Starting phenix.real_space_refine
on Sat Aug 23 10:17:46 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/9qe7_53049/08_2025/9qe7_53049.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/9qe7_53049/08_2025/9qe7_53049.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=4.4
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    model {
      file = "/net/cci-nas-00/data/ceres_data/9qe7_53049/08_2025/9qe7_53049.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/9qe7_53049/08_2025/9qe7_53049.cif"
    real_map_files = "/net/cci-nas-00/data/ceres_data/9qe7_53049/08_2025/9qe7_53049.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/9qe7_53049/08_2025/9qe7_53049.map"
  }
  resolution = 4.4
  write_initial_geo_file = False
  refinement {
    macro_cycles = 10
  }


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

Validating inputs
Origin is already at (0, 0, 0), no shifts will be applied
-------------------------------------------------------------------------------
Processing inputs
*****************
Set random seed
  Set to: 0
Set model cs if undefined
Decide on map wrapping
  Map wrapping is set to: False
Normalize map: mean=0, sd=1
  Input map: mean=   0.001 sd=   0.016
Set stop_for_unknowns flag
  Set to: True
Assert model is a single copy model
Assert all atoms have isotropic ADPs
Construct map_model_manager
Extract box with map and model
Check model and map are aligned
Set scattering table
  Set to: electron
  Number of scattering types: 4
    Type Number    sf(0)   Gaussians
     S      19      5.16       5
     C    6651      2.51       5
     N    1867      2.21       5
     O    2289      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 16 residue(s): 0.01s

  Monomer Library directory:
    "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/chem_data/mon_lib"
  Total number of atoms: 10826
  Number of models: 1
  Model: ""
    Number of chains: 1
    Chain: "A"
      Number of atoms: 10826
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 1483, 10826
          Classifications: {'peptide': 1483}
          Link IDs: {'PCIS': 3, 'PTRANS': 35, 'TRANS': 1444}
  Time building chain proxies: 2.61, per 1000 atoms: 0.24
  Number of scatterers: 10826
  At special positions: 0
  Unit cell: (64.66, 106, 230.02, 90, 90, 90)
  Space group: P 1 (No. 1)
  Number of sites at special positions: 0
  Number of scattering types: 4
    Type Number    sf(0)
     S      19     16.00
     O    2289      8.00
     N    1867      7.00
     C    6651      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: 0.95
  Conformation dependent library (CDL) restraints added in 622.5 milliseconds
  
  Enol-peptide restraints added in 715.3 nanoseconds
  

  2962 Ramachandran restraints generated.
    1481 Oldfield, 0 Emsley, 1481 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  2628

  Finding SS restraints...
    Secondary structure from input PDB file:
      6 helices and 29 sheets defined
      2.0% alpha, 20.7% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 0.40
  Creating SS restraints...
    Processing helix  chain 'A' and resid 588 through 592
    Processing helix  chain 'A' and resid 593 through 597
      removed outlier: 3.528A  pdb=" N   VAL A 597 " --> pdb=" O   PRO A 594 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 1024 through 1029
      removed outlier: 3.895A  pdb=" N   PHE A1028 " --> pdb=" O   ASP A1024 " (cutoff:3.500A)
      removed outlier: 4.121A  pdb=" N   ASN A1029 " --> pdb=" O   PRO A1025 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'A' and resid 1024 through 1029'
    Processing helix  chain 'A' and resid 1055 through 1058
    Processing helix  chain 'A' and resid 1380 through 1384
      removed outlier: 3.634A  pdb=" N   SER A1384 " --> pdb=" O   SER A1381 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 1705 through 1708
    Processing sheet with id=AA1, first strand: chain 'A' and resid 394 through 396
      removed outlier: 6.278A  pdb=" N   VAL A 394 " --> pdb=" O   VAL A 422 " (cutoff:3.500A)
  No H-bonds generated for sheet with id=AA1
    Processing sheet with id=AA2, first strand: chain 'A' and resid 410 through 411
      removed outlier: 5.862A  pdb=" N   ILE A 512 " --> pdb=" O   ASN A 570 " (cutoff:3.500A)
      removed outlier: 6.733A  pdb=" N   ILE A 569 " --> pdb=" O   ASN A 641 " (cutoff:3.500A)
      removed outlier: 5.813A  pdb=" N   ILE A 665 " --> pdb=" O   SER A 743 " (cutoff:3.500A)
    Processing sheet with id=AA3, first strand: chain 'A' and resid 418 through 419
      removed outlier: 7.422A  pdb=" N   ASN A 418 " --> pdb=" O   VAL A 447 " (cutoff:3.500A)
  No H-bonds generated for sheet with id=AA3
    Processing sheet with id=AA4, first strand: chain 'A' and resid 434 through 435
    Processing sheet with id=AA5, first strand: chain 'A' and resid 478 through 479
    Processing sheet with id=AA6, first strand: chain 'A' and resid 488 through 491
      removed outlier: 6.867A  pdb=" N   GLY A 521 " --> pdb=" O   ILE A 488 " (cutoff:3.500A)
      removed outlier: 6.439A  pdb=" N   MET A 579 " --> pdb=" O   GLY A 521 " (cutoff:3.500A)
      removed outlier: 7.045A  pdb=" N   GLN A 523 " --> pdb=" O   MET A 579 " (cutoff:3.500A)
      removed outlier: 6.957A  pdb=" N   THR A 581 " --> pdb=" O   GLN A 523 " (cutoff:3.500A)
      removed outlier: 7.893A  pdb=" N   GLY A 649 " --> pdb=" O   PHE A 577 " (cutoff:3.500A)
      removed outlier: 4.094A  pdb=" N   MET A 579 " --> pdb=" O   GLY A 649 " (cutoff:3.500A)
      removed outlier: 5.957A  pdb=" N   GLY A 699 " --> pdb=" O   ILE A 648 " (cutoff:3.500A)
      removed outlier: 6.434A  pdb=" N   VAL A 698 " --> pdb=" O   GLY A 753 " (cutoff:3.500A)
      removed outlier: 7.687A  pdb=" N   LEU A 755 " --> pdb=" O   VAL A 698 " (cutoff:3.500A)
      removed outlier: 6.510A  pdb=" N   VAL A 700 " --> pdb=" O   LEU A 755 " (cutoff:3.500A)
    Processing sheet with id=AA7, first strand: chain 'A' and resid 532 through 534
    Processing sheet with id=AA8, first strand: chain 'A' and resid 563 through 565
      removed outlier: 5.571A  pdb=" N   ALA A 563 " --> pdb=" O   TYR A 635 " (cutoff:3.500A)
    Processing sheet with id=AA9, first strand: chain 'A' and resid 694 through 695
      removed outlier: 6.136A  pdb=" N   VAL A 694 " --> pdb=" O   THR A 749 " (cutoff:3.500A)
  No H-bonds generated for sheet with id=AA9
    Processing sheet with id=AB1, first strand: chain 'A' and resid 736 through 738
      removed outlier: 5.742A  pdb=" N   VAL A 736 " --> pdb=" O   THR A 790 " (cutoff:3.500A)
  No H-bonds generated for sheet with id=AB1
    Processing sheet with id=AB2, first strand: chain 'A' and resid 761 through 762
      removed outlier: 3.934A  pdb=" N   ILE A 761 " --> pdb=" O   LEU A 783 " (cutoff:3.500A)
    Processing sheet with id=AB3, first strand: chain 'A' and resid 769 through 770
      removed outlier: 6.944A  pdb=" N   THR A 769 " --> pdb=" O   TYR A 827 " (cutoff:3.500A)
      removed outlier: 3.661A  pdb=" N   SER A 815 " --> pdb=" O   ASN A 828 " (cutoff:3.500A)
    Processing sheet with id=AB4, first strand: chain 'A' and resid 838 through 839
    Processing sheet with id=AB5, first strand: chain 'A' and resid 843 through 845
    Processing sheet with id=AB6, first strand: chain 'A' and resid 923 through 924
      removed outlier: 7.485A  pdb=" N   ILE A 923 " --> pdb=" O   LYS A 959 " (cutoff:3.500A)
  No H-bonds generated for sheet with id=AB6
    Processing sheet with id=AB7, first strand: chain 'A' and resid 941 through 943
      removed outlier: 6.322A  pdb=" N   ALA A 966 " --> pdb=" O   ILE A 941 " (cutoff:3.500A)
    Processing sheet with id=AB8, first strand: chain 'A' and resid 975 through 976
      removed outlier: 3.574A  pdb=" N   LYS A1004 " --> pdb=" O   VAL A 976 " (cutoff:3.500A)
      removed outlier: 6.704A  pdb=" N   VAL A1003 " --> pdb=" O   LYS A1033 " (cutoff:3.500A)
    Processing sheet with id=AB9, first strand: chain 'A' and resid 1011 through 1012
      removed outlier: 7.517A  pdb=" N   LEU A1011 " --> pdb=" O   GLU A1043 " (cutoff:3.500A)
  No H-bonds generated for sheet with id=AB9
    Processing sheet with id=AC1, first strand: chain 'A' and resid 1018 through 1022
      removed outlier: 6.918A  pdb=" N   PHE A1050 " --> pdb=" O   VAL A1018 " (cutoff:3.500A)
      removed outlier: 6.474A  pdb=" N   LEU A1088 " --> pdb=" O   THR A1049 " (cutoff:3.500A)
      removed outlier: 7.083A  pdb=" N   VAL A1115 " --> pdb=" O   SER A1087 " (cutoff:3.500A)
      removed outlier: 6.354A  pdb=" N   GLY A1139 " --> pdb=" O   ALA A1114 " (cutoff:3.500A)
      removed outlier: 6.740A  pdb=" N   ALA A1138 " --> pdb=" O   GLY A1169 " (cutoff:3.500A)
      removed outlier: 8.448A  pdb=" N   TYR A1171 " --> pdb=" O   ALA A1138 " (cutoff:3.500A)
      removed outlier: 5.992A  pdb=" N   LEU A1140 " --> pdb=" O   TYR A1171 " (cutoff:3.500A)
      removed outlier: 7.715A  pdb=" N   SER A1173 " --> pdb=" O   LEU A1140 " (cutoff:3.500A)
      removed outlier: 6.048A  pdb=" N   ALA A1142 " --> pdb=" O   SER A1173 " (cutoff:3.500A)
      removed outlier: 6.291A  pdb=" N   GLY A1192 " --> pdb=" O   ILE A1168 " (cutoff:3.500A)
      removed outlier: 6.650A  pdb=" N   VAL A1191 " --> pdb=" O   GLY A1216 " (cutoff:3.500A)
      removed outlier: 8.391A  pdb=" N   TYR A1218 " --> pdb=" O   VAL A1191 " (cutoff:3.500A)
      removed outlier: 6.335A  pdb=" N   ILE A1193 " --> pdb=" O   TYR A1218 " (cutoff:3.500A)
      removed outlier: 8.326A  pdb=" N   GLU A1220 " --> pdb=" O   ILE A1193 " (cutoff:3.500A)
      removed outlier: 6.464A  pdb=" N   GLY A1195 " --> pdb=" O   GLU A1220 " (cutoff:3.500A)
      removed outlier: 7.039A  pdb=" N   ALA A1215 " --> pdb=" O   SER A1240 " (cutoff:3.500A)
      removed outlier: 6.945A  pdb=" N   GLY A1242 " --> pdb=" O   ALA A1215 " (cutoff:3.500A)
      removed outlier: 3.594A  pdb=" N   VAL A1217 " --> pdb=" O   GLY A1242 " (cutoff:3.500A)
      removed outlier: 6.882A  pdb=" N   VAL A1241 " --> pdb=" O   SER A1273 " (cutoff:3.500A)
      removed outlier: 6.633A  pdb=" N   GLY A1275 " --> pdb=" O   VAL A1241 " (cutoff:3.500A)
      removed outlier: 6.541A  pdb=" N   GLY A1303 " --> pdb=" O   ALA A1274 " (cutoff:3.500A)
    Processing sheet with id=AC2, first strand: chain 'A' and resid 1123 through 1126
      removed outlier: 3.899A  pdb=" N   VAL A1124 " --> pdb=" O   VAL A1152 " (cutoff:3.500A)
      removed outlier: 3.581A  pdb=" N   LYS A1154 " --> pdb=" O   VAL A1124 " (cutoff:3.500A)
      removed outlier: 5.650A  pdb=" N   ALA A1153 " --> pdb=" O   GLU A1178 " (cutoff:3.500A)
      removed outlier: 6.092A  pdb=" N   GLY A1177 " --> pdb=" O   LYS A1202 " (cutoff:3.500A)
      removed outlier: 5.764A  pdb=" N   LEU A1201 " --> pdb=" O   ILE A1225 " (cutoff:3.500A)
      removed outlier: 6.538A  pdb=" N   MET A1224 " --> pdb=" O   LYS A1258 " (cutoff:3.500A)
      removed outlier: 6.004A  pdb=" N   LYS A1255 " --> pdb=" O   THR A1287 " (cutoff:3.500A)
      removed outlier: 7.816A  pdb=" N   GLU A1289 " --> pdb=" O   LYS A1255 " (cutoff:3.500A)
      removed outlier: 5.765A  pdb=" N   VAL A1257 " --> pdb=" O   GLU A1289 " (cutoff:3.500A)
      removed outlier: 7.696A  pdb=" N   THR A1320 " --> pdb=" O   LEU A1286 " (cutoff:3.500A)
      removed outlier: 6.285A  pdb=" N   ILE A1288 " --> pdb=" O   THR A1320 " (cutoff:3.500A)
    Processing sheet with id=AC3, first strand: chain 'A' and resid 1158 through 1161
      removed outlier: 3.723A  pdb=" N   SER A1161 " --> pdb=" O   THR A1184 " (cutoff:3.500A)
      removed outlier: 3.649A  pdb=" N   GLU A1208 " --> pdb=" O   ILE A1183 " (cutoff:3.500A)
      removed outlier: 5.076A  pdb=" N   MET A1185 " --> pdb=" O   GLU A1208 " (cutoff:3.500A)
      removed outlier: 5.896A  pdb=" N   ILE A1207 " --> pdb=" O   ILE A1234 " (cutoff:3.500A)
    Processing sheet with id=AC4, first strand: chain 'A' and resid 1262 through 1265
      removed outlier: 5.999A  pdb=" N   ILE A1263 " --> pdb=" O   GLU A1295 " (cutoff:3.500A)
    Processing sheet with id=AC5, first strand: chain 'A' and resid 1333 through 1335
      removed outlier: 6.623A  pdb=" N   GLY A1361 " --> pdb=" O   ILE A1333 " (cutoff:3.500A)
      removed outlier: 6.630A  pdb=" N   ALA A1360 " --> pdb=" O   GLY A1392 " (cutoff:3.500A)
      removed outlier: 7.206A  pdb=" N   SER A1394 " --> pdb=" O   ALA A1360 " (cutoff:3.500A)
      removed outlier: 6.099A  pdb=" N   ILE A1362 " --> pdb=" O   SER A1394 " (cutoff:3.500A)
      removed outlier: 6.739A  pdb=" N   MET A1419 " --> pdb=" O   GLY A1392 " (cutoff:3.500A)
      removed outlier: 6.682A  pdb=" N   SER A1394 " --> pdb=" O   MET A1419 " (cutoff:3.500A)
      removed outlier: 6.806A  pdb=" N   SER A1421 " --> pdb=" O   SER A1394 " (cutoff:3.500A)
      removed outlier: 6.899A  pdb=" N   THR A1417 " --> pdb=" O   GLY A1441 " (cutoff:3.500A)
      removed outlier: 7.608A  pdb=" N   TYR A1443 " --> pdb=" O   THR A1417 " (cutoff:3.500A)
      removed outlier: 5.646A  pdb=" N   MET A1419 " --> pdb=" O   TYR A1443 " (cutoff:3.500A)
      removed outlier: 7.167A  pdb=" N   THR A1445 " --> pdb=" O   MET A1419 " (cutoff:3.500A)
      removed outlier: 5.561A  pdb=" N   SER A1421 " --> pdb=" O   THR A1445 " (cutoff:3.500A)
      removed outlier: 7.243A  pdb=" N   TYR A1470 " --> pdb=" O   VAL A1440 " (cutoff:3.500A)
      removed outlier: 6.186A  pdb=" N   MET A1442 " --> pdb=" O   TYR A1470 " (cutoff:3.500A)
      removed outlier: 7.845A  pdb=" N   LYS A1472 " --> pdb=" O   MET A1442 " (cutoff:3.500A)
      removed outlier: 6.343A  pdb=" N   ALA A1444 " --> pdb=" O   LYS A1472 " (cutoff:3.500A)
      removed outlier: 6.294A  pdb=" N   ILE A1469 " --> pdb=" O   TYR A1503 " (cutoff:3.500A)
      removed outlier: 8.406A  pdb=" N   ILE A1505 " --> pdb=" O   ILE A1469 " (cutoff:3.500A)
      removed outlier: 6.862A  pdb=" N   SER A1471 " --> pdb=" O   ILE A1505 " (cutoff:3.500A)
      removed outlier: 6.066A  pdb=" N   ILE A1502 " --> pdb=" O   TYR A1533 " (cutoff:3.500A)
      removed outlier: 7.781A  pdb=" N   LYS A1535 " --> pdb=" O   ILE A1502 " (cutoff:3.500A)
      removed outlier: 7.460A  pdb=" N   SER A1504 " --> pdb=" O   LYS A1535 " (cutoff:3.500A)
      removed outlier: 7.699A  pdb=" N   LEU A1564 " --> pdb=" O   GLY A1531 " (cutoff:3.500A)
      removed outlier: 4.716A  pdb=" N   TYR A1533 " --> pdb=" O   LEU A1564 " (cutoff:3.500A)
      removed outlier: 7.123A  pdb=" N   ILE A1590 " --> pdb=" O   GLY A1562 " (cutoff:3.500A)
      removed outlier: 7.707A  pdb=" N   LEU A1564 " --> pdb=" O   ILE A1590 " (cutoff:3.500A)
      removed outlier: 7.370A  pdb=" N   GLY A1592 " --> pdb=" O   LEU A1564 " (cutoff:3.500A)
      removed outlier: 6.454A  pdb=" N   GLY A1620 " --> pdb=" O   ALA A1588 " (cutoff:3.500A)
      removed outlier: 4.126A  pdb=" N   GLY A1592 " --> pdb=" O   SER A1622 " (cutoff:3.500A)
      removed outlier: 6.855A  pdb=" N   GLY A1645 " --> pdb=" O   VAL A1619 " (cutoff:3.500A)
      removed outlier: 3.843A  pdb=" N   ALA A1672 " --> pdb=" O   MET A1646 " (cutoff:3.500A)
      removed outlier: 3.564A  pdb=" N   GLY A1648 " --> pdb=" O   ALA A1672 " (cutoff:3.500A)
      removed outlier: 6.055A  pdb=" N   MET A1671 " --> pdb=" O   PHE A1695 " (cutoff:3.500A)
      removed outlier: 7.284A  pdb=" N   LYS A1697 " --> pdb=" O   MET A1671 " (cutoff:3.500A)
      removed outlier: 5.659A  pdb=" N   GLY A1673 " --> pdb=" O   LYS A1697 " (cutoff:3.500A)
    Processing sheet with id=AC6, first strand: chain 'A' and resid 1341 through 1343
      removed outlier: 6.568A  pdb=" N   ILE A1342 " --> pdb=" O   ILE A1371 " (cutoff:3.500A)
  No H-bonds generated for sheet with id=AC6
    Processing sheet with id=AC7, first strand: chain 'A' and resid 1400 through 1403
      removed outlier: 6.476A  pdb=" N   GLY A1401 " --> pdb=" O   THR A1427 " (cutoff:3.500A)
      removed outlier: 5.715A  pdb=" N   ILE A1426 " --> pdb=" O   THR A1450 " (cutoff:3.500A)
  No H-bonds generated for sheet with id=AC7
    Processing sheet with id=AC8, first strand: chain 'A' and resid 1408 through 1409
      removed outlier: 5.988A  pdb=" N   ILE A1432 " --> pdb=" O   PHE A1460 " (cutoff:3.500A)
      removed outlier: 7.523A  pdb=" N   ILE A1522 " --> pdb=" O   GLU A1554 " (cutoff:3.500A)
      removed outlier: 3.704A  pdb=" N   ILE A1581 " --> pdb=" O   ILE A1553 " (cutoff:3.500A)
      removed outlier: 6.977A  pdb=" N   ILE A1603 " --> pdb=" O   ILE A1580 " (cutoff:3.500A)
      removed outlier: 7.881A  pdb=" N   VAL A1582 " --> pdb=" O   ILE A1603 " (cutoff:3.500A)
      removed outlier: 6.469A  pdb=" N   LYS A1605 " --> pdb=" O   VAL A1582 " (cutoff:3.500A)
      removed outlier: 6.139A  pdb=" N   ILE A1604 " --> pdb=" O   THR A1637 " (cutoff:3.500A)
      removed outlier: 5.977A  pdb=" N   ILE A1636 " --> pdb=" O   THR A1661 " (cutoff:3.500A)
    Processing sheet with id=AC9, first strand: chain 'A' and resid 1482 through 1483
      removed outlier: 6.063A  pdb=" N   VAL A1483 " --> pdb=" O   VAL A1517 " (cutoff:3.500A)
      removed outlier: 6.471A  pdb=" N   VAL A1516 " --> pdb=" O   THR A1548 " (cutoff:3.500A)
      removed outlier: 6.292A  pdb=" N   VAL A1547 " --> pdb=" O   THR A1571 " (cutoff:3.500A)
    Processing sheet with id=AD1, first strand: chain 'A' and resid 1627 through 1629
      removed outlier: 5.588A  pdb=" N   ALA A1628 " --> pdb=" O   THR A1655 " (cutoff:3.500A)
      removed outlier: 5.738A  pdb=" N   LEU A1654 " --> pdb=" O   THR A1679 " (cutoff:3.500A)
      removed outlier: 3.750A  pdb=" N   VAL A1678 " --> pdb=" O   THR A1701 " (cutoff:3.500A)
  No H-bonds generated for sheet with id=AD1
    Processing sheet with id=AD2, first strand: chain 'A' and resid 1684 through 1685
      removed outlier: 6.645A  pdb=" N   ILE A1684 " --> pdb=" O   THR A1711 " (cutoff:3.500A)
  No H-bonds generated for sheet with id=AD2

