Starting phenix.real_space_refine
on Wed Sep 17 18:27:09 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/9ken_62292/09_2025/9ken_62292.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/9ken_62292/09_2025/9ken_62292.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=3.63
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/cci-nas-00/data/ceres_data/9ken_62292/09_2025/9ken_62292.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/9ken_62292/09_2025/9ken_62292.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/9ken_62292/09_2025/9ken_62292.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/9ken_62292/09_2025/9ken_62292.cif"
  }
  resolution = 3.63
  write_initial_geo_file = False
  refinement {
    macro_cycles = 10
  }


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

Validating inputs
Origin is already at (0, 0, 0), no shifts will be applied
-------------------------------------------------------------------------------
Processing inputs
*****************
Set random seed
  Set to: 0
Set model cs if undefined
Decide on map wrapping
  Map wrapping is set to: False
Normalize map: mean=0, sd=1
  Input map: mean=   0.000 sd=   0.001
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      63      5.16       5
     C    6438      2.51       5
     N    1708      2.21       5
     O    1874      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 5 residue(s): 0.01s

  Monomer Library directory:
    "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5805/lib/python3.9/site-packages/chem_data/mon_lib"
  Total number of atoms: 10083
  Number of models: 1
  Model: ""
    Number of chains: 3
    Chain: "C"
      Number of atoms: 597
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 76, 597
          Classifications: {'peptide': 76}
          Incomplete info: {'truncation_to_alanine': 1}
          Link IDs: {'PTRANS': 3, 'TRANS': 72}
          Unresolved non-hydrogen bonds: 4
          Unresolved non-hydrogen angles: 5
          Unresolved non-hydrogen dihedrals: 3
          Planarities with less than four sites: {'GLU:plan': 1}
          Unresolved non-hydrogen planarities: 4
    Chain: "D"
      Number of atoms: 581
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 74, 581
          Classifications: {'peptide': 74}
          Incomplete info: {'truncation_to_alanine': 2}
          Link IDs: {'PTRANS': 3, 'TRANS': 70}
          Unresolved non-hydrogen bonds: 9
          Unresolved non-hydrogen angles: 10
          Unresolved non-hydrogen dihedrals: 8
          Planarities with less than four sites: {'ARG:plan': 1}
          Unresolved non-hydrogen planarities: 5
    Chain: "A"
      Number of atoms: 8905
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 1124, 8905
          Classifications: {'peptide': 1124}
          Incomplete info: {'truncation_to_alanine': 10}
          Link IDs: {'PCIS': 2, 'PTRANS': 54, 'TRANS': 1067}
          Chain breaks: 7
          Unresolved non-hydrogen bonds: 37
          Unresolved non-hydrogen angles: 46
          Unresolved non-hydrogen dihedrals: 28
          Unresolved non-hydrogen chiralities: 1
          Planarities with less than four sites: {'ASN:plan1': 1, 'GLN:plan1': 3, 'GLU:plan': 3, 'ASP:plan': 1}
          Unresolved non-hydrogen planarities: 30
  Residues with excluded nonbonded symmetry interactions: 3
    residue:
      pdb=" N   LEU C  73 " occ=0.45
      ... (6 atoms not shown)
      pdb=" CD2 LEU C  73 " occ=0.45
    residue:
      pdb=" N   LEU D  73 " occ=0.45
      ... (6 atoms not shown)
      pdb=" CD2 LEU D  73 " occ=0.45
    residue:
      pdb=" N   ARG D  74 " occ=0.45
      ... (3 atoms not shown)
      pdb=" CB  ARG D  74 " occ=0.45
  Time building chain proxies: 2.25, per 1000 atoms: 0.22
  Number of scatterers: 10083
  At special positions: 0
  Unit cell: (116.352, 84.84, 133.32, 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      63     16.00
     O    1874      8.00
     N    1708      7.00
     C    6438      6.00
    sf(0) = scattering factor at diffraction angle 0.

