Starting phenix.real_space_refine
on Wed Feb  4 13:44:48 2026 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/9lg6_63055/02_2026/9lg6_63055_neut.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/9lg6_63055/02_2026/9lg6_63055.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=3.7
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    model {
      file = "/net/cci-nas-00/data/ceres_data/9lg6_63055/02_2026/9lg6_63055_neut.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/9lg6_63055/02_2026/9lg6_63055_neut.cif"
    real_map_files = "/net/cci-nas-00/data/ceres_data/9lg6_63055/02_2026/9lg6_63055.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/9lg6_63055/02_2026/9lg6_63055.map"
  }
  resolution = 3.7
  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=   0.056
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       2      5.49       5
     S      58      5.16       5
     C    6931      2.51       5
     N    1772      2.21       5
     O    1899      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 35 residue(s): 0.01s

  Monomer Library directory:
    "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5952/lib/python3.9/site-packages/chem_data/mon_lib"
  Total number of atoms: 10662
  Number of models: 1
  Model: ""
    Number of chains: 2
    Chain: "A"
      Number of atoms: 10618
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 1336, 10618
          Classifications: {'peptide': 1336}
          Link IDs: {'PTRANS': 50, 'TRANS': 1285}
          Chain breaks: 8
    Chain: "A"
      Number of atoms: 44
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 1, 44
          Unusual residues: {'GJF': 1}
          Classifications: {'undetermined': 1}
  Time building chain proxies: 2.23, per 1000 atoms: 0.21
  Number of scatterers: 10662
  At special positions: 0
  Unit cell: (89.44, 130, 152.88, 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      58     16.00
     P       2     15.00
     O    1899      8.00
     N    1772      7.00
     C    6931      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: 0.75
  Conformation dependent library (CDL) restraints added in 499.2 milliseconds
  

  2636 Ramachandran restraints generated.
    1318 Oldfield, 0 Emsley, 1318 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  2530

  Finding SS restraints...
    Secondary structure from input PDB file:
      54 helices and 6 sheets defined
      72.1% alpha, 7.1% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 0.39
  Creating SS restraints...
    Processing helix  chain 'A' and resid 17 through 22
      removed outlier: 3.676A  pdb=" N   THR A  21 " --> pdb=" O   GLU A  17 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 30 through 60
      removed outlier: 3.960A  pdb=" N   LEU A  38 " --> pdb=" O   GLN A  34 " (cutoff:3.500A)
      removed outlier: 5.027A  pdb=" N   VAL A  39 " --> pdb=" O   ASN A  35 " (cutoff:3.500A)
      Proline residue:  A  42  - end of helix
      Proline residue:  A  51  - end of helix
      removed outlier: 3.865A  pdb=" N   LEU A  55 " --> pdb=" O   PRO A  51 " (cutoff:3.500A)
      removed outlier: 3.807A  pdb=" N   TYR A  56 " --> pdb=" O   PHE A  52 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 68 through 94
      removed outlier: 3.696A  pdb=" N   LEU A  89 " --> pdb=" O   CYS A  85 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 104 through 130
      removed outlier: 3.578A  pdb=" N   VAL A 108 " --> pdb=" O   PRO A 104 " (cutoff:3.500A)
      Proline residue:  A 110  - end of helix
    Processing helix  chain 'A' and resid 136 through 160
      removed outlier: 4.177A  pdb=" N   TRP A 142 " --> pdb=" O   MET A 138 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 171 through 191
      removed outlier: 3.544A  pdb=" N   PHE A 175 " --> pdb=" O   ARG A 171 " (cutoff:3.500A)
      removed outlier: 4.034A  pdb=" N   PHE A 191 " --> pdb=" O   VAL A 187 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 208 through 212
    Processing helix  chain 'A' and resid 214 through 221
    Processing helix  chain 'A' and resid 224 through 234
    Processing helix  chain 'A' and resid 245 through 248
    Processing helix  chain 'A' and resid 249 through 268
      Proline residue:  A 255  - end of helix
    Processing helix  chain 'A' and resid 312 through 321
      removed outlier: 3.754A  pdb=" N   VAL A 316 " --> pdb=" O   SER A 312 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 321 through 326
    Processing helix  chain 'A' and resid 326 through 355
      removed outlier: 4.164A  pdb=" N   LEU A 330 " --> pdb=" O   LEU A 326 " (cutoff:3.500A)
      removed outlier: 3.616A  pdb=" N   PHE A 331 " --> pdb=" O   MET A 327 " (cutoff:3.500A)
      removed outlier: 3.687A  pdb=" N   GLY A 342 " --> pdb=" O   MET A 338 " (cutoff:3.500A)
      Proline residue:  A 343  - end of helix
    Processing helix  chain 'A' and resid 359 through 410
      removed outlier: 3.987A  pdb=" N   GLY A 363 " --> pdb=" O   PRO A 359 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 411 through 418
      removed outlier: 3.828A  pdb=" N   SER A 417 " --> pdb=" O   ALA A 413 " (cutoff:3.500A)
      removed outlier: 4.146A  pdb=" N   SER A 418 " --> pdb=" O   ALA A 414 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 419 through 438
      removed outlier: 3.936A  pdb=" N   ASP A 430 " --> pdb=" O   LEU A 426 " (cutoff:3.500A)
      removed outlier: 4.485A  pdb=" N   ALA A 431 " --> pdb=" O   MET A 427 " (cutoff:3.500A)
      removed outlier: 3.674A  pdb=" N   ALA A 438 " --> pdb=" O   PHE A 434 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 442 through 462
      Proline residue:  A 448  - end of helix
    Processing helix  chain 'A' and resid 464 through 471
      removed outlier: 4.007A  pdb=" N   ALA A 468 " --> pdb=" O   PRO A 464 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 472 through 511
      Proline residue:  A 478  - end of helix
    Processing helix  chain 'A' and resid 511 through 519
      removed outlier: 3.582A  pdb=" N   LEU A 515 " --> pdb=" O   GLY A 511 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 520 through 572
      removed outlier: 3.814A  pdb=" N   VAL A 538 " --> pdb=" O   GLU A 534 " (cutoff:3.500A)
      removed outlier: 3.708A  pdb=" N   VAL A 548 " --> pdb=" O   TYR A 544 " (cutoff:3.500A)
      Proline residue:  A 557  - end of helix
      removed outlier: 4.012A  pdb=" N   ASP A 572 " --> pdb=" O   TYR A 568 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 579 through 598
      removed outlier: 3.566A  pdb=" N   VAL A 584 " --> pdb=" O   GLN A 580 " (cutoff:3.500A)
      removed outlier: 5.153A  pdb=" N   SER A 585 " --> pdb=" O   LYS A 581 " (cutoff:3.500A)
      removed outlier: 4.066A  pdb=" N   PHE A 594 " --> pdb=" O   ASN A 590 " (cutoff:3.500A)
      Proline residue:  A 595  - end of helix
      removed outlier: 3.538A  pdb=" N   ILE A 598 " --> pdb=" O   PHE A 594 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 598 through 621
    Processing helix  chain 'A' and resid 626 through 630
    Processing helix  chain 'A' and resid 683 through 692
      removed outlier: 3.551A  pdb=" N   LEU A 688 " --> pdb=" O   LYS A 684 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 721 through 728
    Processing helix  chain 'A' and resid 733 through 744
      removed outlier: 4.369A  pdb=" N   GLU A 742 " --> pdb=" O   LYS A 738 " (cutoff:3.500A)
      removed outlier: 3.660A  pdb=" N   ALA A 743 " --> pdb=" O   ALA A 739 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 746 through 753
    Processing helix  chain 'A' and resid 755 through 759
      removed outlier: 3.659A  pdb=" N   ARG A 758 " --> pdb=" O   SER A 755 " (cutoff:3.500A)
      removed outlier: 3.710A  pdb=" N   THR A 759 " --> pdb=" O   GLY A 756 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'A' and resid 755 through 759'
    Processing helix  chain 'A' and resid 769 through 785
    Processing helix  chain 'A' and resid 799 through 810
    Processing helix  chain 'A' and resid 831 through 835
    Processing helix  chain 'A' and resid 851 through 859
    Processing helix  chain 'A' and resid 860 through 869
      removed outlier: 4.015A  pdb=" N   TYR A 869 " --> pdb=" O   PHE A 865 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 959 through 970
      removed outlier: 3.746A  pdb=" N   TRP A 963 " --> pdb=" O   LEU A 959 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 970 through 1000
      removed outlier: 3.550A  pdb=" N   ASP A1000 " --> pdb=" O   SER A 996 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 1011 through 1058
      removed outlier: 3.812A  pdb=" N   LEU A1015 " --> pdb=" O   THR A1011 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 1059 through 1066
      removed outlier: 3.831A  pdb=" N   PHE A1063 " --> pdb=" O   PRO A1059 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 1069 through 1084
      removed outlier: 3.748A  pdb=" N   ASN A1073 " --> pdb=" O   GLY A1069 " (cutoff:3.500A)
      removed outlier: 3.545A  pdb=" N   ARG A1074 " --> pdb=" O   ASN A1070 " (cutoff:3.500A)
      removed outlier: 3.765A  pdb=" N   GLU A1078 " --> pdb=" O   ARG A1074 " (cutoff:3.500A)
      removed outlier: 4.623A  pdb=" N   LEU A1079 " --> pdb=" O   PHE A1075 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 1084 through 1111
      removed outlier: 3.821A  pdb=" N   GLN A1088 " --> pdb=" O   SER A1084 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 1117 through 1167
      removed outlier: 4.087A  pdb=" N   GLN A1138 " --> pdb=" O   ALA A1134 " (cutoff:3.500A)
      removed outlier: 3.641A  pdb=" N   LEU A1139 " --> pdb=" O   SER A1135 " (cutoff:3.500A)
      removed outlier: 3.851A  pdb=" N   ARG A1141 " --> pdb=" O   ARG A1137 " (cutoff:3.500A)
      removed outlier: 3.978A  pdb=" N   SER A1148 " --> pdb=" O   SER A1144 " (cutoff:3.500A)
      Proline residue:  A1149  - end of helix
      removed outlier: 5.806A  pdb=" N   SER A1162 " --> pdb=" O   LEU A1158 " (cutoff:3.500A)
      removed outlier: 6.414A  pdb=" N   VAL A1163 " --> pdb=" O   LEU A1159 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 1169 through 1219
      Proline residue:  A1190  - end of helix
    Processing helix  chain 'A' and resid 1225 through 1264
      removed outlier: 4.542A  pdb=" N   THR A1240 " --> pdb=" O   SER A1236 " (cutoff:3.500A)
      removed outlier: 5.257A  pdb=" N   THR A1241 " --> pdb=" O   LEU A1237 " (cutoff:3.500A)
      removed outlier: 3.745A  pdb=" N   TYR A1242 " --> pdb=" O   GLN A1238 " (cutoff:3.500A)
      removed outlier: 4.312A  pdb=" N   VAL A1258 " --> pdb=" O   GLU A1254 " (cutoff:3.500A)
      removed outlier: 5.317A  pdb=" N   ALA A1259 " --> pdb=" O   THR A1255 " (cutoff:3.500A)
      removed outlier: 4.686A  pdb=" N   VAL A1260 " --> pdb=" O   ASN A1256 " (cutoff:3.500A)
      removed outlier: 3.692A  pdb=" N   GLU A1261 " --> pdb=" O   ILE A1257 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 1331 through 1340
      removed outlier: 3.669A  pdb=" N   THR A1336 " --> pdb=" O   LYS A1332 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 1361 through 1368
    Processing helix  chain 'A' and resid 1382 through 1388
    Processing helix  chain 'A' and resid 1394 through 1405
    Processing helix  chain 'A' and resid 1407 through 1412
    Processing helix  chain 'A' and resid 1416 through 1420
      removed outlier: 3.863A  pdb=" N   HIS A1420 " --> pdb=" O   LYS A1417 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 1430 through 1446
      removed outlier: 3.637A  pdb=" N   LYS A1446 " --> pdb=" O   ALA A1442 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 1463 through 1474
      removed outlier: 3.975A  pdb=" N   GLN A1474 " --> pdb=" O   THR A1470 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 1486 through 1493
      removed outlier: 3.878A  pdb=" N   ILE A1490 " --> pdb=" O   ARG A1486 " (cutoff:3.500A)
      removed outlier: 4.293A  pdb=" N   ASP A1492 " --> pdb=" O   ASN A1488 " (cutoff:3.500A)
      removed outlier: 4.052A  pdb=" N   TYR A1493 " --> pdb=" O   THR A1489 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 1509 through 1514
    Processing sheet with id=AA1, first strand: chain 'A' and resid 661 through 668
      removed outlier: 7.039A  pdb=" N   HIS A 662 " --> pdb=" O   THR A 650 " (cutoff:3.500A)
      removed outlier: 6.446A  pdb=" N   THR A 650 " --> pdb=" O   HIS A 662 " (cutoff:3.500A)
      removed outlier: 5.592A  pdb=" N   ILE A 664 " --> pdb=" O   ASN A 648 " (cutoff:3.500A)
      removed outlier: 6.897A  pdb=" N   VAL A 646 " --> pdb=" O   VAL A 702 " (cutoff:3.500A)
      removed outlier: 7.076A  pdb=" N   VAL A 702 " --> pdb=" O   VAL A 646 " (cutoff:3.500A)
      removed outlier: 7.074A  pdb=" N   ASN A 648 " --> pdb=" O   GLY A 700 " (cutoff:3.500A)
      removed outlier: 3.695A  pdb=" N   GLY A 700 " --> pdb=" O   ASN A 648 " (cutoff:3.500A)
      removed outlier: 6.507A  pdb=" N   THR A 650 " --> pdb=" O   VAL A 698 " (cutoff:3.500A)
    Processing sheet with id=AA2, first strand: chain 'A' and resid 708 through 711
      removed outlier: 6.300A  pdb=" N   TYR A 789 " --> pdb=" O   LEU A 823 " (cutoff:3.500A)
      removed outlier: 7.707A  pdb=" N   VAL A 825 " --> pdb=" O   TYR A 789 " (cutoff:3.500A)
      removed outlier: 6.971A  pdb=" N   LEU A 791 " --> pdb=" O   VAL A 825 " (cutoff:3.500A)
      removed outlier: 6.184A  pdb=" N   LEU A 673 " --> pdb=" O   VAL A 837 " (cutoff:3.500A)
      removed outlier: 7.344A  pdb=" N   ILE A 839 " --> pdb=" O   LEU A 673 " (cutoff:3.500A)
      removed outlier: 6.075A  pdb=" N   ALA A 675 " --> pdb=" O   ILE A 839 " (cutoff:3.500A)
    Processing sheet with id=AA3, first strand: chain 'A' and resid 1003 through 1004
    Processing sheet with id=AA4, first strand: chain 'A' and resid 1309 through 1316
      removed outlier: 5.876A  pdb=" N   LYS A1310 " --> pdb=" O   LEU A1299 " (cutoff:3.500A)
      removed outlier: 7.258A  pdb=" N   LEU A1299 " --> pdb=" O   LYS A1310 " (cutoff:3.500A)
      removed outlier: 7.422A  pdb=" N   VAL A1314 " --> pdb=" O   ARG A1295 " (cutoff:3.500A)
      removed outlier: 4.967A  pdb=" N   ARG A1295 " --> pdb=" O   VAL A1314 " (cutoff:3.500A)
      removed outlier: 7.245A  pdb=" N   ILE A1316 " --> pdb=" O   GLU A1293 " (cutoff:3.500A)
      removed outlier: 5.197A  pdb=" N   GLU A1293 " --> pdb=" O   ILE A1316 " (cutoff:3.500A)
    Processing sheet with id=AA5, first strand: chain 'A' and resid 1309 through 1316
      removed outlier: 5.876A  pdb=" N   LYS A1310 " --> pdb=" O   LEU A1299 " (cutoff:3.500A)
      removed outlier: 7.258A  pdb=" N   LEU A1299 " --> pdb=" O   LYS A1310 " (cutoff:3.500A)
      removed outlier: 7.422A  pdb=" N   VAL A1314 " --> pdb=" O   ARG A1295 " (cutoff:3.500A)
      removed outlier: 4.967A  pdb=" N   ARG A1295 " --> pdb=" O   VAL A1314 " (cutoff:3.500A)
      removed outlier: 7.245A  pdb=" N   ILE A1316 " --> pdb=" O   GLU A1293 " (cutoff:3.500A)
      removed outlier: 5.197A  pdb=" N   GLU A1293 " --> pdb=" O   ILE A1316 " (cutoff:3.500A)
    Processing sheet with id=AA6, first strand: chain 'A' and resid 1369 through 1372
      removed outlier: 6.390A  pdb=" N   LEU A1450 " --> pdb=" O   LEU A1481 " (cutoff:3.500A)
      removed outlier: 8.029A  pdb=" N   ILE A1483 " --> pdb=" O   LEU A1450 " (cutoff:3.500A)
      removed outlier: 6.404A  pdb=" N   LEU A1452 " --> pdb=" O   ILE A1483 " (cutoff:3.500A)
      removed outlier: 6.363A  pdb=" N   GLY A1323 " --> pdb=" O   ILE A1497 " (cutoff:3.500A)
      removed outlier: 7.676A  pdb=" N   LEU A1499 " --> pdb=" O   GLY A1323 " (cutoff:3.500A)
      removed outlier: 6.682A  pdb=" N   VAL A1325 " --> pdb=" O   LEU A1499 " (cutoff:3.500A)
      removed outlier: 7.033A  pdb=" N   VAL A1496 " --> pdb=" O   TRP A1507 " (cutoff:3.500A)
      removed outlier: 4.674A  pdb=" N   TRP A1507 " --> pdb=" O   VAL A1496 " (cutoff:3.500A)
      removed outlier: 6.768A  pdb=" N   VAL A1498 " --> pdb=" O   GLN A1505 " (cutoff:3.500A)

