Starting phenix.real_space_refine
on Wed Mar  4 14:13:48 2026 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/7ync_33958/03_2026/7ync_33958.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/7ync_33958/03_2026/7ync_33958.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=3.14
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/cci-nas-00/data/ceres_data/7ync_33958/03_2026/7ync_33958.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/7ync_33958/03_2026/7ync_33958.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/7ync_33958/03_2026/7ync_33958.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/7ync_33958/03_2026/7ync_33958.cif"
  }
  resolution = 3.14
  write_initial_geo_file = False
  refinement {
    macro_cycles = 10
  }


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

Validating inputs
Origin is already at (0, 0, 0), no shifts will be applied
-------------------------------------------------------------------------------
Processing inputs
*****************
Set random seed
  Set to: 0
Set model cs if undefined
Decide on map wrapping
  Map wrapping is set to: False
Normalize map: mean=0, sd=1
  Input map: mean=   0.000 sd=   0.004
Set stop_for_unknowns flag
  Set to: True
Assert model is a single copy model
Assert all atoms have isotropic ADPs
Construct map_model_manager
Extract box with map and model
Check model and map are aligned
Set scattering table
  Set to: electron
  Number of scattering types: 5
    Type Number    sf(0)   Gaussians
     P      66      5.49       5
     S      57      5.16       5
     C    8497      2.51       5
     N    2467      2.21       5
     O    2761      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 60 residue(s): 0.02s

  Monomer Library directory:
    "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-5986/lib/python3.9/site-packages/chem_data/mon_lib"
  Total number of atoms: 13848
  Number of models: 1
  Model: ""
    Number of chains: 3
    Chain: "A"
      Number of atoms: 12447
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 1536, 12447
          Classifications: {'peptide': 1536}
          Link IDs: {'PTRANS': 84, 'TRANS': 1451}
          Chain breaks: 4
    Chain: "B"
      Number of atoms: 810
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 38, 810
          Classifications: {'RNA': 38}
          Modifications used: {'rna2p_pur': 14, 'rna2p_pyr': 5, 'rna3p_pur': 7, 'rna3p_pyr': 12}
          Link IDs: {'rna2p': 19, 'rna3p': 18}
    Chain: "C"
      Number of atoms: 591
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 28, 591
          Classifications: {'RNA': 28}
          Modifications used: {'rna2p_pur': 2, 'rna2p_pyr': 1, 'rna3p_pur': 11, 'rna3p_pyr': 14}
          Link IDs: {'rna2p': 3, 'rna3p': 24}
  Time building chain proxies: 3.24, per 1000 atoms: 0.23
  Number of scatterers: 13848
  At special positions: 0
  Unit cell: (94.16, 169.06, 133.75, 90, 90, 90)
  Space group: P 1 (No. 1)
  Number of sites at special positions: 0
  Number of scattering types: 5
    Type Number    sf(0)
     S      57     16.00
     P      66     15.00
     O    2761      8.00
     N    2467      7.00
     C    8497      6.00
    sf(0) = scattering factor at diffraction angle 0.

  Number of disulfides: simple=0, symmetry=0

  Automatic linking
    Parameters for automatic linking
      Linking & cutoffs
        Metal                : Auto  - 3.00
        Amino acid           : True  - 1.90
        Carbohydrate         : True  - 1.99
        Ligands              : True  - 1.99
        Small molecules      : False - 1.98
        Amino acid - RNA/DNA : False
      
  Number of custom bonds: simple=0, symmetry=0
  Time building additional restraints: 1.31
  Conformation dependent library (CDL) restraints added in 596.2 milliseconds
  

  3052 Ramachandran restraints generated.
    1526 Oldfield, 0 Emsley, 1526 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  2858