    98 hydrogen bonds defined for protein.
    270 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: 2.66

  Time building geometry restraints manager: 1.21 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: 3683
        1.34 -     1.46: 1938
        1.46 -     1.58: 5285
        1.58 -     1.69: 0
        1.69 -     1.81: 38
  Bond restraints: 10944
  Sorted by residual:
  bond pdb=" CA  LYS A 775 "
       pdb=" C   LYS A 775 "
    ideal  model  delta    sigma   weight residual
    1.522  1.499  0.024 1.39e-02 5.18e+03 2.88e+00
  bond pdb=" N   ASP A 963 "
       pdb=" CA  ASP A 963 "
    ideal  model  delta    sigma   weight residual
    1.457  1.477 -0.020 1.29e-02 6.01e+03 2.32e+00
  bond pdb=" C   LYS A 970 "
       pdb=" N   ASP A 971 "
    ideal  model  delta    sigma   weight residual
    1.325  1.340 -0.015 1.14e-02 7.69e+03 1.66e+00
  bond pdb=" N   ILE A1581 "
       pdb=" CA  ILE A1581 "
    ideal  model  delta    sigma   weight residual
    1.474  1.455  0.019 1.57e-02 4.06e+03 1.48e+00
  bond pdb=" N   ILE A 797 "
       pdb=" CA  ILE A 797 "
    ideal  model  delta    sigma   weight residual
    1.474  1.456  0.018 1.57e-02 4.06e+03 1.37e+00
  ... (remaining 10939 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     2.20: 14434
        2.20 -     4.40: 346
        4.40 -     6.61: 21
        6.61 -     8.81: 3
        8.81 -    11.01: 1
  Bond angle restraints: 14805
  Sorted by residual:
  angle pdb=" N   ILE A1376 "
        pdb=" CA  ILE A1376 "
        pdb=" C   ILE A1376 "
      ideal   model   delta    sigma   weight residual
     111.88  106.30    5.58 1.06e+00 8.90e-01 2.77e+01
  angle pdb=" N   ILE A 678 "
        pdb=" CA  ILE A 678 "
        pdb=" C   ILE A 678 "
      ideal   model   delta    sigma   weight residual
     111.48  106.70    4.78 9.40e-01 1.13e+00 2.59e+01
  angle pdb=" C   THR A1759 "
        pdb=" N   LYS A1760 "
        pdb=" CA  LYS A1760 "
      ideal   model   delta    sigma   weight residual
     120.38  126.71   -6.33 1.46e+00 4.69e-01 1.88e+01
  angle pdb=" C   ASP A 971 "
        pdb=" CA  ASP A 971 "
        pdb=" CB  ASP A 971 "
      ideal   model   delta    sigma   weight residual
     115.79  110.75    5.04 1.19e+00 7.06e-01 1.79e+01
  angle pdb=" N   SER A1452 "
        pdb=" CA  SER A1452 "
        pdb=" C   SER A1452 "
      ideal   model   delta    sigma   weight residual
     114.31  109.03    5.28 1.29e+00 6.01e-01 1.67e+01
  ... (remaining 14800 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    17.72: 6056
       17.72 -    35.44: 476
       35.44 -    53.16: 76
       53.16 -    70.88: 18
       70.88 -    88.60: 7
  Dihedral angle restraints: 6633
    sinusoidal: 2484
      harmonic: 4149
  Sorted by residual:
  dihedral pdb=" CA  ASP A1102 "
           pdb=" C   ASP A1102 "
           pdb=" N   TYR A1103 "
           pdb=" CA  TYR A1103 "
      ideal   model   delta  harmonic     sigma   weight residual
    -180.00 -146.99  -33.01     0      5.00e+00 4.00e-02 4.36e+01
  dihedral pdb=" CA  LYS A1357 "
           pdb=" C   LYS A1357 "
           pdb=" N   LYS A1358 "
           pdb=" CA  LYS A1358 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  156.95   23.05     0      5.00e+00 4.00e-02 2.13e+01
  dihedral pdb=" CA  GLU A1101 "
           pdb=" C   GLU A1101 "
           pdb=" N   ASP A1102 "
           pdb=" CA  ASP A1102 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00 -157.30  -22.70     0      5.00e+00 4.00e-02 2.06e+01
  ... (remaining 6630 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.051: 1333
       0.051 -    0.102: 322
       0.102 -    0.153: 96
       0.153 -    0.204: 3
       0.204 -    0.256: 2
  Chirality restraints: 1756
  Sorted by residual:
  chirality pdb=" CB  ILE A 892 "
            pdb=" CA  ILE A 892 "
            pdb=" CG1 ILE A 892 "
            pdb=" CG2 ILE A 892 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.64    2.39    0.26 2.00e-01 2.50e+01 1.63e+00
  chirality pdb=" CG  LEU A1099 "
            pdb=" CB  LEU A1099 "
            pdb=" CD1 LEU A1099 "
            pdb=" CD2 LEU A1099 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.59   -2.38   -0.21 2.00e-01 2.50e+01 1.10e+00
  chirality pdb=" CB  ILE A 877 "
            pdb=" CA  ILE A 877 "
            pdb=" CG1 ILE A 877 "
            pdb=" CG2 ILE A 877 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.64    2.46    0.19 2.00e-01 2.50e+01 8.58e-01
  ... (remaining 1753 not shown)