  Number of disulfides: simple=1, symmetry=0
    Simple disulfide: pdb=" SG  CYS A 589 " - pdb=" SG  CYS A 625 " distance=2.01

  Automatic linking
    Parameters for automatic linking
      Linking & cutoffs
        Metal                : Auto  - 3.00
        Amino acid           : True  - 1.90
        Carbohydrate         : True  - 1.99
        Ligands              : True  - 1.99
        Small molecules      : False - 1.98
        Amino acid - RNA/DNA : False
      
  Number of custom bonds: simple=0, symmetry=0
  Time building additional restraints: 1.03
  Conformation dependent library (CDL) restraints added in 392.6 milliseconds
  
  Enol-peptide restraints added in 715.3 nanoseconds
  

  2508 Ramachandran restraints generated.
    1254 Oldfield, 0 Emsley, 1254 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  2428

  Finding SS restraints...
    Secondary structure from input PDB file:
      68 helices and 5 sheets defined
      57.3% alpha, 3.1% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 0.41
  Creating SS restraints...
    Processing helix  chain 'C' and resid 22 through 27
    Processing helix  chain 'C' and resid 27 through 35
      removed outlier: 3.625A  pdb=" N   GLN C  31 " --> pdb=" O   LYS C  27 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 24 through 29
    Processing helix  chain 'A' and resid 450 through 467
      removed outlier: 3.952A  pdb=" N   ILE A 459 " --> pdb=" O   LEU A 455 " (cutoff:3.500A)
      removed outlier: 3.695A  pdb=" N   LEU A 465 " --> pdb=" O   MET A 461 " (cutoff:3.500A)
      removed outlier: 3.660A  pdb=" N   MET A 467 " --> pdb=" O   GLN A 463 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 477 through 491
      Proline residue:  A 483  - end of helix
    Processing helix  chain 'A' and resid 494 through 512
      removed outlier: 3.525A  pdb=" N   HIS A 500 " --> pdb=" O   ASP A 496 " (cutoff:3.500A)
      removed outlier: 3.598A  pdb=" N   ALA A 501 " --> pdb=" O   ILE A 497 " (cutoff:3.500A)
      removed outlier: 4.159A  pdb=" N   MET A 509 " --> pdb=" O   LEU A 505 " (cutoff:3.500A)
      removed outlier: 4.376A  pdb=" N   GLU A 510 " --> pdb=" O   THR A 506 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 515 through 520
      removed outlier: 3.796A  pdb=" N   VAL A 520 " --> pdb=" O   SER A 516 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 522 through 532
    Processing helix  chain 'A' and resid 535 through 548
      removed outlier: 3.664A  pdb=" N   GLN A 541 " --> pdb=" O   ASP A 537 " (cutoff:3.500A)
      removed outlier: 3.862A  pdb=" N   THR A 544 " --> pdb=" O   GLU A 540 " (cutoff:3.500A)
      removed outlier: 3.635A  pdb=" N   MET A 548 " --> pdb=" O   THR A 544 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 553 through 560
      removed outlier: 3.621A  pdb=" N   LEU A 558 " --> pdb=" O   SER A 554 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 561 through 567
      removed outlier: 3.979A  pdb=" N   ASP A 565 " --> pdb=" O   GLY A 561 " (cutoff:3.500A)
      removed outlier: 3.631A  pdb=" N   LEU A 567 " --> pdb=" O   LEU A 563 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 574 through 589
      removed outlier: 3.628A  pdb=" N   ALA A 583 " --> pdb=" O   ARG A 579 " (cutoff:3.500A)
      removed outlier: 3.573A  pdb=" N   ASN A 587 " --> pdb=" O   ALA A 583 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 593 through 595
