Starting phenix.real_space_refine
on Wed Jan 14 01:36:21 2026 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/8fac_28950/01_2026/8fac_28950.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/8fac_28950/01_2026/8fac_28950.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=3.92
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/cci-nas-00/data/ceres_data/8fac_28950/01_2026/8fac_28950.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/8fac_28950/01_2026/8fac_28950.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/8fac_28950/01_2026/8fac_28950.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/8fac_28950/01_2026/8fac_28950.cif"
  }
  resolution = 3.92
  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=  -0.003 sd=   0.957
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      75      5.16       5
     C    6997      2.51       5
     N    1870      2.21       5
     O    2011      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 19 residue(s): 0.01s

  Monomer Library directory:
    "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5927/lib/python3.9/site-packages/chem_data/mon_lib"
  Total number of atoms: 10955
  Number of models: 1
  Model: ""
    Number of chains: 2
    Chain: "A"
      Number of atoms: 10927
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 1377, 10927
          Classifications: {'peptide': 1377}
          Link IDs: {'PCIS': 2, 'PTRANS': 69, 'TRANS': 1305}
          Chain breaks: 17
    Chain: "A"
      Number of atoms: 28
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 1, 28
          Unusual residues: {'GDP': 1}
          Classifications: {'undetermined': 1}
  Time building chain proxies: 2.78, per 1000 atoms: 0.25
  Number of scatterers: 10955
  At special positions: 0
  Unit cell: (87.48, 107.73, 158.76, 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      75     16.00
     P       2     15.00
     O    2011      8.00
     N    1870      7.00
     C    6997      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: 0.71
  Conformation dependent library (CDL) restraints added in 521.8 milliseconds
  

  2682 Ramachandran restraints generated.
    1341 Oldfield, 0 Emsley, 1341 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  2616