  Planarity restraints: 1940
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   THR A1455 "   -0.031 5.00e-02 4.00e+02   4.71e-02 3.54e+00
        pdb=" N   PRO A1456 "    0.081 5.00e-02 4.00e+02
        pdb=" CA  PRO A1456 "   -0.026 5.00e-02 4.00e+02
        pdb=" CD  PRO A1456 "   -0.024 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CB  HIS A 814 "    0.014 2.00e-02 2.50e+03   1.41e-02 2.96e+00
        pdb=" CG  HIS A 814 "   -0.030 2.00e-02 2.50e+03
        pdb=" ND1 HIS A 814 "    0.006 2.00e-02 2.50e+03
        pdb=" CD2 HIS A 814 "    0.004 2.00e-02 2.50e+03
        pdb=" CE1 HIS A 814 "   -0.000 2.00e-02 2.50e+03
        pdb=" NE2 HIS A 814 "    0.006 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   VAL A 587 "   -0.028 5.00e-02 4.00e+02   4.23e-02 2.86e+00
        pdb=" N   PRO A 588 "    0.073 5.00e-02 4.00e+02
        pdb=" CA  PRO A 588 "   -0.022 5.00e-02 4.00e+02
        pdb=" CD  PRO A 588 "   -0.024 5.00e-02 4.00e+02
  ... (remaining 1937 not shown)

  Histogram of nonbonded interaction distances:
        2.04 -     2.61: 363
        2.61 -     3.19: 10875
        3.19 -     3.76: 18783
        3.76 -     4.33: 25289
        4.33 -     4.90: 40074
  Nonbonded interactions: 95384
  Sorted by model distance:
  nonbonded pdb=" O   ILE A1079 "
            pdb=" OH  TYR A1103 "
     model   vdw
     2.043 3.040
  nonbonded pdb=" O   LYS A1457 "
            pdb=" OG1 THR A1488 "
     model   vdw
     2.105 3.040
  nonbonded pdb=" OE2 GLU A1133 "
            pdb=" OG1 THR A1162 "
     model   vdw
     2.113 3.040
  nonbonded pdb=" OG  SER A 458 "
            pdb=" OG1 THR A 461 "
     model   vdw
     2.142 3.040
  nonbonded pdb=" O   ILE A1636 "
            pdb=" OG1 THR A1661 "
     model   vdw
     2.146 3.040
  ... (remaining 95379 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:             3.980
  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:          0.110
  Check model and map are aligned:         0.030
  Set scattering table:                    0.010
  Process input model:                     11.790
  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:1.110
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   17.110
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6101
moved from start:          0.0000

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.032  10944  Z= 0.186
  Angle     :  0.816  11.009  14805  Z= 0.511
  Chirality :  0.048   0.256   1756
  Planarity :  0.004   0.047   1940
  Dihedral  : 13.416  88.604   4005
  Min Nonbonded Distance : 2.043

Molprobity Statistics.
  All-atom Clashscore : 29.46
  Ramachandran Plot:
    Outliers :  0.34 %
    Allowed  : 10.80 %
    Favored  : 88.86 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  0.41 %
    Favored  : 99.59 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 7.89 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.07 %

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 aren not related in a simple way.
  whole: -3.15 (0.19), residues: 1481
  helix: -4.83 (0.48), residues: 6
  sheet: -1.47 (0.30), residues: 302
  loop : -2.47 (0.15), residues: 1173

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG A 724 
 TYR   0.018   0.002   TYR A1103 
 PHE   0.016   0.002   PHE A1050 
 TRP   0.005   0.001   TRP A 540 
 HIS   0.014   0.002   HIS A 814 

Details of bonding type rmsd
  covalent geometry    : bond        0.00324 (10944)
  covalent geometry    : angle       0.81554 (14805)
  hydrogen bonds       : bond        0.32729 (   98)
  hydrogen bonds       : angle      11.67021 (  270)

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

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

  2962 Ramachandran restraints generated.
    1481 Oldfield, 0 Emsley, 1481 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2962 Ramachandran restraints generated.
    1481 Oldfield, 0 Emsley, 1481 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  312 residues out of total 1208 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 312
  time to evaluate  : 0.447 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  327 ILE cc_start: 0.8458 (tp) cc_final: 0.8210 (tp)
REVERT: A  344 VAL cc_start: 0.9027 (t) cc_final: 0.8706 (p)
REVERT: A  445 GLN cc_start: 0.8022 (mt0) cc_final: 0.7491 (tp-100)
REVERT: A  503 MET cc_start: 0.0595 (tpt) cc_final: -0.2612 (ppp)
REVERT: A  509 LYS cc_start: 0.8345 (tttt) cc_final: 0.8078 (mtmt)
REVERT: A  522 ILE cc_start: 0.6718 (mp) cc_final: 0.5936 (mt)
REVERT: A  523 GLN cc_start: 0.7477 (tt0) cc_final: 0.7272 (tm-30)
REVERT: A  530 HIS cc_start: 0.7619 (m90) cc_final: 0.7197 (m-70)
REVERT: A  561 MET cc_start: 0.5768 (mtt) cc_final: 0.5339 (mtt)
REVERT: A  579 MET cc_start: 0.8208 (mtp) cc_final: 0.7369 (mmm)
REVERT: A  768 LEU cc_start: 0.8657 (tp) cc_final: 0.8406 (tp)
REVERT: A  802 LYS cc_start: 0.8599 (mppt) cc_final: 0.8325 (mptt)
REVERT: A  803 LYS cc_start: 0.8213 (ptpp) cc_final: 0.7976 (pttm)
REVERT: A  825 LEU cc_start: 0.8360 (tp) cc_final: 0.7968 (mm)
REVERT: A  970 LYS cc_start: 0.6956 (mmmt) cc_final: 0.6166 (tptt)
REVERT: A 1018 VAL cc_start: 0.6576 (t) cc_final: 0.6065 (p)
REVERT: A 1203 ASN cc_start: 0.6228 (t0) cc_final: 0.5994 (t0)
REVERT: A 1218 TYR cc_start: 0.6809 (t80) cc_final: 0.6604 (t80)
REVERT: A 1305 TYR cc_start: 0.6924 (t80) cc_final: 0.6363 (t80)
REVERT: A 1307 LYS cc_start: 0.7090 (mmpt) cc_final: 0.5893 (mmmt)
REVERT: A 1335 ILE cc_start: 0.7973 (mm) cc_final: 0.7709 (mt)
REVERT: A 1336 MET cc_start: 0.7994 (mmm) cc_final: 0.7740 (mmm)
REVERT: A 1367 GLU cc_start: 0.7723 (tp30) cc_final: 0.7414 (tp30)
REVERT: A 1412 ASP cc_start: 0.7597 (t0) cc_final: 0.7129 (t0)
REVERT: A 1421 SER cc_start: 0.8606 (t) cc_final: 0.8263 (m)
REVERT: A 1432 ILE cc_start: 0.7436 (mp) cc_final: 0.7068 (mp)
REVERT: A 1443 TYR cc_start: 0.7881 (t80) cc_final: 0.7510 (t80)
REVERT: A 1519 ASN cc_start: 0.7907 (t0) cc_final: 0.7305 (m-40)
REVERT: A 1522 ILE cc_start: 0.8848 (mt) cc_final: 0.8547 (mm)
REVERT: A 1533 TYR cc_start: 0.6324 (t80) cc_final: 0.5699 (t80)
REVERT: A 1535 LYS cc_start: 0.7733 (mttm) cc_final: 0.5662 (mttm)
REVERT: A 1546 ASP cc_start: 0.5111 (m-30) cc_final: 0.3594 (m-30)
REVERT: A 1572 ASN cc_start: 0.7785 (m-40) cc_final: 0.7522 (m110)
REVERT: A 1646 MET cc_start: 0.7237 (pmm) cc_final: 0.6981 (pmm)
REVERT: A 1709 LYS cc_start: 0.7442 (ptpp) cc_final: 0.7085 (ttpt)
REVERT: A 1763 MET cc_start: 0.2687 (ptt) cc_final: 0.1536 (ttt)
  outliers start: 0
  outliers final: 0
  residues processed: 312
  average time/residue: 0.0976
  time to fit residues: 43.2839
Evaluate side-chains
  244 residues out of total 1208 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 244
  time to evaluate  : 0.357 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 148
   random chunks:
   chunk 98 optimal weight:    0.6980
   chunk 107 optimal weight:    4.9990
   chunk 10 optimal weight:   10.0000
   chunk 66 optimal weight:    3.9990
   chunk 130 optimal weight:    0.9990
   chunk 124 optimal weight:    2.9990
   chunk 103 optimal weight:    3.9990
   chunk 77 optimal weight:    2.9990
   chunk 122 optimal weight:    4.9990
   chunk 91 optimal weight:    4.9990
   chunk 55 optimal weight:    2.9990
   overall best weight:    2.1388

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

Flipped N/Q/H residues before XYZ refinement:
** A 452 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 487 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 493 ASN
** A 499 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 566 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 641 ASN
A 674 GLN
** A 680 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 719 ASN
** A 725 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 932 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 953 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
A 979 ASN
A1189 ASN
** A1236 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A1344 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A1380 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A1526 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A1572 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A1600 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A1704 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
A1750 ASN

Total number of N/Q/H flips: 7

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4402 r_free = 0.4402 target = 0.137155 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 35)----------------|
| r_work = 0.4007 r_free = 0.4007 target = 0.112334 restraints weight = 34978.415|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 30)----------------|
| r_work = 0.4066 r_free = 0.4066 target = 0.115956 restraints weight = 25005.471|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 29)----------------|
| r_work = 0.4111 r_free = 0.4111 target = 0.118731 restraints weight = 19040.780|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 29)----------------|
| r_work = 0.4146 r_free = 0.4146 target = 0.120939 restraints weight = 15126.165|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 29)----------------|
| r_work = 0.4174 r_free = 0.4174 target = 0.122665 restraints weight = 12377.636|
|-----------------------------------------------------------------------------|
r_work (final): 0.4143
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6297
moved from start:          0.4311

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.008   0.063  10944  Z= 0.398
  Angle     :  1.023  11.888  14805  Z= 0.560
  Chirality :  0.062   0.308   1756
  Planarity :  0.007   0.057   1940
  Dihedral  :  8.035  40.618   1537
  Min Nonbonded Distance : 2.409

Molprobity Statistics.
  All-atom Clashscore : 47.15
  Ramachandran Plot:
    Outliers :  0.54 %
    Allowed  : 14.79 %
    Favored  : 84.67 %
  Rotamer:
    Outliers :  1.24 %
    Allowed  : 10.93 %
    Favored  : 87.83 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 7.89 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.07 %

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 aren not related in a simple way.
  whole: -3.81 (0.18), residues: 1481
  helix: -4.83 (0.47), residues: 6
  sheet: -2.01 (0.30), residues: 293
  loop : -2.92 (0.14), residues: 1182