      No H-bonds generated for 'chain 'A' and resid 593 through 595'
    Processing helix  chain 'A' and resid 596 through 611
      removed outlier: 4.393A  pdb=" N   VAL A 600 " --> pdb=" O   GLU A 596 " (cutoff:3.500A)
      removed outlier: 4.080A  pdb=" N   ASP A 602 " --> pdb=" O   HIS A 598 " (cutoff:3.500A)
      removed outlier: 4.288A  pdb=" N   SER A 603 " --> pdb=" O   PHE A 599 " (cutoff:3.500A)
      Proline residue:  A 605  - end of helix
      removed outlier: 3.636A  pdb=" N   GLN A 609 " --> pdb=" O   PRO A 605 " (cutoff:3.500A)
      removed outlier: 3.606A  pdb=" N   LEU A 611 " --> pdb=" O   LEU A 607 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 615 through 630
      removed outlier: 3.630A  pdb=" N   SER A 621 " --> pdb=" O   LYS A 617 " (cutoff:3.500A)
      removed outlier: 4.242A  pdb=" N   LEU A 624 " --> pdb=" O   GLU A 620 " (cutoff:3.500A)
      removed outlier: 3.859A  pdb=" N   CYS A 625 " --> pdb=" O   SER A 621 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 636 through 644
      removed outlier: 3.727A  pdb=" N   GLN A 642 " --> pdb=" O   ASN A 638 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 647 through 657
      removed outlier: 4.173A  pdb=" N   GLN A 653 " --> pdb=" O   LEU A 649 " (cutoff:3.500A)
      removed outlier: 4.075A  pdb=" N   VAL A 657 " --> pdb=" O   GLN A 653 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 667 through 680
      removed outlier: 3.505A  pdb=" N   VAL A 672 " --> pdb=" O   PHE A 668 " (cutoff:3.500A)
      removed outlier: 3.509A  pdb=" N   PHE A 675 " --> pdb=" O   VAL A 671 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 682 through 692
    Processing helix  chain 'A' and resid 693 through 703
      removed outlier: 3.978A  pdb=" N   THR A 697 " --> pdb=" O   ASN A 693 " (cutoff:3.500A)
      removed outlier: 3.672A  pdb=" N   LEU A 702 " --> pdb=" O   LEU A 698 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 722 through 730
      removed outlier: 3.688A  pdb=" N   GLU A 726 " --> pdb=" O   GLN A 722 " (cutoff:3.500A)
      removed outlier: 3.571A  pdb=" N   THR A 728 " --> pdb=" O   LEU A 724 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 731 through 734
      removed outlier: 3.663A  pdb=" N   LEU A 734 " --> pdb=" O   ILE A 731 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'A' and resid 731 through 734'
    Processing helix  chain 'A' and resid 742 through 745
    Processing helix  chain 'A' and resid 746 through 751
      removed outlier: 3.832A  pdb=" N   LYS A 751 " --> pdb=" O   ASP A 747 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 818 through 827
      removed outlier: 3.672A  pdb=" N   LYS A 825 " --> pdb=" O   ALA A 821 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 827 through 849
      removed outlier: 3.592A  pdb=" N   ALA A 831 " --> pdb=" O   ASP A 827 " (cutoff:3.500A)
      removed outlier: 4.497A  pdb=" N   THR A 837 " --> pdb=" O   SER A 833 " (cutoff:3.500A)
      removed outlier: 5.886A  pdb=" N   GLY A 840 " --> pdb=" O   LYS A 836 " (cutoff:3.500A)
      removed outlier: 4.291A  pdb=" N   VAL A 841 " --> pdb=" O   THR A 837 " (cutoff:3.500A)
      removed outlier: 3.779A  pdb=" N   LEU A 842 " --> pdb=" O   LEU A 838 " (cutoff:3.500A)
      removed outlier: 3.663A  pdb=" N   SER A 849 " --> pdb=" O   VAL A 845 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 853 through 869