  Finding SS restraints...
    Secondary structure from input PDB file:
      46 helices and 19 sheets defined
      31.2% alpha, 15.3% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 0.56
  Creating SS restraints...
    Processing helix  chain 'A' and resid 345 through 349
    Processing helix  chain 'A' and resid 396 through 402
      removed outlier: 3.786A  pdb=" N   LEU A 400 " --> pdb=" O   PRO A 396 " (cutoff:3.500A)
      removed outlier: 3.822A  pdb=" N   SER A 402 " --> pdb=" O   LEU A 398 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 443 through 448
      removed outlier: 4.427A  pdb=" N   PHE A 447 " --> pdb=" O   LYS A 443 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 466 through 472
      removed outlier: 4.223A  pdb=" N   LEU A 472 " --> pdb=" O   LEU A 469 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 490 through 494
      removed outlier: 3.659A  pdb=" N   LYS A 493 " --> pdb=" O   PRO A 490 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 543 through 547
      removed outlier: 3.975A  pdb=" N   LEU A 546 " --> pdb=" O   PRO A 543 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 564 through 570
      removed outlier: 3.648A  pdb=" N   LEU A 570 " --> pdb=" O   VAL A 567 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 588 through 594
      removed outlier: 3.832A  pdb=" N   LEU A 594 " --> pdb=" O   LEU A 591 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 623 through 628
    Processing helix  chain 'A' and resid 652 through 660
      removed outlier: 4.118A  pdb=" N   GLU A 656 " --> pdb=" O   SER A 652 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 709 through 713
    Processing helix  chain 'A' and resid 727 through 729
      No H-bonds generated for 'chain 'A' and resid 727 through 729'
    Processing helix  chain 'A' and resid 730 through 747
      removed outlier: 4.426A  pdb=" N   PHE A 738 " --> pdb=" O   ALA A 734 " (cutoff:3.500A)
      removed outlier: 4.331A  pdb=" N   TRP A 739 " --> pdb=" O   ASN A 735 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 766 through 783
      removed outlier: 3.504A  pdb=" N   ALA A 772 " --> pdb=" O   VAL A 768 " (cutoff:3.500A)
      removed outlier: 3.587A  pdb=" N   CYS A 782 " --> pdb=" O   VAL A 778 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 797 through 799
      No H-bonds generated for 'chain 'A' and resid 797 through 799'
    Processing helix  chain 'A' and resid 811 through 823
      removed outlier: 3.517A  pdb=" N   LEU A 815 " --> pdb=" O   GLY A 811 " (cutoff:3.500A)
      removed outlier: 3.557A  pdb=" N   ARG A 816 " --> pdb=" O   GLN A 812 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 844 through 865
      removed outlier: 3.706A  pdb=" N   GLU A 852 " --> pdb=" O   LEU A 848 " (cutoff:3.500A)
      removed outlier: 3.988A  pdb=" N   ALA A 853 " --> pdb=" O   SER A 849 " (cutoff:3.500A)
      removed outlier: 3.603A  pdb=" N   ARG A 863 " --> pdb=" O   GLN A 859 " (cutoff:3.500A)
      removed outlier: 4.027A  pdb=" N   ASP A 864 " --> pdb=" O   ARG A 860 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 871 through 882
      removed outlier: 3.954A  pdb=" N   GLN A 877 " --> pdb=" O   ARG A 873 " (cutoff:3.500A)
      removed outlier: 3.610A  pdb=" N   LEU A 878 " --> pdb=" O   GLN A 874 " (cutoff:3.500A)
      removed outlier: 3.537A  pdb=" N   THR A 882 " --> pdb=" O   LEU A 878 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 889 through 902
      removed outlier: 4.067A  pdb=" N   GLU A 902 " --> pdb=" O   SER A 898 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 923 through 935
    Processing helix  chain 'A' and resid 941 through 945
      removed outlier: 4.278A  pdb=" N   ALA A 944 " --> pdb=" O   ARG A 941 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 967 through 972
    Processing helix  chain 'A' and resid 973 through 978
    Processing helix  chain 'A' and resid 992 through 995
    Processing helix  chain 'A' and resid 1025 through 1046
      removed outlier: 4.654A  pdb=" N   GLN A1029 " --> pdb=" O   VAL A1025 " (cutoff:3.500A)
      removed outlier: 3.640A  pdb=" N   ARG A1030 " --> pdb=" O   GLY A1026 " (cutoff:3.500A)
      removed outlier: 3.703A  pdb=" N   ALA A1033 " --> pdb=" O   GLN A1029 " (cutoff:3.500A)
      removed outlier: 3.753A  pdb=" N   ARG A1034 " --> pdb=" O   ARG A1030 " (cutoff:3.500A)
      removed outlier: 3.555A  pdb=" N   MET A1042 " --> pdb=" O   SER A1038 " (cutoff:3.500A)
      removed outlier: 3.870A  pdb=" N   ASP A1043 " --> pdb=" O   LEU A1039 " (cutoff:3.500A)
      removed outlier: 4.040A  pdb=" N   LEU A1046 " --> pdb=" O   MET A1042 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 1133 through 1145
      removed outlier: 4.058A  pdb=" N   ASP A1142 " --> pdb=" O   ASN A1138 " (cutoff:3.500A)
      removed outlier: 5.087A  pdb=" N   GLN A1143 " --> pdb=" O   SER A1139 " (cutoff:3.500A)
      removed outlier: 3.882A  pdb=" N   TRP A1144 " --> pdb=" O   LEU A1140 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 1165 through 1170
      removed outlier: 3.617A  pdb=" N   THR A1170 " --> pdb=" O   PRO A1166 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 1190 through 1197
      removed outlier: 4.145A  pdb=" N   LEU A1195 " --> pdb=" O   GLU A1191 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 1214 through 1219
    Processing helix  chain 'A' and resid 1220 through 1224
    Processing helix  chain 'A' and resid 1243 through 1247
    Processing helix  chain 'A' and resid 1289 through 1313
      removed outlier: 3.554A  pdb=" N   ASN A1300 " --> pdb=" O   ASP A1296 " (cutoff:3.500A)
      removed outlier: 3.900A  pdb=" N   GLN A1306 " --> pdb=" O   SER A1302 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 1341 through 1350
      removed outlier: 4.243A  pdb=" N   GLU A1348 " --> pdb=" O   THR A1344 " (cutoff:3.500A)
      removed outlier: 4.072A  pdb=" N   ASN A1349 " --> pdb=" O   VAL A1345 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 1359 through 1380
      removed outlier: 4.177A  pdb=" N   GLN A1364 " --> pdb=" O   HIS A1360 " (cutoff:3.500A)
      removed outlier: 3.705A  pdb=" N   ALA A1371 " --> pdb=" O   ALA A1367 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 1388 through 1392
    Processing helix  chain 'A' and resid 1444 through 1459
      removed outlier: 3.539A  pdb=" N   GLY A1451 " --> pdb=" O   MET A1447 " (cutoff:3.500A)
      removed outlier: 3.958A  pdb=" N   MET A1452 " --> pdb=" O   PHE A1448 " (cutoff:3.500A)
      removed outlier: 3.602A  pdb=" N   GLU A1456 " --> pdb=" O   MET A1452 " (cutoff:3.500A)
      removed outlier: 3.719A  pdb=" N   LEU A1457 " --> pdb=" O   VAL A1453 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 1486 through 1491
      removed outlier: 3.599A  pdb=" N   VAL A1490 " --> pdb=" O   GLN A1486 " (cutoff:3.500A)
      removed outlier: 3.820A  pdb=" N   GLN A1491 " --> pdb=" O   PRO A1487 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'A' and resid 1486 through 1491'
    Processing helix  chain 'A' and resid 1492 through 1501
      removed outlier: 3.671A  pdb=" N   GLN A1496 " --> pdb=" O   PHE A1492 " (cutoff:3.500A)
      removed outlier: 4.384A  pdb=" N   LEU A1498 " --> pdb=" O   ARG A1494 " (cutoff:3.500A)
      removed outlier: 3.692A  pdb=" N   MET A1499 " --> pdb=" O   LEU A1495 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 1512 through 1520
    Processing helix  chain 'A' and resid 1523 through 1527
    Processing helix  chain 'A' and resid 1556 through 1559
    Processing helix  chain 'A' and resid 1670 through 1678
    Processing helix  chain 'A' and resid 1685 through 1689
    Processing helix  chain 'A' and resid 1699 through 1702
    Processing helix  chain 'A' and resid 1950 through 1957
      removed outlier: 4.070A  pdb=" N   THR A1954 " --> pdb=" O   ARG A1951 " (cutoff:3.500A)
      Proline residue:  A1955  - end of helix
    Processing helix  chain 'A' and resid 1990 through 2010
      removed outlier: 3.561A  pdb=" N   LEU A2004 " --> pdb=" O   SER A2000 " (cutoff:3.500A)
      removed outlier: 3.562A  pdb=" N   GLY A2005 " --> pdb=" O   TYR A2001 " (cutoff:3.500A)
    Processing sheet with id=AA1, first strand: chain 'A' and resid 356 through 358
      removed outlier: 3.548A  pdb=" N   ASP A 386 " --> pdb=" O   LEU A 357 " (cutoff:3.500A)
      removed outlier: 7.454A  pdb=" N   LEU A 385 " --> pdb=" O   ASN A 410 " (cutoff:3.500A)
    Processing sheet with id=AA2, first strand: chain 'A' and resid 675 through 681
      removed outlier: 3.696A  pdb=" N   THR A 676 " --> pdb=" O   VAL A 697 " (cutoff:3.500A)
      removed outlier: 7.338A  pdb=" N   MET A 639 " --> pdb=" O   ASN A 696 " (cutoff:3.500A)
      removed outlier: 8.003A  pdb=" N   TRP A 698 " --> pdb=" O   MET A 639 " (cutoff:3.500A)
      removed outlier: 6.637A  pdb=" N   MET A 641 " --> pdb=" O   TRP A 698 " (cutoff:3.500A)
      removed outlier: 9.220A  pdb=" N   LEU A 719 " --> pdb=" O   LEU A 638 " (cutoff:3.500A)
      removed outlier: 7.048A  pdb=" N   LYS A 640 " --> pdb=" O   LEU A 719 " (cutoff:3.500A)
      removed outlier: 7.960A  pdb=" N   VAL A 721 " --> pdb=" O   LYS A 640 " (cutoff:3.500A)
      removed outlier: 6.248A  pdb=" N   ILE A 642 " --> pdb=" O   VAL A 721 " (cutoff:3.500A)
      removed outlier: 7.245A  pdb=" N   VAL A 723 " --> pdb=" O   ILE A 642 " (cutoff:3.500A)
      removed outlier: 6.316A  pdb=" N   VAL A 644 " --> pdb=" O   VAL A 723 " (cutoff:3.500A)
      removed outlier: 8.527A  pdb=" N   ASN A 725 " --> pdb=" O   VAL A 644 " (cutoff:3.500A)
      removed outlier: 6.602A  pdb=" N   TYR A 720 " --> pdb=" O   LEU A 753 " (cutoff:3.500A)
      removed outlier: 7.830A  pdb=" N   VAL A 755 " --> pdb=" O   TYR A 720 " (cutoff:3.500A)
      removed outlier: 6.283A  pdb=" N   VAL A 722 " --> pdb=" O   VAL A 755 " (cutoff:3.500A)
      removed outlier: 7.059A  pdb=" N   THR A 757 " --> pdb=" O   VAL A 722 " (cutoff:3.500A)
      removed outlier: 6.197A  pdb=" N   TRP A 724 " --> pdb=" O   THR A 757 " (cutoff:3.500A)
    Processing sheet with id=AA3, first strand: chain 'A' and resid 869 through 870
    Processing sheet with id=AA4, first strand: chain 'A' and resid 948 through 950
      removed outlier: 3.518A  pdb=" N   SER A 988 " --> pdb=" O   VAL A 984 " (cutoff:3.500A)
    Processing sheet with id=AA5, first strand: chain 'A' and resid 1118 through 1120
      removed outlier: 3.947A  pdb=" N   ILE A1014 " --> pdb=" O   CYS A1120 " (cutoff:3.500A)
      removed outlier: 5.979A  pdb=" N   GLN A1015 " --> pdb=" O   PRO A1164 " (cutoff:3.500A)
    Processing sheet with id=AA6, first strand: chain 'A' and resid 1084 through 1085
    Processing sheet with id=AA7, first strand: chain 'A' and resid 1103 through 1105
      removed outlier: 3.768A  pdb=" N   SER A1104 " --> pdb=" O   GLY A1115 " (cutoff:3.500A)
    Processing sheet with id=AA8, first strand: chain 'A' and resid 1239 through 1240
      removed outlier: 3.648A  pdb=" N   ALA A1268 " --> pdb=" O   LEU A1334 " (cutoff:3.500A)
      removed outlier: 3.594A  pdb=" N   PHE A1332 " --> pdb=" O   LYS A1270 " (cutoff:3.500A)
      removed outlier: 4.101A  pdb=" N   GLY A1324 " --> pdb=" O   ALA A1333 " (cutoff:3.500A)
    Processing sheet with id=AA9, first strand: chain 'A' and resid 1393 through 1394
    Processing sheet with id=AB1, first strand: chain 'A' and resid 1528 through 1536
      removed outlier: 6.512A  pdb=" N   PHE A1528 " --> pdb=" O   ARG A1987 " (cutoff:3.500A)
      removed outlier: 5.814A  pdb=" N   ARG A1987 " --> pdb=" O   PHE A1528 " (cutoff:3.500A)
      removed outlier: 3.947A  pdb=" N   TYR A1530 " --> pdb=" O   VAL A1985 " (cutoff:3.500A)
      removed outlier: 6.073A  pdb=" N   TRP A1981 " --> pdb=" O   CYS A1534 " (cutoff:3.500A)
    Processing sheet with id=AB2, first strand: chain 'A' and resid 1528 through 1536
      removed outlier: 6.512A  pdb=" N   PHE A1528 " --> pdb=" O   ARG A1987 " (cutoff:3.500A)
      removed outlier: 5.814A  pdb=" N   ARG A1987 " --> pdb=" O   PHE A1528 " (cutoff:3.500A)
      removed outlier: 3.947A  pdb=" N   TYR A1530 " --> pdb=" O   VAL A1985 " (cutoff:3.500A)
      removed outlier: 6.073A  pdb=" N   TRP A1981 " --> pdb=" O   CYS A1534 " (cutoff:3.500A)
      removed outlier: 6.511A  pdb=" N   VAL A1971 " --> pdb=" O   VAL A1964 " (cutoff:3.500A)
      removed outlier: 5.143A  pdb=" N   VAL A1964 " --> pdb=" O   VAL A1971 " (cutoff:3.500A)
    Processing sheet with id=AB3, first strand: chain 'A' and resid 1553 through 1554
      removed outlier: 6.447A  pdb=" N   TYR A1562 " --> pdb=" O   ARG A1576 " (cutoff:3.500A)
      removed outlier: 3.872A  pdb=" N   ARG A1576 " --> pdb=" O   TYR A1562 " (cutoff:3.500A)
      removed outlier: 4.047A  pdb=" N   VAL A1574 " --> pdb=" O   VAL A1564 " (cutoff:3.500A)
    Processing sheet with id=AB4, first strand: chain 'A' and resid 1584 through 1586
    Processing sheet with id=AB5, first strand: chain 'A' and resid 1584 through 1586
      removed outlier: 4.116A  pdb=" N   LYS A1602 " --> pdb=" O   THR A1598 " (cutoff:3.500A)
    Processing sheet with id=AB6, first strand: chain 'A' and resid 1633 through 1634
    Processing sheet with id=AB7, first strand: chain 'A' and resid 1645 through 1646
    Processing sheet with id=AB8, first strand: chain 'A' and resid 1704 through 1709
    Processing sheet with id=AB9, first strand: chain 'A' and resid 1763 through 1764
      removed outlier: 6.401A  pdb=" N   MET A1763 " --> pdb=" O   CYS A1772 " (cutoff:3.500A)
    Processing sheet with id=AC1, first strand: chain 'A' and resid 1786 through 1787
      removed outlier: 3.533A  pdb=" N   GLY A1942 " --> pdb=" O   PHE A1787 " (cutoff:3.500A)
      removed outlier: 7.572A  pdb=" N   VAL A1930 " --> pdb=" O   ILE A1945 " (cutoff:3.500A)
      removed outlier: 4.693A  pdb=" N   VAL A1947 " --> pdb=" O   VAL A1928 " (cutoff:3.500A)
      removed outlier: 6.260A  pdb=" N   VAL A1928 " --> pdb=" O   VAL A1947 " (cutoff:3.500A)
      removed outlier: 3.595A  pdb=" N   LEU A1913 " --> pdb=" O   TRP A1920 " (cutoff:3.500A)

    326 hydrogen bonds defined for protein.
    843 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: 2.28

