimal weight:    0.5980
   chunk 21 optimal weight:    0.5980
   chunk 135 optimal weight:    9.9990
   chunk 56 optimal weight:    3.9990
   chunk 35 optimal weight:    0.6980
   chunk 79 optimal weight:    0.0570
   chunk 110 optimal weight:    0.7980
   chunk 115 optimal weight:    8.9990
   overall best weight:    0.5098

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

Flipped N/Q/H residues before XYZ refinement:
A 757 ASN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4278 r_free = 0.4278 target = 0.198298 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 57)----------------|
| r_work = 0.3757 r_free = 0.3757 target = 0.146131 restraints weight = 13772.021|
|-----------------------------------------------------------------------------|
r_work (start): 0.3732 rms_B_bonded: 1.92
r_work: 0.3376 rms_B_bonded: 2.77 restraints_weight: 0.5000
r_work: 0.3251 rms_B_bonded: 4.51 restraints_weight: 0.2500
r_work (final): 0.3251
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8200
moved from start:          0.3001

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.034  11411  Z= 0.125
  Angle     :  0.588  12.970  15540  Z= 0.287
  Chirality :  0.041   0.146   1800
  Planarity :  0.004   0.042   1915
  Dihedral  :  7.977  58.409   1981
  Min Nonbonded Distance : 2.155

Molprobity Statistics.
  All-atom Clashscore : 7.17
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.35 %
    Favored  : 96.65 %
  Rotamer:
    Outliers :  2.35 %
    Allowed  : 18.94 %
    Favored  : 78.71 %
  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:  0.62 (0.23), residues: 1373
  helix:  1.08 (0.18), residues: 896
  sheet:  0.68 (0.61), residues: 68
  loop : -1.05 (0.31), residues: 409

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.006   0.000   ARG A1422 
 TYR   0.019   0.001   TYR A 369 
 PHE   0.023   0.001   PHE A 119 
 TRP   0.023   0.001   TRP A 121 
 HIS   0.002   0.000   HIS A 954 

Details of bonding type rmsd
  covalent geometry    : bond        0.00254 (11410)
  covalent geometry    : angle       0.58794 (15538)
  SS BOND              : bond        0.00190 (    1)
  SS BOND              : angle       0.29537 (    2)
  hydrogen bonds       : bond        0.05834 (  620)
  hydrogen bonds       : angle       4.22615 ( 1815)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 3115.06 seconds
wall clock time: 53 minutes 50.04 seconds (3230.04 seconds total)