      removed outlier: 3.629A  pdb=" N   LEU A 859 " --> pdb=" O   ARG A 855 " (cutoff:3.500A)
      removed outlier: 3.914A  pdb=" N   ILE A 862 " --> pdb=" O   CYS A 858 " (cutoff:3.500A)
      removed outlier: 3.503A  pdb=" N   PHE A 868 " --> pdb=" O   ARG A 864 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 870 through 878
      removed outlier: 3.666A  pdb=" N   LEU A 874 " --> pdb=" O   ASP A 870 " (cutoff:3.500A)
      removed outlier: 3.803A  pdb=" N   ASP A 876 " --> pdb=" O   GLU A 872 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 879 through 881
      No H-bonds generated for 'chain 'A' and resid 879 through 881'
    Processing helix  chain 'A' and resid 882 through 892
      removed outlier: 3.754A  pdb=" N   HIS A 886 " --> pdb=" O   ALA A 882 " (cutoff:3.500A)
      removed outlier: 3.764A  pdb=" N   ALA A 888 " --> pdb=" O   SER A 884 " (cutoff:3.500A)
      removed outlier: 3.570A  pdb=" N   SER A 889 " --> pdb=" O   SER A 885 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 896 through 913
      removed outlier: 3.543A  pdb=" N   MET A 910 " --> pdb=" O   ALA A 906 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 925 through 936
    Processing helix  chain 'A' and resid 1082 through 1105
      removed outlier: 3.913A  pdb=" N   ARG A1086 " --> pdb=" O   ILE A1082 " (cutoff:3.500A)
      removed outlier: 4.946A  pdb=" N   GLU A1087 " --> pdb=" O   SER A1083 " (cutoff:3.500A)
      removed outlier: 3.779A  pdb=" N   LYS A1088 " --> pdb=" O   ASN A1084 " (cutoff:3.500A)
      removed outlier: 3.664A  pdb=" N   GLU A1095 " --> pdb=" O   GLY A1091 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 1118 through 1126
    Processing helix  chain 'A' and resid 1138 through 1148
      removed outlier: 3.700A  pdb=" N   VAL A1142 " --> pdb=" O   ALA A1138 " (cutoff:3.500A)
      removed outlier: 4.781A  pdb=" N   ILE A1144 " --> pdb=" O   CYS A1140 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 1164 through 1172
      removed outlier: 4.456A  pdb=" N   TYR A1170 " --> pdb=" O   GLN A1166 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 1181 through 1193
    Processing helix  chain 'A' and resid 1212 through 1230
    Processing helix  chain 'A' and resid 1449 through 1454
      removed outlier: 4.124A  pdb=" N   TYR A1453 " --> pdb=" O   PRO A1449 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 1468 through 1484
      removed outlier: 3.503A  pdb=" N   LEU A1473 " --> pdb=" O   LEU A1469 " (cutoff:3.500A)
      removed outlier: 3.626A  pdb=" N   VAL A1477 " --> pdb=" O   LEU A1473 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 1485 through 1488
    Processing helix  chain 'A' and resid 1505 through 1517
      removed outlier: 3.575A  pdb=" N   ALA A1510 " --> pdb=" O   SER A1506 " (cutoff:3.500A)
      removed outlier: 3.736A  pdb=" N   GLN A1517 " --> pdb=" O   ASN A1513 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 1518 through 1525
      removed outlier: 3.724A  pdb=" N   ILE A1522 " --> pdb=" O   ASP A1518 " (cutoff:3.500A)
      removed outlier: 3.878A  pdb=" N   THR A1524 " --> pdb=" O   LEU A1520 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 1528 through 1538
      removed outlier: 3.938A  pdb=" N   THR A1532 " --> pdb=" O   PRO A1528 " (cutoff:3.500A)
      removed outlier: 3.713A  pdb=" N   GLU A1533 " --> pdb=" O   THR A1529 " (cutoff:3.500A)