  Time building geometry restraints manager: 1.00 seconds

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

  Histogram of bond lengths:
        1.22 -     1.34: 3557
        1.34 -     1.46: 2373
        1.46 -     1.58: 5140
        1.58 -     1.70: 3
        1.70 -     1.82: 110
  Bond restraints: 11183
  Sorted by residual:
  bond pdb=" CA  ASP A 699 "
       pdb=" CB  ASP A 699 "
    ideal  model  delta    sigma   weight residual
    1.524  1.543 -0.018 1.46e-02 4.69e+03 1.55e+00
  bond pdb=" N   GLY A1411 "
       pdb=" CA  GLY A1411 "
    ideal  model  delta    sigma   weight residual
    1.446  1.458 -0.012 1.02e-02 9.61e+03 1.38e+00
  bond pdb=" CB  VAL A1551 "
       pdb=" CG1 VAL A1551 "
    ideal  model  delta    sigma   weight residual
    1.521  1.484  0.037 3.30e-02 9.18e+02 1.27e+00
  bond pdb=" N   GLY A1114 "
       pdb=" CA  GLY A1114 "
    ideal  model  delta    sigma   weight residual
    1.444  1.456 -0.012 1.06e-02 8.90e+03 1.27e+00
  bond pdb=" CB  GLU A1244 "
       pdb=" CG  GLU A1244 "
    ideal  model  delta    sigma   weight residual
    1.520  1.552 -0.032 3.00e-02 1.11e+03 1.13e+00
  ... (remaining 11178 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     1.88: 14837
        1.88 -     3.76: 263
        3.76 -     5.64: 35
        5.64 -     7.53: 13
        7.53 -     9.41: 2
  Bond angle restraints: 15150
  Sorted by residual:
  angle pdb=" C   VAL A1550 "
        pdb=" N   VAL A1551 "
        pdb=" CA  VAL A1551 "
      ideal   model   delta    sigma   weight residual
     121.97  115.66    6.31 1.80e+00 3.09e-01 1.23e+01
  angle pdb=" C   LYS A 945 "
        pdb=" N   ASN A 946 "
        pdb=" CA  ASN A 946 "
      ideal   model   delta    sigma   weight residual
     121.54  127.61   -6.07 1.91e+00 2.74e-01 1.01e+01
  angle pdb=" CA  MET A1696 "
        pdb=" CB  MET A1696 "
        pdb=" CG  MET A1696 "
      ideal   model   delta    sigma   weight residual
     114.10  120.07   -5.97 2.00e+00 2.50e-01 8.92e+00
  angle pdb=" CA  MET A1224 "
        pdb=" CB  MET A1224 "
        pdb=" CG  MET A1224 "
      ideal   model   delta    sigma   weight residual
     114.10  119.82   -5.72 2.00e+00 2.50e-01 8.19e+00
  angle pdb=" C   ASN A1081 "
        pdb=" N   GLN A1082 "
        pdb=" CA  GLN A1082 "
      ideal   model   delta    sigma   weight residual
     121.54  126.78   -5.24 1.91e+00 2.74e-01 7.52e+00
  ... (remaining 15145 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    17.99: 6071
       17.99 -    35.97: 565
       35.97 -    53.96: 114
       53.96 -    71.94: 12
       71.94 -    89.93: 13
  Dihedral angle restraints: 6775
    sinusoidal: 2763
      harmonic: 4012
  Sorted by residual:
  dihedral pdb=" CA  GLN A1082 "
           pdb=" C   GLN A1082 "
           pdb=" N   THR A1083 "
           pdb=" CA  THR A1083 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  157.70   22.30     0      5.00e+00 4.00e-02 1.99e+01
  dihedral pdb=" CA  VAL A 697 "
           pdb=" C   VAL A 697 "
           pdb=" N   TRP A 698 "
           pdb=" CA  TRP A 698 "
      ideal   model   delta  harmonic     sigma   weight residual
    -180.00 -158.80  -21.20     0      5.00e+00 4.00e-02 1.80e+01
  dihedral pdb=" CA  GLY A1747 "
           pdb=" C   GLY A1747 "
           pdb=" N   GLU A1748 "
           pdb=" CA  GLU A1748 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  160.61   19.39     0      5.00e+00 4.00e-02 1.50e+01
  ... (remaining 6772 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.034: 1091
       0.034 -    0.067: 444
       0.067 -    0.101: 134
       0.101 -    0.134: 41
       0.134 -    0.168: 10
  Chirality restraints: 1720
  Sorted by residual:
  chirality pdb=" CA  MET A1224 "
            pdb=" N   MET A1224 "
            pdb=" C   MET A1224 "
            pdb=" CB  MET A1224 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.34    0.17 2.00e-01 2.50e+01 7.04e-01
  chirality pdb=" CB  VAL A 943 "
            pdb=" CA  VAL A 943 "
            pdb=" CG1 VAL A 943 "
            pdb=" CG2 VAL A 943 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.63   -2.46   -0.16 2.00e-01 2.50e+01 6.80e-01
  chirality pdb=" CB  VAL A1219 "
            pdb=" CA  VAL A1219 "
            pdb=" CG1 VAL A1219 "
            pdb=" CG2 VAL A1219 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.63   -2.47   -0.16 2.00e-01 2.50e+01 6.21e-01
  ... (remaining 1717 not shown)

  Planarity restraints: 1926
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  LYS A 945 "    0.007 2.00e-02 2.50e+03   1.49e-02 2.21e+00
        pdb=" C   LYS A 945 "   -0.026 2.00e-02 2.50e+03
        pdb=" O   LYS A 945 "    0.010 2.00e-02 2.50e+03
        pdb=" N   ASN A 946 "    0.009 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   VAL A1023 "    0.022 5.00e-02 4.00e+02   3.38e-02 1.83e+00
        pdb=" N   PRO A1024 "   -0.059 5.00e-02 4.00e+02
        pdb=" CA  PRO A1024 "    0.018 5.00e-02 4.00e+02
        pdb=" CD  PRO A1024 "    0.019 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   VAL A1633 "    0.021 5.00e-02 4.00e+02   3.18e-02 1.62e+00
        pdb=" N   PRO A1634 "   -0.055 5.00e-02 4.00e+02
        pdb=" CA  PRO A1634 "    0.017 5.00e-02 4.00e+02
        pdb=" CD  PRO A1634 "    0.017 5.00e-02 4.00e+02
  ... (remaining 1923 not shown)

  Histogram of nonbonded interaction distances:
        2.19 -     2.73: 609
        2.73 -     3.27: 11567
        3.27 -     3.82: 17653
        3.82 -     4.36: 21423
        4.36 -     4.90: 35193
  Nonbonded interactions: 86445
  Sorted by model distance:
  nonbonded pdb=" O   GLY A1000 "
            pdb=" OG1 THR A1003 "
     model   vdw
     2.189 3.040
  nonbonded pdb=" OG1 THR A1598 "
            pdb=" OD1 ASP A1600 "
     model   vdw
     2.225 3.040
  nonbonded pdb=" O   VAL A1658 "
            pdb=" OG1 THR A1661 "
     model   vdw
     2.237 3.040
  nonbonded pdb=" OG1 THR A1628 "
            pdb=" O   VAL A1693 "
     model   vdw
     2.242 3.040
  nonbonded pdb=" OD1 ASN A1391 "
            pdb=" OG  SER A1408 "
     model   vdw
     2.256 3.040
  ... (remaining 86440 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:             8.120
  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:          0.190
  Check model and map are aligned:         0.030
  Set scattering table:                    0.030
  Process input model:                     11.750
  Find NCS groups from input model:        0.050
  Set up NCS constraints:                  0.020
  Set refine NCS operators:                0.000
  Adjust number of macro_cycles:           0.000
  Reset NCS operators:                     0.000
  Extract rigid body selections:           0.000
  Check and reset occupancies:             0.000
  Load rotamer database and sin/cos tables:1.580
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   21.780
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7061
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      :  0.002   0.037  11183  Z= 0.117
  Angle     :  0.620   9.407  15150  Z= 0.317
  Chirality :  0.042   0.168   1720
  Planarity :  0.003   0.034   1926
  Dihedral  : 14.649  89.929   4159
  Min Nonbonded Distance : 2.189

Molprobity Statistics.
  All-atom Clashscore : 12.20
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  7.38 %
    Favored  : 92.62 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  0.16 %
    Favored  : 99.84 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.82 %
    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: -1.57 (0.23), residues: 1341
  helix: -1.09 (0.28), residues: 305
  sheet: -1.34 (0.37), residues: 222
  loop : -0.88 (0.23), residues: 814

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARG A 933 
 TYR   0.016   0.001   TYR A1641 
 PHE   0.017   0.001   PHE A1492 
 TRP   0.019   0.001   TRP A 698 
 HIS   0.003   0.001   HIS A1136 

Details of bonding type rmsd
  covalent geometry    : bond        0.00238 (11183)
  covalent geometry    : angle       0.62026 (15150)
  hydrogen bonds       : bond        0.29330 (  314)
  hydrogen bonds       : angle       9.44176 (  843)

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

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

  2682 Ramachandran restraints generated.
    1341 Oldfield, 0 Emsley, 1341 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2682 Ramachandran restraints generated.
    1341 Oldfield, 0 Emsley, 1341 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  140 residues out of total 1216 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 140
  time to evaluate  : 0.423 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A 1190 MET cc_start: 0.7677 (tpp) cc_final: 0.7389 (tpt)
REVERT: A 1288 MET cc_start: 0.8155 (ptp) cc_final: 0.7910 (tmm)
REVERT: A 1684 GLU cc_start: 0.8119 (pp20) cc_final: 0.7845 (tm-30)
REVERT: A 1716 ILE cc_start: 0.8663 (tp) cc_final: 0.8459 (tt)
REVERT: A 1731 MET cc_start: 0.6463 (ppp) cc_final: 0.6143 (ppp)
  outliers start: 0
  outliers final: 0
  residues processed: 140
  average time/residue: 0.0927
  time to fit residues: 19.2384
Evaluate side-chains
  107 residues out of total 1216 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 107
  time to evaluate  : 0.411 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 137
   random chunks:
   chunk 98 optimal weight:    0.6980
   chunk 107 optimal weight:    7.9990
   chunk 10 optimal weight:    9.9990
   chunk 66 optimal weight:    1.9990
   chunk 130 optimal weight:    0.0970
   chunk 124 optimal weight:    0.7980
   chunk 103 optimal weight:    0.8980
   chunk 77 optimal weight:    0.9980
   chunk 122 optimal weight:    1.9990
   chunk 91 optimal weight:    2.9990
   chunk 55 optimal weight:    2.9990
   overall best weight:    0.6978