    691 hydrogen bonds defined for protein.
    2031 hydrogen bond angles defined for protein.
    Restraints generated for nucleic acids:
      0 hydrogen bonds
      0 hydrogen bond angles
      0 basepair planarities
      0 basepair parallelities
      0 stacking parallelities
  Total time for adding SS restraints: 2.06

  Time building geometry restraints manager: 1.02 seconds

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

  Histogram of bond lengths:
        1.21 -     1.35: 3337
        1.35 -     1.48: 2557
        1.48 -     1.62: 4915
        1.62 -     1.75: 4
        1.75 -     1.89: 93
  Bond restraints: 10906
  Sorted by residual:
  bond pdb=" P2  GJF A1601 "
       pdb=" S2  GJF A1601 "
    ideal  model  delta    sigma   weight residual
    2.082  1.885  0.197 2.00e-02 2.50e+03 9.66e+01
  bond pdb=" P1  GJF A1601 "
       pdb=" S1  GJF A1601 "
    ideal  model  delta    sigma   weight residual
    2.070  1.886  0.184 2.00e-02 2.50e+03 8.45e+01
  bond pdb=" C14 GJF A1601 "
       pdb=" N7  GJF A1601 "
    ideal  model  delta    sigma   weight residual
    1.336  1.447 -0.111 2.00e-02 2.50e+03 3.06e+01
  bond pdb=" C3  GJF A1601 "
       pdb=" N8  GJF A1601 "
    ideal  model  delta    sigma   weight residual
    1.342  1.447 -0.105 2.00e-02 2.50e+03 2.78e+01
  bond pdb=" C17 GJF A1601 "
       pdb=" C18 GJF A1601 "
    ideal  model  delta    sigma   weight residual
    1.526  1.437  0.089 2.00e-02 2.50e+03 1.98e+01
  ... (remaining 10901 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     3.27: 14641
        3.27 -     6.54: 151
        6.54 -     9.81: 20
        9.81 -    13.08: 2
       13.08 -    16.35: 2
  Bond angle restraints: 14816
  Sorted by residual:
  angle pdb=" N   VAL A1289 "
        pdb=" CA  VAL A1289 "
        pdb=" C   VAL A1289 "
      ideal   model   delta    sigma   weight residual
     113.71  107.66    6.05 9.50e-01 1.11e+00 4.05e+01
  angle pdb=" O6  GJF A1601 "
        pdb=" P2  GJF A1601 "
        pdb=" O9  GJF A1601 "
      ideal   model   delta    sigma   weight residual
     104.39  120.74  -16.35 3.00e+00 1.11e-01 2.97e+01
  angle pdb=" O3  GJF A1601 "
        pdb=" P1  GJF A1601 "
        pdb=" O7  GJF A1601 "
      ideal   model   delta    sigma   weight residual
     102.52  118.81  -16.29 3.00e+00 1.11e-01 2.95e+01
  angle pdb=" N   LEU A 592 "
        pdb=" CA  LEU A 592 "
        pdb=" C   LEU A 592 "
      ideal   model   delta    sigma   weight residual
     113.88  108.01    5.87 1.23e+00 6.61e-01 2.28e+01
  angle pdb=" O5  GJF A1601 "
        pdb=" P2  GJF A1601 "
        pdb=" S2  GJF A1601 "
      ideal   model   delta    sigma   weight residual
     116.54  103.62   12.92 3.00e+00 1.11e-01 1.86e+01
  ... (remaining 14811 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    22.25: 5873
       22.25 -    44.49: 516
       44.49 -    66.73: 88
       66.73 -    88.98: 27
       88.98 -   111.22: 8
  Dihedral angle restraints: 6512
    sinusoidal: 2610
      harmonic: 3902
  Sorted by residual:
  dihedral pdb=" C9  GJF A1601 "
           pdb=" O6  GJF A1601 "
           pdb=" P2  GJF A1601 "
           pdb=" S2  GJF A1601 "
      ideal   model   delta sinusoidal    sigma   weight residual
    -116.32   -5.10 -111.22     1      3.00e+01 1.11e-03 1.45e+01
  dihedral pdb=" CG  ARG A1472 "
           pdb=" CD  ARG A1472 "
           pdb=" NE  ARG A1472 "
           pdb=" CZ  ARG A1472 "
      ideal   model   delta sinusoidal    sigma   weight residual
     -90.00  -40.22  -49.78     2      1.50e+01 4.44e-03 1.24e+01
  dihedral pdb=" C9  GJF A1601 "
           pdb=" O6  GJF A1601 "
           pdb=" P2  GJF A1601 "
           pdb=" O9  GJF A1601 "
      ideal   model   delta sinusoidal    sigma   weight residual
     132.63 -129.60  -97.77     1      3.00e+01 1.11e-03 1.21e+01
  ... (remaining 6509 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.077: 1445
       0.077 -    0.153: 242
       0.153 -    0.230: 38
       0.230 -    0.306: 0
       0.306 -    0.382: 1
  Chirality restraints: 1726
  Sorted by residual:
  chirality pdb=" C16 GJF A1601 "
            pdb=" C15 GJF A1601 "
            pdb=" C17 GJF A1601 "
            pdb=" O8  GJF A1601 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.40    2.78   -0.38 2.00e-01 2.50e+01 3.66e+00
  chirality pdb=" CA  ILE A 137 "
            pdb=" N   ILE A 137 "
            pdb=" C   ILE A 137 "
            pdb=" CB  ILE A 137 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.43    2.65   -0.21 2.00e-01 2.50e+01 1.14e+00
  chirality pdb=" CA  CYS A  43 "
            pdb=" N   CYS A  43 "
            pdb=" C   CYS A  43 "
            pdb=" CB  CYS A  43 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.72   -0.21 2.00e-01 2.50e+01 1.06e+00
  ... (remaining 1723 not shown)