      removed outlier: 3.519A  pdb=" N   THR A1537 " --> pdb=" O   GLU A1533 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 1539 through 1542
    Processing helix  chain 'A' and resid 1543 through 1555
      removed outlier: 3.938A  pdb=" N   VAL A1553 " --> pdb=" O   MET A1549 " (cutoff:3.500A)
      removed outlier: 3.566A  pdb=" N   ALA A1555 " --> pdb=" O   PHE A1551 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 1559 through 1569
      removed outlier: 3.583A  pdb=" N   THR A1568 " --> pdb=" O   ARG A1564 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 1597 through 1606
    Processing helix  chain 'A' and resid 1627 through 1642
      removed outlier: 4.121A  pdb=" N   THR A1631 " --> pdb=" O   GLY A1627 " (cutoff:3.500A)
      removed outlier: 4.096A  pdb=" N   ALA A1636 " --> pdb=" O   LEU A1632 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 1686 through 1694
      removed outlier: 3.748A  pdb=" N   ALA A1691 " --> pdb=" O   PRO A1687 " (cutoff:3.500A)
      removed outlier: 3.757A  pdb=" N   VAL A1693 " --> pdb=" O   HIS A1689 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 1695 through 1710
      removed outlier: 3.545A  pdb=" N   LYS A1706 " --> pdb=" O   LYS A1702 " (cutoff:3.500A)
      removed outlier: 3.520A  pdb=" N   ILE A1708 " --> pdb=" O   MET A1704 " (cutoff:3.500A)
      removed outlier: 3.518A  pdb=" N   MET A1709 " --> pdb=" O   ALA A1705 " (cutoff:3.500A)
      removed outlier: 3.700A  pdb=" N   ASP A1710 " --> pdb=" O   LYS A1706 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 1719 through 1727
      removed outlier: 4.079A  pdb=" N   TYR A1723 " --> pdb=" O   GLY A1719 " (cutoff:3.500A)
      removed outlier: 3.795A  pdb=" N   LYS A1724 " --> pdb=" O   LEU A1720 " (cutoff:3.500A)
      removed outlier: 3.595A  pdb=" N   TRP A1725 " --> pdb=" O   PRO A1721 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 1729 through 1733
      removed outlier: 3.702A  pdb=" N   LEU A1733 " --> pdb=" O   GLU A1730 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 1734 through 1739
      removed outlier: 3.798A  pdb=" N   PHE A1739 " --> pdb=" O   SER A1735 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 1744 through 1764
      removed outlier: 3.837A  pdb=" N   SER A1748 " --> pdb=" O   VAL A1744 " (cutoff:3.500A)
      removed outlier: 4.250A  pdb=" N   ILE A1755 " --> pdb=" O   HIS A1751 " (cutoff:3.500A)
      removed outlier: 3.690A  pdb=" N   LEU A1762 " --> pdb=" O   GLN A1758 " (cutoff:3.500A)
      removed outlier: 3.817A  pdb=" N   GLN A1764 " --> pdb=" O   LYS A1760 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 1781 through 1785
      removed outlier: 3.716A  pdb=" N   GLY A1784 " --> pdb=" O   THR A1781 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 1786 through 1791
      removed outlier: 3.712A  pdb=" N   LEU A1790 " --> pdb=" O   SER A1786 " (cutoff:3.500A)
      removed outlier: 3.645A  pdb=" N   GLY A1791 " --> pdb=" O   VAL A1787 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'A' and resid 1786 through 1791'
    Processing helix  chain 'A' and resid 1807 through 1811
    Processing helix  chain 'A' and resid 1817 through 1831
      removed outlier: 3.778A  pdb=" N   ILE A1826 " --> pdb=" O   LEU A1822 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 1834 through 1846
      removed outlier: 3.627A  pdb=" N   PHE A1838 " --> pdb=" O   VAL A1834 " (cutoff:3.500A)