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

Flipped N/Q/H residues before XYZ refinement:
A 383 GLN
A 407 ASN
** A 711 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 802 HIS

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4364 r_free = 0.4364 target = 0.163199 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 34)----------------|
| r_work = 0.3930 r_free = 0.3930 target = 0.130381 restraints weight = 24498.327|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 30)----------------|
| r_work = 0.3890 r_free = 0.3890 target = 0.128982 restraints weight = 23527.212|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 27)----------------|
| r_work = 0.3903 r_free = 0.3903 target = 0.130037 restraints weight = 24274.076|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 25)----------------|
| r_work = 0.3926 r_free = 0.3926 target = 0.131857 restraints weight = 16278.829|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 23)----------------|
| r_work = 0.3928 r_free = 0.3928 target = 0.132046 restraints weight = 14028.974|
|-----------------------------------------------------------------------------|
r_work (final): 0.3925
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7203
moved from start:          0.1223

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.037  11183  Z= 0.151
  Angle     :  0.647   8.556  15150  Z= 0.330
  Chirality :  0.044   0.161   1720
  Planarity :  0.004   0.032   1926
  Dihedral  :  4.374  25.573   1478
  Min Nonbonded Distance : 2.498

Molprobity Statistics.
  All-atom Clashscore : 10.70
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  7.53 %
    Favored  : 92.47 %
  Rotamer:
    Outliers :  1.07 %
    Allowed  :  9.79 %
    Favored  : 89.14 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.82 %
    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: -1.51 (0.23), residues: 1341
  helix: -0.74 (0.28), residues: 317
  sheet: -1.66 (0.35), residues: 221
  loop : -0.86 (0.23), residues: 803

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.000   ARG A 861 
 TYR   0.020   0.001   TYR A1707 
 PHE   0.022   0.001   PHE A1525 
 TRP   0.024   0.001   TRP A 698 
 HIS   0.006   0.001   HIS A1316 

Details of bonding type rmsd
  covalent geometry    : bond        0.00338 (11183)
  covalent geometry    : angle       0.64707 (15150)
  hydrogen bonds       : bond        0.05357 (  314)
  hydrogen bonds       : angle       6.51777 (  843)

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

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

  2682 Ramachandran restraints generated.
    1341 Oldfield, 0 Emsley, 1341 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2682 Ramachandran restraints generated.
    1341 Oldfield, 0 Emsley, 1341 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  133 residues out of total 1216 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 120
  time to evaluate  : 0.455 
Fit side-chains
   revert: symmetry clash
REVERT: A  802 HIS cc_start: 0.6952 (OUTLIER) cc_final: 0.6179 (m90)
REVERT: A 1130 MET cc_start: 0.8201 (mmp) cc_final: 0.7521 (mmt)
REVERT: A 1288 MET cc_start: 0.8366 (ptp) cc_final: 0.7753 (tmm)
REVERT: A 1520 MET cc_start: 0.7856 (mmt) cc_final: 0.7611 (mmt)
  outliers start: 13
  outliers final: 11
  residues processed: 125
  average time/residue: 0.0886
  time to fit residues: 17.0229
Evaluate side-chains
  118 residues out of total 1216 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 106
  time to evaluate  : 0.432 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  576 LEU
Chi-restraints excluded: chain A residue  578 LEU
Chi-restraints excluded: chain A residue  673 ILE
Chi-restraints excluded: chain A residue  741 LEU
Chi-restraints excluded: chain A residue  754 VAL
Chi-restraints excluded: chain A residue  802 HIS
Chi-restraints excluded: chain A residue  963 PHE
Chi-restraints excluded: chain A residue 1023 VAL
Chi-restraints excluded: chain A residue 1668 TYR
Chi-restraints excluded: chain A residue 1740 VAL
Chi-restraints excluded: chain A residue 1741 CYS
Chi-restraints excluded: chain A residue 1944 VAL
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 137
   random chunks:
   chunk 83 optimal weight:    0.5980
   chunk 127 optimal weight:    1.9990
   chunk 63 optimal weight:    0.9980
   chunk 92 optimal weight:    0.9990
   chunk 84 optimal weight:    1.9990
   chunk 15 optimal weight:   20.0000
   chunk 8 optimal weight:    0.8980
   chunk 56 optimal weight:    1.9990
   chunk 112 optimal weight:    3.9990
   chunk 104 optimal weight:    4.9990
   chunk 70 optimal weight:    0.0170
   overall best weight:    0.7020

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

Flipped N/Q/H residues before XYZ refinement:
** A 711 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 802 HIS
A 851 GLN
A1566 ASN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4357 r_free = 0.4357 target = 0.162492 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.3920 r_free = 0.3920 target = 0.129627 restraints weight = 24566.645|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 28)----------------|
| r_work = 0.3867 r_free = 0.3867 target = 0.127586 restraints weight = 24775.304|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 27)----------------|
| r_work = 0.3885 r_free = 0.3885 target = 0.128914 restraints weight = 25035.479|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 25)----------------|
| r_work = 0.3900 r_free = 0.3900 target = 0.130185 restraints weight = 16376.908|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 23)----------------|
| r_work = 0.3905 r_free = 0.3905 target = 0.130519 restraints weight = 14839.073|
|-----------------------------------------------------------------------------|
r_work (final): 0.3904
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7242
moved from start:          0.1521

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.032  11183  Z= 0.140
  Angle     :  0.607   8.429  15150  Z= 0.308
  Chirality :  0.044   0.171   1720
  Planarity :  0.004   0.039   1926
  Dihedral  :  4.363  25.967   1478
  Min Nonbonded Distance : 2.498

Molprobity Statistics.
  All-atom Clashscore : 10.97
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  7.01 %
    Favored  : 92.99 %
  Rotamer:
    Outliers :  1.56 %
    Allowed  : 12.99 %
    Favored  : 85.44 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.82 %
    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: -1.52 (0.24), residues: 1341
  helix: -0.70 (0.29), residues: 327
  sheet: -1.94 (0.35), residues: 220
  loop : -0.80 (0.23), residues: 794

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARG A 861 
 TYR   0.015   0.001   TYR A1707 
 PHE   0.021   0.001   PHE A 738 
 TRP   0.017   0.001   TRP A 698 
 HIS   0.008   0.001   HIS A 802 

Details of bonding type rmsd
  covalent geometry    : bond        0.00317 (11183)
  covalent geometry    : angle       0.60743 (15150)
  hydrogen bonds       : bond        0.04795 (  314)
  hydrogen bonds       : angle       6.03584 (  843)

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

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

  2682 Ramachandran restraints generated.
    1341 Oldfield, 0 Emsley, 1341 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2682 Ramachandran restraints generated.
    1341 Oldfield, 0 Emsley, 1341 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  136 residues out of total 1216 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 19
    poor density    : 117
  time to evaluate  : 0.385 
Fit side-chains
   revert: symmetry clash
REVERT: A  802 HIS cc_start: 0.7093 (OUTLIER) cc_final: 0.6060 (m90)
REVERT: A  923 ASP cc_start: 0.7730 (t0) cc_final: 0.7515 (t0)
REVERT: A 1116 MET cc_start: 0.8016 (mmm) cc_final: 0.7741 (mmm)
REVERT: A 1130 MET cc_start: 0.8178 (mmp) cc_final: 0.7867 (mmt)
REVERT: A 1190 MET cc_start: 0.7598 (tpp) cc_final: 0.7385 (tpt)
REVERT: A 1288 MET cc_start: 0.8200 (ptp) cc_final: 0.7790 (tmm)
REVERT: A 1529 MET cc_start: 0.8187 (mtp) cc_final: 0.7974 (mtp)
REVERT: A 1716 ILE cc_start: 0.8547 (tp) cc_final: 0.8315 (tt)
REVERT: A 1763 MET cc_start: 0.7074 (tpt) cc_final: 0.6808 (tpt)
  outliers start: 19
  outliers final: 12
  residues processed: 127
  average time/residue: 0.0892
  time to fit residues: 17.4089
Evaluate side-chains
  114 residues out of total 1216 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 101
  time to evaluate  : 0.443 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  576 LEU
Chi-restraints excluded: chain A residue  578 LEU
Chi-restraints excluded: chain A residue  673 ILE
Chi-restraints excluded: chain A residue  721 VAL
Chi-restraints excluded: chain A residue  754 VAL
Chi-restraints excluded: chain A residue  802 HIS
Chi-restraints excluded: chain A residue  963 PHE
Chi-restraints excluded: chain A residue 1023 VAL
Chi-restraints excluded: chain A residue 1668 TYR
Chi-restraints excluded: chain A residue 1696 MET
Chi-restraints excluded: chain A residue 1740 VAL
Chi-restraints excluded: chain A residue 1741 CYS
Chi-restraints excluded: chain A residue 1944 VAL
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 137
   random chunks:
   chunk 37 optimal weight:    1.9990
   chunk 59 optimal weight:    1.9990
   chunk 69 optimal weight:    0.9980
   chunk 131 optimal weight:    1.9990
   chunk 11 optimal weight:    0.0060
   chunk 0 optimal weight:   40.0000
   chunk 2 optimal weight:   10.0000
   chunk 13 optimal weight:    0.9990
   chunk 81 optimal weight:    0.9990
   chunk 5 optimal weight:   40.0000
   chunk 7 optimal weight:    8.9990
   overall best weight:    1.0002

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

Flipped N/Q/H residues before XYZ refinement:
** A 711 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 802 HIS
A 993 HIS
A1208 HIS
** A1496 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
A1566 ASN
A1709 ASN