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.008   0.001   ARG A 604 
 TYR   0.032   0.004   TYR A 600 
 PHE   0.028   0.004   PHE A1050 
 TRP   0.034   0.004   TRP A 375 
 HIS   0.021   0.003   HIS A 814 

Details of bonding type rmsd
  covalent geometry    : bond        0.00819 (10944)
  covalent geometry    : angle       1.02252 (14805)
  hydrogen bonds       : bond        0.07615 (   98)
  hydrogen bonds       : angle      10.64141 (  270)

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

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

  2962 Ramachandran restraints generated.
    1481 Oldfield, 0 Emsley, 1481 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2962 Ramachandran restraints generated.
    1481 Oldfield, 0 Emsley, 1481 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  296 residues out of total 1208 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 15
    poor density    : 281
  time to evaluate  : 0.262 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  322 ILE cc_start: 0.8348 (OUTLIER) cc_final: 0.8127 (mm)
REVERT: A  344 VAL cc_start: 0.8836 (t) cc_final: 0.8597 (p)
REVERT: A  351 VAL cc_start: 0.8649 (p) cc_final: 0.8418 (p)
REVERT: A  355 VAL cc_start: 0.8561 (t) cc_final: 0.8358 (m)
REVERT: A  444 SER cc_start: 0.6220 (m) cc_final: 0.5965 (t)
REVERT: A  445 GLN cc_start: 0.8118 (mt0) cc_final: 0.7839 (tp40)
REVERT: A  460 SER cc_start: 0.6243 (t) cc_final: 0.5790 (p)
REVERT: A  503 MET cc_start: 0.1172 (tpt) cc_final: 0.0845 (tpt)
REVERT: A  554 LYS cc_start: 0.7933 (ttpp) cc_final: 0.7721 (ttpt)
REVERT: A  579 MET cc_start: 0.8337 (mtp) cc_final: 0.7693 (mtp)
REVERT: A  724 ARG cc_start: 0.8376 (tmm160) cc_final: 0.8081 (tmm-80)
REVERT: A  725 ASN cc_start: 0.8389 (t0) cc_final: 0.8177 (t0)
REVERT: A  750 GLN cc_start: 0.8734 (pt0) cc_final: 0.8229 (pm20)
REVERT: A  770 GLU cc_start: 0.6926 (mp0) cc_final: 0.6699 (mp0)
REVERT: A  782 LYS cc_start: 0.7784 (mmpt) cc_final: 0.7577 (mmpt)
REVERT: A  802 LYS cc_start: 0.8574 (mppt) cc_final: 0.8340 (mppt)
REVERT: A  805 TYR cc_start: 0.7252 (m-10) cc_final: 0.6759 (m-10)
REVERT: A  845 ILE cc_start: 0.3942 (OUTLIER) cc_final: 0.3668 (mm)
REVERT: A  855 MET cc_start: 0.6216 (tpt) cc_final: 0.5908 (tpt)
REVERT: A 1022 SER cc_start: 0.6632 (t) cc_final: 0.5510 (p)
REVERT: A 1078 ASN cc_start: 0.7190 (p0) cc_final: 0.6513 (m-40)
REVERT: A 1105 VAL cc_start: 0.6038 (OUTLIER) cc_final: 0.4479 (m)
REVERT: A 1207 ILE cc_start: 0.8271 (OUTLIER) cc_final: 0.7950 (mp)
REVERT: A 1213 SER cc_start: 0.8246 (m) cc_final: 0.7856 (t)
REVERT: A 1264 GLU cc_start: 0.7905 (mt-10) cc_final: 0.7594 (mt-10)
REVERT: A 1265 ILE cc_start: 0.8039 (mt) cc_final: 0.7767 (mm)
REVERT: A 1335 ILE cc_start: 0.8670 (mm) cc_final: 0.8392 (mt)
REVERT: A 1410 LYS cc_start: 0.7455 (ptpp) cc_final: 0.7229 (ptpp)
REVERT: A 1431 LYS cc_start: 0.8731 (tmtt) cc_final: 0.8482 (tptt)
REVERT: A 1432 ILE cc_start: 0.7998 (mp) cc_final: 0.7732 (mp)
REVERT: A 1443 TYR cc_start: 0.8012 (t80) cc_final: 0.7155 (t80)
REVERT: A 1504 SER cc_start: 0.7553 (m) cc_final: 0.6769 (t)
REVERT: A 1519 ASN cc_start: 0.8303 (t0) cc_final: 0.7775 (m-40)
REVERT: A 1535 LYS cc_start: 0.7249 (mttm) cc_final: 0.6750 (mttp)
REVERT: A 1720 MET cc_start: 0.7544 (ppp) cc_final: 0.7032 (ppp)
REVERT: A 1763 MET cc_start: 0.3227 (ptt) cc_final: 0.2838 (ttp)
  outliers start: 15
  outliers final: 5
  residues processed: 295
  average time/residue: 0.0949
  time to fit residues: 40.1686
Evaluate side-chains
  244 residues out of total 1208 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 9
    poor density    : 235
  time to evaluate  : 0.442 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 148
   random chunks:
   chunk 44 optimal weight:    0.6980
   chunk 143 optimal weight:    3.9990
   chunk 64 optimal weight:    0.9980
   chunk 131 optimal weight:    2.9990
   chunk 22 optimal weight:    0.3980
   chunk 27 optimal weight:    1.9990
   chunk 104 optimal weight:    0.9990
   chunk 96 optimal weight:    1.9990
   chunk 135 optimal weight:    1.9990
   chunk 16 optimal weight:    0.0020
   chunk 89 optimal weight:    1.9990
   overall best weight:    0.6190

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

Flipped N/Q/H residues before XYZ refinement:
A 455 HIS
A 493 ASN
A 500 ASN
** A 523 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 530 HIS
A 680 ASN
A 725 ASN
A 833 HIS
A 926 ASN
A1071 ASN
** A1135 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A1156 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A1312 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
A1380 ASN
A1485 ASN
** A1526 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
A1600 ASN
** A1704 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
A1750 ASN

Total number of N/Q/H flips: 13

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4495 r_free = 0.4495 target = 0.147830 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.4106 r_free = 0.4106 target = 0.120832 restraints weight = 33769.000|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 30)----------------|
| r_work = 0.4158 r_free = 0.4158 target = 0.124357 restraints weight = 24909.536|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 35)----------------|
| r_work = 0.4198 r_free = 0.4198 target = 0.127117 restraints weight = 19458.705|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 30)----------------|
| r_work = 0.4230 r_free = 0.4230 target = 0.129306 restraints weight = 15829.095|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 27)----------------|
| r_work = 0.4254 r_free = 0.4254 target = 0.131040 restraints weight = 13266.852|
|-----------------------------------------------------------------------------|
r_work (final): 0.4220
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6126
moved from start:          0.4622

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.052  10944  Z= 0.179
  Angle     :  0.750  11.391  14805  Z= 0.408
  Chirality :  0.054   0.187   1756
  Planarity :  0.005   0.062   1940
  Dihedral  :  6.762  34.134   1537
  Min Nonbonded Distance : 2.444

Molprobity Statistics.
  All-atom Clashscore : 28.63
  Ramachandran Plot:
    Outliers :  0.34 %
    Allowed  : 11.28 %
    Favored  : 88.39 %
  Rotamer:
    Outliers :  0.33 %
    Allowed  :  5.63 %
    Favored  : 94.04 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 7.89 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.07 %

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 aren not related in a simple way.
  whole: -3.78 (0.18), residues: 1481
  helix: -3.79 (0.72), residues: 12
  sheet: -2.06 (0.29), residues: 298
  loop : -2.88 (0.14), residues: 1171

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.001   ARG A 604 
 TYR   0.028   0.003   TYR A1103 
 PHE   0.016   0.003   PHE A 583 
 TRP   0.008   0.001   TRP A 375 
 HIS   0.013   0.002   HIS A 814 

Details of bonding type rmsd
  covalent geometry    : bond        0.00389 (10944)
  covalent geometry    : angle       0.75023 (14805)
  hydrogen bonds       : bond        0.04862 (   98)
  hydrogen bonds       : angle       9.25661 (  270)

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

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

  2962 Ramachandran restraints generated.
    1481 Oldfield, 0 Emsley, 1481 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2962 Ramachandran restraints generated.
    1481 Oldfield, 0 Emsley, 1481 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  262 residues out of total 1208 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 4
    poor density    : 258
  time to evaluate  : 0.278 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  318 ILE cc_start: 0.8119 (OUTLIER) cc_final: 0.7585 (pt)
REVERT: A  355 VAL cc_start: 0.8511 (t) cc_final: 0.8260 (m)
REVERT: A  444 SER cc_start: 0.6801 (m) cc_final: 0.6592 (t)
REVERT: A  445 GLN cc_start: 0.7976 (mt0) cc_final: 0.7575 (tp-100)
REVERT: A  460 SER cc_start: 0.6474 (t) cc_final: 0.6098 (p)
REVERT: A  525 LYS cc_start: 0.7655 (ptpt) cc_final: 0.7280 (ptpp)
REVERT: A  554 LYS cc_start: 0.7974 (ttpp) cc_final: 0.7626 (tmmt)
REVERT: A  579 MET cc_start: 0.8036 (mtp) cc_final: 0.7793 (mtp)
REVERT: A  750 GLN cc_start: 0.8590 (pt0) cc_final: 0.7860 (pm20)
REVERT: A  775 LYS cc_start: 0.8645 (mptt) cc_final: 0.8352 (mmtt)
REVERT: A  783 LEU cc_start: 0.8512 (tp) cc_final: 0.8225 (tt)
REVERT: A  805 TYR cc_start: 0.7162 (m-10) cc_final: 0.6940 (m-10)
REVERT: A  853 PHE cc_start: 0.6513 (t80) cc_final: 0.6240 (t80)
REVERT: A  855 MET cc_start: 0.5821 (tpt) cc_final: 0.5317 (tpt)
REVERT: A 1022 SER cc_start: 0.6321 (t) cc_final: 0.5706 (p)
REVERT: A 1078 ASN cc_start: 0.6981 (p0) cc_final: 0.6685 (m-40)
REVERT: A 1113 THR cc_start: 0.4258 (m) cc_final: 0.3917 (m)
REVERT: A 1119 ASN cc_start: 0.8339 (m-40) cc_final: 0.8109 (t0)
REVERT: A 1176 ASN cc_start: 0.7402 (m-40) cc_final: 0.7115 (m-40)
REVERT: A 1208 GLU cc_start: 0.7412 (pm20) cc_final: 0.7131 (pp20)
REVERT: A 1258 LYS cc_start: 0.8196 (mmpt) cc_final: 0.7424 (mmpt)
REVERT: A 1259 ASN cc_start: 0.8604 (t0) cc_final: 0.8085 (t0)
REVERT: A 1290 ASN cc_start: 0.7396 (t0) cc_final: 0.5798 (t0)
REVERT: A 1298 GLN cc_start: 0.7859 (pm20) cc_final: 0.6437 (pt0)
REVERT: A 1319 VAL cc_start: 0.8216 (m) cc_final: 0.8010 (p)
REVERT: A 1320 THR cc_start: 0.8046 (t) cc_final: 0.7777 (p)
REVERT: A 1326 LYS cc_start: 0.7434 (mmpt) cc_final: 0.7209 (mmpt)
REVERT: A 1419 MET cc_start: 0.7335 (mmp) cc_final: 0.6917 (mmp)
REVERT: A 1442 MET cc_start: 0.7381 (mmp) cc_final: 0.7173 (mtt)
REVERT: A 1443 TYR cc_start: 0.7811 (t80) cc_final: 0.7020 (t80)
REVERT: A 1467 VAL cc_start: 0.8465 (t) cc_final: 0.7932 (p)
REVERT: A 1504 SER cc_start: 0.7765 (m) cc_final: 0.6656 (t)
REVERT: A 1519 ASN cc_start: 0.8232 (t0) cc_final: 0.7808 (m-40)
REVERT: A 1535 LYS cc_start: 0.7793 (mttm) cc_final: 0.7287 (mttp)
REVERT: A 1598 ILE cc_start: 0.8352 (mt) cc_final: 0.8019 (mt)
REVERT: A 1646 MET cc_start: 0.6881 (pmm) cc_final: 0.6640 (pmm)
REVERT: A 1720 MET cc_start: 0.7915 (ppp) cc_final: 0.7314 (ppp)
  outliers start: 4
  outliers final: 0
  residues processed: 262
  average time/residue: 0.0959
  time to fit residues: 36.2399
Evaluate side-chains
  211 residues out of total 1208 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 210
  time to evaluate  : 0.378 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 148
   random chunks:
   chunk 17 optimal weight:    4.9990
   chunk 5 optimal weight:    3.9990
   chunk 7 optimal weight:   20.0000
   chunk 29 optimal weight:    1.9990
   chunk 103 optimal weight:    1.9990
   chunk 138 optimal weight:    7.9990
   chunk 136 optimal weight:    0.9980
   chunk 135 optimal weight:    3.9990
   chunk 2 optimal weight:    0.8980
   chunk 74 optimal weight:    5.9990
   chunk 144 optimal weight:    6.9990
   overall best weight:    1.9786