  Planarity restraints: 1827
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CD  ARG A1165 "    0.282 9.50e-02 1.11e+02   1.26e-01 9.80e+00
        pdb=" NE  ARG A1165 "   -0.017 2.00e-02 2.50e+03
        pdb=" CZ  ARG A1165 "   -0.001 2.00e-02 2.50e+03
        pdb=" NH1 ARG A1165 "   -0.003 2.00e-02 2.50e+03
        pdb=" NH2 ARG A1165 "    0.009 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CD  ARG A1434 "    0.258 9.50e-02 1.11e+02   1.16e-01 8.22e+00
        pdb=" NE  ARG A1434 "   -0.015 2.00e-02 2.50e+03
        pdb=" CZ  ARG A1434 "   -0.003 2.00e-02 2.50e+03
        pdb=" NH1 ARG A1434 "   -0.002 2.00e-02 2.50e+03
        pdb=" NH2 ARG A1434 "    0.009 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   ASP A1375 "    0.039 5.00e-02 4.00e+02   6.03e-02 5.83e+00
        pdb=" N   PRO A1376 "   -0.104 5.00e-02 4.00e+02
        pdb=" CA  PRO A1376 "    0.032 5.00e-02 4.00e+02
        pdb=" CD  PRO A1376 "    0.032 5.00e-02 4.00e+02
  ... (remaining 1824 not shown)

  Histogram of nonbonded interaction distances:
        2.21 -     2.75: 1128
        2.75 -     3.29: 11282
        3.29 -     3.82: 18049
        3.82 -     4.36: 20641
        4.36 -     4.90: 35534
  Nonbonded interactions: 86634
  Sorted by model distance:
  nonbonded pdb=" OD1 ASN A 992 "
            pdb=" OH  TYR A1235 "
     model   vdw
     2.209 3.040
  nonbonded pdb=" O   VAL A 571 "
            pdb=" OD1 ASP A 572 "
     model   vdw
     2.236 3.040
  nonbonded pdb=" NH1 ARG A1341 "
            pdb=" O   ILE A1357 "
     model   vdw
     2.345 3.120
  nonbonded pdb=" O   VAL A 316 "
            pdb=" OG1 THR A 320 "
     model   vdw
     2.354 3.040
  nonbonded pdb=" NZ  LYS A 396 "
            pdb=" OD1 ASN A1184 "
     model   vdw
     2.375 3.120
  ... (remaining 86629 not shown)

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

  No NCS relation were found !!!

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

Found NCS groups:
  found none.
Set up NCS constraints
  No NCS constraints will be used in refinement.
Set refine NCS operators
Adjust number of macro_cycles
  Number of macro_cycles: 10
Reset NCS operators
Extract rigid body selections
Check and reset occupancies
  Occupancies: min=1.00 max=1.00 mean=1.00
Load rotamer database and sin/cos tables
Set ADP refinement strategy
  ADPs will be refined as group one per residue
Make a string to write initial .geo file
Internal consistency checks
Time:
  Set random seed:                         0.000
  Set model cs if undefined:               0.000
  Decide on map wrapping:                  0.000
  Normalize map: mean=0, sd=1:             2.200
  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:          0.150
  Check model and map are aligned:         0.030
  Set scattering table:                    0.040
  Process input model:                     10.380
  Find NCS groups from input model:        0.040
  Set up NCS constraints:                  0.020
  Set refine NCS operators:                0.000
  Adjust number of macro_cycles:           0.000
  Reset NCS operators:                     0.000
  Extract rigid body selections:           0.000
  Check and reset occupancies:             0.000
  Load rotamer database and sin/cos tables:1.280
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   14.150
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6875
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      :  0.008   0.197  10906  Z= 0.487
  Angle     :  0.946  16.349  14816  Z= 0.613
  Chirality :  0.057   0.382   1726
  Planarity :  0.008   0.126   1827
  Dihedral  : 17.455 111.222   3982
  Min Nonbonded Distance : 2.209

Molprobity Statistics.
  All-atom Clashscore : 10.17
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.88 %
    Favored  : 97.12 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  : 20.77 %
    Favored  : 79.23 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  0.20 (0.23), residues: 1318
  helix:  0.84 (0.18), residues: 867
  sheet: -0.48 (0.57), residues: 71
  loop : -1.27 (0.30), residues: 380

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.014   0.001   ARG A 735 
 TYR   0.019   0.001   TYR A 318 
 PHE   0.030   0.002   PHE A 981 
 TRP   0.025   0.002   TRP A 459 
 HIS   0.004   0.001   HIS A 805 

Details of bonding type rmsd
  covalent geometry    : bond        0.00751 (10906)
  covalent geometry    : angle       0.94610 (14816)
  hydrogen bonds       : bond        0.16065 (  689)
  hydrogen bonds       : angle       6.35387 ( 2031)

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

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

  2636 Ramachandran restraints generated.
    1318 Oldfield, 0 Emsley, 1318 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2636 Ramachandran restraints generated.
    1318 Oldfield, 0 Emsley, 1318 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  272 residues out of total 1175 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 272
  time to evaluate  : 0.376 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  138 MET cc_start: 0.6405 (mmm) cc_final: 0.6165 (tpp)
REVERT: A  473 MET cc_start: 0.7958 (mtt) cc_final: 0.7693 (mtt)
REVERT: A  544 TYR cc_start: 0.7085 (t80) cc_final: 0.6612 (m-10)
REVERT: A  613 LEU cc_start: 0.7932 (mt) cc_final: 0.7355 (tt)
REVERT: A  789 TYR cc_start: 0.8348 (m-80) cc_final: 0.7668 (m-80)
REVERT: A  793 ASP cc_start: 0.7396 (t0) cc_final: 0.7169 (m-30)
REVERT: A  959 LEU cc_start: 0.7680 (tp) cc_final: 0.7205 (pt)
REVERT: A 1094 MET cc_start: 0.6578 (ttp) cc_final: 0.6271 (tpp)
REVERT: A 1203 GLU cc_start: 0.6967 (mm-30) cc_final: 0.6431 (mp0)
REVERT: A 1220 SER cc_start: 0.7131 (t) cc_final: 0.6852 (p)
REVERT: A 1357 ILE cc_start: 0.8438 (mm) cc_final: 0.8183 (mt)
  outliers start: 0
  outliers final: 0
  residues processed: 272
  average time/residue: 0.1164
  time to fit residues: 42.8105
Evaluate side-chains
  149 residues out of total 1175 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 149
  time to evaluate  : 0.389 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 133
   random chunks:
   chunk 98 optimal weight:    2.9990
   chunk 107 optimal weight:    0.7980
   chunk 10 optimal weight:    0.9980
   chunk 66 optimal weight:    0.0980
   chunk 130 optimal weight:    8.9990
   chunk 124 optimal weight:   20.0000
   chunk 103 optimal weight:    0.9990
   chunk 77 optimal weight:    1.9990
   chunk 122 optimal weight:    8.9990
   chunk 91 optimal weight:    0.7980
   chunk 55 optimal weight:    0.6980
   overall best weight:    0.6780

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

Flipped N/Q/H residues before XYZ refinement:
A  34 GLN
A  71 ASN
A 590 ASN
A 774 GLN
A1010 HIS
A1207 ASN
A1363 HIS
A1374 GLN
** A1420 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
A1474 GLN

Total number of N/Q/H flips: 9

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3996 r_free = 0.3996 target = 0.151315 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 32)----------------|
| r_work = 0.3539 r_free = 0.3539 target = 0.111192 restraints weight = 16741.752|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 32)----------------|
| r_work = 0.3550 r_free = 0.3550 target = 0.113291 restraints weight = 10247.760|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 23)----------------|
| r_work = 0.3555 r_free = 0.3555 target = 0.113809 restraints weight = 7365.089|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 23)----------------|
| r_work = 0.3564 r_free = 0.3564 target = 0.114497 restraints weight = 5947.086|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 23)----------------|
| r_work = 0.3567 r_free = 0.3567 target = 0.114784 restraints weight = 5371.290|
|-----------------------------------------------------------------------------|
r_work (final): 0.3554
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7310
moved from start:          0.2686

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.044  10906  Z= 0.163
  Angle     :  0.675  10.795  14816  Z= 0.336
  Chirality :  0.043   0.298   1726
  Planarity :  0.005   0.049   1827
  Dihedral  :  9.622  84.907   1496
  Min Nonbonded Distance : 2.501

Molprobity Statistics.
  All-atom Clashscore : 9.34
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.43 %
    Favored  : 97.57 %
  Rotamer:
    Outliers :  3.15 %
    Allowed  : 22.13 %
    Favored  : 74.72 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  1.22 (0.23), residues: 1318
  helix:  1.74 (0.18), residues: 867
  sheet: -0.40 (0.59), residues: 73
  loop : -1.14 (0.30), residues: 378

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.001   ARG A1472 
 TYR   0.018   0.001   TYR A  64 
 PHE   0.043   0.002   PHE A 558 
 TRP   0.016   0.001   TRP A 459 
 HIS   0.006   0.001   HIS A 382 

Details of bonding type rmsd
  covalent geometry    : bond        0.00351 (10906)
  covalent geometry    : angle       0.67529 (14816)
  hydrogen bonds       : bond        0.05255 (  689)
  hydrogen bonds       : angle       4.40471 ( 2031)

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

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

  2636 Ramachandran restraints generated.
    1318 Oldfield, 0 Emsley, 1318 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2636 Ramachandran restraints generated.
    1318 Oldfield, 0 Emsley, 1318 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  207 residues out of total 1175 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 37
    poor density    : 170
  time to evaluate  : 0.389 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   54 PHE cc_start: 0.7212 (OUTLIER) cc_final: 0.6822 (t80)
REVERT: A   89 LEU cc_start: 0.8404 (tp) cc_final: 0.8002 (tp)
REVERT: A  138 MET cc_start: 0.7231 (mmm) cc_final: 0.6660 (tpp)
REVERT: A  234 GLN cc_start: 0.7288 (tm-30) cc_final: 0.7082 (tm-30)
REVERT: A  395 ILE cc_start: 0.8203 (OUTLIER) cc_final: 0.7958 (mt)
REVERT: A  432 GLN cc_start: 0.8288 (mm-40) cc_final: 0.7893 (mm-40)
REVERT: A  435 MET cc_start: 0.7617 (ttt) cc_final: 0.7238 (ttp)
REVERT: A  520 TRP cc_start: 0.7977 (m-10) cc_final: 0.7736 (m-10)
REVERT: A  544 TYR cc_start: 0.7208 (t80) cc_final: 0.6726 (m-10)
REVERT: A  613 LEU cc_start: 0.8279 (mt) cc_final: 0.7611 (tt)
REVERT: A  695 MET cc_start: 0.7311 (mmm) cc_final: 0.6944 (mmm)
REVERT: A  738 LYS cc_start: 0.8489 (pttm) cc_final: 0.8123 (tptp)
REVERT: A  764 LYS cc_start: 0.7888 (mmmt) cc_final: 0.7637 (mttt)
REVERT: A  789 TYR cc_start: 0.8283 (m-80) cc_final: 0.7332 (m-80)
REVERT: A  793 ASP cc_start: 0.7538 (t0) cc_final: 0.7300 (m-30)
REVERT: A  959 LEU cc_start: 0.8201 (tp) cc_final: 0.7469 (pt)
REVERT: A 1094 MET cc_start: 0.6745 (ttp) cc_final: 0.6193 (tpp)
REVERT: A 1105 ILE cc_start: 0.8438 (tt) cc_final: 0.8175 (mm)
REVERT: A 1220 SER cc_start: 0.7288 (t) cc_final: 0.6988 (p)
REVERT: A 1276 GLN cc_start: 0.7908 (pm20) cc_final: 0.7260 (pm20)
REVERT: A 1340 PHE cc_start: 0.7446 (m-10) cc_final: 0.7230 (m-80)
REVERT: A 1385 MET cc_start: 0.7747 (tmm) cc_final: 0.7532 (tmm)
REVERT: A 1448 LYS cc_start: 0.8245 (mmtm) cc_final: 0.7973 (tppt)
  outliers start: 37
  outliers final: 14
  residues processed: 193
  average time/residue: 0.0792
  time to fit residues: 23.1744
Evaluate side-chains
  156 residues out of total 1175 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 140
  time to evaluate  : 0.382 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   47 TRP
Chi-restraints excluded: chain A residue   54 PHE
Chi-restraints excluded: chain A residue  258 VAL
Chi-restraints excluded: chain A residue  326 LEU
Chi-restraints excluded: chain A residue  378 THR
Chi-restraints excluded: chain A residue  395 ILE
Chi-restraints excluded: chain A residue  411 THR
Chi-restraints excluded: chain A residue  475 LEU
Chi-restraints excluded: chain A residue  492 VAL
Chi-restraints excluded: chain A residue  555 CYS
Chi-restraints excluded: chain A residue  677 VAL
Chi-restraints excluded: chain A residue  835 MET
Chi-restraints excluded: chain A residue 1058 SER
Chi-restraints excluded: chain A residue 1218 VAL
Chi-restraints excluded: chain A residue 1363 HIS
Chi-restraints excluded: chain A residue 1372 ILE
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 133
   random chunks:
   chunk 62 optimal weight:    4.9990
   chunk 27 optimal weight:    0.9980
   chunk 35 optimal weight:    2.9990
   chunk 51 optimal weight:    0.0170
   chunk 77 optimal weight:    5.9990
   chunk 70 optimal weight:    0.6980
   chunk 119 optimal weight:    0.8980
   chunk 66 optimal weight:    0.0570
   chunk 57 optimal weight:    0.8980
   chunk 15 optimal weight:    0.6980
   chunk 132 optimal weight:   20.0000
   overall best weight:    0.4736