Total number of N/Q/H flips: 5

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4332 r_free = 0.4332 target = 0.160657 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 32)----------------|
| r_work = 0.3886 r_free = 0.3886 target = 0.127160 restraints weight = 24493.717|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 28)----------------|
| r_work = 0.3834 r_free = 0.3834 target = 0.125390 restraints weight = 24098.140|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 27)----------------|
| r_work = 0.3851 r_free = 0.3851 target = 0.126624 restraints weight = 24009.636|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 25)----------------|
| r_work = 0.3868 r_free = 0.3868 target = 0.128009 restraints weight = 15874.648|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 23)----------------|
| r_work = 0.3872 r_free = 0.3872 target = 0.128233 restraints weight = 14205.315|
|-----------------------------------------------------------------------------|
r_work (final): 0.3873
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7303
moved from start:          0.1835

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.038  11183  Z= 0.165
  Angle     :  0.619   8.997  15150  Z= 0.314
  Chirality :  0.044   0.155   1720
  Planarity :  0.004   0.032   1926
  Dihedral  :  4.465  26.999   1478
  Min Nonbonded Distance : 2.496

Molprobity Statistics.
  All-atom Clashscore : 11.07
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  7.90 %
    Favored  : 92.10 %
  Rotamer:
    Outliers :  2.63 %
    Allowed  : 13.82 %
    Favored  : 83.55 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.82 %
    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: -1.50 (0.24), residues: 1341
  helix: -0.55 (0.29), residues: 331
  sheet: -1.71 (0.36), residues: 213
  loop : -0.94 (0.23), residues: 797

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARG A 861 
 TYR   0.017   0.001   TYR A1707 
 PHE   0.016   0.001   PHE A1525 
 TRP   0.023   0.001   TRP A 698 
 HIS   0.005   0.001   HIS A1328 

Details of bonding type rmsd
  covalent geometry    : bond        0.00385 (11183)
  covalent geometry    : angle       0.61931 (15150)
  hydrogen bonds       : bond        0.04266 (  314)
  hydrogen bonds       : angle       5.79339 (  843)

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

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

  2682 Ramachandran restraints generated.
    1341 Oldfield, 0 Emsley, 1341 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2682 Ramachandran restraints generated.
    1341 Oldfield, 0 Emsley, 1341 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  146 residues out of total 1216 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 32
    poor density    : 114
  time to evaluate  : 0.436 
Fit side-chains
   revert: symmetry clash
REVERT: A  802 HIS cc_start: 0.7252 (OUTLIER) cc_final: 0.6173 (m90)
REVERT: A  923 ASP cc_start: 0.7875 (t0) cc_final: 0.7639 (t0)
REVERT: A 1130 MET cc_start: 0.8249 (mmp) cc_final: 0.8009 (mmt)
REVERT: A 1288 MET cc_start: 0.8155 (ptp) cc_final: 0.7798 (tmm)
  outliers start: 32
  outliers final: 24
  residues processed: 133
  average time/residue: 0.0847
  time to fit residues: 17.3463
Evaluate side-chains
  124 residues out of total 1216 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 25
    poor density    : 99
  time to evaluate  : 0.424 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  576 LEU
Chi-restraints excluded: chain A residue  578 LEU
Chi-restraints excluded: chain A residue  643 ILE
Chi-restraints excluded: chain A residue  673 ILE
Chi-restraints excluded: chain A residue  721 VAL
Chi-restraints excluded: chain A residue  741 LEU
Chi-restraints excluded: chain A residue  754 VAL
Chi-restraints excluded: chain A residue  802 HIS
Chi-restraints excluded: chain A residue  815 LEU
Chi-restraints excluded: chain A residue  963 PHE
Chi-restraints excluded: chain A residue 1023 VAL
Chi-restraints excluded: chain A residue 1159 MET
Chi-restraints excluded: chain A residue 1163 VAL
Chi-restraints excluded: chain A residue 1310 MET
Chi-restraints excluded: chain A residue 1339 LEU
Chi-restraints excluded: chain A residue 1486 GLN
Chi-restraints excluded: chain A residue 1566 ASN
Chi-restraints excluded: chain A residue 1567 THR
Chi-restraints excluded: chain A residue 1668 TYR
Chi-restraints excluded: chain A residue 1696 MET
Chi-restraints excluded: chain A residue 1736 VAL
Chi-restraints excluded: chain A residue 1740 VAL
Chi-restraints excluded: chain A residue 1741 CYS
Chi-restraints excluded: chain A residue 1751 VAL
Chi-restraints excluded: chain A residue 1944 VAL
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 137
   random chunks:
   chunk 129 optimal weight:    0.4980
   chunk 89 optimal weight:    0.5980
   chunk 77 optimal weight:    0.0770
   chunk 78 optimal weight:    0.0970
   chunk 34 optimal weight:    0.6980
   chunk 125 optimal weight:    2.9990
   chunk 8 optimal weight:    1.9990
   chunk 4 optimal weight:    9.9990
   chunk 92 optimal weight:    1.9990
   chunk 60 optimal weight:    0.6980
   chunk 117 optimal weight:    4.9990
   overall best weight:    0.3936

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

Flipped N/Q/H residues before XYZ refinement:
** A 711 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 802 HIS
A 993 HIS
A1015 GLN
A1208 HIS
** A1496 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
A1566 ASN

Total number of N/Q/H flips: 5

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4352 r_free = 0.4352 target = 0.162313 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 40)----------------|
| r_work = 0.3921 r_free = 0.3921 target = 0.129695 restraints weight = 24116.142|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 30)----------------|
| r_work = 0.3871 r_free = 0.3871 target = 0.128125 restraints weight = 24154.000|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 24)----------------|
| r_work = 0.3892 r_free = 0.3892 target = 0.129579 restraints weight = 24671.717|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 27)----------------|
| r_work = 0.3896 r_free = 0.3896 target = 0.129916 restraints weight = 15824.253|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 25)----------------|
| r_work = 0.3919 r_free = 0.3919 target = 0.131705 restraints weight = 14423.736|
|-----------------------------------------------------------------------------|
r_work (final): 0.3924
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7216
moved from start:          0.1929

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.041  11183  Z= 0.118
  Angle     :  0.602   9.107  15150  Z= 0.301
  Chirality :  0.043   0.191   1720
  Planarity :  0.003   0.030   1926
  Dihedral  :  4.392  26.114   1478
  Min Nonbonded Distance : 2.500

Molprobity Statistics.
  All-atom Clashscore : 10.29
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  7.31 %
    Favored  : 92.69 %
  Rotamer:
    Outliers :  2.80 %
    Allowed  : 14.06 %
    Favored  : 83.14 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.82 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -1.46 (0.24), residues: 1341
  helix: -0.47 (0.29), residues: 332
  sheet: -1.77 (0.37), residues: 197
  loop : -0.93 (0.23), residues: 812

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG A 861 
 TYR   0.017   0.001   TYR A1641 
 PHE   0.020   0.001   PHE A 738 
 TRP   0.015   0.001   TRP A 698 
 HIS   0.011   0.001   HIS A 802 

Details of bonding type rmsd
  covalent geometry    : bond        0.00265 (11183)
  covalent geometry    : angle       0.60234 (15150)
  hydrogen bonds       : bond        0.03802 (  314)
  hydrogen bonds       : angle       5.59627 (  843)

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

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

  2682 Ramachandran restraints generated.
    1341 Oldfield, 0 Emsley, 1341 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2682 Ramachandran restraints generated.
    1341 Oldfield, 0 Emsley, 1341 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  142 residues out of total 1216 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 34
    poor density    : 108
  time to evaluate  : 0.326 
Fit side-chains
REVERT: A  802 HIS cc_start: 0.7205 (OUTLIER) cc_final: 0.6059 (m90)
REVERT: A  923 ASP cc_start: 0.7785 (t0) cc_final: 0.7549 (t0)
REVERT: A 1288 MET cc_start: 0.8019 (ptp) cc_final: 0.7798 (tmm)
REVERT: A 1384 PHE cc_start: 0.8149 (OUTLIER) cc_final: 0.7762 (m-80)
  outliers start: 34
  outliers final: 21
  residues processed: 131
  average time/residue: 0.0855
  time to fit residues: 17.0927
Evaluate side-chains
  130 residues out of total 1216 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 23
    poor density    : 107
  time to evaluate  : 0.401 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  576 LEU
Chi-restraints excluded: chain A residue  578 LEU
Chi-restraints excluded: chain A residue  643 ILE
Chi-restraints excluded: chain A residue  673 ILE
Chi-restraints excluded: chain A residue  741 LEU
Chi-restraints excluded: chain A residue  754 VAL
Chi-restraints excluded: chain A residue  802 HIS
Chi-restraints excluded: chain A residue  963 PHE
Chi-restraints excluded: chain A residue 1023 VAL
Chi-restraints excluded: chain A residue 1078 VAL
Chi-restraints excluded: chain A residue 1159 MET
Chi-restraints excluded: chain A residue 1163 VAL
Chi-restraints excluded: chain A residue 1310 MET
Chi-restraints excluded: chain A residue 1362 LEU
Chi-restraints excluded: chain A residue 1384 PHE
Chi-restraints excluded: chain A residue 1458 LEU
Chi-restraints excluded: chain A residue 1588 LEU
Chi-restraints excluded: chain A residue 1668 TYR
Chi-restraints excluded: chain A residue 1696 MET
Chi-restraints excluded: chain A residue 1736 VAL
Chi-restraints excluded: chain A residue 1751 VAL
Chi-restraints excluded: chain A residue 1944 VAL
Chi-restraints excluded: chain A residue 2011 THR
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 137
   random chunks:
   chunk 64 optimal weight:    0.9980
   chunk 37 optimal weight:    2.9990
   chunk 11 optimal weight:    9.9990
   chunk 107 optimal weight:    0.5980
   chunk 16 optimal weight:    5.9990
   chunk 47 optimal weight:    0.9990
   chunk 128 optimal weight:    0.5980
   chunk 57 optimal weight:    0.9990
   chunk 69 optimal weight:    0.7980
   chunk 112 optimal weight:    0.8980
   chunk 86 optimal weight:    0.3980
   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 711 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 993 HIS
** A1496 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A1566 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4347 r_free = 0.4347 target = 0.161719 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 37)----------------|
| r_work = 0.3912 r_free = 0.3912 target = 0.129007 restraints weight = 24310.699|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 30)----------------|
| r_work = 0.3861 r_free = 0.3861 target = 0.127420 restraints weight = 24605.652|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 27)----------------|
| r_work = 0.3876 r_free = 0.3876 target = 0.128528 restraints weight = 24979.333|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 25)----------------|
| r_work = 0.3900 r_free = 0.3900 target = 0.130284 restraints weight = 16102.216|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 23)----------------|
| r_work = 0.3902 r_free = 0.3902 target = 0.130497 restraints weight = 13668.466|
|-----------------------------------------------------------------------------|
r_work (final): 0.3906
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7242
moved from start:          0.2064