      removed outlier: 4.137A  pdb=" N   SER A1840 " --> pdb=" O   ARG A1836 " (cutoff:3.500A)
      removed outlier: 3.645A  pdb=" N   ASP A1843 " --> pdb=" O   ASP A1839 " (cutoff:3.500A)
      removed outlier: 3.872A  pdb=" N   GLU A1846 " --> pdb=" O   ARG A1842 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 1852 through 1857
      removed outlier: 4.240A  pdb=" N   TYR A1856 " --> pdb=" O   HIS A1853 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 1862 through 1867
      removed outlier: 3.728A  pdb=" N   LEU A1866 " --> pdb=" O   LEU A1862 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 1875 through 1883
      removed outlier: 3.524A  pdb=" N   GLU A1881 " --> pdb=" O   LYS A1877 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 1893 through 1904
      removed outlier: 3.815A  pdb=" N   GLU A1901 " --> pdb=" O   LYS A1897 " (cutoff:3.500A)
      removed outlier: 3.849A  pdb=" N   ILE A1902 " --> pdb=" O   PHE A1898 " (cutoff:3.500A)
      removed outlier: 3.633A  pdb=" N   SER A1904 " --> pdb=" O   PHE A1900 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 1909 through 1919
    Processing helix  chain 'A' and resid 1927 through 1932
      removed outlier: 4.108A  pdb=" N   ARG A1930 " --> pdb=" O   GLY A1927 " (cutoff:3.500A)
      removed outlier: 3.790A  pdb=" N   SER A1931 " --> pdb=" O   GLY A1928 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 1948 through 1952
      removed outlier: 3.787A  pdb=" N   PHE A1952 " --> pdb=" O   PRO A1949 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 1970 through 1984
      removed outlier: 4.270A  pdb=" N   MET A1974 " --> pdb=" O   SER A1970 " (cutoff:3.500A)
      removed outlier: 4.202A  pdb=" N   LEU A1979 " --> pdb=" O   ARG A1975 " (cutoff:3.500A)
      removed outlier: 3.552A  pdb=" N   ARG A1983 " --> pdb=" O   LEU A1979 " (cutoff:3.500A)
    Processing sheet with id=AA1, first strand: chain 'C' and resid 13 through 15
      removed outlier: 3.534A  pdb=" N   LEU C  15 " --> pdb=" O   ILE C   3 " (cutoff:3.500A)
      removed outlier: 3.654A  pdb=" N   ILE C   3 " --> pdb=" O   LEU C  15 " (cutoff:3.500A)
      removed outlier: 6.843A  pdb=" N   PHE C   4 " --> pdb=" O   LEU C  67 " (cutoff:3.500A)
      removed outlier: 7.923A  pdb=" N   LEU C  69 " --> pdb=" O   PHE C   4 " (cutoff:3.500A)
    Processing sheet with id=AA2, first strand: chain 'D' and resid 13 through 16
      removed outlier: 9.482A  pdb=" N   LEU D  67 " --> pdb=" O   GLN D   2 " (cutoff:3.500A)
      removed outlier: 7.182A  pdb=" N   PHE D   4 " --> pdb=" O   LEU D  67 " (cutoff:3.500A)
      removed outlier: 8.144A  pdb=" N   LEU D  69 " --> pdb=" O   PHE D   4 " (cutoff:3.500A)
      removed outlier: 4.001A  pdb=" N   LYS D  48 " --> pdb=" O   PHE D  45 " (cutoff:3.500A)
    Processing sheet with id=AA3, first strand: chain 'A' and resid 1588 through 1590
      removed outlier: 6.790A  pdb=" N   LYS A1589 " --> pdb=" O   GLU A1617 " (cutoff:3.500A)
  No H-bonds generated for sheet with id=AA3
    Processing sheet with id=AA4, first strand: chain 'A' and resid 1653 through 1654
      removed outlier: 3.708A  pdb=" N   GLU A1653 " --> pdb=" O   GLN A1671 " (cutoff:3.500A)
    Processing sheet with id=AA5, first strand: chain 'A' and resid 1884 through 1886
      removed outlier: 3.506A  pdb=" N   ILE A1938 " --> pdb=" O   ARG A1884 " (cutoff:3.500A)