  Finding SS restraints...
    Secondary structure from input PDB file:
      32 helices and 19 sheets defined
      21.4% alpha, 19.6% beta
      16 base pairs and 23 stacking pairs defined.
    Time for finding SS restraints: 1.82
  Creating SS restraints...
    Processing helix  chain 'A' and resid 57 through 74
      removed outlier: 4.187A  pdb=" N   LEU A  61 " --> pdb=" O   THR A  57 " (cutoff:3.500A)
      removed outlier: 3.749A  pdb=" N   THR A  74 " --> pdb=" O   GLU A  70 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 123 through 130
    Processing helix  chain 'A' and resid 213 through 225
    Processing helix  chain 'A' and resid 261 through 276
      removed outlier: 3.537A  pdb=" N   ASN A 276 " --> pdb=" O   ILE A 272 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 281 through 290
    Processing helix  chain 'A' and resid 291 through 294
      removed outlier: 4.078A  pdb=" N   ARG A 294 " --> pdb=" O   SER A 291 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'A' and resid 291 through 294'
    Processing helix  chain 'A' and resid 295 through 302
      removed outlier: 3.983A  pdb=" N   LEU A 298 " --> pdb=" O   SER A 295 " (cutoff:3.500A)
      removed outlier: 3.963A  pdb=" N   VAL A 299 " --> pdb=" O   SER A 296 " (cutoff:3.500A)
      removed outlier: 4.310A  pdb=" N   ALA A 300 " --> pdb=" O   LYS A 297 " (cutoff:3.500A)
      removed outlier: 3.512A  pdb=" N   GLY A 301 " --> pdb=" O   LEU A 298 " (cutoff:3.500A)
      removed outlier: 3.864A  pdb=" N   LEU A 302 " --> pdb=" O   VAL A 299 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'A' and resid 295 through 302'
    Processing helix  chain 'A' and resid 328 through 336
    Processing helix  chain 'A' and resid 344 through 365
      removed outlier: 4.125A  pdb=" N   ASP A 365 " --> pdb=" O   LEU A 361 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 443 through 459
      removed outlier: 3.573A  pdb=" N   VAL A 447 " --> pdb=" O   PRO A 443 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 542 through 553
    Processing helix  chain 'A' and resid 562 through 566
    Processing helix  chain 'A' and resid 587 through 594
      removed outlier: 4.114A  pdb=" N   ASN A 594 " --> pdb=" O   ASP A 590 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 599 through 607
    Processing helix  chain 'A' and resid 642 through 649
    Processing helix  chain 'A' and resid 675 through 689
      removed outlier: 3.570A  pdb=" N   PHE A 679 " --> pdb=" O   LYS A 675 " (cutoff:3.500A)
      removed outlier: 3.538A  pdb=" N   ARG A 689 " --> pdb=" O   SER A 685 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 780 through 784
      removed outlier: 3.755A  pdb=" N   GLU A 784 " --> pdb=" O   ARG A 780 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'A' and resid 780 through 784'
    Processing helix  chain 'A' and resid 787 through 801
      removed outlier: 3.727A  pdb=" N   ALA A 791 " --> pdb=" O   GLU A 787 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 809 through 813
      removed outlier: 3.582A  pdb=" N   ILE A 812 " --> pdb=" O   LYS A 809 " (cutoff:3.500A)
      removed outlier: 3.582A  pdb=" N   GLY A 813 " --> pdb=" O   SER A 810 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'A' and resid 809 through 813'
    Processing helix  chain 'A' and resid 946 through 962
      removed outlier: 4.205A  pdb=" N   LEU A 950 " --> pdb=" O   PRO A 946 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 1101 through 1105
      removed outlier: 3.552A  pdb=" N   ASP A1104 " --> pdb=" O   ASP A1101 " (cutoff:3.500A)
      removed outlier: 3.638A  pdb=" N   GLN A1105 " --> pdb=" O   ASN A1102 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'A' and resid 1101 through 1105'
    Processing helix  chain 'A' and resid 1231 through 1247
      removed outlier: 3.901A  pdb=" N   ARG A1235 " --> pdb=" O   PRO A1231 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 1259 through 1264
      removed outlier: 3.526A  pdb=" N   GLU A1264 " --> pdb=" O   ARG A1260 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 1300 through 1305
      removed outlier: 3.608A  pdb=" N   LYS A1303 " --> pdb=" O   MET A1300 " (cutoff:3.500A)
      removed outlier: 3.651A  pdb=" N   ARG A1304 " --> pdb=" O   ILE A1301 " (cutoff:3.500A)
      removed outlier: 4.014A  pdb=" N   MET A1305 " --> pdb=" O   GLY A1302 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'A' and resid 1300 through 1305'
    Processing helix  chain 'A' and resid 1343 through 1348
      removed outlier: 4.192A  pdb=" N   LEU A1347 " --> pdb=" O   PRO A1343 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 1420 through 1427
      removed outlier: 3.856A  pdb=" N   ILE A1424 " --> pdb=" O   ALA A1420 " (cutoff:3.500A)
      removed outlier: 3.708A  pdb=" N   ASP A1426 " --> pdb=" O   LYS A1422 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 1466 through 1476
    Processing helix  chain 'A' and resid 1515 through 1517
      No H-bonds generated for 'chain 'A' and resid 1515 through 1517'
    Processing helix  chain 'A' and resid 1518 through 1534
      removed outlier: 3.713A  pdb=" N   GLY A1524 " --> pdb=" O   PRO A1520 " (cutoff:3.500A)
      removed outlier: 3.705A  pdb=" N   PHE A1534 " --> pdb=" O   LEU A1530 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 1538 through 1548
    Processing helix  chain 'A' and resid 1575 through 1580
      removed outlier: 3.572A  pdb=" N   LYS A1580 " --> pdb=" O   TYR A1576 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 1588 through 1595
      removed outlier: 3.528A  pdb=" N   THR A1595 " --> pdb=" O   LYS A1591 " (cutoff:3.500A)
    Processing sheet with id=AA1, first strand: chain 'A' and resid 148 through 150
    Processing sheet with id=AA2, first strand: chain 'A' and resid 15 through 17
      removed outlier: 3.746A  pdb=" N   PHE A 187 " --> pdb=" O   LEU A 173 " (cutoff:3.500A)
      removed outlier: 3.669A  pdb=" N   GLU A 191 " --> pdb=" O   SER A 169 " (cutoff:3.500A)
      removed outlier: 3.589A  pdb=" N   SER A 169 " --> pdb=" O   GLU A 191 " (cutoff:3.500A)
    Processing sheet with id=AA3, first strand: chain 'A' and resid 41 through 44
    Processing sheet with id=AA4, first strand: chain 'A' and resid 483 through 484
      removed outlier: 3.705A  pdb=" N   GLU A 403 " --> pdb=" O   LEU A 580 " (cutoff:3.500A)
      removed outlier: 3.556A  pdb=" N   LYS A 576 " --> pdb=" O   CYS A 407 " (cutoff:3.500A)
      removed outlier: 4.565A  pdb=" N   GLU A 409 " --> pdb=" O   ASN A 574 " (cutoff:3.500A)
      removed outlier: 4.993A  pdb=" N   ASN A 574 " --> pdb=" O   GLU A 409 " (cutoff:3.500A)
      removed outlier: 6.945A  pdb=" N   VAL A 411 " --> pdb=" O   MET A 572 " (cutoff:3.500A)
      removed outlier: 5.575A  pdb=" N   MET A 572 " --> pdb=" O   VAL A 411 " (cutoff:3.500A)
    Processing sheet with id=AA5, first strand: chain 'A' and resid 497 through 504
      removed outlier: 3.770A  pdb=" N   GLU A 497 " --> pdb=" O   VAL A 521 " (cutoff:3.500A)
      removed outlier: 3.938A  pdb=" N   ARG A 503 " --> pdb=" O   ALA A 515 " (cutoff:3.500A)
      removed outlier: 5.979A  pdb=" N   ALA A 515 " --> pdb=" O   ARG A 503 " (cutoff:3.500A)
    Processing sheet with id=AA6, first strand: chain 'A' and resid 723 through 724
      removed outlier: 6.803A  pdb=" N   ASN A 629 " --> pdb=" O   ILE A 822 " (cutoff:3.500A)
      removed outlier: 4.412A  pdb=" N   ILE A 822 " --> pdb=" O   ASN A 629 " (cutoff:3.500A)
      removed outlier: 6.805A  pdb=" N   SER A 631 " --> pdb=" O   LEU A 820 " (cutoff:3.500A)
      removed outlier: 4.525A  pdb=" N   LEU A 820 " --> pdb=" O   SER A 631 " (cutoff:3.500A)
      removed outlier: 6.904A  pdb=" N   GLU A 633 " --> pdb=" O   LYS A 818 " (cutoff:3.500A)
    Processing sheet with id=AA7, first strand: chain 'A' and resid 659 through 663
    Processing sheet with id=AA8, first strand: chain 'A' and resid 739 through 744
      removed outlier: 3.646A  pdb=" N   PHE A 757 " --> pdb=" O   HIS A 741 " (cutoff:3.500A)
      removed outlier: 3.510A  pdb=" N   ALA A 743 " --> pdb=" O   LYS A 755 " (cutoff:3.500A)
      removed outlier: 6.743A  pdb=" N   LYS A 755 " --> pdb=" O   ALA A 743 " (cutoff:3.500A)
    Processing sheet with id=AA9, first strand: chain 'A' and resid 861 through 862
    Processing sheet with id=AB1, first strand: chain 'A' and resid 944 through 945
      removed outlier: 5.463A  pdb=" N   LEU A 891 " --> pdb=" O   ASN A1462 " (cutoff:3.500A)
    Processing sheet with id=AB2, first strand: chain 'A' and resid 944 through 945
    Processing sheet with id=AB3, first strand: chain 'A' and resid 908 through 909
      removed outlier: 4.459A  pdb=" N   ALA A 935 " --> pdb=" O   ASP A 909 " (cutoff:3.500A)
    Processing sheet with id=AB4, first strand: chain 'A' and resid 976 through 978
    Processing sheet with id=AB5, first strand: chain 'A' and resid 1001 through 1012
      removed outlier: 41.983A  pdb=" N   VAL A1121 " --> pdb=" O   ILE A1002 " (cutoff:3.500A)
      removed outlier: 35.885A  pdb=" N   LYS A1004 " --> pdb=" O   VAL A1121 " (cutoff:3.500A)
      removed outlier: 29.703A  pdb=" N   ASP A1123 " --> pdb=" O   LYS A1004 " (cutoff:3.500A)
      removed outlier: 23.731A  pdb=" N   SER A1006 " --> pdb=" O   ASP A1123 " (cutoff:3.500A)
      removed outlier: 17.731A  pdb=" N   ARG A1125 " --> pdb=" O   SER A1006 " (cutoff:3.500A)
      removed outlier: 14.195A  pdb=" N   THR A1008 " --> pdb=" O   ARG A1125 " (cutoff:3.500A)
      removed outlier: 7.622A  pdb=" N   GLN A1127 " --> pdb=" O   THR A1008 " (cutoff:3.500A)
      removed outlier: 3.795A  pdb=" N   ARG A1010 " --> pdb=" O   GLN A1127 " (cutoff:3.500A)
      removed outlier: 3.538A  pdb=" N   ALA A1129 " --> pdb=" O   ARG A1010 " (cutoff:3.500A)
      removed outlier: 3.921A  pdb=" N   TRP A1120 " --> pdb=" O   SER A1047 " (cutoff:3.500A)
      removed outlier: 3.557A  pdb=" N   SER A1047 " --> pdb=" O   TRP A1120 " (cutoff:3.500A)
      removed outlier: 3.566A  pdb=" N   ARG A1122 " --> pdb=" O   ARG A1045 " (cutoff:3.500A)
      removed outlier: 3.719A  pdb=" N   ARG A1041 " --> pdb=" O   TYR A1126 " (cutoff:3.500A)
      removed outlier: 7.292A  pdb=" N   LYS A1128 " --> pdb=" O   VAL A1039 " (cutoff:3.500A)
      removed outlier: 4.970A  pdb=" N   VAL A1039 " --> pdb=" O   LYS A1128 " (cutoff:3.500A)
      removed outlier: 6.545A  pdb=" N   PHE A1130 " --> pdb=" O   MET A1037 " (cutoff:3.500A)
      removed outlier: 5.103A  pdb=" N   MET A1037 " --> pdb=" O   PHE A1130 " (cutoff:3.500A)
      removed outlier: 3.669A  pdb=" N   MET A1037 " --> pdb=" O   LYS A1144 " (cutoff:3.500A)
      removed outlier: 19.244A  pdb=" N   CYS A1143 " --> pdb=" O   LYS A1223 " (cutoff:3.500A)
      removed outlier: 14.148A  pdb=" N   LYS A1223 " --> pdb=" O   CYS A1143 " (cutoff:3.500A)
      removed outlier: 8.653A  pdb=" N   GLU A1145 " --> pdb=" O   ASP A1221 " (cutoff:3.500A)
      removed outlier: 3.733A  pdb=" N   PHE A1220 " --> pdb=" O   GLU A1007 " (cutoff:3.500A)
      removed outlier: 4.095A  pdb=" N   GLU A1007 " --> pdb=" O   PHE A1220 " (cutoff:3.500A)
      removed outlier: 6.801A  pdb=" N   LEU A1222 " --> pdb=" O   PHE A1005 " (cutoff:3.500A)
      removed outlier: 7.049A  pdb=" N   PHE A1005 " --> pdb=" O   LEU A1222 " (cutoff:3.500A)
      removed outlier: 8.096A  pdb=" N   GLU A1224 " --> pdb=" O   GLN A1003 " (cutoff:3.500A)
      removed outlier: 8.641A  pdb=" N   GLN A1003 " --> pdb=" O   GLU A1224 " (cutoff:3.500A)
      removed outlier: 10.428A  pdb=" N   GLU A1226 " --> pdb=" O   HIS A1001 " (cutoff:3.500A)
      removed outlier: 9.592A  pdb=" N   HIS A1001 " --> pdb=" O   GLU A1226 " (cutoff:3.500A)
      removed outlier: 3.900A  pdb=" N   VAL A1275 " --> pdb=" O   GLY A 993 " (cutoff:3.500A)
      removed outlier: 6.611A  pdb=" N   TYR A1276 " --> pdb=" O   ILE A1287 " (cutoff:3.500A)
      removed outlier: 4.617A  pdb=" N   ILE A1287 " --> pdb=" O   TYR A1276 " (cutoff:3.500A)
      removed outlier: 6.526A  pdb=" N   LYS A1278 " --> pdb=" O   GLU A1285 " (cutoff:3.500A)
      removed outlier: 3.535A  pdb=" N   TYR A1283 " --> pdb=" O   ASN A1280 " (cutoff:3.500A)
      removed outlier: 8.150A  pdb=" N   VAL A1284 " --> pdb=" O   GLU A1227 " (cutoff:3.500A)
      removed outlier: 7.393A  pdb=" N   GLU A1229 " --> pdb=" O   VAL A1284 " (cutoff:3.500A)
      removed outlier: 8.591A  pdb=" N   ASP A1286 " --> pdb=" O   GLU A1229 " (cutoff:3.500A)
    Processing sheet with id=AB6, first strand: chain 'A' and resid 1070 through 1071
    Processing sheet with id=AB7, first strand: chain 'A' and resid 1081 through 1086
      removed outlier: 3.623A  pdb=" N   PHE A1083 " --> pdb=" O   LEU A1096 " (cutoff:3.500A)
      removed outlier: 3.598A  pdb=" N   LEU A1096 " --> pdb=" O   PHE A1083 " (cutoff:3.500A)
      removed outlier: 3.642A  pdb=" N   VAL A1085 " --> pdb=" O   PHE A1094 " (cutoff:3.500A)
      removed outlier: 3.566A  pdb=" N   PHE A1094 " --> pdb=" O   VAL A1085 " (cutoff:3.500A)
    Processing sheet with id=AB8, first strand: chain 'A' and resid 1187 through 1188
    Processing sheet with id=AB9, first strand: chain 'A' and resid 1200 through 1202
      removed outlier: 3.519A  pdb=" N   TYR A1209 " --> pdb=" O   CYS A1201 " (cutoff:3.500A)
    Processing sheet with id=AC1, first strand: chain 'A' and resid 1385 through 1387

    302 hydrogen bonds defined for protein.
    858 hydrogen bond angles defined for protein.
    Restraints generated for nucleic acids:
      39 hydrogen bonds
      78 hydrogen bond angles
      0 basepair planarities
      16 basepair parallelities
      23 stacking parallelities
  Total time for adding SS restraints: 2.99