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

Flipped N/Q/H residues before XYZ refinement:
A 510 ASN
A1363 HIS

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3992 r_free = 0.3992 target = 0.150835 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 36)----------------|
| r_work = 0.3541 r_free = 0.3541 target = 0.111343 restraints weight = 17071.170|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 26)----------------|
| r_work = 0.3553 r_free = 0.3553 target = 0.113504 restraints weight = 10119.742|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 27)----------------|
| r_work = 0.3560 r_free = 0.3560 target = 0.114192 restraints weight = 7411.472|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 23)----------------|
| r_work = 0.3567 r_free = 0.3567 target = 0.114759 restraints weight = 5709.424|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 23)----------------|
| r_work = 0.3570 r_free = 0.3570 target = 0.115025 restraints weight = 5257.235|
|-----------------------------------------------------------------------------|
r_work (final): 0.3556
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7310
moved from start:          0.3149

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.048  10906  Z= 0.140
  Angle     :  0.625  10.524  14816  Z= 0.309
  Chirality :  0.042   0.292   1726
  Planarity :  0.004   0.042   1827
  Dihedral  :  9.325  80.310   1496
  Min Nonbonded Distance : 2.463

Molprobity Statistics.
  All-atom Clashscore : 8.87
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.28 %
    Favored  : 97.72 %
  Rotamer:
    Outliers :  2.55 %
    Allowed  : 23.40 %
    Favored  : 74.04 %
  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:  1.31 (0.24), residues: 1318
  helix:  1.83 (0.18), residues: 875
  sheet: -0.86 (0.56), residues: 83
  loop : -1.10 (0.31), residues: 360

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.007   0.001   ARG A1384 
 TYR   0.019   0.001   TYR A 318 
 PHE   0.051   0.002   PHE A  93 
 TRP   0.018   0.001   TRP A1286 
 HIS   0.007   0.001   HIS A 985 

Details of bonding type rmsd
  covalent geometry    : bond        0.00304 (10906)
  covalent geometry    : angle       0.62475 (14816)
  hydrogen bonds       : bond        0.04767 (  689)
  hydrogen bonds       : angle       4.24269 ( 2031)

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

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

  2636 Ramachandran restraints generated.
    1318 Oldfield, 0 Emsley, 1318 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2636 Ramachandran restraints generated.
    1318 Oldfield, 0 Emsley, 1318 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  186 residues out of total 1175 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 30
    poor density    : 156
  time to evaluate  : 0.336 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   54 PHE cc_start: 0.7260 (OUTLIER) cc_final: 0.6793 (t80)
REVERT: A   82 TRP cc_start: 0.6749 (t60) cc_final: 0.6498 (t60)
REVERT: A  138 MET cc_start: 0.7149 (mmm) cc_final: 0.6536 (tpp)
REVERT: A  370 LEU cc_start: 0.8661 (OUTLIER) cc_final: 0.8304 (tt)
REVERT: A  395 ILE cc_start: 0.8199 (OUTLIER) cc_final: 0.7945 (mt)
REVERT: A  432 GLN cc_start: 0.8331 (mm-40) cc_final: 0.7981 (mm-40)
REVERT: A  435 MET cc_start: 0.7657 (ttt) cc_final: 0.7343 (ttp)
REVERT: A  520 TRP cc_start: 0.8069 (m-10) cc_final: 0.7455 (m-10)
REVERT: A  613 LEU cc_start: 0.8396 (mt) cc_final: 0.7633 (tt)
REVERT: A  695 MET cc_start: 0.7446 (mmm) cc_final: 0.7004 (mmm)
REVERT: A  738 LYS cc_start: 0.8527 (pttm) cc_final: 0.8000 (tptp)
REVERT: A  764 LYS cc_start: 0.7941 (mmmt) cc_final: 0.7670 (mttt)
REVERT: A  789 TYR cc_start: 0.8243 (m-80) cc_final: 0.7227 (m-80)
REVERT: A  793 ASP cc_start: 0.7538 (t0) cc_final: 0.7296 (m-30)
REVERT: A  959 LEU cc_start: 0.8197 (tp) cc_final: 0.7490 (pt)
REVERT: A 1094 MET cc_start: 0.6684 (ttp) cc_final: 0.6231 (tpp)
REVERT: A 1105 ILE cc_start: 0.8438 (tt) cc_final: 0.8146 (mm)
REVERT: A 1220 SER cc_start: 0.7399 (t) cc_final: 0.7086 (p)
  outliers start: 30
  outliers final: 13
  residues processed: 172
  average time/residue: 0.0775
  time to fit residues: 20.0092
Evaluate side-chains
  156 residues out of total 1175 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 140
  time to evaluate  : 0.376 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   20 VAL
Chi-restraints excluded: chain A residue   47 TRP
Chi-restraints excluded: chain A residue   52 PHE
Chi-restraints excluded: chain A residue   54 PHE
Chi-restraints excluded: chain A residue  124 ILE
Chi-restraints excluded: chain A residue  219 ILE
Chi-restraints excluded: chain A residue  258 VAL
Chi-restraints excluded: chain A residue  370 LEU
Chi-restraints excluded: chain A residue  378 THR
Chi-restraints excluded: chain A residue  395 ILE
Chi-restraints excluded: chain A residue  682 CYS
Chi-restraints excluded: chain A residue  835 MET
Chi-restraints excluded: chain A residue 1036 VAL
Chi-restraints excluded: chain A residue 1058 SER
Chi-restraints excluded: chain A residue 1218 VAL
Chi-restraints excluded: chain A residue 1372 ILE
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 133
   random chunks:
   chunk 77 optimal weight:    5.9990
   chunk 75 optimal weight:    3.9990
   chunk 118 optimal weight:    0.6980
   chunk 85 optimal weight:    6.9990
   chunk 79 optimal weight:    3.9990
   chunk 67 optimal weight:    0.9980
   chunk 88 optimal weight:    2.9990
   chunk 54 optimal weight:    0.9980
   chunk 80 optimal weight:    0.9990
   chunk 6 optimal weight:    5.9990
   chunk 125 optimal weight:    6.9990
   overall best weight:    1.3384

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

Flipped N/Q/H residues before XYZ refinement:
A 362 GLN
A 510 ASN
A1406 HIS
** A1420 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3922 r_free = 0.3922 target = 0.145368 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 46)----------------|
| r_work = 0.3366 r_free = 0.3366 target = 0.100388 restraints weight = 17341.846|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 46)----------------|
| r_work = 0.3412 r_free = 0.3412 target = 0.103572 restraints weight = 9553.646|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 45)----------------|
| r_work = 0.3442 r_free = 0.3442 target = 0.105769 restraints weight = 6476.426|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 52)----------------|
| r_work = 0.3462 r_free = 0.3462 target = 0.107207 restraints weight = 5027.501|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 32)----------------|
| r_work = 0.3471 r_free = 0.3471 target = 0.107901 restraints weight = 4287.442|
|-----------------------------------------------------------------------------|
r_work (final): 0.3456
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7485
moved from start:          0.3664

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.040  10906  Z= 0.194
  Angle     :  0.679  13.002  14816  Z= 0.337
  Chirality :  0.044   0.309   1726
  Planarity :  0.004   0.045   1827
  Dihedral  :  9.393  83.554   1496
  Min Nonbonded Distance : 2.500

Molprobity Statistics.
  All-atom Clashscore : 9.48
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.66 %
    Favored  : 97.34 %
  Rotamer:
    Outliers :  3.91 %
    Allowed  : 23.15 %
    Favored  : 72.94 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.08 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  1.13 (0.23), residues: 1318
  helix:  1.68 (0.18), residues: 868
  sheet: -0.80 (0.57), residues: 83
  loop : -1.12 (0.31), residues: 367

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.001   ARG A1201 
 TYR   0.021   0.002   TYR A 318 
 PHE   0.036   0.002   PHE A  93 
 TRP   0.022   0.002   TRP A1286 
 HIS   0.006   0.001   HIS A1420 

Details of bonding type rmsd
  covalent geometry    : bond        0.00456 (10906)
  covalent geometry    : angle       0.67888 (14816)
  hydrogen bonds       : bond        0.05055 (  689)
  hydrogen bonds       : angle       4.29632 ( 2031)

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

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

  2636 Ramachandran restraints generated.
    1318 Oldfield, 0 Emsley, 1318 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2636 Ramachandran restraints generated.
    1318 Oldfield, 0 Emsley, 1318 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  195 residues out of total 1175 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 46
    poor density    : 149
  time to evaluate  : 0.289 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   54 PHE cc_start: 0.7301 (OUTLIER) cc_final: 0.6839 (t80)
REVERT: A   79 PHE cc_start: 0.7716 (m-80) cc_final: 0.7171 (m-10)
REVERT: A   82 TRP cc_start: 0.6959 (t60) cc_final: 0.6570 (t60)
REVERT: A  117 MET cc_start: 0.5911 (mmp) cc_final: 0.5393 (mmp)
REVERT: A  138 MET cc_start: 0.7634 (mmm) cc_final: 0.7179 (tpp)
REVERT: A  370 LEU cc_start: 0.8693 (OUTLIER) cc_final: 0.8318 (tt)
REVERT: A  395 ILE cc_start: 0.8362 (OUTLIER) cc_final: 0.8061 (mt)
REVERT: A  520 TRP cc_start: 0.8256 (m-10) cc_final: 0.7637 (m-10)
REVERT: A  662 HIS cc_start: 0.6497 (OUTLIER) cc_final: 0.6118 (m90)
REVERT: A  695 MET cc_start: 0.8076 (mmm) cc_final: 0.7194 (mmm)
REVERT: A  736 TYR cc_start: 0.6615 (t80) cc_final: 0.6327 (t80)
REVERT: A  738 LYS cc_start: 0.8583 (pttm) cc_final: 0.8036 (tptp)
REVERT: A  764 LYS cc_start: 0.8020 (mmmt) cc_final: 0.7667 (mttt)
REVERT: A  789 TYR cc_start: 0.8290 (m-80) cc_final: 0.7038 (m-80)
REVERT: A  862 PHE cc_start: 0.7282 (t80) cc_final: 0.7024 (t80)
REVERT: A  959 LEU cc_start: 0.8350 (tp) cc_final: 0.8140 (tp)
REVERT: A 1105 ILE cc_start: 0.8543 (tt) cc_final: 0.8297 (mm)
REVERT: A 1220 SER cc_start: 0.7910 (t) cc_final: 0.7603 (p)
REVERT: A 1309 LEU cc_start: 0.8811 (OUTLIER) cc_final: 0.8496 (mp)
REVERT: A 1448 LYS cc_start: 0.7894 (tppt) cc_final: 0.7411 (tppt)
  outliers start: 46
  outliers final: 25
  residues processed: 180
  average time/residue: 0.0770
  time to fit residues: 20.8300
Evaluate side-chains
  169 residues out of total 1175 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 30
    poor density    : 139
  time to evaluate  : 0.287 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   47 TRP
Chi-restraints excluded: chain A residue   52 PHE
Chi-restraints excluded: chain A residue   54 PHE
Chi-restraints excluded: chain A residue  124 ILE
Chi-restraints excluded: chain A residue  219 ILE
Chi-restraints excluded: chain A residue  258 VAL
Chi-restraints excluded: chain A residue  370 LEU
Chi-restraints excluded: chain A residue  375 CYS
Chi-restraints excluded: chain A residue  378 THR
Chi-restraints excluded: chain A residue  395 ILE
Chi-restraints excluded: chain A residue  399 VAL
Chi-restraints excluded: chain A residue  411 THR
Chi-restraints excluded: chain A residue  466 VAL
Chi-restraints excluded: chain A residue  492 VAL
Chi-restraints excluded: chain A residue  550 THR
Chi-restraints excluded: chain A residue  626 ASP
Chi-restraints excluded: chain A residue  662 HIS
Chi-restraints excluded: chain A residue  682 CYS
Chi-restraints excluded: chain A residue  835 MET
Chi-restraints excluded: chain A residue 1032 TYR
Chi-restraints excluded: chain A residue 1036 VAL
Chi-restraints excluded: chain A residue 1058 SER
Chi-restraints excluded: chain A residue 1159 LEU
Chi-restraints excluded: chain A residue 1218 VAL
Chi-restraints excluded: chain A residue 1309 LEU
Chi-restraints excluded: chain A residue 1321 LYS
Chi-restraints excluded: chain A residue 1372 ILE
Chi-restraints excluded: chain A residue 1418 LEU
Chi-restraints excluded: chain A residue 1431 VAL
Chi-restraints excluded: chain A residue 1436 LEU
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 133
   random chunks:
   chunk 119 optimal weight:    6.9990
   chunk 80 optimal weight:    3.9990
   chunk 55 optimal weight:    0.1980
   chunk 15 optimal weight:    0.9990
   chunk 63 optimal weight:    1.9990
   chunk 92 optimal weight:    0.6980
   chunk 129 optimal weight:    1.9990
   chunk 116 optimal weight:    0.7980
   chunk 26 optimal weight:    0.6980
   chunk 27 optimal weight:    0.8980
   chunk 45 optimal weight:    0.8980
   overall best weight:    0.6580