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.035  11183  Z= 0.132
  Angle     :  0.605  10.239  15150  Z= 0.302
  Chirality :  0.043   0.156   1720
  Planarity :  0.003   0.038   1926
  Dihedral  :  4.374  26.744   1478
  Min Nonbonded Distance : 2.498

Molprobity Statistics.
  All-atom Clashscore : 10.70
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  7.46 %
    Favored  : 92.54 %
  Rotamer:
    Outliers :  3.21 %
    Allowed  : 14.97 %
    Favored  : 81.83 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.82 %
    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: -1.39 (0.24), residues: 1341
  helix: -0.37 (0.29), residues: 333
  sheet: -1.67 (0.37), residues: 202
  loop : -0.92 (0.23), residues: 806

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.006   0.000   ARG A1016 
 TYR   0.018   0.001   TYR A1641 
 PHE   0.021   0.001   PHE A1132 
 TRP   0.018   0.001   TRP A 698 
 HIS   0.004   0.001   HIS A1328 

Details of bonding type rmsd
  covalent geometry    : bond        0.00306 (11183)
  covalent geometry    : angle       0.60475 (15150)
  hydrogen bonds       : bond        0.03626 (  314)
  hydrogen bonds       : angle       5.44931 (  843)

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

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

  2682 Ramachandran restraints generated.
    1341 Oldfield, 0 Emsley, 1341 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2682 Ramachandran restraints generated.
    1341 Oldfield, 0 Emsley, 1341 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  147 residues out of total 1216 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 39
    poor density    : 108
  time to evaluate  : 0.427 
Fit side-chains
REVERT: A  923 ASP cc_start: 0.7747 (t0) cc_final: 0.7478 (t0)
REVERT: A 1384 PHE cc_start: 0.8135 (OUTLIER) cc_final: 0.7716 (m-80)
REVERT: A 1549 THR cc_start: 0.8384 (OUTLIER) cc_final: 0.8141 (p)
  outliers start: 39
  outliers final: 27
  residues processed: 134
  average time/residue: 0.0859
  time to fit residues: 17.9205
Evaluate side-chains
  133 residues out of total 1216 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 29
    poor density    : 104
  time to evaluate  : 0.359 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  576 LEU
Chi-restraints excluded: chain A residue  578 LEU
Chi-restraints excluded: chain A residue  643 ILE
Chi-restraints excluded: chain A residue  673 ILE
Chi-restraints excluded: chain A residue  741 LEU
Chi-restraints excluded: chain A residue  754 VAL
Chi-restraints excluded: chain A residue  781 LEU
Chi-restraints excluded: chain A residue  804 ILE
Chi-restraints excluded: chain A residue  815 LEU
Chi-restraints excluded: chain A residue  905 THR
Chi-restraints excluded: chain A residue  963 PHE
Chi-restraints excluded: chain A residue 1023 VAL
Chi-restraints excluded: chain A residue 1078 VAL
Chi-restraints excluded: chain A residue 1159 MET
Chi-restraints excluded: chain A residue 1163 VAL
Chi-restraints excluded: chain A residue 1310 MET
Chi-restraints excluded: chain A residue 1339 LEU
Chi-restraints excluded: chain A residue 1362 LEU
Chi-restraints excluded: chain A residue 1384 PHE
Chi-restraints excluded: chain A residue 1549 THR
Chi-restraints excluded: chain A residue 1588 LEU
Chi-restraints excluded: chain A residue 1668 TYR
Chi-restraints excluded: chain A residue 1696 MET
Chi-restraints excluded: chain A residue 1736 VAL
Chi-restraints excluded: chain A residue 1741 CYS
Chi-restraints excluded: chain A residue 1751 VAL
Chi-restraints excluded: chain A residue 1779 VAL
Chi-restraints excluded: chain A residue 1944 VAL
Chi-restraints excluded: chain A residue 2011 THR
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 137
   random chunks:
   chunk 82 optimal weight:    1.9990
   chunk 14 optimal weight:    8.9990
   chunk 110 optimal weight:   10.0000
   chunk 104 optimal weight:    3.9990
   chunk 6 optimal weight:   30.0000
   chunk 78 optimal weight:    0.0970
   chunk 16 optimal weight:    1.9990
   chunk 53 optimal weight:    0.7980
   chunk 26 optimal weight:    0.5980
   chunk 11 optimal weight:    7.9990
   chunk 100 optimal weight:    1.9990
   overall best weight:    1.0982

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

Flipped N/Q/H residues before XYZ refinement:
** A 711 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A1496 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A1566 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4320 r_free = 0.4320 target = 0.159569 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 37)----------------|
| r_work = 0.3876 r_free = 0.3876 target = 0.126434 restraints weight = 23999.911|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 26)----------------|
| r_work = 0.3827 r_free = 0.3827 target = 0.124703 restraints weight = 24944.524|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 27)----------------|
| r_work = 0.3841 r_free = 0.3841 target = 0.125924 restraints weight = 26055.392|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 25)----------------|
| r_work = 0.3863 r_free = 0.3863 target = 0.127615 restraints weight = 17148.822|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 23)----------------|
| r_work = 0.3865 r_free = 0.3865 target = 0.127856 restraints weight = 14860.518|
|-----------------------------------------------------------------------------|
r_work (final): 0.3871
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7305
moved from start:          0.2284

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.042  11183  Z= 0.175
  Angle     :  0.640  10.047  15150  Z= 0.323
  Chirality :  0.044   0.167   1720
  Planarity :  0.004   0.033   1926
  Dihedral  :  4.553  28.279   1478
  Min Nonbonded Distance : 2.496

Molprobity Statistics.
  All-atom Clashscore : 11.29
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  7.90 %
    Favored  : 92.10 %
  Rotamer:
    Outliers :  3.12 %
    Allowed  : 15.54 %
    Favored  : 81.33 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.82 %
    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: -1.43 (0.24), residues: 1341
  helix: -0.38 (0.29), residues: 334
  sheet: -1.74 (0.36), residues: 230
  loop : -0.90 (0.24), residues: 777

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARG A 861 
 TYR   0.018   0.002   TYR A1707 
 PHE   0.027   0.002   PHE A 738 
 TRP   0.027   0.001   TRP A 698 
 HIS   0.006   0.001   HIS A1328 

Details of bonding type rmsd
  covalent geometry    : bond        0.00412 (11183)
  covalent geometry    : angle       0.63994 (15150)
  hydrogen bonds       : bond        0.03679 (  314)
  hydrogen bonds       : angle       5.45109 (  843)

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

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

  2682 Ramachandran restraints generated.
    1341 Oldfield, 0 Emsley, 1341 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2682 Ramachandran restraints generated.
    1341 Oldfield, 0 Emsley, 1341 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  145 residues out of total 1216 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 38
    poor density    : 107
  time to evaluate  : 0.422 
Fit side-chains
   revert: symmetry clash
REVERT: A  923 ASP cc_start: 0.7772 (t0) cc_final: 0.7557 (t0)
REVERT: A 1384 PHE cc_start: 0.8232 (OUTLIER) cc_final: 0.7702 (m-80)
REVERT: A 1549 THR cc_start: 0.8510 (OUTLIER) cc_final: 0.8236 (p)
  outliers start: 38
  outliers final: 28
  residues processed: 131
  average time/residue: 0.0854
  time to fit residues: 17.4513
Evaluate side-chains
  132 residues out of total 1216 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 30
    poor density    : 102
  time to evaluate  : 0.424 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  576 LEU
Chi-restraints excluded: chain A residue  578 LEU
Chi-restraints excluded: chain A residue  673 ILE
Chi-restraints excluded: chain A residue  741 LEU
Chi-restraints excluded: chain A residue  754 VAL
Chi-restraints excluded: chain A residue  781 LEU
Chi-restraints excluded: chain A residue  804 ILE
Chi-restraints excluded: chain A residue  815 LEU
Chi-restraints excluded: chain A residue  905 THR
Chi-restraints excluded: chain A residue  963 PHE
Chi-restraints excluded: chain A residue  984 VAL
Chi-restraints excluded: chain A residue 1023 VAL
Chi-restraints excluded: chain A residue 1078 VAL
Chi-restraints excluded: chain A residue 1132 PHE
Chi-restraints excluded: chain A residue 1159 MET
Chi-restraints excluded: chain A residue 1163 VAL
Chi-restraints excluded: chain A residue 1310 MET
Chi-restraints excluded: chain A residue 1339 LEU
Chi-restraints excluded: chain A residue 1362 LEU
Chi-restraints excluded: chain A residue 1384 PHE
Chi-restraints excluded: chain A residue 1458 LEU
Chi-restraints excluded: chain A residue 1549 THR
Chi-restraints excluded: chain A residue 1567 THR
Chi-restraints excluded: chain A residue 1588 LEU
Chi-restraints excluded: chain A residue 1668 TYR
Chi-restraints excluded: chain A residue 1736 VAL
Chi-restraints excluded: chain A residue 1741 CYS
Chi-restraints excluded: chain A residue 1751 VAL
Chi-restraints excluded: chain A residue 1944 VAL
Chi-restraints excluded: chain A residue 2011 THR
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 137
   random chunks:
   chunk 91 optimal weight:    0.8980
   chunk 61 optimal weight:    0.6980
   chunk 66 optimal weight:    3.9990
   chunk 22 optimal weight:   20.0000
   chunk 134 optimal weight:    0.9990
   chunk 37 optimal weight:    1.9990
   chunk 28 optimal weight:    0.6980
   chunk 113 optimal weight:    7.9990
   chunk 131 optimal weight:    0.8980
   chunk 109 optimal weight:    0.9990
   chunk 74 optimal weight:    1.9990
   overall best weight:    0.8382