  Time building geometry restraints manager: 1.69 seconds

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

  Histogram of bond lengths:
        1.22 -     1.34: 4227
        1.34 -     1.45: 2635
        1.45 -     1.57: 7235
        1.57 -     1.69: 130
        1.69 -     1.81: 82
  Bond restraints: 14309
  Sorted by residual:
  bond pdb=" N   CYS A 965 "
       pdb=" CA  CYS A 965 "
    ideal  model  delta    sigma   weight residual
    1.456  1.490 -0.034 1.22e-02 6.72e+03 7.79e+00
  bond pdb=" N   CYS A  86 "
       pdb=" CA  CYS A  86 "
    ideal  model  delta    sigma   weight residual
    1.452  1.491 -0.038 1.41e-02 5.03e+03 7.42e+00
  bond pdb=" N   CYS A1342 "
       pdb=" CA  CYS A1342 "
    ideal  model  delta    sigma   weight residual
    1.452  1.489 -0.037 1.41e-02 5.03e+03 6.98e+00
  bond pdb=" N   CYS A 711 "
       pdb=" CA  CYS A 711 "
    ideal  model  delta    sigma   weight residual
    1.456  1.489 -0.032 1.31e-02 5.83e+03 6.08e+00
  bond pdb=" N   CYS A 708 "
       pdb=" CA  CYS A 708 "
    ideal  model  delta    sigma   weight residual
    1.453  1.486 -0.033 1.37e-02 5.33e+03 5.87e+00
  ... (remaining 14304 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     1.48: 18830
        1.48 -     2.95: 637
        2.95 -     4.43: 98
        4.43 -     5.90: 22
        5.90 -     7.38: 9
  Bond angle restraints: 19596
  Sorted by residual:
  angle pdb=" N   ARG A1346 "
        pdb=" CA  ARG A1346 "
        pdb=" C   ARG A1346 "
      ideal   model   delta    sigma   weight residual
     114.04  108.63    5.41 1.24e+00 6.50e-01 1.91e+01
  angle pdb=" N   TYR A 866 "
        pdb=" CA  TYR A 866 "
        pdb=" C   TYR A 866 "
      ideal   model   delta    sigma   weight residual
     111.02  115.93   -4.91 1.25e+00 6.40e-01 1.54e+01
  angle pdb=" N   CYS A 123 "
        pdb=" CA  CYS A 123 "
        pdb=" C   CYS A 123 "
      ideal   model   delta    sigma   weight residual
     110.39  105.74    4.65 1.30e+00 5.92e-01 1.28e+01
  angle pdb=" CA  CYS A1312 "
        pdb=" C   CYS A1312 "
        pdb=" O   CYS A1312 "
      ideal   model   delta    sigma   weight residual
     122.64  118.52    4.12 1.25e+00 6.40e-01 1.09e+01
  angle pdb=" C   ALA A 919 "
        pdb=" N   ASP A 920 "
        pdb=" CA  ASP A 920 "
      ideal   model   delta    sigma   weight residual
     122.46  126.98   -4.52 1.41e+00 5.03e-01 1.03e+01
  ... (remaining 19591 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    31.39: 8253
       31.39 -    62.79: 415
       62.79 -    94.18: 70
       94.18 -   125.58: 4
      125.58 -   156.97: 1
  Dihedral angle restraints: 8743
    sinusoidal: 4312
      harmonic: 4431
  Sorted by residual:
  dihedral pdb=" CA  GLY A1411 "
           pdb=" C   GLY A1411 "
           pdb=" N   ARG A1412 "
           pdb=" CA  ARG A1412 "
      ideal   model   delta  harmonic     sigma   weight residual
    -180.00 -159.59  -20.41     0      5.00e+00 4.00e-02 1.67e+01
  dihedral pdb=" CA  HIS A 383 "
           pdb=" C   HIS A 383 "
           pdb=" N   GLY A 384 "
           pdb=" CA  GLY A 384 "
      ideal   model   delta  harmonic     sigma   weight residual
    -180.00 -160.01  -19.99     0      5.00e+00 4.00e-02 1.60e+01
  dihedral pdb=" C4'   U B -14 "
           pdb=" C3'   U B -14 "
           pdb=" O3'   U B -14 "
           pdb=" P     G B -13 "
      ideal   model   delta sinusoidal    sigma   weight residual
     220.00   63.03  156.97     1      3.50e+01 8.16e-04 1.50e+01
  ... (remaining 8740 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.042: 1535
       0.042 -    0.084: 429
       0.084 -    0.126: 108
       0.126 -    0.168: 25
       0.168 -    0.210: 2
  Chirality restraints: 2099
  Sorted by residual:
  chirality pdb=" CA  CYS A 123 "
            pdb=" N   CYS A 123 "
            pdb=" C   CYS A 123 "
            pdb=" CB  CYS A 123 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.72   -0.21 2.00e-01 2.50e+01 1.11e+00
  chirality pdb=" C1'   A C   6 "
            pdb=" O4'   A C   6 "
            pdb=" C2'   A C   6 "
            pdb=" N9    A C   6 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.46    2.29    0.17 2.00e-01 2.50e+01 7.30e-01
  chirality pdb=" CA  ASN A1061 "
            pdb=" N   ASN A1061 "
            pdb=" C   ASN A1061 "
            pdb=" CB  ASN A1061 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.35    0.16 2.00e-01 2.50e+01 6.24e-01
  ... (remaining 2096 not shown)

  Planarity restraints: 2318
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   THR A 435 "    0.051 5.00e-02 4.00e+02   7.74e-02 9.59e+00
        pdb=" N   PRO A 436 "   -0.134 5.00e-02 4.00e+02
        pdb=" CA  PRO A 436 "    0.040 5.00e-02 4.00e+02
        pdb=" CD  PRO A 436 "    0.043 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   TYR A 863 "   -0.040 5.00e-02 4.00e+02   6.04e-02 5.83e+00
        pdb=" N   PRO A 864 "    0.104 5.00e-02 4.00e+02
        pdb=" CA  PRO A 864 "   -0.032 5.00e-02 4.00e+02
        pdb=" CD  PRO A 864 "   -0.033 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   SER A 636 "   -0.039 5.00e-02 4.00e+02   5.97e-02 5.70e+00
        pdb=" N   PRO A 637 "    0.103 5.00e-02 4.00e+02
        pdb=" CA  PRO A 637 "   -0.031 5.00e-02 4.00e+02
        pdb=" CD  PRO A 637 "   -0.033 5.00e-02 4.00e+02
  ... (remaining 2315 not shown)

  Histogram of nonbonded interaction distances:
        2.13 -     2.68: 408
        2.68 -     3.24: 11818
        3.24 -     3.79: 20054
        3.79 -     4.35: 27001
        4.35 -     4.90: 45936
  Nonbonded interactions: 105217
  Sorted by model distance:
  nonbonded pdb=" O2'   A B  11 "
            pdb=" O4'   C B  12 "
     model   vdw
     2.130 3.040
  nonbonded pdb=" OE1 GLU A  70 "
            pdb=" NH2 ARG A 104 "
     model   vdw
     2.246 3.120
  nonbonded pdb=" O   ARG A 330 "
            pdb=" OG1 THR A 334 "
     model   vdw
     2.262 3.040
  nonbonded pdb=" O   SER A 180 "
            pdb=" OG  SER A 180 "
     model   vdw
     2.305 3.040
  nonbonded pdb=" NH2 ARG A 917 "
            pdb=" O   GLU A 922 "
     model   vdw
     2.308 3.120
  ... (remaining 105212 not shown)

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

  No NCS relation were found !!!

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

Found NCS groups:
  found none.
Set up NCS constraints
  No NCS constraints will be used in refinement.
Set refine NCS operators
Adjust number of macro_cycles
  Number of macro_cycles: 10
Reset NCS operators
Extract rigid body selections
Check and reset occupancies
  Occupancies: min=1.00 max=1.00 mean=1.00
Load rotamer database and sin/cos tables
Set ADP refinement strategy
  ADPs will be refined as 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:             3.110
  Set stop_for_unknowns flag:              0.000
  Assert model is a single copy model:     0.000
  Assert all atoms have isotropic ADPs:    0.000
  Construct map_model_manager:             0.010
  Extract box with map and model:          0.240
  Check model and map are aligned:         0.020
  Set scattering table:                    0.030
  Process input model:                     16.110
  Find NCS groups from input model:        0.050
  Set up NCS constraints:                  0.030
  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:1.390
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   20.990
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8123
moved from start:          0.0000

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.040  14309  Z= 0.159
  Angle     :  0.651   7.377  19596  Z= 0.383
  Chirality :  0.043   0.210   2099
  Planarity :  0.006   0.077   2318
  Dihedral  : 18.049 156.972   5885
  Min Nonbonded Distance : 2.130

Molprobity Statistics.
  All-atom Clashscore : 6.89
  Ramachandran Plot:
    Outliers :  0.07 %
    Allowed  : 10.55 %
    Favored  : 89.38 %
  Rotamer:
    Outliers :  1.04 %
    Allowed  : 10.94 %
    Favored  : 88.02 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -4.51 (0.17), residues: 1526
  helix: -2.16 (0.24), residues: 293
  sheet: -1.75 (0.29), residues: 267
  loop : -3.90 (0.14), residues: 966

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG A 967 
 TYR   0.010   0.001   TYR A 313 
 PHE   0.012   0.001   PHE A 416 
 TRP   0.035   0.001   TRP A1600 
 HIS   0.004   0.001   HIS A 691 

Details of bonding type rmsd
  covalent geometry    : bond        0.00312 (14309)
  covalent geometry    : angle       0.65056 (19596)
  hydrogen bonds       : bond        0.19880 (  335)
  hydrogen bonds       : angle       7.10924 (  936)

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

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

  3052 Ramachandran restraints generated.
    1526 Oldfield, 0 Emsley, 1526 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3052 Ramachandran restraints generated.
    1526 Oldfield, 0 Emsley, 1526 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  146 residues out of total 1344 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 132
  time to evaluate  : 0.518 
Fit side-chains
REVERT: A  393 ARG cc_start: 0.7549 (mpp80) cc_final: 0.7202 (ptt-90)
REVERT: A  437 ASP cc_start: 0.7376 (p0) cc_final: 0.7173 (t0)
REVERT: A  577 TYR cc_start: 0.8005 (p90) cc_final: 0.7725 (p90)
REVERT: A  621 ARG cc_start: 0.7930 (OUTLIER) cc_final: 0.7647 (mmt-90)
REVERT: A  634 MET cc_start: 0.8421 (mtt) cc_final: 0.8206 (mtm)
  outliers start: 14
  outliers final: 9
  residues processed: 145
  average time/residue: 0.1756
  time to fit residues: 34.3080
Evaluate side-chains
  98 residues out of total 1344 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 88
  time to evaluate  : 0.520 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   86 CYS
Chi-restraints excluded: chain A residue  621 ARG
Chi-restraints excluded: chain A residue  659 VAL
Chi-restraints excluded: chain A residue  742 VAL
Chi-restraints excluded: chain A residue  837 PHE
Chi-restraints excluded: chain A residue  965 CYS
Chi-restraints excluded: chain A residue 1049 VAL
Chi-restraints excluded: chain A residue 1252 VAL
Chi-restraints excluded: chain A residue 1559 VAL
Chi-restraints excluded: chain A residue 1590 GLN
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 158
   random chunks:
   chunk 98 optimal weight:    0.0670
   chunk 107 optimal weight:    6.9990
   chunk 10 optimal weight:    2.9990
   chunk 66 optimal weight:    1.9990
   chunk 130 optimal weight:    1.9990
   chunk 124 optimal weight:    0.0170
   chunk 103 optimal weight:   10.0000
   chunk 77 optimal weight:    2.9990
   chunk 122 optimal weight:    7.9990
   chunk 91 optimal weight:    0.6980
   chunk 149 optimal weight:    2.9990
   overall best weight:    0.9560