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

Flipped N/Q/H residues before XYZ refinement:
A 452 GLN
** A 487 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 493 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 515 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 523 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 530 HIS
** A 572 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 584 ASN
A 641 ASN
** A 683 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 888 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 932 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 953 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** A1071 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A1155 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A1156 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A1312 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A1344 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A1372 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
A1485 ASN
** A1526 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A1542 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
A1750 ASN

Total number of N/Q/H flips: 6

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4400 r_free = 0.4400 target = 0.143166 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.4000 r_free = 0.4000 target = 0.116234 restraints weight = 34242.624|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 27)----------------|
| r_work = 0.4054 r_free = 0.4054 target = 0.119708 restraints weight = 25618.190|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 26)----------------|
| r_work = 0.4095 r_free = 0.4095 target = 0.122405 restraints weight = 20100.776|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 31)----------------|
| r_work = 0.4127 r_free = 0.4127 target = 0.124526 restraints weight = 16430.419|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 31)----------------|
| r_work = 0.4152 r_free = 0.4152 target = 0.126195 restraints weight = 13827.276|
|-----------------------------------------------------------------------------|
r_work (final): 0.4092
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6338
moved from start:          0.6040

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.007   0.076  10944  Z= 0.356
  Angle     :  0.977  13.350  14805  Z= 0.532
  Chirality :  0.061   0.335   1756
  Planarity :  0.006   0.059   1940
  Dihedral  :  8.259  38.855   1537
  Min Nonbonded Distance : 2.429

Molprobity Statistics.
  All-atom Clashscore : 45.62
  Ramachandran Plot:
    Outliers :  0.34 %
    Allowed  : 16.48 %
    Favored  : 83.19 %
  Rotamer:
    Outliers :  0.08 %
    Allowed  :  8.61 %
    Favored  : 91.31 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 7.89 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.14 %

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 aren not related in a simple way.
  whole: -4.12 (0.17), residues: 1481
  helix: -4.90 (0.42), residues: 6
  sheet: -2.17 (0.30), residues: 275
  loop : -3.17 (0.14), residues: 1200

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.001   ARG A 604 
 TYR   0.057   0.004   TYR A1218 
 PHE   0.024   0.004   PHE A 701 
 TRP   0.031   0.004   TRP A 375 
 HIS   0.014   0.003   HIS A 814 

Details of bonding type rmsd
  covalent geometry    : bond        0.00744 (10944)
  covalent geometry    : angle       0.97657 (14805)
  hydrogen bonds       : bond        0.06940 (   98)
  hydrogen bonds       : angle      10.64068 (  270)

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

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

  2962 Ramachandran restraints generated.
    1481 Oldfield, 0 Emsley, 1481 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2962 Ramachandran restraints generated.
    1481 Oldfield, 0 Emsley, 1481 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  272 residues out of total 1208 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 271
  time to evaluate  : 0.310 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  330 LEU cc_start: 0.7832 (pp) cc_final: 0.7569 (pp)
REVERT: A  387 GLU cc_start: 0.7292 (mp0) cc_final: 0.6361 (pp20)
REVERT: A  445 GLN cc_start: 0.8026 (mt0) cc_final: 0.7623 (tp-100)
REVERT: A  506 MET cc_start: 0.7127 (tpt) cc_final: 0.6426 (tpt)
REVERT: A  511 GLU cc_start: 0.6742 (pp20) cc_final: 0.6429 (pp20)
REVERT: A  525 LYS cc_start: 0.7674 (ptpt) cc_final: 0.7467 (ptpp)
REVERT: A  554 LYS cc_start: 0.7948 (ttpp) cc_final: 0.7603 (tmmt)
REVERT: A  561 MET cc_start: 0.5498 (mtm) cc_final: 0.5233 (mtm)
REVERT: A  603 LEU cc_start: 0.8642 (mm) cc_final: 0.8385 (mp)
REVERT: A  657 GLN cc_start: 0.4318 (tp40) cc_final: 0.3463 (tm-30)
REVERT: A  707 MET cc_start: 0.7054 (tmm) cc_final: 0.6706 (tmm)
REVERT: A  805 TYR cc_start: 0.7155 (m-10) cc_final: 0.6728 (m-10)
REVERT: A  855 MET cc_start: 0.6105 (tpt) cc_final: 0.5738 (tpt)
REVERT: A  902 LYS cc_start: 0.7221 (mmtm) cc_final: 0.6983 (mmtm)
REVERT: A 1078 ASN cc_start: 0.7076 (p0) cc_final: 0.6502 (m-40)
REVERT: A 1119 ASN cc_start: 0.8265 (m-40) cc_final: 0.8064 (m-40)
REVERT: A 1131 LYS cc_start: 0.7412 (mtmm) cc_final: 0.7087 (mtmm)
REVERT: A 1143 ILE cc_start: 0.8459 (mm) cc_final: 0.8223 (mm)
REVERT: A 1202 LYS cc_start: 0.8410 (pttp) cc_final: 0.7995 (ptmm)
REVERT: A 1204 THR cc_start: 0.7390 (m) cc_final: 0.7178 (m)
REVERT: A 1208 GLU cc_start: 0.7668 (pm20) cc_final: 0.7378 (pm20)
REVERT: A 1305 TYR cc_start: 0.7336 (t80) cc_final: 0.6944 (t80)
REVERT: A 1435 GLU cc_start: 0.6569 (mp0) cc_final: 0.6045 (mp0)
REVERT: A 1443 TYR cc_start: 0.7947 (t80) cc_final: 0.7053 (t80)
REVERT: A 1504 SER cc_start: 0.7545 (m) cc_final: 0.6495 (t)
REVERT: A 1519 ASN cc_start: 0.8400 (t0) cc_final: 0.8101 (m-40)
REVERT: A 1533 TYR cc_start: 0.6307 (t80) cc_final: 0.5914 (t80)
REVERT: A 1535 LYS cc_start: 0.7532 (mttm) cc_final: 0.5015 (mttp)
REVERT: A 1720 MET cc_start: 0.7121 (ppp) cc_final: 0.6773 (ppp)
REVERT: A 1759 THR cc_start: 0.7130 (t) cc_final: 0.6892 (m)
REVERT: A 1763 MET cc_start: 0.3194 (ptt) cc_final: 0.2502 (pmm)
  outliers start: 1
  outliers final: 0
  residues processed: 271
  average time/residue: 0.0971
  time to fit residues: 37.2883
Evaluate side-chains
  226 residues out of total 1208 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 226
  time to evaluate  : 0.240 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 148
   random chunks:
   chunk 12 optimal weight:    1.9990
   chunk 123 optimal weight:    0.7980
   chunk 144 optimal weight:    4.9990
   chunk 132 optimal weight:    5.9990
   chunk 80 optimal weight:    1.9990
   chunk 69 optimal weight:    1.9990
   chunk 124 optimal weight:    0.1980
   chunk 37 optimal weight:    0.6980
   chunk 32 optimal weight:    0.0270
   chunk 141 optimal weight:    3.9990
   chunk 4 optimal weight:    0.9980
   overall best weight:    0.5438

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

Flipped N/Q/H residues before XYZ refinement:
A 347 GLN
A 440 ASN
** A 487 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 493 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 515 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 523 GLN
A 530 HIS
** A 572 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 639 ASN
A 641 ASN
** A 680 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 683 ASN
** A 888 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 926 ASN
** A 953 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** A1071 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A1312 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A1372 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A1526 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
A1653 GLN

Total number of N/Q/H flips: 9

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4477 r_free = 0.4477 target = 0.145511 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 29)----------------|
| r_work = 0.4123 r_free = 0.4123 target = 0.121745 restraints weight = 33258.044|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 35)----------------|
| r_work = 0.4176 r_free = 0.4176 target = 0.125263 restraints weight = 24165.513|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 24)----------------|
| r_work = 0.4216 r_free = 0.4216 target = 0.127956 restraints weight = 18461.708|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 34)----------------|
| r_work = 0.4247 r_free = 0.4247 target = 0.130026 restraints weight = 14707.440|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 32)----------------|
| r_work = 0.4271 r_free = 0.4271 target = 0.131690 restraints weight = 12132.909|
|-----------------------------------------------------------------------------|
r_work (final): 0.4264
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6104
moved from start:          0.5947

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.043  10944  Z= 0.174
  Angle     :  0.761  11.238  14805  Z= 0.411
  Chirality :  0.055   0.222   1756
  Planarity :  0.005   0.054   1940
  Dihedral  :  7.059  37.039   1537
  Min Nonbonded Distance : 2.461

Molprobity Statistics.
  All-atom Clashscore : 30.15
  Ramachandran Plot:
    Outliers :  0.34 %
    Allowed  : 12.36 %
    Favored  : 87.31 %
  Rotamer:
    Outliers :  0.08 %
    Allowed  :  4.80 %
    Favored  : 95.12 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 7.89 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.07 %

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 aren not related in a simple way.
  whole: -3.92 (0.18), residues: 1481
  helix: -3.66 (0.88), residues: 12
  sheet: -2.09 (0.29), residues: 317
  loop : -3.01 (0.15), residues: 1152

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.008   0.001   ARG A1163 
 TYR   0.051   0.003   TYR A1218 
 PHE   0.030   0.003   PHE A 577 
 TRP   0.036   0.003   TRP A 532 
 HIS   0.012   0.002   HIS A 814 

Details of bonding type rmsd
  covalent geometry    : bond        0.00380 (10944)
  covalent geometry    : angle       0.76066 (14805)
  hydrogen bonds       : bond        0.04283 (   98)
  hydrogen bonds       : angle       8.94930 (  270)

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

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

  2962 Ramachandran restraints generated.
    1481 Oldfield, 0 Emsley, 1481 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2962 Ramachandran restraints generated.
    1481 Oldfield, 0 Emsley, 1481 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  271 residues out of total 1208 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 270
  time to evaluate  : 0.245 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  445 GLN cc_start: 0.8040 (mt0) cc_final: 0.7434 (tp-100)
REVERT: A  525 LYS cc_start: 0.7750 (ptpt) cc_final: 0.7325 (ptpp)
REVERT: A  554 LYS cc_start: 0.7983 (ttpp) cc_final: 0.7680 (tmmt)
REVERT: A  561 MET cc_start: 0.5314 (mtm) cc_final: 0.5027 (mtm)
REVERT: A  707 MET cc_start: 0.7537 (tmm) cc_final: 0.7141 (tmm)
REVERT: A  763 LEU cc_start: 0.7419 (mt) cc_final: 0.7112 (mt)
REVERT: A  855 MET cc_start: 0.5547 (tpt) cc_final: 0.5110 (tpt)
REVERT: A  879 PHE cc_start: 0.7273 (m-10) cc_final: 0.7067 (m-10)
REVERT: A 1078 ASN cc_start: 0.6713 (p0) cc_final: 0.6490 (t0)
REVERT: A 1119 ASN cc_start: 0.8445 (m-40) cc_final: 0.8234 (m-40)
REVERT: A 1156 ASN cc_start: 0.7050 (t0) cc_final: 0.6660 (t0)
REVERT: A 1202 LYS cc_start: 0.8344 (pttp) cc_final: 0.7969 (ptmm)
REVERT: A 1210 GLU cc_start: 0.6842 (pm20) cc_final: 0.6247 (pm20)
REVERT: A 1225 ILE cc_start: 0.8391 (tt) cc_final: 0.8154 (tt)
REVERT: A 1258 LYS cc_start: 0.8205 (mmpt) cc_final: 0.7208 (mmpt)
REVERT: A 1289 GLU cc_start: 0.7958 (pm20) cc_final: 0.7743 (pm20)
REVERT: A 1319 VAL cc_start: 0.8276 (m) cc_final: 0.8050 (p)
REVERT: A 1321 ASN cc_start: 0.7945 (t0) cc_final: 0.7667 (t0)
REVERT: A 1326 LYS cc_start: 0.7628 (mmpt) cc_final: 0.7387 (mmpt)
REVERT: A 1335 ILE cc_start: 0.8381 (mm) cc_final: 0.8162 (mm)
REVERT: A 1336 MET cc_start: 0.8167 (mmt) cc_final: 0.7763 (mmm)
REVERT: A 1409 ILE cc_start: 0.7410 (tp) cc_final: 0.7106 (mt)
REVERT: A 1443 TYR cc_start: 0.7813 (t80) cc_final: 0.6859 (t80)
REVERT: A 1470 TYR cc_start: 0.7002 (t80) cc_final: 0.4963 (t80)
REVERT: A 1503 TYR cc_start: 0.6300 (t80) cc_final: 0.5348 (t80)
REVERT: A 1504 SER cc_start: 0.7563 (m) cc_final: 0.6539 (t)
REVERT: A 1506 ILE cc_start: 0.7213 (pt) cc_final: 0.6886 (mm)
REVERT: A 1720 MET cc_start: 0.7420 (ppp) cc_final: 0.6783 (ppp)
REVERT: A 1763 MET cc_start: 0.2699 (ptt) cc_final: 0.2121 (pmm)
  outliers start: 1
  outliers final: 0
  residues processed: 271
  average time/residue: 0.0993
  time to fit residues: 38.2877
Evaluate side-chains
  234 residues out of total 1208 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 234
  time to evaluate  : 0.237 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 148
   random chunks:
   chunk 64 optimal weight:    2.9990
   chunk 101 optimal weight:    2.9990
   chunk 23 optimal weight:    4.9990
   chunk 67 optimal weight:    0.6980
   chunk 86 optimal weight:    2.9990
   chunk 12 optimal weight:    1.9990
   chunk 36 optimal weight:    0.9980
   chunk 137 optimal weight:    2.9990
   chunk 104 optimal weight:    1.9990
   chunk 32 optimal weight:    2.9990
   chunk 47 optimal weight:    0.7980
   overall best weight:    1.2984