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

Flipped N/Q/H residues before XYZ refinement:
A 432 GLN
A 510 ASN
** A1420 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3946 r_free = 0.3946 target = 0.147583 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 44)----------------|
| r_work = 0.3408 r_free = 0.3408 target = 0.103252 restraints weight = 17190.140|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 42)----------------|
| r_work = 0.3454 r_free = 0.3454 target = 0.106541 restraints weight = 9395.975|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 32)----------------|
| r_work = 0.3482 r_free = 0.3482 target = 0.108675 restraints weight = 6309.124|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 37)----------------|
| r_work = 0.3503 r_free = 0.3503 target = 0.110195 restraints weight = 4875.302|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 49)----------------|
| r_work = 0.3516 r_free = 0.3516 target = 0.111146 restraints weight = 4137.631|
|-----------------------------------------------------------------------------|
r_work (final): 0.3497
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7406
moved from start:          0.3906

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.033  10906  Z= 0.136
  Angle     :  0.605  13.389  14816  Z= 0.295
  Chirality :  0.041   0.200   1726
  Planarity :  0.004   0.042   1827
  Dihedral  :  9.179  84.347   1496
  Min Nonbonded Distance : 2.522

Molprobity Statistics.
  All-atom Clashscore : 8.97
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.97 %
    Favored  : 98.03 %
  Rotamer:
    Outliers :  3.15 %
    Allowed  : 24.60 %
    Favored  : 72.26 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.08 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  1.36 (0.24), residues: 1318
  helix:  1.87 (0.18), residues: 868
  sheet: -0.68 (0.58), residues: 83
  loop : -1.08 (0.31), residues: 367

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG A1046 
 TYR   0.018   0.001   TYR A  64 
 PHE   0.043   0.002   PHE A  93 
 TRP   0.013   0.001   TRP A1286 
 HIS   0.005   0.001   HIS A 985 

Details of bonding type rmsd
  covalent geometry    : bond        0.00303 (10906)
  covalent geometry    : angle       0.60536 (14816)
  hydrogen bonds       : bond        0.04518 (  689)
  hydrogen bonds       : angle       4.08845 ( 2031)

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

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

  2636 Ramachandran restraints generated.
    1318 Oldfield, 0 Emsley, 1318 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2636 Ramachandran restraints generated.
    1318 Oldfield, 0 Emsley, 1318 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  183 residues out of total 1175 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 37
    poor density    : 146
  time to evaluate  : 0.322 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   54 PHE cc_start: 0.7250 (OUTLIER) cc_final: 0.6842 (t80)
REVERT: A   79 PHE cc_start: 0.7688 (m-80) cc_final: 0.7202 (m-10)
REVERT: A   82 TRP cc_start: 0.6976 (t60) cc_final: 0.6569 (t60)
REVERT: A  138 MET cc_start: 0.7438 (mmm) cc_final: 0.7058 (tpp)
REVERT: A  370 LEU cc_start: 0.8586 (OUTLIER) cc_final: 0.8270 (tt)
REVERT: A  395 ILE cc_start: 0.8262 (OUTLIER) cc_final: 0.8028 (mt)
REVERT: A  545 LEU cc_start: 0.7197 (tp) cc_final: 0.6955 (tt)
REVERT: A  695 MET cc_start: 0.8023 (mmm) cc_final: 0.7326 (mmm)
REVERT: A  738 LYS cc_start: 0.8616 (pttm) cc_final: 0.7990 (tptp)
REVERT: A  764 LYS cc_start: 0.7957 (mmmt) cc_final: 0.7652 (mttt)
REVERT: A  789 TYR cc_start: 0.8280 (m-80) cc_final: 0.7051 (m-80)
REVERT: A  959 LEU cc_start: 0.8301 (tp) cc_final: 0.7572 (pt)
REVERT: A 1053 HIS cc_start: 0.8391 (OUTLIER) cc_final: 0.8179 (t-90)
REVERT: A 1105 ILE cc_start: 0.8478 (tt) cc_final: 0.8200 (mm)
REVERT: A 1127 PHE cc_start: 0.6969 (OUTLIER) cc_final: 0.5757 (m-10)
REVERT: A 1220 SER cc_start: 0.7835 (t) cc_final: 0.7529 (p)
REVERT: A 1309 LEU cc_start: 0.8845 (OUTLIER) cc_final: 0.8233 (tt)
REVERT: A 1490 ILE cc_start: 0.7893 (OUTLIER) cc_final: 0.7589 (mt)
  outliers start: 37
  outliers final: 21
  residues processed: 172
  average time/residue: 0.0755
  time to fit residues: 20.0411
Evaluate side-chains
  164 residues out of total 1175 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 28
    poor density    : 136
  time to evaluate  : 0.345 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   47 TRP
Chi-restraints excluded: chain A residue   54 PHE
Chi-restraints excluded: chain A residue  124 ILE
Chi-restraints excluded: chain A residue  219 ILE
Chi-restraints excluded: chain A residue  225 THR
Chi-restraints excluded: chain A residue  239 THR
Chi-restraints excluded: chain A residue  258 VAL
Chi-restraints excluded: chain A residue  370 LEU
Chi-restraints excluded: chain A residue  378 THR
Chi-restraints excluded: chain A residue  395 ILE
Chi-restraints excluded: chain A residue  466 VAL
Chi-restraints excluded: chain A residue  472 VAL
Chi-restraints excluded: chain A residue  670 GLU
Chi-restraints excluded: chain A residue  682 CYS
Chi-restraints excluded: chain A residue  835 MET
Chi-restraints excluded: chain A residue 1032 TYR
Chi-restraints excluded: chain A residue 1053 HIS
Chi-restraints excluded: chain A residue 1058 SER
Chi-restraints excluded: chain A residue 1109 LEU
Chi-restraints excluded: chain A residue 1127 PHE
Chi-restraints excluded: chain A residue 1158 LEU
Chi-restraints excluded: chain A residue 1159 LEU
Chi-restraints excluded: chain A residue 1224 LEU
Chi-restraints excluded: chain A residue 1309 LEU
Chi-restraints excluded: chain A residue 1372 ILE
Chi-restraints excluded: chain A residue 1418 LEU
Chi-restraints excluded: chain A residue 1431 VAL
Chi-restraints excluded: chain A residue 1490 ILE
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 133
   random chunks:
   chunk 123 optimal weight:    7.9990
   chunk 58 optimal weight:    0.9990
   chunk 43 optimal weight:    1.9990
   chunk 71 optimal weight:    0.2980
   chunk 130 optimal weight:    1.9990
   chunk 88 optimal weight:    0.6980
   chunk 104 optimal weight:    0.9990
   chunk 45 optimal weight:    0.6980
   chunk 55 optimal weight:    1.9990
   chunk 115 optimal weight:   10.0000
   chunk 32 optimal weight:    1.9990
   overall best weight:    0.7384

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

Flipped N/Q/H residues before XYZ refinement:
A 510 ASN
** A1420 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3942 r_free = 0.3942 target = 0.146872 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 50)----------------|
| r_work = 0.3397 r_free = 0.3397 target = 0.102404 restraints weight = 17152.795|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 38)----------------|
| r_work = 0.3443 r_free = 0.3443 target = 0.105639 restraints weight = 9362.207|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 39)----------------|
| r_work = 0.3473 r_free = 0.3473 target = 0.107829 restraints weight = 6301.530|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 33)----------------|
| r_work = 0.3492 r_free = 0.3492 target = 0.109258 restraints weight = 4880.315|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 29)----------------|
| r_work = 0.3501 r_free = 0.3501 target = 0.110052 restraints weight = 4157.528|
|-----------------------------------------------------------------------------|
r_work (final): 0.3486
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7440
moved from start:          0.4128

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.046  10906  Z= 0.140
  Angle     :  0.599  14.325  14816  Z= 0.294
  Chirality :  0.041   0.175   1726
  Planarity :  0.004   0.043   1827
  Dihedral  :  9.056  83.996   1496
  Min Nonbonded Distance : 2.535

Molprobity Statistics.
  All-atom Clashscore : 9.01
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.66 %
    Favored  : 97.34 %
  Rotamer:
    Outliers :  3.32 %
    Allowed  : 25.28 %
    Favored  : 71.40 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.08 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  1.31 (0.24), residues: 1318
  helix:  1.77 (0.18), residues: 878
  sheet: -0.65 (0.58), residues: 83
  loop : -1.02 (0.31), residues: 357

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARG A 632 
 TYR   0.026   0.001   TYR A  64 
 PHE   0.046   0.002   PHE A 558 
 TRP   0.022   0.001   TRP A1286 
 HIS   0.005   0.001   HIS A1420 

Details of bonding type rmsd
  covalent geometry    : bond        0.00317 (10906)
  covalent geometry    : angle       0.59889 (14816)
  hydrogen bonds       : bond        0.04430 (  689)
  hydrogen bonds       : angle       4.07244 ( 2031)