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

Flipped N/Q/H residues before XYZ refinement:
** A 100 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 113 ASN
A 306 HIS
A 456 GLN
A 464 ASN
A 531 GLN
** A 587 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 985 ASN
A1098 HIS
A1113 ASN
A1127 GLN
A1313 HIS
A1483 HIS
A1590 GLN

Total number of N/Q/H flips: 12

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3612 r_free = 0.3612 target = 0.130524 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 37)----------------|
| r_work = 0.3193 r_free = 0.3193 target = 0.097571 restraints weight = 19429.504|
|-----------------------------------------------------------------------------|
r_work (start): 0.3174 rms_B_bonded: 2.18
r_work: 0.3009 rms_B_bonded: 2.97 restraints_weight: 0.5000
r_work: 0.2869 rms_B_bonded: 4.84 restraints_weight: 0.2500
r_work (final): 0.2869
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8428
moved from start:          0.1123

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.040  14309  Z= 0.140
  Angle     :  0.621  10.138  19596  Z= 0.326
  Chirality :  0.043   0.191   2099
  Planarity :  0.005   0.070   2318
  Dihedral  : 16.304 161.944   2691
  Min Nonbonded Distance : 2.467

Molprobity Statistics.
  All-atom Clashscore : 3.91
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  : 11.34 %
    Favored  : 88.66 %
  Rotamer:
    Outliers :  2.01 %
    Allowed  : 13.24 %
    Favored  : 84.75 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -3.51 (0.18), residues: 1526
  helix: -0.40 (0.30), residues: 296
  sheet: -1.30 (0.31), residues: 262
  loop : -3.52 (0.15), residues: 968

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG A1356 
 TYR   0.009   0.001   TYR A1276 
 PHE   0.012   0.001   PHE A 187 
 TRP   0.026   0.001   TRP A1600 
 HIS   0.005   0.001   HIS A1149 

Details of bonding type rmsd
  covalent geometry    : bond        0.00321 (14309)
  covalent geometry    : angle       0.62102 (19596)
  hydrogen bonds       : bond        0.04439 (  335)
  hydrogen bonds       : angle       4.66981 (  936)

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

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

  3052 Ramachandran restraints generated.
    1526 Oldfield, 0 Emsley, 1526 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3052 Ramachandran restraints generated.
    1526 Oldfield, 0 Emsley, 1526 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  121 residues out of total 1344 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 27
    poor density    : 94
  time to evaluate  : 0.499 
Fit side-chains
REVERT: A  314 LEU cc_start: 0.8851 (OUTLIER) cc_final: 0.8513 (pt)
REVERT: A  393 ARG cc_start: 0.7718 (mpp80) cc_final: 0.7005 (ptt-90)
REVERT: A  437 ASP cc_start: 0.7611 (p0) cc_final: 0.7363 (t0)
REVERT: A  634 MET cc_start: 0.8726 (mtt) cc_final: 0.8471 (mtt)
REVERT: A  759 ASP cc_start: 0.8844 (p0) cc_final: 0.8644 (p0)
REVERT: A 1082 TYR cc_start: 0.7188 (t80) cc_final: 0.6570 (m-80)
REVERT: A 1211 MET cc_start: 0.7789 (OUTLIER) cc_final: 0.6466 (tmm)
  outliers start: 27
  outliers final: 15
  residues processed: 115
  average time/residue: 0.1344
  time to fit residues: 22.3885
Evaluate side-chains
  106 residues out of total 1344 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 17
    poor density    : 89
  time to evaluate  : 0.506 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   21 GLN
Chi-restraints excluded: chain A residue  176 VAL
Chi-restraints excluded: chain A residue  314 LEU
Chi-restraints excluded: chain A residue  410 LEU
Chi-restraints excluded: chain A residue  659 VAL
Chi-restraints excluded: chain A residue  742 VAL
Chi-restraints excluded: chain A residue  900 ILE
Chi-restraints excluded: chain A residue  968 ILE
Chi-restraints excluded: chain A residue 1048 LEU
Chi-restraints excluded: chain A residue 1049 VAL
Chi-restraints excluded: chain A residue 1193 ARG
Chi-restraints excluded: chain A residue 1211 MET
Chi-restraints excluded: chain A residue 1217 THR
Chi-restraints excluded: chain A residue 1266 VAL
Chi-restraints excluded: chain A residue 1275 VAL
Chi-restraints excluded: chain A residue 1554 ASP
Chi-restraints excluded: chain A residue 1594 THR
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 158
   random chunks:
   chunk 5 optimal weight:    0.7980
   chunk 47 optimal weight:    2.9990
   chunk 66 optimal weight:    1.9990
   chunk 121 optimal weight:    0.9990
   chunk 130 optimal weight:    2.9990
   chunk 68 optimal weight:    0.9990
   chunk 134 optimal weight:    0.0970
   chunk 54 optimal weight:    0.9990
   chunk 90 optimal weight:    3.9990
   chunk 156 optimal weight:    7.9990
   chunk 106 optimal weight:    0.0040
   overall best weight:    0.5794

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

Flipped N/Q/H residues before XYZ refinement:
** A 100 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 587 GLN
A1113 ASN
A1313 HIS

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3626 r_free = 0.3626 target = 0.131754 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 54)----------------|
| r_work = 0.3165 r_free = 0.3165 target = 0.096879 restraints weight = 19511.862|
|-----------------------------------------------------------------------------|
r_work (start): 0.3173 rms_B_bonded: 2.40
r_work: 0.3043 rms_B_bonded: 2.89 restraints_weight: 0.5000
r_work: 0.2903 rms_B_bonded: 4.72 restraints_weight: 0.2500
r_work (final): 0.2903
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8331
moved from start:          0.1396

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.040  14309  Z= 0.111
  Angle     :  0.566  10.643  19596  Z= 0.295
  Chirality :  0.041   0.193   2099
  Planarity :  0.005   0.066   2318
  Dihedral  : 16.092 161.952   2678
  Min Nonbonded Distance : 2.378

Molprobity Statistics.
  All-atom Clashscore : 4.25
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  9.76 %
    Favored  : 90.24 %
  Rotamer:
    Outliers :  1.79 %
    Allowed  : 14.96 %
    Favored  : 83.26 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -2.97 (0.19), residues: 1526
  helix:  0.47 (0.32), residues: 302
  sheet: -1.02 (0.31), residues: 262
  loop : -3.32 (0.16), residues: 962

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG A 470 
 TYR   0.008   0.001   TYR A1276 
 PHE   0.010   0.001   PHE A 747 
 TRP   0.022   0.001   TRP A1600 
 HIS   0.004   0.001   HIS A1149 

Details of bonding type rmsd
  covalent geometry    : bond        0.00251 (14309)
  covalent geometry    : angle       0.56608 (19596)
  hydrogen bonds       : bond        0.03661 (  335)
  hydrogen bonds       : angle       4.28890 (  936)

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

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

  3052 Ramachandran restraints generated.
    1526 Oldfield, 0 Emsley, 1526 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3052 Ramachandran restraints generated.
    1526 Oldfield, 0 Emsley, 1526 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  120 residues out of total 1344 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 24
    poor density    : 96
  time to evaluate  : 0.511 
Fit side-chains
REVERT: A  314 LEU cc_start: 0.8730 (OUTLIER) cc_final: 0.8354 (pt)
REVERT: A  393 ARG cc_start: 0.7800 (mpp80) cc_final: 0.6958 (ptt-90)
REVERT: A  634 MET cc_start: 0.8705 (mtt) cc_final: 0.8441 (mtp)
REVERT: A  692 MET cc_start: 0.8769 (tpp) cc_final: 0.8160 (tpt)
REVERT: A  759 ASP cc_start: 0.8805 (p0) cc_final: 0.8595 (p0)
REVERT: A 1211 MET cc_start: 0.7650 (OUTLIER) cc_final: 0.6256 (tmm)
  outliers start: 24
  outliers final: 13
  residues processed: 113
  average time/residue: 0.1261
  time to fit residues: 21.0819
Evaluate side-chains
  101 residues out of total 1344 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 15
    poor density    : 86
  time to evaluate  : 0.535 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   21 GLN
Chi-restraints excluded: chain A residue   86 CYS
Chi-restraints excluded: chain A residue  314 LEU
Chi-restraints excluded: chain A residue  659 VAL
Chi-restraints excluded: chain A residue  742 VAL
Chi-restraints excluded: chain A residue  842 VAL
Chi-restraints excluded: chain A residue  900 ILE
Chi-restraints excluded: chain A residue  968 ILE
Chi-restraints excluded: chain A residue 1008 THR
Chi-restraints excluded: chain A residue 1049 VAL
Chi-restraints excluded: chain A residue 1193 ARG
Chi-restraints excluded: chain A residue 1211 MET
Chi-restraints excluded: chain A residue 1217 THR
Chi-restraints excluded: chain A residue 1444 THR
Chi-restraints excluded: chain A residue 1554 ASP
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 158
   random chunks:
   chunk 6 optimal weight:    4.9990
   chunk 36 optimal weight:    1.9990
   chunk 8 optimal weight:    1.9990
   chunk 16 optimal weight:    0.8980
   chunk 11 optimal weight:    7.9990
   chunk 62 optimal weight:    3.9990
   chunk 86 optimal weight:    3.9990
   chunk 85 optimal weight:    0.5980
   chunk 112 optimal weight:    7.9990
   chunk 12 optimal weight:    1.9990
   chunk 66 optimal weight:    2.9990
   overall best weight:    1.4986