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

Flipped N/Q/H residues before XYZ refinement:
A 484 ASN
** A 487 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 493 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 515 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 530 HIS
** A 572 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 641 ASN
A 657 GLN
** A 680 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 725 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 888 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 926 ASN
** A 953 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** A1071 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A1155 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A1226 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A1312 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A1344 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A1372 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A1526 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A1542 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 5

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4423 r_free = 0.4423 target = 0.142199 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 35)----------------|
| r_work = 0.4059 r_free = 0.4059 target = 0.118537 restraints weight = 33500.706|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 32)----------------|
| r_work = 0.4114 r_free = 0.4114 target = 0.121964 restraints weight = 24291.409|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 32)----------------|
| r_work = 0.4154 r_free = 0.4154 target = 0.124568 restraints weight = 18641.504|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 35)----------------|
| r_work = 0.4186 r_free = 0.4186 target = 0.126593 restraints weight = 14954.879|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 25)----------------|
| r_work = 0.4208 r_free = 0.4208 target = 0.128101 restraints weight = 12401.001|
|-----------------------------------------------------------------------------|
r_work (final): 0.4181
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6221
moved from start:          0.6580

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.048  10944  Z= 0.257
  Angle     :  0.852  12.036  14805  Z= 0.462
  Chirality :  0.057   0.195   1756
  Planarity :  0.006   0.057   1940
  Dihedral  :  7.639  37.914   1537
  Min Nonbonded Distance : 2.355

Molprobity Statistics.
  All-atom Clashscore : 39.94
  Ramachandran Plot:
    Outliers :  0.34 %
    Allowed  : 15.80 %
    Favored  : 83.86 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  5.46 %
    Favored  : 94.54 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 7.89 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.14 %

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 aren not related in a simple way.
  whole: -4.13 (0.18), residues: 1481
  helix: -4.95 (0.39), residues: 6
  sheet: -2.23 (0.29), residues: 296
  loop : -3.16 (0.14), residues: 1179

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.007   0.001   ARG A 558 
 TYR   0.046   0.003   TYR A1218 
 PHE   0.019   0.003   PHE A1082 
 TRP   0.021   0.003   TRP A 375 
 HIS   0.010   0.002   HIS A 814 

Details of bonding type rmsd
  covalent geometry    : bond        0.00549 (10944)
  covalent geometry    : angle       0.85159 (14805)
  hydrogen bonds       : bond        0.05511 (   98)
  hydrogen bonds       : angle       9.63732 (  270)

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

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

  2962 Ramachandran restraints generated.
    1481 Oldfield, 0 Emsley, 1481 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2962 Ramachandran restraints generated.
    1481 Oldfield, 0 Emsley, 1481 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  257 residues out of total 1208 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 257
  time to evaluate  : 0.425 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  445 GLN cc_start: 0.8089 (mt0) cc_final: 0.7624 (tp40)
REVERT: A  525 LYS cc_start: 0.7700 (ptpt) cc_final: 0.7327 (ptpp)
REVERT: A  554 LYS cc_start: 0.8018 (ttpp) cc_final: 0.7726 (tmmt)
REVERT: A  561 MET cc_start: 0.5620 (mtm) cc_final: 0.5304 (mtm)
REVERT: A  603 LEU cc_start: 0.8333 (mt) cc_final: 0.7980 (mp)
REVERT: A  707 MET cc_start: 0.7238 (tmm) cc_final: 0.6985 (tmm)
REVERT: A  750 GLN cc_start: 0.8654 (pt0) cc_final: 0.7152 (pp30)
REVERT: A  855 MET cc_start: 0.5654 (tpt) cc_final: 0.5275 (tpt)
REVERT: A 1078 ASN cc_start: 0.6895 (p0) cc_final: 0.6558 (m-40)
REVERT: A 1119 ASN cc_start: 0.8462 (m-40) cc_final: 0.8245 (m-40)
REVERT: A 1143 ILE cc_start: 0.8514 (mm) cc_final: 0.8247 (mm)
REVERT: A 1168 ILE cc_start: 0.8230 (tt) cc_final: 0.7771 (tt)
REVERT: A 1202 LYS cc_start: 0.8458 (pttp) cc_final: 0.8102 (ptmm)
REVERT: A 1224 MET cc_start: 0.8392 (pmm) cc_final: 0.8006 (pmm)
REVERT: A 1258 LYS cc_start: 0.7912 (mmpt) cc_final: 0.6959 (mmpt)
REVERT: A 1335 ILE cc_start: 0.8531 (mm) cc_final: 0.8300 (mm)
REVERT: A 1426 ILE cc_start: 0.8217 (pt) cc_final: 0.7910 (mm)
REVERT: A 1443 TYR cc_start: 0.7871 (t80) cc_final: 0.6897 (t80)
REVERT: A 1489 ILE cc_start: 0.7703 (mp) cc_final: 0.7412 (mp)
REVERT: A 1504 SER cc_start: 0.7683 (m) cc_final: 0.6710 (t)
REVERT: A 1527 LYS cc_start: 0.7581 (mmtt) cc_final: 0.7351 (mmmt)
REVERT: A 1535 LYS cc_start: 0.7293 (mttm) cc_final: 0.5071 (mttm)
REVERT: A 1646 MET cc_start: 0.6883 (pmm) cc_final: 0.6665 (pmm)
REVERT: A 1720 MET cc_start: 0.7222 (ppp) cc_final: 0.6476 (ppp)
REVERT: A 1763 MET cc_start: 0.2839 (ptt) cc_final: 0.1981 (ptm)
  outliers start: 0
  outliers final: 0
  residues processed: 257
  average time/residue: 0.0886
  time to fit residues: 32.2342
Evaluate side-chains
  218 residues out of total 1208 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 218
  time to evaluate  : 0.311 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 148
   random chunks:
   chunk 88 optimal weight:    3.9990
   chunk 6 optimal weight:    0.6980
   chunk 28 optimal weight:    0.8980
   chunk 5 optimal weight:    1.9990
   chunk 60 optimal weight:    0.0470
   chunk 121 optimal weight:    0.8980
   chunk 138 optimal weight:    1.9990
   chunk 105 optimal weight:    0.9980
   chunk 86 optimal weight:    0.9990
   chunk 73 optimal weight:    3.9990
   chunk 30 optimal weight:    0.8980
   overall best weight:    0.6878

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

Flipped N/Q/H residues before XYZ refinement:
A 347 GLN
** A 487 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 493 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 515 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 530 HIS
** A 572 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 639 ASN
A 641 ASN
** A 657 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 680 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 888 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 926 ASN
** A 953 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** A1071 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A1155 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A1372 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A1526 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
A1753 ASN

Total number of N/Q/H flips: 6

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4477 r_free = 0.4477 target = 0.148983 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 44)----------------|
| r_work = 0.4103 r_free = 0.4103 target = 0.123639 restraints weight = 32394.411|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 32)----------------|
| r_work = 0.4161 r_free = 0.4161 target = 0.127514 restraints weight = 23200.878|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 34)----------------|
| r_work = 0.4206 r_free = 0.4206 target = 0.130483 restraints weight = 17524.660|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 29)----------------|
| r_work = 0.4240 r_free = 0.4240 target = 0.132741 restraints weight = 13832.546|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 29)----------------|
| r_work = 0.4268 r_free = 0.4268 target = 0.134587 restraints weight = 11241.833|
|-----------------------------------------------------------------------------|
r_work (final): 0.4230
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6134
moved from start:          0.6667

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.066  10944  Z= 0.186
  Angle     :  0.783  11.048  14805  Z= 0.423
  Chirality :  0.055   0.243   1756
  Planarity :  0.005   0.056   1940
  Dihedral  :  7.121  36.980   1537
  Min Nonbonded Distance : 2.441

Molprobity Statistics.
  All-atom Clashscore : 32.23
  Ramachandran Plot:
    Outliers :  0.34 %
    Allowed  : 12.76 %
    Favored  : 86.90 %
  Rotamer:
    Outliers :  0.08 %
    Allowed  :  3.39 %
    Favored  : 96.52 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 7.89 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.07 %

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 aren not related in a simple way.
  whole: -3.96 (0.18), residues: 1481
  helix: -4.94 (0.39), residues: 6
  sheet: -2.04 (0.30), residues: 296
  loop : -3.07 (0.14), residues: 1179

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.001   ARG A1163 
 TYR   0.036   0.003   TYR A 600 
 PHE   0.018   0.002   PHE A 577 
 TRP   0.036   0.004   TRP A 532 
 HIS   0.009   0.002   HIS A 814 

Details of bonding type rmsd
  covalent geometry    : bond        0.00414 (10944)
  covalent geometry    : angle       0.78348 (14805)
  hydrogen bonds       : bond        0.04365 (   98)
  hydrogen bonds       : angle       8.74833 (  270)

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

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

  2962 Ramachandran restraints generated.
    1481 Oldfield, 0 Emsley, 1481 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2962 Ramachandran restraints generated.
    1481 Oldfield, 0 Emsley, 1481 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  255 residues out of total 1208 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 254
  time to evaluate  : 0.329 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  445 GLN cc_start: 0.8131 (mt0) cc_final: 0.7619 (tp-100)
REVERT: A  525 LYS cc_start: 0.7688 (ptpt) cc_final: 0.7339 (ptpp)
REVERT: A  554 LYS cc_start: 0.8015 (ttpp) cc_final: 0.7705 (tmmt)
REVERT: A  561 MET cc_start: 0.5487 (mtm) cc_final: 0.5208 (mtm)
REVERT: A  579 MET cc_start: 0.7896 (mtp) cc_final: 0.7296 (mmm)
REVERT: A  639 ASN cc_start: 0.6528 (t0) cc_final: 0.5768 (t0)
REVERT: A  750 GLN cc_start: 0.8529 (pt0) cc_final: 0.6994 (pp30)
REVERT: A  763 LEU cc_start: 0.7181 (mt) cc_final: 0.6827 (mt)
REVERT: A  853 PHE cc_start: 0.6666 (t80) cc_final: 0.6435 (t80)
REVERT: A  855 MET cc_start: 0.5124 (tpt) cc_final: 0.4914 (tpt)
REVERT: A 1078 ASN cc_start: 0.7070 (p0) cc_final: 0.6704 (m-40)
REVERT: A 1143 ILE cc_start: 0.8500 (mm) cc_final: 0.8261 (mm)
REVERT: A 1156 ASN cc_start: 0.7061 (t0) cc_final: 0.6425 (t0)
REVERT: A 1202 LYS cc_start: 0.8453 (pttp) cc_final: 0.8012 (ptmm)
REVERT: A 1290 ASN cc_start: 0.7562 (t0) cc_final: 0.7247 (t0)
REVERT: A 1321 ASN cc_start: 0.7953 (t0) cc_final: 0.7664 (t0)
REVERT: A 1324 LEU cc_start: 0.6628 (tp) cc_final: 0.5991 (mt)
REVERT: A 1335 ILE cc_start: 0.8590 (mm) cc_final: 0.8371 (mm)
REVERT: A 1393 ILE cc_start: 0.8170 (mt) cc_final: 0.7870 (mt)
REVERT: A 1431 LYS cc_start: 0.8255 (tptp) cc_final: 0.7910 (tptt)
REVERT: A 1442 MET cc_start: 0.7390 (mtt) cc_final: 0.7063 (mtm)
REVERT: A 1443 TYR cc_start: 0.7923 (t80) cc_final: 0.6818 (t80)
REVERT: A 1504 SER cc_start: 0.7662 (m) cc_final: 0.6715 (t)
REVERT: A 1506 ILE cc_start: 0.7314 (pt) cc_final: 0.6973 (mm)
REVERT: A 1527 LYS cc_start: 0.7356 (mmtt) cc_final: 0.7113 (mmmt)
REVERT: A 1583 SER cc_start: 0.8682 (m) cc_final: 0.8428 (p)
REVERT: A 1720 MET cc_start: 0.7258 (ppp) cc_final: 0.6622 (ppp)
REVERT: A 1753 ASN cc_start: 0.3732 (OUTLIER) cc_final: 0.3368 (m110)
REVERT: A 1763 MET cc_start: 0.2742 (ptt) cc_final: 0.2376 (pmm)
  outliers start: 1
  outliers final: 0
  residues processed: 255
  average time/residue: 0.0967
  time to fit residues: 34.9680
Evaluate side-chains
  218 residues out of total 1208 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 217
  time to evaluate  : 0.365 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 148
   random chunks:
   chunk 32 optimal weight:    3.9990
   chunk 120 optimal weight:    0.9980
   chunk 46 optimal weight:    4.9990
   chunk 136 optimal weight:    0.0980
   chunk 90 optimal weight:    0.7980
   chunk 18 optimal weight:    3.9990
   chunk 111 optimal weight:    4.9990
   chunk 27 optimal weight:    0.9980
   chunk 134 optimal weight:    0.7980
   chunk 80 optimal weight:    1.9990
   chunk 42 optimal weight:    0.3980
   overall best weight:    0.6180