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

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

  2636 Ramachandran restraints generated.
    1318 Oldfield, 0 Emsley, 1318 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2636 Ramachandran restraints generated.
    1318 Oldfield, 0 Emsley, 1318 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  176 residues out of total 1175 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 39
    poor density    : 137
  time to evaluate  : 0.380 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   35 ASN cc_start: 0.7767 (m-40) cc_final: 0.7079 (p0)
REVERT: A   54 PHE cc_start: 0.7268 (OUTLIER) cc_final: 0.6833 (t80)
REVERT: A   79 PHE cc_start: 0.7709 (m-80) cc_final: 0.7225 (m-10)
REVERT: A   82 TRP cc_start: 0.6998 (t60) cc_final: 0.6522 (t60)
REVERT: A  117 MET cc_start: 0.5948 (mmp) cc_final: 0.5465 (mmp)
REVERT: A  138 MET cc_start: 0.7554 (mmm) cc_final: 0.7234 (tpp)
REVERT: A  370 LEU cc_start: 0.8638 (OUTLIER) cc_final: 0.8290 (tt)
REVERT: A  395 ILE cc_start: 0.8271 (OUTLIER) cc_final: 0.8030 (mt)
REVERT: A  479 LEU cc_start: 0.7520 (OUTLIER) cc_final: 0.7196 (tt)
REVERT: A  662 HIS cc_start: 0.6687 (OUTLIER) cc_final: 0.6330 (m90)
REVERT: A  695 MET cc_start: 0.8015 (mmm) cc_final: 0.7245 (mmm)
REVERT: A  738 LYS cc_start: 0.8615 (pttm) cc_final: 0.7940 (tptp)
REVERT: A  764 LYS cc_start: 0.7950 (mmmt) cc_final: 0.7648 (mttt)
REVERT: A  789 TYR cc_start: 0.8337 (m-80) cc_final: 0.7035 (m-80)
REVERT: A  829 ILE cc_start: 0.7405 (OUTLIER) cc_final: 0.7175 (pt)
REVERT: A  959 LEU cc_start: 0.8314 (tp) cc_final: 0.7576 (pt)
REVERT: A 1105 ILE cc_start: 0.8519 (tt) cc_final: 0.8227 (mm)
REVERT: A 1127 PHE cc_start: 0.7050 (OUTLIER) cc_final: 0.5809 (m-10)
REVERT: A 1220 SER cc_start: 0.7878 (t) cc_final: 0.7583 (p)
REVERT: A 1309 LEU cc_start: 0.8805 (OUTLIER) cc_final: 0.8179 (tt)
  outliers start: 39
  outliers final: 23
  residues processed: 165
  average time/residue: 0.0620
  time to fit residues: 15.9854
Evaluate side-chains
  161 residues out of total 1175 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 31
    poor density    : 130
  time to evaluate  : 0.325 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   47 TRP
Chi-restraints excluded: chain A residue   52 PHE
Chi-restraints excluded: chain A residue   54 PHE
Chi-restraints excluded: chain A residue  124 ILE
Chi-restraints excluded: chain A residue  219 ILE
Chi-restraints excluded: chain A residue  225 THR
Chi-restraints excluded: chain A residue  239 THR
Chi-restraints excluded: chain A residue  258 VAL
Chi-restraints excluded: chain A residue  370 LEU
Chi-restraints excluded: chain A residue  378 THR
Chi-restraints excluded: chain A residue  395 ILE
Chi-restraints excluded: chain A residue  411 THR
Chi-restraints excluded: chain A residue  466 VAL
Chi-restraints excluded: chain A residue  479 LEU
Chi-restraints excluded: chain A residue  618 VAL
Chi-restraints excluded: chain A residue  626 ASP
Chi-restraints excluded: chain A residue  662 HIS
Chi-restraints excluded: chain A residue  682 CYS
Chi-restraints excluded: chain A residue  829 ILE
Chi-restraints excluded: chain A residue  835 MET
Chi-restraints excluded: chain A residue 1032 TYR
Chi-restraints excluded: chain A residue 1058 SER
Chi-restraints excluded: chain A residue 1109 LEU
Chi-restraints excluded: chain A residue 1127 PHE
Chi-restraints excluded: chain A residue 1158 LEU
Chi-restraints excluded: chain A residue 1159 LEU
Chi-restraints excluded: chain A residue 1218 VAL
Chi-restraints excluded: chain A residue 1309 LEU
Chi-restraints excluded: chain A residue 1372 ILE
Chi-restraints excluded: chain A residue 1418 LEU
Chi-restraints excluded: chain A residue 1431 VAL
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 133
   random chunks:
   chunk 92 optimal weight:    0.9990
   chunk 55 optimal weight:    1.9990
   chunk 41 optimal weight:    2.9990
   chunk 119 optimal weight:    6.9990
   chunk 85 optimal weight:    4.9990
   chunk 62 optimal weight:    1.9990
   chunk 73 optimal weight:    2.9990
   chunk 9 optimal weight:    2.9990
   chunk 18 optimal weight:    0.9980
   chunk 52 optimal weight:    2.9990
   chunk 15 optimal weight:    0.6980
   overall best weight:    1.3386

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

Flipped N/Q/H residues before XYZ refinement:
A 510 ASN
A 719 ASN
** A1420 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3916 r_free = 0.3916 target = 0.144404 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 32)----------------|
| r_work = 0.3425 r_free = 0.3425 target = 0.104181 restraints weight = 17564.423|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 28)----------------|
| r_work = 0.3416 r_free = 0.3416 target = 0.103977 restraints weight = 10411.784|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 26)----------------|
| r_work = 0.3419 r_free = 0.3419 target = 0.104355 restraints weight = 7358.284|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 28)----------------|
| r_work = 0.3425 r_free = 0.3425 target = 0.104888 restraints weight = 7127.071|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 26)----------------|
| r_work = 0.3432 r_free = 0.3432 target = 0.105404 restraints weight = 6390.125|
|-----------------------------------------------------------------------------|
r_work (final): 0.3413
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7542
moved from start:          0.4333

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.051  10906  Z= 0.188
  Angle     :  0.654  12.691  14816  Z= 0.319
  Chirality :  0.043   0.211   1726
  Planarity :  0.004   0.044   1827
  Dihedral  :  9.021  84.256   1496
  Min Nonbonded Distance : 2.550

Molprobity Statistics.
  All-atom Clashscore : 9.48
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.50 %
    Favored  : 97.50 %
  Rotamer:
    Outliers :  3.74 %
    Allowed  : 25.19 %
    Favored  : 71.06 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.08 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  1.15 (0.23), residues: 1318
  helix:  1.60 (0.18), residues: 884
  sheet: -0.40 (0.60), residues: 78
  loop : -1.04 (0.31), residues: 356

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.001   ARG A1165 
 TYR   0.018   0.002   TYR A 318 
 PHE   0.043   0.002   PHE A  93 
 TRP   0.020   0.001   TRP A1286 
 HIS   0.003   0.001   HIS A1420 

Details of bonding type rmsd
  covalent geometry    : bond        0.00444 (10906)
  covalent geometry    : angle       0.65441 (14816)
  hydrogen bonds       : bond        0.04804 (  689)
  hydrogen bonds       : angle       4.20041 ( 2031)

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

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

  2636 Ramachandran restraints generated.
    1318 Oldfield, 0 Emsley, 1318 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2636 Ramachandran restraints generated.
    1318 Oldfield, 0 Emsley, 1318 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  183 residues out of total 1175 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 44
    poor density    : 139
  time to evaluate  : 0.380 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   35 ASN cc_start: 0.7801 (m-40) cc_final: 0.7076 (p0)
REVERT: A   54 PHE cc_start: 0.7298 (OUTLIER) cc_final: 0.6910 (t80)
REVERT: A   64 TYR cc_start: 0.7206 (p90) cc_final: 0.6935 (p90)
REVERT: A   79 PHE cc_start: 0.7673 (m-80) cc_final: 0.7378 (m-10)
REVERT: A   82 TRP cc_start: 0.7011 (t60) cc_final: 0.6596 (t60)
REVERT: A  117 MET cc_start: 0.6000 (mmp) cc_final: 0.5446 (mmp)
REVERT: A  370 LEU cc_start: 0.8806 (OUTLIER) cc_final: 0.8430 (tt)
REVERT: A  479 LEU cc_start: 0.7530 (OUTLIER) cc_final: 0.7171 (tt)
REVERT: A  662 HIS cc_start: 0.6827 (OUTLIER) cc_final: 0.6373 (m90)
REVERT: A  695 MET cc_start: 0.8223 (mmm) cc_final: 0.7409 (mmm)
REVERT: A  738 LYS cc_start: 0.8764 (pttm) cc_final: 0.8043 (tptp)
REVERT: A  789 TYR cc_start: 0.8455 (m-80) cc_final: 0.7038 (m-80)
REVERT: A  829 ILE cc_start: 0.7691 (OUTLIER) cc_final: 0.7451 (pt)
REVERT: A  959 LEU cc_start: 0.8412 (tp) cc_final: 0.7622 (pt)
REVERT: A 1053 HIS cc_start: 0.8422 (OUTLIER) cc_final: 0.8164 (t-90)
REVERT: A 1094 MET cc_start: 0.7077 (ttp) cc_final: 0.6710 (tpp)
REVERT: A 1105 ILE cc_start: 0.8618 (tt) cc_final: 0.8346 (mm)
REVERT: A 1127 PHE cc_start: 0.7158 (OUTLIER) cc_final: 0.5965 (m-10)
REVERT: A 1182 ASP cc_start: 0.8395 (t70) cc_final: 0.8111 (t0)
REVERT: A 1220 SER cc_start: 0.8165 (t) cc_final: 0.7894 (p)
REVERT: A 1309 LEU cc_start: 0.8865 (OUTLIER) cc_final: 0.8210 (tt)
REVERT: A 1448 LYS cc_start: 0.7843 (tppt) cc_final: 0.7378 (tppt)
REVERT: A 1490 ILE cc_start: 0.7891 (OUTLIER) cc_final: 0.7581 (mt)
  outliers start: 44
  outliers final: 31
  residues processed: 171
  average time/residue: 0.0725
  time to fit residues: 19.1436
Evaluate side-chains
  171 residues out of total 1175 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 40
    poor density    : 131
  time to evaluate  : 0.387 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   47 TRP
Chi-restraints excluded: chain A residue   54 PHE
Chi-restraints excluded: chain A residue  124 ILE
Chi-restraints excluded: chain A residue  139 LEU
Chi-restraints excluded: chain A residue  219 ILE
Chi-restraints excluded: chain A residue  225 THR
Chi-restraints excluded: chain A residue  239 THR
Chi-restraints excluded: chain A residue  258 VAL
Chi-restraints excluded: chain A residue  370 LEU
Chi-restraints excluded: chain A residue  378 THR
Chi-restraints excluded: chain A residue  399 VAL
Chi-restraints excluded: chain A residue  411 THR
Chi-restraints excluded: chain A residue  466 VAL
Chi-restraints excluded: chain A residue  472 VAL
Chi-restraints excluded: chain A residue  477 VAL
Chi-restraints excluded: chain A residue  479 LEU
Chi-restraints excluded: chain A residue  550 THR
Chi-restraints excluded: chain A residue  618 VAL
Chi-restraints excluded: chain A residue  626 ASP
Chi-restraints excluded: chain A residue  662 HIS
Chi-restraints excluded: chain A residue  670 GLU
Chi-restraints excluded: chain A residue  677 VAL
Chi-restraints excluded: chain A residue  682 CYS
Chi-restraints excluded: chain A residue  829 ILE
Chi-restraints excluded: chain A residue  835 MET
Chi-restraints excluded: chain A residue  841 MET
Chi-restraints excluded: chain A residue 1032 TYR
Chi-restraints excluded: chain A residue 1036 VAL
Chi-restraints excluded: chain A residue 1053 HIS
Chi-restraints excluded: chain A residue 1058 SER
Chi-restraints excluded: chain A residue 1109 LEU
Chi-restraints excluded: chain A residue 1127 PHE
Chi-restraints excluded: chain A residue 1158 LEU
Chi-restraints excluded: chain A residue 1159 LEU
Chi-restraints excluded: chain A residue 1218 VAL
Chi-restraints excluded: chain A residue 1309 LEU
Chi-restraints excluded: chain A residue 1372 ILE
Chi-restraints excluded: chain A residue 1418 LEU
Chi-restraints excluded: chain A residue 1431 VAL
Chi-restraints excluded: chain A residue 1490 ILE
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 133
   random chunks:
   chunk 13 optimal weight:    6.9990
   chunk 61 optimal weight:    0.9990
   chunk 119 optimal weight:    3.9990
   chunk 122 optimal weight:   10.0000
   chunk 121 optimal weight:    0.9990
   chunk 14 optimal weight:    0.3980
   chunk 20 optimal weight:    0.0870
   chunk 47 optimal weight:    0.4980
   chunk 58 optimal weight:    3.9990
   chunk 83 optimal weight:    4.9990
   chunk 32 optimal weight:    0.9980
   overall best weight:    0.5960