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

Flipped N/Q/H residues before XYZ refinement:
** A 100 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 587 GLN
A1113 ASN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3564 r_free = 0.3564 target = 0.126855 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 36)----------------|
| r_work = 0.3125 r_free = 0.3125 target = 0.093685 restraints weight = 19602.292|
|-----------------------------------------------------------------------------|
r_work (start): 0.3123 rms_B_bonded: 2.50
r_work: 0.2957 rms_B_bonded: 2.89 restraints_weight: 0.5000
r_work: 0.2816 rms_B_bonded: 4.69 restraints_weight: 0.2500
r_work (final): 0.2816
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8486
moved from start:          0.1740

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.044  14309  Z= 0.180
  Angle     :  0.644  16.170  19596  Z= 0.335
  Chirality :  0.045   0.189   2099
  Planarity :  0.005   0.070   2318
  Dihedral  : 16.093 158.143   2678
  Min Nonbonded Distance : 2.376

Molprobity Statistics.
  All-atom Clashscore : 4.21
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  : 12.84 %
    Favored  : 87.16 %
  Rotamer:
    Outliers :  2.46 %
    Allowed  : 15.70 %
    Favored  : 81.85 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -2.74 (0.20), residues: 1526
  helix:  0.77 (0.32), residues: 308
  sheet: -1.01 (0.31), residues: 284
  loop : -3.22 (0.16), residues: 934

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG A 444 
 TYR   0.011   0.001   TYR A1276 
 PHE   0.015   0.002   PHE A 187 
 TRP   0.023   0.001   TRP A1600 
 HIS   0.005   0.001   HIS A1149 

Details of bonding type rmsd
  covalent geometry    : bond        0.00425 (14309)
  covalent geometry    : angle       0.64400 (19596)
  hydrogen bonds       : bond        0.04786 (  335)
  hydrogen bonds       : angle       4.31762 (  936)

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

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

  3052 Ramachandran restraints generated.
    1526 Oldfield, 0 Emsley, 1526 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3052 Ramachandran restraints generated.
    1526 Oldfield, 0 Emsley, 1526 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  118 residues out of total 1344 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 33
    poor density    : 85
  time to evaluate  : 0.519 
Fit side-chains
REVERT: A  314 LEU cc_start: 0.8950 (OUTLIER) cc_final: 0.8643 (pt)
REVERT: A  393 ARG cc_start: 0.7814 (mpp80) cc_final: 0.7022 (ptt-90)
REVERT: A  634 MET cc_start: 0.8742 (mtt) cc_final: 0.8487 (mtp)
REVERT: A  759 ASP cc_start: 0.8889 (p0) cc_final: 0.8648 (p0)
REVERT: A 1024 LEU cc_start: 0.7720 (mt) cc_final: 0.7510 (mp)
REVERT: A 1097 TRP cc_start: 0.8306 (m-10) cc_final: 0.8037 (m-10)
REVERT: A 1211 MET cc_start: 0.7903 (OUTLIER) cc_final: 0.6722 (tmm)
  outliers start: 33
  outliers final: 23
  residues processed: 109
  average time/residue: 0.1309
  time to fit residues: 20.8050
Evaluate side-chains
  108 residues out of total 1344 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 25
    poor density    : 83
  time to evaluate  : 0.579 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   21 GLN
Chi-restraints excluded: chain A residue  176 VAL
Chi-restraints excluded: chain A residue  314 LEU
Chi-restraints excluded: chain A residue  410 LEU
Chi-restraints excluded: chain A residue  414 THR
Chi-restraints excluded: chain A residue  622 ASP
Chi-restraints excluded: chain A residue  636 SER
Chi-restraints excluded: chain A residue  659 VAL
Chi-restraints excluded: chain A residue  742 VAL
Chi-restraints excluded: chain A residue  772 LEU
Chi-restraints excluded: chain A residue  842 VAL
Chi-restraints excluded: chain A residue  900 ILE
Chi-restraints excluded: chain A residue 1008 THR
Chi-restraints excluded: chain A residue 1048 LEU
Chi-restraints excluded: chain A residue 1049 VAL
Chi-restraints excluded: chain A residue 1185 THR
Chi-restraints excluded: chain A residue 1193 ARG
Chi-restraints excluded: chain A residue 1211 MET
Chi-restraints excluded: chain A residue 1217 THR
Chi-restraints excluded: chain A residue 1252 VAL
Chi-restraints excluded: chain A residue 1266 VAL
Chi-restraints excluded: chain A residue 1275 VAL
Chi-restraints excluded: chain A residue 1309 LEU
Chi-restraints excluded: chain A residue 1444 THR
Chi-restraints excluded: chain A residue 1554 ASP
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 158
   random chunks:
   chunk 97 optimal weight:    7.9990
   chunk 41 optimal weight:    1.9990
   chunk 119 optimal weight:    3.9990
   chunk 26 optimal weight:    3.9990
   chunk 15 optimal weight:    4.9990
   chunk 20 optimal weight:    4.9990
   chunk 143 optimal weight:    3.9990
   chunk 33 optimal weight:    4.9990
   chunk 90 optimal weight:    2.9990
   chunk 107 optimal weight:    5.9990
   chunk 37 optimal weight:    1.9990
   overall best weight:    2.9990

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

Flipped N/Q/H residues before XYZ refinement:
** A 100 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 587 GLN
A 691 HIS
A1113 ASN
A1279 HIS
A1337 HIS
A1428 ASN

Total number of N/Q/H flips: 6

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3555 r_free = 0.3555 target = 0.124469 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 33)----------------|
| r_work = 0.3138 r_free = 0.3138 target = 0.092498 restraints weight = 19967.864|
|-----------------------------------------------------------------------------|
r_work (start): 0.3113 rms_B_bonded: 2.03
r_work: 0.2925 rms_B_bonded: 2.88 restraints_weight: 0.5000
r_work: 0.2787 rms_B_bonded: 4.65 restraints_weight: 0.2500
r_work (final): 0.2787
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8626
moved from start:          0.2183

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.008   0.079  14309  Z= 0.332
  Angle     :  0.787  16.541  19596  Z= 0.412
  Chirality :  0.052   0.245   2099
  Planarity :  0.006   0.072   2318
  Dihedral  : 16.251 154.684   2678
  Min Nonbonded Distance : 2.391

Molprobity Statistics.
  All-atom Clashscore : 4.40
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  : 13.37 %
    Favored  : 86.63 %
  Rotamer:
    Outliers :  3.35 %
    Allowed  : 15.55 %
    Favored  : 81.10 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -2.78 (0.20), residues: 1526
  helix:  0.59 (0.32), residues: 305
  sheet: -0.84 (0.32), residues: 283
  loop : -3.25 (0.17), residues: 938

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.007   0.001   ARG A 444 
 TYR   0.015   0.002   TYR A 930 
 PHE   0.020   0.002   PHE A1013 
 TRP   0.029   0.002   TRP A1600 
 HIS   0.010   0.002   HIS A1149 

Details of bonding type rmsd
  covalent geometry    : bond        0.00815 (14309)
  covalent geometry    : angle       0.78695 (19596)
  hydrogen bonds       : bond        0.06314 (  335)
  hydrogen bonds       : angle       4.58328 (  936)

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

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

  3052 Ramachandran restraints generated.
    1526 Oldfield, 0 Emsley, 1526 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3052 Ramachandran restraints generated.
    1526 Oldfield, 0 Emsley, 1526 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  127 residues out of total 1344 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 45
    poor density    : 82
  time to evaluate  : 0.503 
Fit side-chains
REVERT: A  314 LEU cc_start: 0.9162 (OUTLIER) cc_final: 0.8936 (pt)
REVERT: A  393 ARG cc_start: 0.7850 (mpp80) cc_final: 0.7171 (ptt-90)
REVERT: A  634 MET cc_start: 0.8838 (mtt) cc_final: 0.8583 (mtp)
REVERT: A  759 ASP cc_start: 0.8971 (p0) cc_final: 0.8710 (p0)
REVERT: A 1024 LEU cc_start: 0.7858 (mt) cc_final: 0.7537 (mp)
REVERT: A 1113 ASN cc_start: 0.6027 (OUTLIER) cc_final: 0.5631 (t0)
REVERT: A 1188 PHE cc_start: 0.8648 (m-80) cc_final: 0.8285 (m-80)
REVERT: A 1211 MET cc_start: 0.8046 (OUTLIER) cc_final: 0.7285 (tmm)
REVERT: A 1260 ARG cc_start: 0.8466 (ttp-170) cc_final: 0.7953 (ttt-90)
REVERT: A 1268 LYS cc_start: 0.8199 (mttm) cc_final: 0.7780 (mtmm)
REVERT: A 1300 MET cc_start: 0.8787 (mtm) cc_final: 0.8557 (mtp)
REVERT: A 1485 LEU cc_start: 0.9384 (OUTLIER) cc_final: 0.8981 (pt)
  outliers start: 45
  outliers final: 31
  residues processed: 120
  average time/residue: 0.1395
  time to fit residues: 24.4595
Evaluate side-chains
  117 residues out of total 1344 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 35
    poor density    : 82
  time to evaluate  : 0.488 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   21 GLN
Chi-restraints excluded: chain A residue   75 LEU
Chi-restraints excluded: chain A residue  169 SER
Chi-restraints excluded: chain A residue  176 VAL
Chi-restraints excluded: chain A residue  225 THR
Chi-restraints excluded: chain A residue  314 LEU
Chi-restraints excluded: chain A residue  414 THR
Chi-restraints excluded: chain A residue  587 GLN
Chi-restraints excluded: chain A residue  636 SER
Chi-restraints excluded: chain A residue  659 VAL
Chi-restraints excluded: chain A residue  742 VAL
Chi-restraints excluded: chain A residue  772 LEU
Chi-restraints excluded: chain A residue  842 VAL
Chi-restraints excluded: chain A residue  844 VAL
Chi-restraints excluded: chain A residue  900 ILE
Chi-restraints excluded: chain A residue  986 VAL
Chi-restraints excluded: chain A residue 1008 THR
Chi-restraints excluded: chain A residue 1048 LEU
Chi-restraints excluded: chain A residue 1049 VAL
Chi-restraints excluded: chain A residue 1113 ASN
Chi-restraints excluded: chain A residue 1185 THR
Chi-restraints excluded: chain A residue 1193 ARG
Chi-restraints excluded: chain A residue 1211 MET
Chi-restraints excluded: chain A residue 1217 THR
Chi-restraints excluded: chain A residue 1252 VAL
Chi-restraints excluded: chain A residue 1266 VAL
Chi-restraints excluded: chain A residue 1275 VAL
Chi-restraints excluded: chain A residue 1295 THR
Chi-restraints excluded: chain A residue 1309 LEU
Chi-restraints excluded: chain A residue 1436 ILE
Chi-restraints excluded: chain A residue 1444 THR
Chi-restraints excluded: chain A residue 1485 LEU
Chi-restraints excluded: chain A residue 1487 MET
Chi-restraints excluded: chain A residue 1554 ASP
Chi-restraints excluded: chain A residue 1594 THR
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 158
   random chunks:
   chunk 13 optimal weight:    4.9990
   chunk 10 optimal weight:    0.7980
   chunk 96 optimal weight:    1.9990
   chunk 65 optimal weight:    0.7980
   chunk 114 optimal weight:    5.9990
   chunk 139 optimal weight:    0.9990
   chunk 36 optimal weight:    0.6980
   chunk 23 optimal weight:    0.8980
   chunk 141 optimal weight:    0.7980
   chunk 68 optimal weight:    0.6980
   chunk 121 optimal weight:    0.9980
   overall best weight:    0.7580