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

Flipped N/Q/H residues before XYZ refinement:
A 347 GLN
** A 487 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 515 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 530 HIS
** A 572 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 641 ASN
A 657 GLN
** A 680 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 888 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 926 ASN
** A 953 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** A1312 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A1372 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A1526 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A1572 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
A1753 ASN

Total number of N/Q/H flips: 6

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4470 r_free = 0.4470 target = 0.145753 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 42)----------------|
| r_work = 0.4117 r_free = 0.4117 target = 0.122883 restraints weight = 33074.884|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 35)----------------|
| r_work = 0.4170 r_free = 0.4170 target = 0.126249 restraints weight = 23612.114|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 34)----------------|
| r_work = 0.4211 r_free = 0.4211 target = 0.128883 restraints weight = 17884.747|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 29)----------------|
| r_work = 0.4243 r_free = 0.4243 target = 0.130952 restraints weight = 14076.488|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 40)----------------|
| r_work = 0.4269 r_free = 0.4269 target = 0.132572 restraints weight = 11393.715|
|-----------------------------------------------------------------------------|
r_work (final): 0.4240
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6076
moved from start:          0.6806

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.045  10944  Z= 0.175
  Angle     :  0.771  10.017  14805  Z= 0.414
  Chirality :  0.055   0.286   1756
  Planarity :  0.005   0.058   1940
  Dihedral  :  6.948  39.171   1537
  Min Nonbonded Distance : 2.458

Molprobity Statistics.
  All-atom Clashscore : 30.57
  Ramachandran Plot:
    Outliers :  0.27 %
    Allowed  : 13.03 %
    Favored  : 86.70 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  2.32 %
    Favored  : 97.68 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 7.89 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.07 %

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 aren not related in a simple way.
  whole: -3.93 (0.18), residues: 1481
  helix: -4.95 (0.39), residues: 6
  sheet: -2.09 (0.30), residues: 299
  loop : -3.01 (0.15), residues: 1176

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.001   ARG A 604 
 TYR   0.049   0.003   TYR A1103 
 PHE   0.017   0.002   PHE A 577 
 TRP   0.019   0.002   TRP A 532 
 HIS   0.009   0.002   HIS A 814 

Details of bonding type rmsd
  covalent geometry    : bond        0.00390 (10944)
  covalent geometry    : angle       0.77061 (14805)
  hydrogen bonds       : bond        0.04075 (   98)
  hydrogen bonds       : angle       8.44306 (  270)

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

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

  2962 Ramachandran restraints generated.
    1481 Oldfield, 0 Emsley, 1481 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2962 Ramachandran restraints generated.
    1481 Oldfield, 0 Emsley, 1481 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  262 residues out of total 1208 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 262
  time to evaluate  : 0.257 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  506 MET cc_start: 0.5901 (tpt) cc_final: 0.5478 (mmt)
REVERT: A  554 LYS cc_start: 0.8037 (ttpp) cc_final: 0.7780 (tmmt)
REVERT: A  561 MET cc_start: 0.5100 (mtm) cc_final: 0.4741 (mtm)
REVERT: A  579 MET cc_start: 0.7631 (mtp) cc_final: 0.7062 (mmm)
REVERT: A  600 TYR cc_start: 0.7720 (t80) cc_final: 0.7294 (t80)
REVERT: A  657 GLN cc_start: 0.3789 (tp40) cc_final: 0.3493 (tp-100)
REVERT: A  763 LEU cc_start: 0.7010 (mt) cc_final: 0.6715 (mt)
REVERT: A  855 MET cc_start: 0.5001 (tpt) cc_final: 0.4670 (tpt)
REVERT: A 1143 ILE cc_start: 0.8393 (mm) cc_final: 0.8159 (mm)
REVERT: A 1156 ASN cc_start: 0.6891 (t0) cc_final: 0.6209 (t0)
REVERT: A 1194 LEU cc_start: 0.8077 (tp) cc_final: 0.7646 (tp)
REVERT: A 1202 LYS cc_start: 0.8424 (pttm) cc_final: 0.7939 (ptmm)
REVERT: A 1225 ILE cc_start: 0.8285 (tt) cc_final: 0.8049 (tt)
REVERT: A 1258 LYS cc_start: 0.7413 (mmpt) cc_final: 0.7002 (mmpt)
REVERT: A 1290 ASN cc_start: 0.7351 (t0) cc_final: 0.6987 (t0)
REVERT: A 1294 ILE cc_start: 0.7948 (pt) cc_final: 0.7746 (pt)
REVERT: A 1321 ASN cc_start: 0.7799 (t0) cc_final: 0.7539 (t0)
REVERT: A 1324 LEU cc_start: 0.6956 (tp) cc_final: 0.6464 (mp)
REVERT: A 1326 LYS cc_start: 0.7784 (mmpt) cc_final: 0.7484 (mmtm)
REVERT: A 1336 MET cc_start: 0.8339 (mmt) cc_final: 0.8068 (mmm)
REVERT: A 1412 ASP cc_start: 0.7127 (t0) cc_final: 0.6900 (t0)
REVERT: A 1435 GLU cc_start: 0.6209 (mp0) cc_final: 0.5763 (mp0)
REVERT: A 1443 TYR cc_start: 0.7591 (t80) cc_final: 0.6824 (t80)
REVERT: A 1467 VAL cc_start: 0.8553 (t) cc_final: 0.8099 (p)
REVERT: A 1489 ILE cc_start: 0.7521 (mp) cc_final: 0.7294 (mp)
REVERT: A 1504 SER cc_start: 0.7568 (m) cc_final: 0.6643 (t)
REVERT: A 1506 ILE cc_start: 0.7340 (pt) cc_final: 0.7049 (mm)
REVERT: A 1527 LYS cc_start: 0.7315 (mmtt) cc_final: 0.7028 (mmmt)
REVERT: A 1720 MET cc_start: 0.7276 (ppp) cc_final: 0.6605 (ppp)
REVERT: A 1763 MET cc_start: 0.2777 (ptt) cc_final: 0.2393 (pmm)
  outliers start: 0
  outliers final: 0
  residues processed: 262
  average time/residue: 0.0859
  time to fit residues: 32.3600
Evaluate side-chains
  225 residues out of total 1208 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 225
  time to evaluate  : 0.345 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 148
   random chunks:
   chunk 45 optimal weight:    2.9990
   chunk 112 optimal weight:    1.9990
   chunk 35 optimal weight:    1.9990
   chunk 74 optimal weight:    0.9980
   chunk 135 optimal weight:    1.9990
   chunk 5 optimal weight:    2.9990
   chunk 91 optimal weight:    3.9990
   chunk 69 optimal weight:    0.9990
   chunk 17 optimal weight:    1.9990
   chunk 104 optimal weight:    2.9990
   chunk 83 optimal weight:    0.3980
   overall best weight:    1.2786

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

Flipped N/Q/H residues before XYZ refinement:
A 392 ASN
** A 487 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 515 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 530 HIS
** A 566 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 572 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 888 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 926 ASN
** A 953 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
A1137 ASN
** A1155 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A1312 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A1344 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A1372 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A1526 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A1542 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
A1704 ASN

Total number of N/Q/H flips: 5

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4422 r_free = 0.4422 target = 0.143222 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 42)----------------|
| r_work = 0.4059 r_free = 0.4059 target = 0.120168 restraints weight = 34129.571|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 30)----------------|
| r_work = 0.4115 r_free = 0.4115 target = 0.123631 restraints weight = 24213.149|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 30)----------------|
| r_work = 0.4156 r_free = 0.4156 target = 0.126257 restraints weight = 18257.527|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 33)----------------|
| r_work = 0.4190 r_free = 0.4190 target = 0.128363 restraints weight = 14342.733|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 34)----------------|
| r_work = 0.4216 r_free = 0.4216 target = 0.129987 restraints weight = 11604.581|
|-----------------------------------------------------------------------------|
r_work (final): 0.4183
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6205
moved from start:          0.7317

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.006   0.060  10944  Z= 0.260
  Angle     :  0.882  11.404  14805  Z= 0.475
  Chirality :  0.058   0.311   1756
  Planarity :  0.006   0.056   1940
  Dihedral  :  7.745  43.018   1537
  Min Nonbonded Distance : 2.368

Molprobity Statistics.
  All-atom Clashscore : 39.02
  Ramachandran Plot:
    Outliers :  0.27 %
    Allowed  : 15.80 %
    Favored  : 83.93 %
  Rotamer:
    Outliers :  0.08 %
    Allowed  :  1.90 %
    Favored  : 98.01 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 7.89 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.14 %

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 aren not related in a simple way.
  whole: -4.25 (0.17), residues: 1481
  helix: -4.10 (0.58), residues: 12
  sheet: -2.34 (0.29), residues: 304
  loop : -3.24 (0.14), residues: 1165

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.010   0.002   ARG A 622 
 TYR   0.061   0.003   TYR A1103 
 PHE   0.020   0.003   PHE A 583 
 TRP   0.025   0.003   TRP A 375 
 HIS   0.007   0.002   HIS A 814 

Details of bonding type rmsd
  covalent geometry    : bond        0.00567 (10944)
  covalent geometry    : angle       0.88177 (14805)
  hydrogen bonds       : bond        0.05327 (   98)
  hydrogen bonds       : angle       9.26485 (  270)