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

Flipped N/Q/H residues before XYZ refinement:
** A1420 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
A1485 HIS

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3940 r_free = 0.3940 target = 0.146877 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 46)----------------|
| r_work = 0.3393 r_free = 0.3393 target = 0.102146 restraints weight = 17431.223|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 46)----------------|
| r_work = 0.3439 r_free = 0.3439 target = 0.105456 restraints weight = 9511.308|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 46)----------------|
| r_work = 0.3469 r_free = 0.3469 target = 0.107694 restraints weight = 6385.261|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 33)----------------|
| r_work = 0.3486 r_free = 0.3486 target = 0.109037 restraints weight = 4936.339|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 51)----------------|
| r_work = 0.3500 r_free = 0.3500 target = 0.110042 restraints weight = 4217.812|
|-----------------------------------------------------------------------------|
r_work (final): 0.3481
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7443
moved from start:          0.4443

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.040  10906  Z= 0.131
  Angle     :  0.608  14.928  14816  Z= 0.293
  Chirality :  0.041   0.178   1726
  Planarity :  0.004   0.043   1827
  Dihedral  :  8.678  80.502   1496
  Min Nonbonded Distance : 2.530

Molprobity Statistics.
  All-atom Clashscore : 8.92
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.35 %
    Favored  : 97.65 %
  Rotamer:
    Outliers :  2.89 %
    Allowed  : 26.13 %
    Favored  : 70.98 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.08 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  1.34 (0.24), residues: 1318
  helix:  1.75 (0.18), residues: 883
  sheet: -0.53 (0.58), residues: 84
  loop : -0.95 (0.32), residues: 351

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG A1165 
 TYR   0.017   0.001   TYR A  64 
 PHE   0.047   0.002   PHE A  93 
 TRP   0.021   0.001   TRP A1286 
 HIS   0.004   0.001   HIS A 985 

Details of bonding type rmsd
  covalent geometry    : bond        0.00291 (10906)
  covalent geometry    : angle       0.60798 (14816)
  hydrogen bonds       : bond        0.04440 (  689)
  hydrogen bonds       : angle       4.07796 ( 2031)

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

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

  2636 Ramachandran restraints generated.
    1318 Oldfield, 0 Emsley, 1318 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2636 Ramachandran restraints generated.
    1318 Oldfield, 0 Emsley, 1318 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  167 residues out of total 1175 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 34
    poor density    : 133
  time to evaluate  : 0.323 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   35 ASN cc_start: 0.7797 (m-40) cc_final: 0.7064 (p0)
REVERT: A   54 PHE cc_start: 0.7137 (OUTLIER) cc_final: 0.6741 (t80)
REVERT: A   79 PHE cc_start: 0.7560 (m-80) cc_final: 0.7332 (m-80)
REVERT: A   82 TRP cc_start: 0.6907 (t60) cc_final: 0.6560 (t60)
REVERT: A  117 MET cc_start: 0.5733 (mmp) cc_final: 0.5301 (mmp)
REVERT: A  370 LEU cc_start: 0.8629 (OUTLIER) cc_final: 0.8288 (tt)
REVERT: A  479 LEU cc_start: 0.7480 (OUTLIER) cc_final: 0.7165 (tt)
REVERT: A  695 MET cc_start: 0.8158 (mmm) cc_final: 0.7423 (mmm)
REVERT: A  738 LYS cc_start: 0.8659 (pttm) cc_final: 0.8097 (tptp)
REVERT: A  764 LYS cc_start: 0.7889 (mmmt) cc_final: 0.7610 (mttt)
REVERT: A  789 TYR cc_start: 0.8386 (m-80) cc_final: 0.7032 (m-80)
REVERT: A  829 ILE cc_start: 0.7282 (OUTLIER) cc_final: 0.7053 (pt)
REVERT: A  959 LEU cc_start: 0.8322 (tp) cc_final: 0.7581 (pt)
REVERT: A 1053 HIS cc_start: 0.8394 (OUTLIER) cc_final: 0.8164 (t-90)
REVERT: A 1105 ILE cc_start: 0.8515 (tt) cc_final: 0.8210 (mm)
REVERT: A 1127 PHE cc_start: 0.7058 (OUTLIER) cc_final: 0.5865 (m-10)
REVERT: A 1220 SER cc_start: 0.8045 (t) cc_final: 0.7761 (p)
REVERT: A 1309 LEU cc_start: 0.8832 (OUTLIER) cc_final: 0.8225 (tt)
REVERT: A 1448 LYS cc_start: 0.7871 (tppt) cc_final: 0.7426 (tppt)
  outliers start: 34
  outliers final: 25
  residues processed: 157
  average time/residue: 0.0700
  time to fit residues: 17.0883
Evaluate side-chains
  162 residues out of total 1175 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 32
    poor density    : 130
  time to evaluate  : 0.236 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   47 TRP
Chi-restraints excluded: chain A residue   52 PHE
Chi-restraints excluded: chain A residue   54 PHE
Chi-restraints excluded: chain A residue   80 LEU
Chi-restraints excluded: chain A residue  124 ILE
Chi-restraints excluded: chain A residue  139 LEU
Chi-restraints excluded: chain A residue  219 ILE
Chi-restraints excluded: chain A residue  225 THR
Chi-restraints excluded: chain A residue  258 VAL
Chi-restraints excluded: chain A residue  370 LEU
Chi-restraints excluded: chain A residue  378 THR
Chi-restraints excluded: chain A residue  399 VAL
Chi-restraints excluded: chain A residue  466 VAL
Chi-restraints excluded: chain A residue  475 LEU
Chi-restraints excluded: chain A residue  479 LEU
Chi-restraints excluded: chain A residue  550 THR
Chi-restraints excluded: chain A residue  571 VAL
Chi-restraints excluded: chain A residue  618 VAL
Chi-restraints excluded: chain A residue  626 ASP
Chi-restraints excluded: chain A residue  677 VAL
Chi-restraints excluded: chain A residue  682 CYS
Chi-restraints excluded: chain A residue  702 VAL
Chi-restraints excluded: chain A residue  829 ILE
Chi-restraints excluded: chain A residue  835 MET
Chi-restraints excluded: chain A residue 1032 TYR
Chi-restraints excluded: chain A residue 1053 HIS
Chi-restraints excluded: chain A residue 1127 PHE
Chi-restraints excluded: chain A residue 1159 LEU
Chi-restraints excluded: chain A residue 1309 LEU
Chi-restraints excluded: chain A residue 1418 LEU
Chi-restraints excluded: chain A residue 1431 VAL
Chi-restraints excluded: chain A residue 1451 VAL
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 133
   random chunks:
   chunk 122 optimal weight:    8.9990
   chunk 46 optimal weight:    0.7980
   chunk 27 optimal weight:    0.5980
   chunk 51 optimal weight:    0.6980
   chunk 2 optimal weight:    4.9990
   chunk 1 optimal weight:    2.9990
   chunk 110 optimal weight:    0.7980
   chunk 90 optimal weight:    0.8980
   chunk 70 optimal weight:    3.9990
   chunk 62 optimal weight:    0.6980
   chunk 16 optimal weight:    0.0050
   overall best weight:    0.5594

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

Flipped N/Q/H residues before XYZ refinement:
A 719 ASN
** A1420 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3946 r_free = 0.3946 target = 0.147365 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 32)----------------|
| r_work = 0.3481 r_free = 0.3481 target = 0.107475 restraints weight = 17201.811|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 30)----------------|
| r_work = 0.3494 r_free = 0.3494 target = 0.109593 restraints weight = 10914.784|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 29)----------------|
| r_work = 0.3499 r_free = 0.3499 target = 0.110050 restraints weight = 7646.806|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 23)----------------|
| r_work = 0.3506 r_free = 0.3506 target = 0.110586 restraints weight = 6422.791|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 26)----------------|
| r_work = 0.3509 r_free = 0.3509 target = 0.110883 restraints weight = 5903.634|
|-----------------------------------------------------------------------------|
r_work (final): 0.3495
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7413
moved from start:          0.4554

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.039  10906  Z= 0.129
  Angle     :  0.610  14.228  14816  Z= 0.294
  Chirality :  0.040   0.173   1726
  Planarity :  0.004   0.042   1827
  Dihedral  :  8.363  76.200   1496
  Min Nonbonded Distance : 2.506

Molprobity Statistics.
  All-atom Clashscore : 8.32
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.35 %
    Favored  : 97.65 %
  Rotamer:
    Outliers :  3.06 %
    Allowed  : 26.04 %
    Favored  : 70.89 %
  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:  1.37 (0.24), residues: 1318
  helix:  1.75 (0.18), residues: 883
  sheet: -0.35 (0.59), residues: 84
  loop : -0.92 (0.32), residues: 351

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG A1165 
 TYR   0.027   0.001   TYR A  64 
 PHE   0.072   0.002   PHE A 558 
 TRP   0.024   0.001   TRP A1286 
 HIS   0.004   0.001   HIS A 985 

Details of bonding type rmsd
  covalent geometry    : bond        0.00284 (10906)
  covalent geometry    : angle       0.60959 (14816)
  hydrogen bonds       : bond        0.04361 (  689)
  hydrogen bonds       : angle       4.00671 ( 2031)

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

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

  2636 Ramachandran restraints generated.
    1318 Oldfield, 0 Emsley, 1318 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2636 Ramachandran restraints generated.
    1318 Oldfield, 0 Emsley, 1318 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  168 residues out of total 1175 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 36
    poor density    : 132
  time to evaluate  : 0.249 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   54 PHE cc_start: 0.7202 (OUTLIER) cc_final: 0.6789 (t80)
REVERT: A   82 TRP cc_start: 0.6849 (t60) cc_final: 0.6540 (t60)
REVERT: A  117 MET cc_start: 0.5761 (mmp) cc_final: 0.5329 (mmp)
REVERT: A  354 ASN cc_start: 0.8385 (OUTLIER) cc_final: 0.8151 (t0)
REVERT: A  370 LEU cc_start: 0.8665 (OUTLIER) cc_final: 0.8322 (tt)
REVERT: A  479 LEU cc_start: 0.7532 (OUTLIER) cc_final: 0.7228 (tt)
REVERT: A  662 HIS cc_start: 0.6949 (OUTLIER) cc_final: 0.6462 (m90)
REVERT: A  695 MET cc_start: 0.8155 (mmm) cc_final: 0.7468 (mmm)
REVERT: A  738 LYS cc_start: 0.8716 (pttm) cc_final: 0.8173 (tptp)
REVERT: A  764 LYS cc_start: 0.7884 (mmmt) cc_final: 0.7592 (mttt)
REVERT: A  789 TYR cc_start: 0.8426 (m-80) cc_final: 0.7117 (m-80)
REVERT: A  829 ILE cc_start: 0.7376 (OUTLIER) cc_final: 0.7163 (pt)
REVERT: A  959 LEU cc_start: 0.8356 (tp) cc_final: 0.7600 (pt)
REVERT: A 1053 HIS cc_start: 0.8383 (OUTLIER) cc_final: 0.8122 (t-90)
REVERT: A 1105 ILE cc_start: 0.8542 (tt) cc_final: 0.8221 (mm)
REVERT: A 1127 PHE cc_start: 0.7048 (OUTLIER) cc_final: 0.5812 (m-10)
REVERT: A 1220 SER cc_start: 0.8051 (t) cc_final: 0.7774 (p)
REVERT: A 1309 LEU cc_start: 0.8766 (OUTLIER) cc_final: 0.8196 (tt)
REVERT: A 1448 LYS cc_start: 0.7969 (tppt) cc_final: 0.7595 (tppt)
  outliers start: 36
  outliers final: 24
  residues processed: 158
  average time/residue: 0.0752
  time to fit residues: 18.2356
Evaluate side-chains
  166 residues out of total 1175 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 33
    poor density    : 133
  time to evaluate  : 0.320 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   47 TRP
Chi-restraints excluded: chain A residue   52 PHE
Chi-restraints excluded: chain A residue   54 PHE
Chi-restraints excluded: chain A residue   80 LEU
Chi-restraints excluded: chain A residue  124 ILE
Chi-restraints excluded: chain A residue  219 ILE
Chi-restraints excluded: chain A residue  225 THR
Chi-restraints excluded: chain A residue  258 VAL
Chi-restraints excluded: chain A residue  354 ASN
Chi-restraints excluded: chain A residue  370 LEU
Chi-restraints excluded: chain A residue  378 THR
Chi-restraints excluded: chain A residue  399 VAL
Chi-restraints excluded: chain A residue  411 THR
Chi-restraints excluded: chain A residue  466 VAL
Chi-restraints excluded: chain A residue  479 LEU
Chi-restraints excluded: chain A residue  536 LEU
Chi-restraints excluded: chain A residue  550 THR
Chi-restraints excluded: chain A residue  571 VAL
Chi-restraints excluded: chain A residue  618 VAL
Chi-restraints excluded: chain A residue  626 ASP
Chi-restraints excluded: chain A residue  662 HIS
Chi-restraints excluded: chain A residue  682 CYS
Chi-restraints excluded: chain A residue  702 VAL
Chi-restraints excluded: chain A residue  829 ILE
Chi-restraints excluded: chain A residue  835 MET
Chi-restraints excluded: chain A residue 1032 TYR
Chi-restraints excluded: chain A residue 1053 HIS
Chi-restraints excluded: chain A residue 1127 PHE
Chi-restraints excluded: chain A residue 1159 LEU
Chi-restraints excluded: chain A residue 1309 LEU
Chi-restraints excluded: chain A residue 1339 LEU
Chi-restraints excluded: chain A residue 1418 LEU
Chi-restraints excluded: chain A residue 1431 VAL
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 133
   random chunks:
   chunk 79 optimal weight:    0.0370
   chunk 106 optimal weight:    0.9990
   chunk 78 optimal weight:    0.9990
   chunk 120 optimal weight:    2.9990
   chunk 3 optimal weight:    0.6980
   chunk 98 optimal weight:    2.9990
   chunk 0 optimal weight:    7.9990
   chunk 71 optimal weight:    2.9990
   chunk 91 optimal weight:    0.8980
   chunk 75 optimal weight:    2.9990
   chunk 45 optimal weight:    0.8980
   overall best weight:    0.7060