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

Flipped N/Q/H residues before XYZ refinement:
** A 100 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 518 ASN
A 587 GLN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3595 r_free = 0.3595 target = 0.127897 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 37)----------------|
| r_work = 0.3177 r_free = 0.3177 target = 0.096219 restraints weight = 19269.672|
|-----------------------------------------------------------------------------|
r_work (start): 0.3155 rms_B_bonded: 2.32
r_work: 0.3000 rms_B_bonded: 2.76 restraints_weight: 0.5000
r_work: 0.2863 rms_B_bonded: 4.51 restraints_weight: 0.2500
r_work (final): 0.2863
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8484
moved from start:          0.2089

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.037  14309  Z= 0.124
  Angle     :  0.600  15.035  19596  Z= 0.312
  Chirality :  0.043   0.194   2099
  Planarity :  0.005   0.069   2318
  Dihedral  : 16.176 159.088   2678
  Min Nonbonded Distance : 2.452

Molprobity Statistics.
  All-atom Clashscore : 4.58
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  : 10.88 %
    Favored  : 89.12 %
  Rotamer:
    Outliers :  2.31 %
    Allowed  : 16.96 %
    Favored  : 80.73 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -2.45 (0.20), residues: 1526
  helix:  1.03 (0.32), residues: 304
  sheet: -0.63 (0.32), residues: 275
  loop : -3.07 (0.17), residues: 947

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG A 470 
 TYR   0.011   0.001   TYR A1276 
 PHE   0.012   0.001   PHE A 416 
 TRP   0.027   0.001   TRP A1600 
 HIS   0.011   0.001   HIS A1149 

Details of bonding type rmsd
  covalent geometry    : bond        0.00279 (14309)
  covalent geometry    : angle       0.59957 (19596)
  hydrogen bonds       : bond        0.03820 (  335)
  hydrogen bonds       : angle       4.25351 (  936)

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

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

  3052 Ramachandran restraints generated.
    1526 Oldfield, 0 Emsley, 1526 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3052 Ramachandran restraints generated.
    1526 Oldfield, 0 Emsley, 1526 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  116 residues out of total 1344 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 31
    poor density    : 85
  time to evaluate  : 0.498 
Fit side-chains
REVERT: A  314 LEU cc_start: 0.9002 (OUTLIER) cc_final: 0.8742 (pt)
REVERT: A  393 ARG cc_start: 0.7805 (mpp80) cc_final: 0.7076 (ptt-90)
REVERT: A  600 GLU cc_start: 0.7238 (mm-30) cc_final: 0.7020 (tp30)
REVERT: A  634 MET cc_start: 0.8679 (mtt) cc_final: 0.8428 (mtt)
REVERT: A  759 ASP cc_start: 0.8883 (p0) cc_final: 0.8647 (p0)
REVERT: A 1024 LEU cc_start: 0.7794 (mt) cc_final: 0.7579 (mp)
REVERT: A 1211 MET cc_start: 0.7845 (OUTLIER) cc_final: 0.6769 (tmm)
REVERT: A 1268 LYS cc_start: 0.7988 (mttm) cc_final: 0.7566 (mtmm)
REVERT: A 1300 MET cc_start: 0.8643 (mtm) cc_final: 0.8423 (mtp)
  outliers start: 31
  outliers final: 22
  residues processed: 111
  average time/residue: 0.1370
  time to fit residues: 21.9443
Evaluate side-chains
  107 residues out of total 1344 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 24
    poor density    : 83
  time to evaluate  : 0.928 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   21 GLN
Chi-restraints excluded: chain A residue  176 VAL
Chi-restraints excluded: chain A residue  314 LEU
Chi-restraints excluded: chain A residue  410 LEU
Chi-restraints excluded: chain A residue  414 THR
Chi-restraints excluded: chain A residue  466 GLU
Chi-restraints excluded: chain A residue  636 SER
Chi-restraints excluded: chain A residue  659 VAL
Chi-restraints excluded: chain A residue  742 VAL
Chi-restraints excluded: chain A residue  844 VAL
Chi-restraints excluded: chain A residue  900 ILE
Chi-restraints excluded: chain A residue  986 VAL
Chi-restraints excluded: chain A residue 1008 THR
Chi-restraints excluded: chain A residue 1048 LEU
Chi-restraints excluded: chain A residue 1049 VAL
Chi-restraints excluded: chain A residue 1185 THR
Chi-restraints excluded: chain A residue 1193 ARG
Chi-restraints excluded: chain A residue 1210 THR
Chi-restraints excluded: chain A residue 1211 MET
Chi-restraints excluded: chain A residue 1252 VAL
Chi-restraints excluded: chain A residue 1275 VAL
Chi-restraints excluded: chain A residue 1309 LEU
Chi-restraints excluded: chain A residue 1444 THR
Chi-restraints excluded: chain A residue 1554 ASP
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 158
   random chunks:
   chunk 26 optimal weight:    4.9990
   chunk 96 optimal weight:    2.9990
   chunk 11 optimal weight:    0.0170
   chunk 8 optimal weight:    2.9990
   chunk 127 optimal weight:    4.9990
   chunk 118 optimal weight:    4.9990
   chunk 77 optimal weight:    4.9990
   chunk 4 optimal weight:    2.9990
   chunk 112 optimal weight:    5.9990
   chunk 15 optimal weight:    0.6980
   chunk 1 optimal weight:    0.2980
   overall best weight:    1.4022

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

Flipped N/Q/H residues before XYZ refinement:
** A 100 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 587 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3550 r_free = 0.3550 target = 0.126109 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 33)----------------|
| r_work = 0.3129 r_free = 0.3129 target = 0.093225 restraints weight = 19622.381|
|-----------------------------------------------------------------------------|
r_work (start): 0.3114 rms_B_bonded: 2.17
r_work: 0.2932 rms_B_bonded: 3.02 restraints_weight: 0.5000
r_work: 0.2791 rms_B_bonded: 4.88 restraints_weight: 0.2500
r_work (final): 0.2791
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8508
moved from start:          0.2172

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.046  14309  Z= 0.171
  Angle     :  0.628  14.612  19596  Z= 0.327
  Chirality :  0.045   0.188   2099
  Planarity :  0.005   0.072   2318
  Dihedral  : 16.115 158.092   2678
  Min Nonbonded Distance : 2.463

Molprobity Statistics.
  All-atom Clashscore : 4.43
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  : 12.65 %
    Favored  : 87.35 %
  Rotamer:
    Outliers :  2.75 %
    Allowed  : 16.89 %
    Favored  : 80.36 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -2.39 (0.21), residues: 1526
  helix:  0.98 (0.32), residues: 312
  sheet: -0.48 (0.32), residues: 277
  loop : -3.08 (0.17), residues: 937

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARG A 470 
 TYR   0.010   0.001   TYR A1276 
 PHE   0.014   0.002   PHE A 776 
 TRP   0.026   0.001   TRP A1600 
 HIS   0.009   0.001   HIS A1149 

Details of bonding type rmsd
  covalent geometry    : bond        0.00406 (14309)
  covalent geometry    : angle       0.62793 (19596)
  hydrogen bonds       : bond        0.04360 (  335)
  hydrogen bonds       : angle       4.20491 (  936)

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

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

  3052 Ramachandran restraints generated.
    1526 Oldfield, 0 Emsley, 1526 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3052 Ramachandran restraints generated.
    1526 Oldfield, 0 Emsley, 1526 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  120 residues out of total 1344 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 37
    poor density    : 83
  time to evaluate  : 0.492 
Fit side-chains
REVERT: A  314 LEU cc_start: 0.8980 (OUTLIER) cc_final: 0.8710 (pt)
REVERT: A  393 ARG cc_start: 0.7814 (mpp80) cc_final: 0.7030 (ptt-90)
REVERT: A  600 GLU cc_start: 0.7385 (mm-30) cc_final: 0.7034 (tp30)
REVERT: A  634 MET cc_start: 0.8735 (mtt) cc_final: 0.8479 (mtp)
REVERT: A  759 ASP cc_start: 0.8930 (p0) cc_final: 0.8707 (p0)
REVERT: A 1024 LEU cc_start: 0.7602 (mt) cc_final: 0.7352 (mp)
REVERT: A 1211 MET cc_start: 0.7953 (OUTLIER) cc_final: 0.6855 (tmm)
REVERT: A 1268 LYS cc_start: 0.8048 (mttm) cc_final: 0.7603 (mtmm)
REVERT: A 1300 MET cc_start: 0.8702 (mtm) cc_final: 0.8464 (mtp)
  outliers start: 37
  outliers final: 29
  residues processed: 113
  average time/residue: 0.1299
  time to fit residues: 21.1846
Evaluate side-chains
  113 residues out of total 1344 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 31
    poor density    : 82
  time to evaluate  : 0.505 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   21 GLN
Chi-restraints excluded: chain A residue  176 VAL
Chi-restraints excluded: chain A residue  314 LEU
Chi-restraints excluded: chain A residue  410 LEU
Chi-restraints excluded: chain A residue  414 THR
Chi-restraints excluded: chain A residue  466 GLU
Chi-restraints excluded: chain A residue  636 SER
Chi-restraints excluded: chain A residue  659 VAL
Chi-restraints excluded: chain A residue  742 VAL
Chi-restraints excluded: chain A residue  772 LEU
Chi-restraints excluded: chain A residue  842 VAL
Chi-restraints excluded: chain A residue  844 VAL
Chi-restraints excluded: chain A residue  900 ILE
Chi-restraints excluded: chain A residue  986 VAL
Chi-restraints excluded: chain A residue 1008 THR
Chi-restraints excluded: chain A residue 1048 LEU
Chi-restraints excluded: chain A residue 1049 VAL
Chi-restraints excluded: chain A residue 1096 LEU
Chi-restraints excluded: chain A residue 1151 VAL
Chi-restraints excluded: chain A residue 1185 THR
Chi-restraints excluded: chain A residue 1193 ARG
Chi-restraints excluded: chain A residue 1210 THR
Chi-restraints excluded: chain A residue 1211 MET
Chi-restraints excluded: chain A residue 1217 THR
Chi-restraints excluded: chain A residue 1252 VAL
Chi-restraints excluded: chain A residue 1266 VAL
Chi-restraints excluded: chain A residue 1275 VAL
Chi-restraints excluded: chain A residue 1295 THR
Chi-restraints excluded: chain A residue 1309 LEU
Chi-restraints excluded: chain A residue 1444 THR
Chi-restraints excluded: chain A residue 1554 ASP
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 158
   random chunks:
   chunk 74 optimal weight:    3.9990
   chunk 146 optimal weight:    0.9990
   chunk 127 optimal weight:    5.9990
   chunk 157 optimal weight:    5.9990
   chunk 84 optimal weight:    2.9990
   chunk 78 optimal weight:    0.8980
   chunk 141 optimal weight:    2.9990
   chunk 10 optimal weight:    0.6980
   chunk 76 optimal weight:    1.9990
   chunk 134 optimal weight:    2.9990
   chunk 80 optimal weight:    0.8980
   overall best weight:    1.0984