    374 hydrogen bonds defined for protein.
    1080 hydrogen bond angles defined for protein.
    Restraints generated for nucleic acids:
      0 hydrogen bonds
      0 hydrogen bond angles
      0 basepair planarities
      0 basepair parallelities
      0 stacking parallelities
  Total time for adding SS restraints: 1.65

  Time building geometry restraints manager: 1.33 seconds

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

  Histogram of bond lengths:
        1.21 -     1.33: 3060
        1.33 -     1.46: 1936
        1.46 -     1.58: 5177
        1.58 -     1.70: 0
        1.70 -     1.82: 99
  Bond restraints: 10272
  Sorted by residual:
  bond pdb=" CB  ILE A1498 "
       pdb=" CG2 ILE A1498 "
    ideal  model  delta    sigma   weight residual
    1.521  1.431  0.090 3.30e-02 9.18e+02 7.36e+00
  bond pdb=" C   LEU A1198 "
       pdb=" N   PRO A1199 "
    ideal  model  delta    sigma   weight residual
    1.332  1.360 -0.028 1.12e-02 7.97e+03 6.42e+00
  bond pdb=" CG  LEU A1700 "
       pdb=" CD2 LEU A1700 "
    ideal  model  delta    sigma   weight residual
    1.521  1.456  0.065 3.30e-02 9.18e+02 3.87e+00
  bond pdb=" CB  VAL A1918 "
       pdb=" CG1 VAL A1918 "
    ideal  model  delta    sigma   weight residual
    1.521  1.456  0.065 3.30e-02 9.18e+02 3.85e+00
  bond pdb=" N   ILE D  13 "
       pdb=" CA  ILE D  13 "
    ideal  model  delta    sigma   weight residual
    1.459  1.435  0.024 1.25e-02 6.40e+03 3.76e+00
  ... (remaining 10267 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     2.56: 13466
        2.56 -     5.11: 392
        5.11 -     7.67: 32
        7.67 -    10.23: 2
       10.23 -    12.79: 1
  Bond angle restraints: 13893
  Sorted by residual:
  angle pdb=" C   VAL A1848 "
        pdb=" N   PHE A1849 "
        pdb=" CA  PHE A1849 "
      ideal   model   delta    sigma   weight residual
     122.26  127.04   -4.78 1.10e+00 8.26e-01 1.89e+01
  angle pdb=" C   ASP C  21 "
        pdb=" N   THR C  22 "
        pdb=" CA  THR C  22 "
      ideal   model   delta    sigma   weight residual
     120.95  127.65   -6.70 1.78e+00 3.16e-01 1.42e+01
  angle pdb=" C   PRO C  19 "
        pdb=" N   SER C  20 "
        pdb=" CA  SER C  20 "
      ideal   model   delta    sigma   weight residual
     121.54  128.72   -7.18 1.91e+00 2.74e-01 1.41e+01
  angle pdb=" N   ARG C  74 "
        pdb=" CA  ARG C  74 "
        pdb=" C   ARG C  74 "
      ideal   model   delta    sigma   weight residual
     114.75  110.19    4.56 1.26e+00 6.30e-01 1.31e+01
  angle pdb=" C   ARG C  72 "
        pdb=" N   LEU C  73 "
        pdb=" CA  LEU C  73 "
      ideal   model   delta    sigma   weight residual
     122.44  118.16    4.28 1.19e+00 7.06e-01 1.29e+01
  ... (remaining 13888 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    14.82: 5939
       14.82 -    29.64: 311
       29.64 -    44.46: 46
       44.46 -    59.28: 2
       59.28 -    74.10: 3
  Dihedral angle restraints: 6301
    sinusoidal: 2580
      harmonic: 3721
  Sorted by residual:
  dihedral pdb=" CA  HIS A1160 "
           pdb=" C   HIS A1160 "
           pdb=" N   SER A1161 "
           pdb=" CA  SER A1161 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  145.60   34.40     0      5.00e+00 4.00e-02 4.73e+01
  dihedral pdb=" CA  GLU A1128 "
           pdb=" C   GLU A1128 "
           pdb=" N   GLN A1129 "
           pdb=" CA  GLN A1129 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  147.68   32.32     0      5.00e+00 4.00e-02 4.18e+01
  dihedral pdb=" CA  VAL A1848 "
           pdb=" C   VAL A1848 "
           pdb=" N   PHE A1849 "
           pdb=" CA  PHE A1849 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00 -151.13  -28.87     0      5.00e+00 4.00e-02 3.33e+01
  ... (remaining 6298 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.052: 1053
       0.052 -    0.103: 442
       0.103 -    0.155: 91
       0.155 -    0.206: 14
       0.206 -    0.258: 2
  Chirality restraints: 1602
  Sorted by residual:
  chirality pdb=" CB  ILE D  61 "
            pdb=" CA  ILE D  61 "
            pdb=" CG1 ILE D  61 "
            pdb=" CG2 ILE D  61 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.64    2.39    0.26 2.00e-01 2.50e+01 1.66e+00
  chirality pdb=" CB  VAL D  26 "
            pdb=" CA  VAL D  26 "
            pdb=" CG1 VAL D  26 "
            pdb=" CG2 VAL D  26 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.63   -2.42   -0.21 2.00e-01 2.50e+01 1.13e+00
  chirality pdb=" CA  LEU A 604 "
            pdb=" N   LEU A 604 "
            pdb=" C   LEU A 604 "
            pdb=" CB  LEU A 604 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.31    0.20 2.00e-01 2.50e+01 9.85e-01
  ... (remaining 1599 not shown)