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

Flipped N/Q/H residues before XYZ refinement:
** A 711 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A1496 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A1566 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4329 r_free = 0.4329 target = 0.160291 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 37)----------------|
| r_work = 0.3890 r_free = 0.3890 target = 0.127298 restraints weight = 23857.305|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 26)----------------|
| r_work = 0.3837 r_free = 0.3837 target = 0.125248 restraints weight = 24711.032|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 27)----------------|
| r_work = 0.3852 r_free = 0.3852 target = 0.126473 restraints weight = 25672.244|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 25)----------------|
| r_work = 0.3871 r_free = 0.3871 target = 0.127982 restraints weight = 16962.730|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 23)----------------|
| r_work = 0.3873 r_free = 0.3873 target = 0.128204 restraints weight = 14816.263|
|-----------------------------------------------------------------------------|
r_work (final): 0.3875
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7292
moved from start:          0.2365

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.050  11183  Z= 0.148
  Angle     :  0.635  11.394  15150  Z= 0.318
  Chirality :  0.044   0.160   1720
  Planarity :  0.003   0.032   1926
  Dihedral  :  4.533  27.973   1478
  Min Nonbonded Distance : 2.497

Molprobity Statistics.
  All-atom Clashscore : 10.84
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  7.76 %
    Favored  : 92.24 %
  Rotamer:
    Outliers :  3.12 %
    Allowed  : 16.12 %
    Favored  : 80.76 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.82 %
    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: 1341
  helix: -0.25 (0.29), residues: 336
  sheet: -1.71 (0.36), residues: 224
  loop : -0.92 (0.24), residues: 781

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARG A1746 
 TYR   0.022   0.001   TYR A1262 
 PHE   0.014   0.001   PHE A 738 
 TRP   0.018   0.001   TRP A 698 
 HIS   0.004   0.001   HIS A1328 

Details of bonding type rmsd
  covalent geometry    : bond        0.00348 (11183)
  covalent geometry    : angle       0.63470 (15150)
  hydrogen bonds       : bond        0.03423 (  314)
  hydrogen bonds       : angle       5.32516 (  843)

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

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

  2682 Ramachandran restraints generated.
    1341 Oldfield, 0 Emsley, 1341 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2682 Ramachandran restraints generated.
    1341 Oldfield, 0 Emsley, 1341 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  144 residues out of total 1216 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 38
    poor density    : 106
  time to evaluate  : 0.357 
Fit side-chains
   revert: symmetry clash
REVERT: A  923 ASP cc_start: 0.7722 (t0) cc_final: 0.7494 (t0)
REVERT: A 1288 MET cc_start: 0.8487 (tmm) cc_final: 0.7809 (ppp)
REVERT: A 1384 PHE cc_start: 0.8250 (OUTLIER) cc_final: 0.7650 (m-80)
REVERT: A 1402 HIS cc_start: 0.6420 (OUTLIER) cc_final: 0.6204 (m-70)
REVERT: A 1549 THR cc_start: 0.8488 (OUTLIER) cc_final: 0.8234 (p)
  outliers start: 38
  outliers final: 28
  residues processed: 131
  average time/residue: 0.0846
  time to fit residues: 17.3438
Evaluate side-chains
  133 residues out of total 1216 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 31
    poor density    : 102
  time to evaluate  : 0.523 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  578 LEU
Chi-restraints excluded: chain A residue  673 ILE
Chi-restraints excluded: chain A residue  741 LEU
Chi-restraints excluded: chain A residue  754 VAL
Chi-restraints excluded: chain A residue  781 LEU
Chi-restraints excluded: chain A residue  804 ILE
Chi-restraints excluded: chain A residue  815 LEU
Chi-restraints excluded: chain A residue  905 THR
Chi-restraints excluded: chain A residue  963 PHE
Chi-restraints excluded: chain A residue  984 VAL
Chi-restraints excluded: chain A residue 1023 VAL
Chi-restraints excluded: chain A residue 1078 VAL
Chi-restraints excluded: chain A residue 1132 PHE
Chi-restraints excluded: chain A residue 1159 MET
Chi-restraints excluded: chain A residue 1163 VAL
Chi-restraints excluded: chain A residue 1310 MET
Chi-restraints excluded: chain A residue 1339 LEU
Chi-restraints excluded: chain A residue 1362 LEU
Chi-restraints excluded: chain A residue 1384 PHE
Chi-restraints excluded: chain A residue 1402 HIS
Chi-restraints excluded: chain A residue 1458 LEU
Chi-restraints excluded: chain A residue 1486 GLN
Chi-restraints excluded: chain A residue 1549 THR
Chi-restraints excluded: chain A residue 1567 THR
Chi-restraints excluded: chain A residue 1588 LEU
Chi-restraints excluded: chain A residue 1668 TYR
Chi-restraints excluded: chain A residue 1736 VAL
Chi-restraints excluded: chain A residue 1741 CYS
Chi-restraints excluded: chain A residue 1751 VAL
Chi-restraints excluded: chain A residue 1944 VAL
Chi-restraints excluded: chain A residue 2011 THR
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 137
   random chunks:
   chunk 72 optimal weight:    1.9990
   chunk 18 optimal weight:    0.2980
   chunk 57 optimal weight:    1.9990
   chunk 111 optimal weight:    0.9980
   chunk 41 optimal weight:    5.9990
   chunk 133 optimal weight:    0.8980
   chunk 13 optimal weight:   20.0000
   chunk 118 optimal weight:    0.8980
   chunk 63 optimal weight:    0.0670
   chunk 39 optimal weight:    6.9990
   chunk 84 optimal weight:    0.0040
   overall best weight:    0.4330

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

Flipped N/Q/H residues before XYZ refinement:
** A 711 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A1496 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A1566 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4345 r_free = 0.4345 target = 0.161514 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 43)----------------|
| r_work = 0.3913 r_free = 0.3913 target = 0.128958 restraints weight = 23963.699|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 26)----------------|
| r_work = 0.3864 r_free = 0.3864 target = 0.126995 restraints weight = 23179.012|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 27)----------------|
| r_work = 0.3878 r_free = 0.3878 target = 0.128320 restraints weight = 24285.028|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 25)----------------|
| r_work = 0.3893 r_free = 0.3893 target = 0.129510 restraints weight = 16517.625|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 23)----------------|
| r_work = 0.3895 r_free = 0.3895 target = 0.129727 restraints weight = 14787.340|
|-----------------------------------------------------------------------------|
r_work (final): 0.3897
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7250
moved from start:          0.2393

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.035  11183  Z= 0.118
  Angle     :  0.631  12.701  15150  Z= 0.314
  Chirality :  0.043   0.152   1720
  Planarity :  0.003   0.031   1926
  Dihedral  :  4.491  27.551   1478
  Min Nonbonded Distance : 2.499

Molprobity Statistics.
  All-atom Clashscore : 10.57
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  7.53 %
    Favored  : 92.47 %
  Rotamer:
    Outliers :  3.04 %
    Allowed  : 16.61 %
    Favored  : 80.35 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.82 %
    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: -1.34 (0.24), residues: 1341
  helix: -0.19 (0.29), residues: 336
  sheet: -1.66 (0.36), residues: 219
  loop : -0.92 (0.24), residues: 786

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG A1016 
 TYR   0.018   0.001   TYR A1262 
 PHE   0.033   0.001   PHE A 738 
 TRP   0.010   0.001   TRP A 698 
 HIS   0.003   0.001   HIS A1765 

Details of bonding type rmsd
  covalent geometry    : bond        0.00271 (11183)
  covalent geometry    : angle       0.63148 (15150)
  hydrogen bonds       : bond        0.03217 (  314)
  hydrogen bonds       : angle       5.21264 (  843)