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

Flipped N/Q/H residues before XYZ refinement:
** A 100 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 587 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3568 r_free = 0.3568 target = 0.127494 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 36)----------------|
| r_work = 0.3137 r_free = 0.3137 target = 0.094405 restraints weight = 19533.401|
|-----------------------------------------------------------------------------|
r_work (start): 0.3135 rms_B_bonded: 2.47
r_work: 0.2971 rms_B_bonded: 2.87 restraints_weight: 0.5000
r_work: 0.2830 rms_B_bonded: 4.67 restraints_weight: 0.2500
r_work (final): 0.2830
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8474
moved from start:          0.2212

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.041  14309  Z= 0.144
  Angle     :  0.596  14.129  19596  Z= 0.309
  Chirality :  0.043   0.191   2099
  Planarity :  0.005   0.074   2318
  Dihedral  : 16.069 158.877   2678
  Min Nonbonded Distance : 2.473

Molprobity Statistics.
  All-atom Clashscore : 4.51
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  : 11.27 %
    Favored  : 88.73 %
  Rotamer:
    Outliers :  2.75 %
    Allowed  : 16.89 %
    Favored  : 80.36 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -2.23 (0.21), residues: 1526
  helix:  1.20 (0.32), residues: 306
  sheet: -0.48 (0.31), residues: 281
  loop : -2.95 (0.17), residues: 939

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG A 470 
 TYR   0.009   0.001   TYR A1276 
 PHE   0.013   0.001   PHE A 776 
 TRP   0.026   0.001   TRP A1600 
 HIS   0.008   0.001   HIS A1149 

Details of bonding type rmsd
  covalent geometry    : bond        0.00339 (14309)
  covalent geometry    : angle       0.59557 (19596)
  hydrogen bonds       : bond        0.03922 (  335)
  hydrogen bonds       : angle       4.11140 (  936)

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

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

  3052 Ramachandran restraints generated.
    1526 Oldfield, 0 Emsley, 1526 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3052 Ramachandran restraints generated.
    1526 Oldfield, 0 Emsley, 1526 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  125 residues out of total 1344 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 37
    poor density    : 88
  time to evaluate  : 0.438 
Fit side-chains
REVERT: A  314 LEU cc_start: 0.8961 (OUTLIER) cc_final: 0.8685 (pt)
REVERT: A  393 ARG cc_start: 0.7807 (mpp80) cc_final: 0.7093 (ptt-90)
REVERT: A  600 GLU cc_start: 0.7350 (mm-30) cc_final: 0.7073 (tp30)
REVERT: A  634 MET cc_start: 0.8709 (mtt) cc_final: 0.8442 (mtp)
REVERT: A  759 ASP cc_start: 0.8849 (p0) cc_final: 0.8627 (p0)
REVERT: A 1024 LEU cc_start: 0.7556 (mt) cc_final: 0.7331 (mp)
REVERT: A 1211 MET cc_start: 0.7913 (OUTLIER) cc_final: 0.6634 (tmm)
REVERT: A 1268 LYS cc_start: 0.8042 (mttm) cc_final: 0.7619 (mtmm)
REVERT: A 1300 MET cc_start: 0.8697 (mtm) cc_final: 0.8465 (mtp)
  outliers start: 37
  outliers final: 32
  residues processed: 120
  average time/residue: 0.1262
  time to fit residues: 21.8630
Evaluate side-chains
  119 residues out of total 1344 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 34
    poor density    : 85
  time to evaluate  : 0.487 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   21 GLN
Chi-restraints excluded: chain A residue  176 VAL
Chi-restraints excluded: chain A residue  299 VAL
Chi-restraints excluded: chain A residue  314 LEU
Chi-restraints excluded: chain A residue  410 LEU
Chi-restraints excluded: chain A residue  414 THR
Chi-restraints excluded: chain A residue  466 GLU
Chi-restraints excluded: chain A residue  636 SER
Chi-restraints excluded: chain A residue  659 VAL
Chi-restraints excluded: chain A residue  742 VAL
Chi-restraints excluded: chain A residue  772 LEU
Chi-restraints excluded: chain A residue  842 VAL
Chi-restraints excluded: chain A residue  844 VAL
Chi-restraints excluded: chain A residue  900 ILE
Chi-restraints excluded: chain A residue  986 VAL
Chi-restraints excluded: chain A residue 1008 THR
Chi-restraints excluded: chain A residue 1048 LEU
Chi-restraints excluded: chain A residue 1049 VAL
Chi-restraints excluded: chain A residue 1151 VAL
Chi-restraints excluded: chain A residue 1185 THR
Chi-restraints excluded: chain A residue 1193 ARG
Chi-restraints excluded: chain A residue 1210 THR
Chi-restraints excluded: chain A residue 1211 MET
Chi-restraints excluded: chain A residue 1217 THR
Chi-restraints excluded: chain A residue 1252 VAL
Chi-restraints excluded: chain A residue 1266 VAL
Chi-restraints excluded: chain A residue 1275 VAL
Chi-restraints excluded: chain A residue 1284 VAL
Chi-restraints excluded: chain A residue 1295 THR
Chi-restraints excluded: chain A residue 1309 LEU
Chi-restraints excluded: chain A residue 1399 SER
Chi-restraints excluded: chain A residue 1444 THR
Chi-restraints excluded: chain A residue 1554 ASP
Chi-restraints excluded: chain A residue 1594 THR
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 158
   random chunks:
   chunk 82 optimal weight:    1.9990
   chunk 0 optimal weight:    5.9990
   chunk 103 optimal weight:    9.9990
   chunk 155 optimal weight:    3.9990
   chunk 91 optimal weight:    0.2980
   chunk 156 optimal weight:    7.9990
   chunk 149 optimal weight:    0.0870
   chunk 130 optimal weight:    1.9990
   chunk 50 optimal weight:    3.9990
   chunk 48 optimal weight:    1.9990
   chunk 140 optimal weight:    0.6980
   overall best weight:    1.0162

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

Flipped N/Q/H residues before XYZ refinement:
** A 100 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 587 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3628 r_free = 0.3628 target = 0.130188 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 40)----------------|
| r_work = 0.3225 r_free = 0.3225 target = 0.098597 restraints weight = 19529.226|
|-----------------------------------------------------------------------------|
r_work (start): 0.3210 rms_B_bonded: 2.20
r_work: 0.3037 rms_B_bonded: 2.73 restraints_weight: 0.5000
r_work: 0.2899 rms_B_bonded: 4.46 restraints_weight: 0.2500
r_work (final): 0.2899
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8517
moved from start:          0.2257

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.053  14309  Z= 0.138
  Angle     :  0.597  13.940  19596  Z= 0.309
  Chirality :  0.043   0.193   2099
  Planarity :  0.005   0.074   2318
  Dihedral  : 16.031 159.001   2678
  Min Nonbonded Distance : 2.432

Molprobity Statistics.
  All-atom Clashscore : 4.36
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  : 11.14 %
    Favored  : 88.86 %
  Rotamer:
    Outliers :  2.90 %
    Allowed  : 17.19 %
    Favored  : 79.91 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -2.23 (0.21), residues: 1526
  helix:  1.17 (0.32), residues: 312
  sheet: -0.39 (0.32), residues: 274
  loop : -2.98 (0.17), residues: 940

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARG A 470 
 TYR   0.009   0.001   TYR A1126 
 PHE   0.013   0.001   PHE A 776 
 TRP   0.025   0.001   TRP A1600 
 HIS   0.007   0.001   HIS A1149 

Details of bonding type rmsd
  covalent geometry    : bond        0.00324 (14309)
  covalent geometry    : angle       0.59734 (19596)
  hydrogen bonds       : bond        0.03839 (  335)
  hydrogen bonds       : angle       4.05817 (  936)