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

Flipped N/Q/H residues before XYZ refinement:
** A1420 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3937 r_free = 0.3937 target = 0.146830 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 59)----------------|
| r_work = 0.3397 r_free = 0.3397 target = 0.102521 restraints weight = 17110.802|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 44)----------------|
| r_work = 0.3443 r_free = 0.3443 target = 0.105762 restraints weight = 9395.342|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 47)----------------|
| r_work = 0.3473 r_free = 0.3473 target = 0.107959 restraints weight = 6336.290|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 37)----------------|
| r_work = 0.3491 r_free = 0.3491 target = 0.109302 restraints weight = 4914.910|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 32)----------------|
| r_work = 0.3501 r_free = 0.3501 target = 0.110099 restraints weight = 4206.851|
|-----------------------------------------------------------------------------|
r_work (final): 0.3485
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7444
moved from start:          0.4656

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.042  10906  Z= 0.135
  Angle     :  0.612  14.086  14816  Z= 0.297
  Chirality :  0.040   0.173   1726
  Planarity :  0.004   0.042   1827
  Dihedral  :  8.149  73.213   1496
  Min Nonbonded Distance : 2.486

Molprobity Statistics.
  All-atom Clashscore : 8.41
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.35 %
    Favored  : 97.65 %
  Rotamer:
    Outliers :  3.06 %
    Allowed  : 26.04 %
    Favored  : 70.89 %
  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:  1.38 (0.24), residues: 1318
  helix:  1.78 (0.18), residues: 881
  sheet: -0.28 (0.59), residues: 84
  loop : -0.95 (0.32), residues: 353

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG A1165 
 TYR   0.018   0.001   TYR A  64 
 PHE   0.064   0.002   PHE A 558 
 TRP   0.026   0.001   TRP A1286 
 HIS   0.004   0.001   HIS A 985 

Details of bonding type rmsd
  covalent geometry    : bond        0.00306 (10906)
  covalent geometry    : angle       0.61177 (14816)
  hydrogen bonds       : bond        0.04344 (  689)
  hydrogen bonds       : angle       4.00648 ( 2031)

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

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

  2636 Ramachandran restraints generated.
    1318 Oldfield, 0 Emsley, 1318 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2636 Ramachandran restraints generated.
    1318 Oldfield, 0 Emsley, 1318 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  170 residues out of total 1175 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 36
    poor density    : 134
  time to evaluate  : 0.381 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   35 ASN cc_start: 0.7789 (m-40) cc_final: 0.7156 (p0)
REVERT: A   54 PHE cc_start: 0.7150 (OUTLIER) cc_final: 0.6748 (t80)
REVERT: A   82 TRP cc_start: 0.7066 (t60) cc_final: 0.6684 (t60)
REVERT: A  117 MET cc_start: 0.5777 (mmp) cc_final: 0.5275 (mmp)
REVERT: A  354 ASN cc_start: 0.8391 (OUTLIER) cc_final: 0.8150 (t0)
REVERT: A  370 LEU cc_start: 0.8628 (OUTLIER) cc_final: 0.8286 (tt)
REVERT: A  479 LEU cc_start: 0.7497 (OUTLIER) cc_final: 0.7178 (tt)
REVERT: A  662 HIS cc_start: 0.7060 (OUTLIER) cc_final: 0.6546 (m90)
REVERT: A  695 MET cc_start: 0.8133 (mmm) cc_final: 0.7436 (mmm)
REVERT: A  738 LYS cc_start: 0.8644 (pttm) cc_final: 0.8061 (tptp)
REVERT: A  764 LYS cc_start: 0.7856 (mmmt) cc_final: 0.7594 (mttt)
REVERT: A  829 ILE cc_start: 0.7308 (OUTLIER) cc_final: 0.7098 (pt)
REVERT: A  959 LEU cc_start: 0.8299 (tp) cc_final: 0.7583 (pt)
REVERT: A 1053 HIS cc_start: 0.8405 (OUTLIER) cc_final: 0.8166 (t-90)
REVERT: A 1085 MET cc_start: 0.7116 (mmm) cc_final: 0.6499 (mmm)
REVERT: A 1105 ILE cc_start: 0.8514 (tt) cc_final: 0.8195 (mm)
REVERT: A 1127 PHE cc_start: 0.7085 (OUTLIER) cc_final: 0.5851 (m-10)
REVERT: A 1220 SER cc_start: 0.8131 (t) cc_final: 0.7867 (p)
REVERT: A 1309 LEU cc_start: 0.8837 (OUTLIER) cc_final: 0.8198 (tt)
REVERT: A 1385 MET cc_start: 0.8151 (ppp) cc_final: 0.7789 (ppp)
REVERT: A 1448 LYS cc_start: 0.7884 (tppt) cc_final: 0.7439 (tppt)
  outliers start: 36
  outliers final: 25
  residues processed: 160
  average time/residue: 0.0658
  time to fit residues: 16.3281
Evaluate side-chains
  165 residues out of total 1175 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 34
    poor density    : 131
  time to evaluate  : 0.403 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   47 TRP
Chi-restraints excluded: chain A residue   54 PHE
Chi-restraints excluded: chain A residue   80 LEU
Chi-restraints excluded: chain A residue  124 ILE
Chi-restraints excluded: chain A residue  219 ILE
Chi-restraints excluded: chain A residue  225 THR
Chi-restraints excluded: chain A residue  258 VAL
Chi-restraints excluded: chain A residue  354 ASN
Chi-restraints excluded: chain A residue  370 LEU
Chi-restraints excluded: chain A residue  378 THR
Chi-restraints excluded: chain A residue  399 VAL
Chi-restraints excluded: chain A residue  411 THR
Chi-restraints excluded: chain A residue  466 VAL
Chi-restraints excluded: chain A residue  479 LEU
Chi-restraints excluded: chain A residue  536 LEU
Chi-restraints excluded: chain A residue  550 THR
Chi-restraints excluded: chain A residue  571 VAL
Chi-restraints excluded: chain A residue  618 VAL
Chi-restraints excluded: chain A residue  626 ASP
Chi-restraints excluded: chain A residue  662 HIS
Chi-restraints excluded: chain A residue  677 VAL
Chi-restraints excluded: chain A residue  682 CYS
Chi-restraints excluded: chain A residue  702 VAL
Chi-restraints excluded: chain A residue  829 ILE
Chi-restraints excluded: chain A residue  835 MET
Chi-restraints excluded: chain A residue 1032 TYR
Chi-restraints excluded: chain A residue 1053 HIS
Chi-restraints excluded: chain A residue 1127 PHE
Chi-restraints excluded: chain A residue 1158 LEU
Chi-restraints excluded: chain A residue 1224 LEU
Chi-restraints excluded: chain A residue 1309 LEU
Chi-restraints excluded: chain A residue 1339 LEU
Chi-restraints excluded: chain A residue 1418 LEU
Chi-restraints excluded: chain A residue 1431 VAL
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 133
   random chunks:
   chunk 39 optimal weight:    1.9990
   chunk 86 optimal weight:    0.6980
   chunk 88 optimal weight:    2.9990
   chunk 25 optimal weight:    0.9990
   chunk 69 optimal weight:    4.9990
   chunk 27 optimal weight:    0.5980
   chunk 15 optimal weight:    4.9990
   chunk 77 optimal weight:    0.9990
   chunk 1 optimal weight:    0.2980
   chunk 63 optimal weight:    1.9990
   chunk 33 optimal weight:    0.5980
   overall best weight:    0.6382

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

Flipped N/Q/H residues before XYZ refinement:
** A1420 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3945 r_free = 0.3945 target = 0.147504 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 32)----------------|
| r_work = 0.3484 r_free = 0.3484 target = 0.107759 restraints weight = 17292.082|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 32)----------------|
| r_work = 0.3493 r_free = 0.3493 target = 0.109698 restraints weight = 10927.701|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 29)----------------|
| r_work = 0.3499 r_free = 0.3499 target = 0.110239 restraints weight = 7865.277|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 23)----------------|
| r_work = 0.3507 r_free = 0.3507 target = 0.110848 restraints weight = 6387.592|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 26)----------------|
| r_work = 0.3511 r_free = 0.3511 target = 0.111153 restraints weight = 5848.773|
|-----------------------------------------------------------------------------|
r_work (final): 0.3499
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7417
moved from start:          0.4745

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.050  10906  Z= 0.130
  Angle     :  0.607  13.745  14816  Z= 0.292
  Chirality :  0.040   0.181   1726
  Planarity :  0.004   0.042   1827
  Dihedral  :  7.967  70.599   1496
  Min Nonbonded Distance : 2.468

Molprobity Statistics.
  All-atom Clashscore : 8.36
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.28 %
    Favored  : 97.72 %
  Rotamer:
    Outliers :  2.98 %
    Allowed  : 26.64 %
    Favored  : 70.38 %
  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:  1.47 (0.24), residues: 1318
  helix:  1.83 (0.18), residues: 879
  sheet: -0.12 (0.60), residues: 81
  loop : -0.90 (0.32), residues: 358

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG A1165 
 TYR   0.016   0.001   TYR A  64 
 PHE   0.055   0.002   PHE A 558 
 TRP   0.021   0.001   TRP A1286 
 HIS   0.004   0.001   HIS A 985 

Details of bonding type rmsd
  covalent geometry    : bond        0.00293 (10906)
  covalent geometry    : angle       0.60656 (14816)
  hydrogen bonds       : bond        0.04271 (  689)
  hydrogen bonds       : angle       3.96924 ( 2031)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 1594.53 seconds
wall clock time: 28 minutes 19.33 seconds (1699.33 seconds total)