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

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

  2682 Ramachandran restraints generated.
    1341 Oldfield, 0 Emsley, 1341 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2682 Ramachandran restraints generated.
    1341 Oldfield, 0 Emsley, 1341 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  146 residues out of total 1216 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 37
    poor density    : 109
  time to evaluate  : 0.378 
Fit side-chains
   revert: symmetry clash
REVERT: A 1288 MET cc_start: 0.8548 (tmm) cc_final: 0.8035 (ppp)
REVERT: A 1384 PHE cc_start: 0.8209 (OUTLIER) cc_final: 0.7594 (m-80)
REVERT: A 1549 THR cc_start: 0.8437 (OUTLIER) cc_final: 0.8172 (p)
  outliers start: 37
  outliers final: 29
  residues processed: 134
  average time/residue: 0.0900
  time to fit residues: 18.6527
Evaluate side-chains
  133 residues out of total 1216 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 31
    poor density    : 102
  time to evaluate  : 0.493 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  576 LEU
Chi-restraints excluded: chain A residue  578 LEU
Chi-restraints excluded: chain A residue  643 ILE
Chi-restraints excluded: chain A residue  673 ILE
Chi-restraints excluded: chain A residue  741 LEU
Chi-restraints excluded: chain A residue  754 VAL
Chi-restraints excluded: chain A residue  781 LEU
Chi-restraints excluded: chain A residue  804 ILE
Chi-restraints excluded: chain A residue  815 LEU
Chi-restraints excluded: chain A residue  905 THR
Chi-restraints excluded: chain A residue  963 PHE
Chi-restraints excluded: chain A residue  984 VAL
Chi-restraints excluded: chain A residue 1023 VAL
Chi-restraints excluded: chain A residue 1078 VAL
Chi-restraints excluded: chain A residue 1132 PHE
Chi-restraints excluded: chain A residue 1159 MET
Chi-restraints excluded: chain A residue 1163 VAL
Chi-restraints excluded: chain A residue 1310 MET
Chi-restraints excluded: chain A residue 1339 LEU
Chi-restraints excluded: chain A residue 1362 LEU
Chi-restraints excluded: chain A residue 1384 PHE
Chi-restraints excluded: chain A residue 1549 THR
Chi-restraints excluded: chain A residue 1567 THR
Chi-restraints excluded: chain A residue 1587 GLN
Chi-restraints excluded: chain A residue 1668 TYR
Chi-restraints excluded: chain A residue 1736 VAL
Chi-restraints excluded: chain A residue 1741 CYS
Chi-restraints excluded: chain A residue 1751 VAL
Chi-restraints excluded: chain A residue 1779 VAL
Chi-restraints excluded: chain A residue 1944 VAL
Chi-restraints excluded: chain A residue 2011 THR
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 137
   random chunks:
   chunk 70 optimal weight:    3.9990
   chunk 86 optimal weight:    2.9990
   chunk 13 optimal weight:   10.0000
   chunk 8 optimal weight:    7.9990
   chunk 3 optimal weight:   20.0000
   chunk 33 optimal weight:    0.0050
   chunk 119 optimal weight:    0.8980
   chunk 83 optimal weight:    1.9990
   chunk 117 optimal weight:    0.7980
   chunk 132 optimal weight:    3.9990
   chunk 14 optimal weight:    0.0020
   overall best weight:    0.7404

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

Flipped N/Q/H residues before XYZ refinement:
** A 711 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 737 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A1496 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A1566 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4334 r_free = 0.4334 target = 0.160664 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 32)----------------|
| r_work = 0.3906 r_free = 0.3906 target = 0.128571 restraints weight = 24002.298|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 28)----------------|
| r_work = 0.3855 r_free = 0.3855 target = 0.126592 restraints weight = 25085.235|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 27)----------------|
| r_work = 0.3871 r_free = 0.3871 target = 0.127879 restraints weight = 24111.377|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 23)----------------|
| r_work = 0.3883 r_free = 0.3883 target = 0.128751 restraints weight = 16005.436|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 23)----------------|
| r_work = 0.3887 r_free = 0.3887 target = 0.129095 restraints weight = 14590.860|
|-----------------------------------------------------------------------------|
r_work (final): 0.3892
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7262
moved from start:          0.2465

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.040  11183  Z= 0.142
  Angle     :  0.635  13.211  15150  Z= 0.316
  Chirality :  0.044   0.206   1720
  Planarity :  0.003   0.032   1926
  Dihedral  :  4.496  28.869   1478
  Min Nonbonded Distance : 2.497

Molprobity Statistics.
  All-atom Clashscore : 11.16
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  7.98 %
    Favored  : 92.02 %
  Rotamer:
    Outliers :  2.88 %
    Allowed  : 16.69 %
    Favored  : 80.43 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.82 %
    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: -1.34 (0.24), residues: 1341
  helix: -0.19 (0.29), residues: 337
  sheet: -1.67 (0.36), residues: 219
  loop : -0.93 (0.24), residues: 785

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG A 861 
 TYR   0.016   0.001   TYR A1262 
 PHE   0.016   0.001   PHE A 738 
 TRP   0.018   0.001   TRP A 698 
 HIS   0.011   0.001   HIS A1402 

Details of bonding type rmsd
  covalent geometry    : bond        0.00334 (11183)
  covalent geometry    : angle       0.63522 (15150)
  hydrogen bonds       : bond        0.03284 (  314)
  hydrogen bonds       : angle       5.16192 (  843)

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

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

  2682 Ramachandran restraints generated.
    1341 Oldfield, 0 Emsley, 1341 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2682 Ramachandran restraints generated.
    1341 Oldfield, 0 Emsley, 1341 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  138 residues out of total 1216 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 35
    poor density    : 103
  time to evaluate  : 0.355 
Fit side-chains
   revert: symmetry clash
REVERT: A  979 GLU cc_start: 0.8440 (mm-30) cc_final: 0.8079 (mm-30)
REVERT: A 1288 MET cc_start: 0.8568 (tmm) cc_final: 0.8086 (ppp)
REVERT: A 1384 PHE cc_start: 0.8240 (OUTLIER) cc_final: 0.7638 (m-80)
REVERT: A 1549 THR cc_start: 0.8477 (OUTLIER) cc_final: 0.8214 (p)
  outliers start: 35
  outliers final: 30
  residues processed: 125
  average time/residue: 0.0881
  time to fit residues: 17.1490
Evaluate side-chains
  134 residues out of total 1216 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 32
    poor density    : 102
  time to evaluate  : 0.420 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  576 LEU
Chi-restraints excluded: chain A residue  578 LEU
Chi-restraints excluded: chain A residue  673 ILE
Chi-restraints excluded: chain A residue  741 LEU
Chi-restraints excluded: chain A residue  754 VAL
Chi-restraints excluded: chain A residue  781 LEU
Chi-restraints excluded: chain A residue  804 ILE
Chi-restraints excluded: chain A residue  815 LEU
Chi-restraints excluded: chain A residue  905 THR
Chi-restraints excluded: chain A residue  963 PHE
Chi-restraints excluded: chain A residue  984 VAL
Chi-restraints excluded: chain A residue 1023 VAL
Chi-restraints excluded: chain A residue 1078 VAL
Chi-restraints excluded: chain A residue 1132 PHE
Chi-restraints excluded: chain A residue 1159 MET
Chi-restraints excluded: chain A residue 1163 VAL
Chi-restraints excluded: chain A residue 1310 MET
Chi-restraints excluded: chain A residue 1339 LEU
Chi-restraints excluded: chain A residue 1362 LEU
Chi-restraints excluded: chain A residue 1384 PHE
Chi-restraints excluded: chain A residue 1458 LEU
Chi-restraints excluded: chain A residue 1549 THR
Chi-restraints excluded: chain A residue 1567 THR
Chi-restraints excluded: chain A residue 1587 GLN
Chi-restraints excluded: chain A residue 1668 TYR
Chi-restraints excluded: chain A residue 1696 MET
Chi-restraints excluded: chain A residue 1736 VAL
Chi-restraints excluded: chain A residue 1741 CYS
Chi-restraints excluded: chain A residue 1751 VAL
Chi-restraints excluded: chain A residue 1779 VAL
Chi-restraints excluded: chain A residue 1944 VAL
Chi-restraints excluded: chain A residue 2011 THR
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 137
   random chunks:
   chunk 27 optimal weight:    4.9990
   chunk 66 optimal weight:    4.9990
   chunk 70 optimal weight:    0.8980
   chunk 73 optimal weight:    0.8980
   chunk 15 optimal weight:   10.0000
   chunk 118 optimal weight:    0.8980
   chunk 8 optimal weight:    1.9990
   chunk 37 optimal weight:    0.0870
   chunk 22 optimal weight:   20.0000
   chunk 96 optimal weight:    2.9990
   chunk 20 optimal weight:    0.7980
   overall best weight:    0.7158

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

Flipped N/Q/H residues before XYZ refinement:
** A 711 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A1496 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A1566 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4332 r_free = 0.4332 target = 0.160586 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 37)----------------|
| r_work = 0.3892 r_free = 0.3892 target = 0.127549 restraints weight = 24376.966|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 26)----------------|
| r_work = 0.3837 r_free = 0.3837 target = 0.125403 restraints weight = 24645.029|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 27)----------------|
| r_work = 0.3853 r_free = 0.3853 target = 0.126685 restraints weight = 25421.326|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 25)----------------|
| r_work = 0.3871 r_free = 0.3871 target = 0.128197 restraints weight = 17052.820|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 23)----------------|
| r_work = 0.3875 r_free = 0.3875 target = 0.128545 restraints weight = 14983.290|
|-----------------------------------------------------------------------------|
r_work (final): 0.3880
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7284
moved from start:          0.2551

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.041  11183  Z= 0.137
  Angle     :  0.631  12.639  15150  Z= 0.315
  Chirality :  0.044   0.176   1720
  Planarity :  0.003   0.031   1926
  Dihedral  :  4.480  28.937   1478
  Min Nonbonded Distance : 2.496

Molprobity Statistics.
  All-atom Clashscore : 11.07
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  7.90 %
    Favored  : 92.10 %
  Rotamer:
    Outliers :  3.12 %
    Allowed  : 17.02 %
    Favored  : 79.85 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.82 %
    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: -1.30 (0.24), residues: 1341
  helix: -0.14 (0.29), residues: 338
  sheet: -1.69 (0.35), residues: 229
  loop : -0.87 (0.24), residues: 774

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG A1016 
 TYR   0.015   0.001   TYR A1262 
 PHE   0.038   0.001   PHE A 738 
 TRP   0.019   0.001   TRP A 698 
 HIS   0.003   0.001   HIS A1328 

Details of bonding type rmsd
  covalent geometry    : bond        0.00322 (11183)
  covalent geometry    : angle       0.63067 (15150)
  hydrogen bonds       : bond        0.03197 (  314)
  hydrogen bonds       : angle       5.12766 (  843)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 1671.15 seconds
wall clock time: 29 minutes 54.77 seconds (1794.77 seconds total)