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

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

  2962 Ramachandran restraints generated.
    1481 Oldfield, 0 Emsley, 1481 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2962 Ramachandran restraints generated.
    1481 Oldfield, 0 Emsley, 1481 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  253 residues out of total 1208 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 252
  time to evaluate  : 0.281 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  439 ILE cc_start: 0.8049 (mm) cc_final: 0.7837 (mm)
REVERT: A  445 GLN cc_start: 0.7992 (mt0) cc_final: 0.7565 (tp40)
REVERT: A  506 MET cc_start: 0.6129 (tpt) cc_final: 0.5732 (mmt)
REVERT: A  525 LYS cc_start: 0.7716 (ptpt) cc_final: 0.7262 (ptpp)
REVERT: A  554 LYS cc_start: 0.7974 (ttpp) cc_final: 0.7755 (tmmt)
REVERT: A  561 MET cc_start: 0.5598 (mtm) cc_final: 0.5298 (mtm)
REVERT: A  600 TYR cc_start: 0.7799 (t80) cc_final: 0.7076 (t80)
REVERT: A  602 ASN cc_start: 0.7496 (t0) cc_final: 0.6573 (t0)
REVERT: A  604 ARG cc_start: 0.6374 (mtm110) cc_final: 0.6032 (mtt90)
REVERT: A  750 GLN cc_start: 0.8576 (pt0) cc_final: 0.7553 (pp30)
REVERT: A  775 LYS cc_start: 0.8516 (mmtm) cc_final: 0.8074 (mmtm)
REVERT: A  803 LYS cc_start: 0.8114 (pttm) cc_final: 0.7856 (pttp)
REVERT: A  855 MET cc_start: 0.5197 (tpt) cc_final: 0.4857 (tpt)
REVERT: A 1119 ASN cc_start: 0.8551 (m-40) cc_final: 0.8237 (m-40)
REVERT: A 1143 ILE cc_start: 0.8437 (mm) cc_final: 0.8223 (mm)
REVERT: A 1156 ASN cc_start: 0.7142 (t0) cc_final: 0.6454 (t0)
REVERT: A 1194 LEU cc_start: 0.8439 (tp) cc_final: 0.7847 (tp)
REVERT: A 1202 LYS cc_start: 0.8456 (pttm) cc_final: 0.8016 (ptmm)
REVERT: A 1225 ILE cc_start: 0.8306 (tt) cc_final: 0.8087 (tt)
REVERT: A 1258 LYS cc_start: 0.7599 (mmpt) cc_final: 0.7245 (mmpt)
REVERT: A 1290 ASN cc_start: 0.7240 (t0) cc_final: 0.6967 (t0)
REVERT: A 1294 ILE cc_start: 0.8036 (pt) cc_final: 0.7662 (pt)
REVERT: A 1305 TYR cc_start: 0.7357 (t80) cc_final: 0.6921 (t80)
REVERT: A 1321 ASN cc_start: 0.7955 (t0) cc_final: 0.7736 (t0)
REVERT: A 1326 LYS cc_start: 0.7873 (mmpt) cc_final: 0.7554 (mmtp)
REVERT: A 1336 MET cc_start: 0.8424 (mmt) cc_final: 0.8166 (mmt)
REVERT: A 1412 ASP cc_start: 0.7411 (t0) cc_final: 0.7147 (t0)
REVERT: A 1435 GLU cc_start: 0.6411 (mp0) cc_final: 0.5878 (mp0)
REVERT: A 1443 TYR cc_start: 0.7892 (t80) cc_final: 0.7105 (t80)
REVERT: A 1459 ILE cc_start: 0.8075 (mp) cc_final: 0.7702 (mp)
REVERT: A 1467 VAL cc_start: 0.8542 (t) cc_final: 0.7945 (p)
REVERT: A 1470 TYR cc_start: 0.7390 (t80) cc_final: 0.7082 (t80)
REVERT: A 1506 ILE cc_start: 0.7663 (pt) cc_final: 0.7405 (mm)
REVERT: A 1527 LYS cc_start: 0.7521 (mmtt) cc_final: 0.7317 (mmmt)
REVERT: A 1535 LYS cc_start: 0.6935 (mtpp) cc_final: 0.4850 (mttt)
REVERT: A 1564 LEU cc_start: 0.8188 (mt) cc_final: 0.7907 (mt)
REVERT: A 1581 ILE cc_start: 0.8315 (mp) cc_final: 0.8104 (mp)
REVERT: A 1694 ILE cc_start: 0.8470 (pt) cc_final: 0.8209 (pt)
REVERT: A 1720 MET cc_start: 0.6991 (ppp) cc_final: 0.6227 (ppp)
REVERT: A 1763 MET cc_start: 0.3192 (ptt) cc_final: 0.2781 (pmm)
  outliers start: 1
  outliers final: 0
  residues processed: 253
  average time/residue: 0.0914
  time to fit residues: 32.5308
Evaluate side-chains
  221 residues out of total 1208 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 221
  time to evaluate  : 0.308 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 148
   random chunks:
   chunk 120 optimal weight:    0.6980
   chunk 46 optimal weight:    3.9990
   chunk 6 optimal weight:    0.9990
   chunk 141 optimal weight:    7.9990
   chunk 12 optimal weight:    1.9990
   chunk 112 optimal weight:    0.3980
   chunk 73 optimal weight:    0.9980
   chunk 28 optimal weight:    0.3980
   chunk 78 optimal weight:    1.9990
   chunk 130 optimal weight:    1.9990
   chunk 64 optimal weight:    5.9990
   overall best weight:    0.6982

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

Flipped N/Q/H residues before XYZ refinement:
** A 487 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 493 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 500 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 515 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 530 HIS
** A 566 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 572 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 680 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 888 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 926 ASN
** A 953 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
A1137 ASN
** A1155 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A1312 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A1344 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A1372 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A1526 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A1542 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A1572 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
A1704 ASN

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4456 r_free = 0.4456 target = 0.145178 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 48)----------------|
| r_work = 0.4103 r_free = 0.4103 target = 0.122066 restraints weight = 33900.017|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 31)----------------|
| r_work = 0.4159 r_free = 0.4159 target = 0.125574 restraints weight = 24116.648|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 36)----------------|
| r_work = 0.4200 r_free = 0.4200 target = 0.128245 restraints weight = 18120.448|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 34)----------------|
| r_work = 0.4232 r_free = 0.4232 target = 0.130333 restraints weight = 14226.183|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 36)----------------|
| r_work = 0.4257 r_free = 0.4257 target = 0.131944 restraints weight = 11500.279|
|-----------------------------------------------------------------------------|
r_work (final): 0.4253
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6121
moved from start:          0.7298

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.052  10944  Z= 0.184
  Angle     :  0.803  10.721  14805  Z= 0.427
  Chirality :  0.057   0.351   1756
  Planarity :  0.005   0.059   1940
  Dihedral  :  7.110  39.849   1537
  Min Nonbonded Distance : 2.431

Molprobity Statistics.
  All-atom Clashscore : 31.91
  Ramachandran Plot:
    Outliers :  0.27 %
    Allowed  : 14.11 %
    Favored  : 85.62 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  0.75 %
    Favored  : 99.25 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 7.89 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.07 %

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 aren not related in a simple way.
  whole: -4.12 (0.18), residues: 1481
  helix: -3.92 (0.69), residues: 12
  sheet: -2.19 (0.30), residues: 297
  loop : -3.17 (0.14), residues: 1172

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.007   0.001   ARG A 604 
 TYR   0.053   0.003   TYR A1103 
 PHE   0.015   0.002   PHE A 577 
 TRP   0.018   0.002   TRP A 532 
 HIS   0.007   0.001   HIS A 814 

Details of bonding type rmsd
  covalent geometry    : bond        0.00414 (10944)
  covalent geometry    : angle       0.80303 (14805)
  hydrogen bonds       : bond        0.04317 (   98)
  hydrogen bonds       : angle       8.52451 (  270)

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

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

  2962 Ramachandran restraints generated.
    1481 Oldfield, 0 Emsley, 1481 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2962 Ramachandran restraints generated.
    1481 Oldfield, 0 Emsley, 1481 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  251 residues out of total 1208 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 251
  time to evaluate  : 0.294 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  445 GLN cc_start: 0.8019 (mt0) cc_final: 0.7599 (tp40)
REVERT: A  506 MET cc_start: 0.6051 (tpt) cc_final: 0.5555 (mmt)
REVERT: A  525 LYS cc_start: 0.7782 (ptpt) cc_final: 0.7522 (ptpt)
REVERT: A  554 LYS cc_start: 0.7946 (ttpp) cc_final: 0.7721 (tmmt)
REVERT: A  561 MET cc_start: 0.5378 (mtm) cc_final: 0.5080 (mtm)
REVERT: A  579 MET cc_start: 0.7746 (mtp) cc_final: 0.7169 (mmm)
REVERT: A  600 TYR cc_start: 0.7824 (t80) cc_final: 0.6747 (t80)
REVERT: A  602 ASN cc_start: 0.7053 (t0) cc_final: 0.5486 (t0)
REVERT: A  604 ARG cc_start: 0.6211 (mtm110) cc_final: 0.5335 (mtp85)
REVERT: A  750 GLN cc_start: 0.8427 (pt0) cc_final: 0.7374 (pp30)
REVERT: A  763 LEU cc_start: 0.6941 (mt) cc_final: 0.6675 (mt)
REVERT: A  775 LYS cc_start: 0.8377 (mmtm) cc_final: 0.8011 (mmtm)
REVERT: A  855 MET cc_start: 0.4845 (tpt) cc_final: 0.4600 (tpt)
REVERT: A  902 LYS cc_start: 0.7089 (mmtm) cc_final: 0.6856 (mmtm)
REVERT: A 1119 ASN cc_start: 0.8511 (m-40) cc_final: 0.8289 (m-40)
REVERT: A 1143 ILE cc_start: 0.8426 (mm) cc_final: 0.8198 (mm)
REVERT: A 1156 ASN cc_start: 0.7043 (t0) cc_final: 0.6352 (t0)
REVERT: A 1166 LYS cc_start: 0.7328 (mptt) cc_final: 0.7045 (mmtt)
REVERT: A 1168 ILE cc_start: 0.8081 (tt) cc_final: 0.7784 (tt)
REVERT: A 1194 LEU cc_start: 0.8089 (tp) cc_final: 0.7617 (tp)
REVERT: A 1202 LYS cc_start: 0.8445 (pttm) cc_final: 0.8010 (ptmm)
REVERT: A 1225 ILE cc_start: 0.8309 (tt) cc_final: 0.8095 (tt)
REVERT: A 1258 LYS cc_start: 0.7442 (mmpt) cc_final: 0.7039 (mmpt)
REVERT: A 1290 ASN cc_start: 0.7213 (t0) cc_final: 0.6807 (t0)
REVERT: A 1305 TYR cc_start: 0.7111 (t80) cc_final: 0.6821 (t80)
REVERT: A 1321 ASN cc_start: 0.8123 (t0) cc_final: 0.7869 (t0)
REVERT: A 1324 LEU cc_start: 0.6998 (tp) cc_final: 0.6064 (mp)
REVERT: A 1332 SER cc_start: 0.7962 (m) cc_final: 0.7713 (p)
REVERT: A 1335 ILE cc_start: 0.8564 (mm) cc_final: 0.8271 (mm)
REVERT: A 1336 MET cc_start: 0.8369 (mmt) cc_final: 0.7793 (mmm)
REVERT: A 1412 ASP cc_start: 0.7325 (t0) cc_final: 0.7050 (t0)
REVERT: A 1435 GLU cc_start: 0.6269 (mp0) cc_final: 0.5759 (mp0)
REVERT: A 1443 TYR cc_start: 0.7733 (t80) cc_final: 0.6934 (t80)
REVERT: A 1470 TYR cc_start: 0.7318 (t80) cc_final: 0.6887 (t80)
REVERT: A 1506 ILE cc_start: 0.7629 (pt) cc_final: 0.7329 (mm)
REVERT: A 1527 LYS cc_start: 0.7445 (mmtt) cc_final: 0.6879 (mmmm)
REVERT: A 1535 LYS cc_start: 0.6821 (mtpp) cc_final: 0.4985 (mttt)
REVERT: A 1720 MET cc_start: 0.6985 (ppp) cc_final: 0.6309 (ppp)
  outliers start: 0
  outliers final: 0
  residues processed: 251
  average time/residue: 0.0912
  time to fit residues: 32.3094
Evaluate side-chains
  219 residues out of total 1208 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 219
  time to evaluate  : 0.239 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 148
   random chunks:
   chunk 47 optimal weight:    1.9990
   chunk 59 optimal weight:    0.9980
   chunk 2 optimal weight:    1.9990
   chunk 50 optimal weight:    0.1980
   chunk 38 optimal weight:    0.0470
   chunk 60 optimal weight:    0.0980
   chunk 109 optimal weight:    0.0000
   chunk 108 optimal weight:    3.9990
   chunk 53 optimal weight:    0.9980
   chunk 48 optimal weight:    0.7980
   chunk 26 optimal weight:    2.9990
   overall best weight:    0.2282

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

Flipped N/Q/H residues before XYZ refinement:
** A 493 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 515 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 530 HIS
** A 566 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 572 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 641 ASN
A 657 GLN
** A 888 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 926 ASN
** A1312 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
A1372 ASN
** A1572 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
A1704 ASN

Total number of N/Q/H flips: 6

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4465 r_free = 0.4465 target = 0.138818 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.4104 r_free = 0.4104 target = 0.116005 restraints weight = 33944.794|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 34)----------------|
| r_work = 0.4164 r_free = 0.4164 target = 0.119576 restraints weight = 24279.917|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 34)----------------|
| r_work = 0.4209 r_free = 0.4209 target = 0.122346 restraints weight = 18258.950|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 31)----------------|
| r_work = 0.4243 r_free = 0.4243 target = 0.124465 restraints weight = 14255.732|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 33)----------------|
| r_work = 0.4270 r_free = 0.4270 target = 0.126175 restraints weight = 11446.597|
|-----------------------------------------------------------------------------|
r_work (final): 0.4310
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.5999
moved from start:          0.7305

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.044  10944  Z= 0.145
  Angle     :  0.758   9.658  14805  Z= 0.404
  Chirality :  0.056   0.284   1756
  Planarity :  0.005   0.059   1940
  Dihedral  :  6.533  36.302   1537
  Min Nonbonded Distance : 2.452

Molprobity Statistics.
  All-atom Clashscore : 25.68
  Ramachandran Plot:
    Outliers :  0.34 %
    Allowed  : 11.68 %
    Favored  : 87.98 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  0.75 %
    Favored  : 99.25 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 7.89 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.07 %

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 aren not related in a simple way.
  whole: -3.92 (0.18), residues: 1481
  helix: -4.14 (0.56), residues: 12
  sheet: -2.28 (0.29), residues: 318
  loop : -2.93 (0.15), residues: 1151

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.006   0.001   ARG A 604 
 TYR   0.042   0.002   TYR A1103 
 PHE   0.029   0.002   PHE A 577 
 TRP   0.008   0.001   TRP A 532 
 HIS   0.007   0.001   HIS A 814 

Details of bonding type rmsd
  covalent geometry    : bond        0.00330 (10944)
  covalent geometry    : angle       0.75830 (14805)
  hydrogen bonds       : bond        0.03713 (   98)
  hydrogen bonds       : angle       8.05304 (  270)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 1871.48 seconds
wall clock time: 33 minutes 40.19 seconds (2020.19 seconds total)