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

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

  3052 Ramachandran restraints generated.
    1526 Oldfield, 0 Emsley, 1526 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3052 Ramachandran restraints generated.
    1526 Oldfield, 0 Emsley, 1526 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  124 residues out of total 1344 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 39
    poor density    : 85
  time to evaluate  : 0.504 
Fit side-chains
REVERT: A  314 LEU cc_start: 0.9075 (OUTLIER) cc_final: 0.8819 (pt)
REVERT: A  393 ARG cc_start: 0.7850 (mpp80) cc_final: 0.7265 (ptt-90)
REVERT: A  600 GLU cc_start: 0.7295 (mm-30) cc_final: 0.7093 (tp30)
REVERT: A  634 MET cc_start: 0.8652 (mtt) cc_final: 0.8377 (mtp)
REVERT: A  759 ASP cc_start: 0.8810 (p0) cc_final: 0.8552 (p0)
REVERT: A 1024 LEU cc_start: 0.7694 (mt) cc_final: 0.7457 (mp)
REVERT: A 1211 MET cc_start: 0.7921 (OUTLIER) cc_final: 0.6555 (tmm)
REVERT: A 1268 LYS cc_start: 0.8013 (mttm) cc_final: 0.7611 (mtmm)
REVERT: A 1300 MET cc_start: 0.8695 (mtm) cc_final: 0.8492 (mtp)
  outliers start: 39
  outliers final: 32
  residues processed: 117
  average time/residue: 0.1313
  time to fit residues: 22.3948
Evaluate side-chains
  118 residues out of total 1344 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 34
    poor density    : 84
  time to evaluate  : 0.485 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   21 GLN
Chi-restraints excluded: chain A residue  176 VAL
Chi-restraints excluded: chain A residue  299 VAL
Chi-restraints excluded: chain A residue  314 LEU
Chi-restraints excluded: chain A residue  410 LEU
Chi-restraints excluded: chain A residue  414 THR
Chi-restraints excluded: chain A residue  466 GLU
Chi-restraints excluded: chain A residue  636 SER
Chi-restraints excluded: chain A residue  659 VAL
Chi-restraints excluded: chain A residue  742 VAL
Chi-restraints excluded: chain A residue  772 LEU
Chi-restraints excluded: chain A residue  842 VAL
Chi-restraints excluded: chain A residue  844 VAL
Chi-restraints excluded: chain A residue  900 ILE
Chi-restraints excluded: chain A residue  986 VAL
Chi-restraints excluded: chain A residue 1008 THR
Chi-restraints excluded: chain A residue 1048 LEU
Chi-restraints excluded: chain A residue 1049 VAL
Chi-restraints excluded: chain A residue 1096 LEU
Chi-restraints excluded: chain A residue 1133 ILE
Chi-restraints excluded: chain A residue 1151 VAL
Chi-restraints excluded: chain A residue 1185 THR
Chi-restraints excluded: chain A residue 1193 ARG
Chi-restraints excluded: chain A residue 1211 MET
Chi-restraints excluded: chain A residue 1217 THR
Chi-restraints excluded: chain A residue 1252 VAL
Chi-restraints excluded: chain A residue 1266 VAL
Chi-restraints excluded: chain A residue 1275 VAL
Chi-restraints excluded: chain A residue 1295 THR
Chi-restraints excluded: chain A residue 1309 LEU
Chi-restraints excluded: chain A residue 1399 SER
Chi-restraints excluded: chain A residue 1444 THR
Chi-restraints excluded: chain A residue 1554 ASP
Chi-restraints excluded: chain A residue 1594 THR
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 158
   random chunks:
   chunk 119 optimal weight:    2.9990
   chunk 3 optimal weight:    4.9990
   chunk 97 optimal weight:    1.9990
   chunk 19 optimal weight:    3.9990
   chunk 96 optimal weight:    0.5980
   chunk 107 optimal weight:    9.9990
   chunk 57 optimal weight:    4.9990
   chunk 6 optimal weight:    2.9990
   chunk 125 optimal weight:    0.8980
   chunk 115 optimal weight:    5.9990
   chunk 55 optimal weight:    0.6980
   overall best weight:    1.4384

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

Flipped N/Q/H residues before XYZ refinement:
** A 100 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 587 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3554 r_free = 0.3554 target = 0.126413 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 33)----------------|
| r_work = 0.3132 r_free = 0.3132 target = 0.093504 restraints weight = 19513.390|
|-----------------------------------------------------------------------------|
r_work (start): 0.3116 rms_B_bonded: 2.17
r_work: 0.2935 rms_B_bonded: 3.01 restraints_weight: 0.5000
r_work: 0.2794 rms_B_bonded: 4.88 restraints_weight: 0.2500
r_work (final): 0.2794
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8503
moved from start:          0.2302

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.047  14309  Z= 0.173
  Angle     :  0.624  14.031  19596  Z= 0.324
  Chirality :  0.045   0.186   2099
  Planarity :  0.005   0.077   2318
  Dihedral  : 16.039 157.952   2678
  Min Nonbonded Distance : 2.378

Molprobity Statistics.
  All-atom Clashscore : 4.40
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  : 12.39 %
    Favored  : 87.61 %
  Rotamer:
    Outliers :  2.83 %
    Allowed  : 17.26 %
    Favored  : 79.91 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -2.18 (0.21), residues: 1526
  helix:  1.23 (0.32), residues: 306
  sheet: -0.35 (0.32), residues: 274
  loop : -2.93 (0.17), residues: 946

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARG A 470 
 TYR   0.010   0.001   TYR A1276 
 PHE   0.014   0.002   PHE A 776 
 TRP   0.025   0.001   TRP A1600 
 HIS   0.008   0.001   HIS A1149 

Details of bonding type rmsd
  covalent geometry    : bond        0.00415 (14309)
  covalent geometry    : angle       0.62448 (19596)
  hydrogen bonds       : bond        0.04320 (  335)
  hydrogen bonds       : angle       4.11600 (  936)

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

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

  3052 Ramachandran restraints generated.
    1526 Oldfield, 0 Emsley, 1526 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3052 Ramachandran restraints generated.
    1526 Oldfield, 0 Emsley, 1526 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  121 residues out of total 1344 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 38
    poor density    : 83
  time to evaluate  : 0.505 
Fit side-chains
REVERT: A  314 LEU cc_start: 0.8989 (OUTLIER) cc_final: 0.8729 (pt)
REVERT: A  393 ARG cc_start: 0.7838 (mpp80) cc_final: 0.7165 (ptt-90)
REVERT: A  600 GLU cc_start: 0.7390 (mm-30) cc_final: 0.7095 (tp30)
REVERT: A  634 MET cc_start: 0.8751 (mtt) cc_final: 0.8489 (mtp)
REVERT: A  759 ASP cc_start: 0.8871 (p0) cc_final: 0.8640 (p0)
REVERT: A 1024 LEU cc_start: 0.7584 (mt) cc_final: 0.7336 (mp)
REVERT: A 1211 MET cc_start: 0.7939 (OUTLIER) cc_final: 0.6638 (tmm)
REVERT: A 1268 LYS cc_start: 0.8057 (mttm) cc_final: 0.7634 (mtmm)
REVERT: A 1300 MET cc_start: 0.8727 (mtm) cc_final: 0.8492 (mtp)
  outliers start: 38
  outliers final: 33
  residues processed: 114
  average time/residue: 0.1382
  time to fit residues: 22.8499
Evaluate side-chains
  118 residues out of total 1344 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 35
    poor density    : 83
  time to evaluate  : 0.495 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   21 GLN
Chi-restraints excluded: chain A residue  176 VAL
Chi-restraints excluded: chain A residue  299 VAL
Chi-restraints excluded: chain A residue  314 LEU
Chi-restraints excluded: chain A residue  410 LEU
Chi-restraints excluded: chain A residue  414 THR
Chi-restraints excluded: chain A residue  466 GLU
Chi-restraints excluded: chain A residue  636 SER
Chi-restraints excluded: chain A residue  659 VAL
Chi-restraints excluded: chain A residue  742 VAL
Chi-restraints excluded: chain A residue  772 LEU
Chi-restraints excluded: chain A residue  842 VAL
Chi-restraints excluded: chain A residue  844 VAL
Chi-restraints excluded: chain A residue  900 ILE
Chi-restraints excluded: chain A residue  986 VAL
Chi-restraints excluded: chain A residue 1008 THR
Chi-restraints excluded: chain A residue 1048 LEU
Chi-restraints excluded: chain A residue 1049 VAL
Chi-restraints excluded: chain A residue 1096 LEU
Chi-restraints excluded: chain A residue 1133 ILE
Chi-restraints excluded: chain A residue 1151 VAL
Chi-restraints excluded: chain A residue 1185 THR
Chi-restraints excluded: chain A residue 1211 MET
Chi-restraints excluded: chain A residue 1217 THR
Chi-restraints excluded: chain A residue 1252 VAL
Chi-restraints excluded: chain A residue 1266 VAL
Chi-restraints excluded: chain A residue 1275 VAL
Chi-restraints excluded: chain A residue 1284 VAL
Chi-restraints excluded: chain A residue 1295 THR
Chi-restraints excluded: chain A residue 1309 LEU
Chi-restraints excluded: chain A residue 1399 SER
Chi-restraints excluded: chain A residue 1436 ILE
Chi-restraints excluded: chain A residue 1444 THR
Chi-restraints excluded: chain A residue 1554 ASP
Chi-restraints excluded: chain A residue 1594 THR
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 158
   random chunks:
   chunk 48 optimal weight:    0.7980
   chunk 116 optimal weight:    4.9990
   chunk 103 optimal weight:    9.9990
   chunk 86 optimal weight:    2.9990
   chunk 68 optimal weight:    0.4980
   chunk 118 optimal weight:    2.9990
   chunk 29 optimal weight:    2.9990
   chunk 115 optimal weight:    0.5980
   chunk 88 optimal weight:    3.9990
   chunk 77 optimal weight:    3.9990
   chunk 40 optimal weight:    1.9990
   overall best weight:    1.3784

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

Flipped N/Q/H residues before XYZ refinement:
** A 100 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 587 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3610 r_free = 0.3610 target = 0.128831 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.3187 r_free = 0.3187 target = 0.097363 restraints weight = 19505.305|
|-----------------------------------------------------------------------------|
r_work (start): 0.3191 rms_B_bonded: 2.35
r_work: 0.3024 rms_B_bonded: 2.66 restraints_weight: 0.5000
r_work: 0.2886 rms_B_bonded: 4.35 restraints_weight: 0.2500
r_work (final): 0.2886
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8525
moved from start:          0.2338

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.052  14309  Z= 0.168
  Angle     :  0.625  13.933  19596  Z= 0.325
  Chirality :  0.045   0.185   2099
  Planarity :  0.005   0.077   2318
  Dihedral  : 16.049 157.964   2678
  Min Nonbonded Distance : 2.396

Molprobity Statistics.
  All-atom Clashscore : 4.40
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  : 11.93 %
    Favored  : 88.07 %
  Rotamer:
    Outliers :  2.90 %
    Allowed  : 17.49 %
    Favored  : 79.61 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -2.21 (0.21), residues: 1526
  helix:  1.13 (0.32), residues: 312
  sheet: -0.31 (0.32), residues: 273
  loop : -2.97 (0.17), residues: 941

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARG A 470 
 TYR   0.010   0.001   TYR A1276 
 PHE   0.014   0.002   PHE A 776 
 TRP   0.025   0.001   TRP A1600 
 HIS   0.008   0.001   HIS A1149 

Details of bonding type rmsd
  covalent geometry    : bond        0.00402 (14309)
  covalent geometry    : angle       0.62528 (19596)
  hydrogen bonds       : bond        0.04261 (  335)
  hydrogen bonds       : angle       4.10579 (  936)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 3655.32 seconds
wall clock time: 63 minutes 14.43 seconds (3794.43 seconds total)