  Planarity restraints: 1785
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   SER A 720 "   -0.053 5.00e-02 4.00e+02   8.02e-02 1.03e+01
        pdb=" N   PRO A 721 "    0.139 5.00e-02 4.00e+02
        pdb=" CA  PRO A 721 "   -0.042 5.00e-02 4.00e+02
        pdb=" CD  PRO A 721 "   -0.044 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   LEU A 604 "   -0.047 5.00e-02 4.00e+02   7.08e-02 8.01e+00
        pdb=" N   PRO A 605 "    0.122 5.00e-02 4.00e+02
        pdb=" CA  PRO A 605 "   -0.035 5.00e-02 4.00e+02
        pdb=" CD  PRO A 605 "   -0.040 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   GLU C  18 "   -0.039 5.00e-02 4.00e+02   6.03e-02 5.82e+00
        pdb=" N   PRO C  19 "    0.104 5.00e-02 4.00e+02
        pdb=" CA  PRO C  19 "   -0.031 5.00e-02 4.00e+02
        pdb=" CD  PRO C  19 "   -0.034 5.00e-02 4.00e+02
  ... (remaining 1782 not shown)

  Histogram of nonbonded interaction distances:
        2.23 -     2.76: 2052
        2.76 -     3.30: 9203
        3.30 -     3.83: 16082
        3.83 -     4.37: 19721
        4.37 -     4.90: 31911
  Nonbonded interactions: 78969
  Sorted by model distance:
  nonbonded pdb=" OG1 THR D  22 "
            pdb=" OH  TYR A1962 "
     model   vdw
     2.231 3.040
  nonbonded pdb=" OG  SER A 665 "
            pdb=" OE2 GLU A 723 "
     model   vdw
     2.259 3.040
  nonbonded pdb=" O   GLN A 609 "
            pdb=" OG1 THR A 612 "
     model   vdw
     2.292 3.040
  nonbonded pdb=" OD2 ASP A1466 "
            pdb=" OG  SER A1468 "
     model   vdw
     2.299 3.040
  nonbonded pdb=" O   LEU A1915 "
            pdb=" OG1 THR A1919 "
     model   vdw
     2.301 3.040
  ... (remaining 78964 not shown)

  NOTE: a complete listing of the restraints can be obtained by requesting
        output of .geo file.
Find NCS groups from input model
Time spend for trying shortcut: 0.00
Found NCS groups:
ncs_group {
  reference = (chain 'C' and ((resid 1 and (name N or name CA or name C or name O or name CB ) \ 
) or resid 2 through 28 or resid 30 through 73 or (resid 74 and (name N or name  \ 
CA or name C or name O or name CB ))))
  selection = (chain 'D' and (resid 1 through 28 or resid 30 through 50 or (resid 51 and (name \ 
 N or name CA or name C or name O or name CB )) or resid 52 through 74))
}

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=0.45 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:             1.680
  Set stop_for_unknowns flag:              0.000
  Assert model is a single copy model:     0.000
  Assert all atoms have isotropic ADPs:    0.000
  Construct map_model_manager:             0.010
  Extract box with map and model:          0.150
  Check model and map are aligned:         0.010
  Set scattering table:                    0.030
  Process input model:                     10.890
  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:             0.010
  Load rotamer database and sin/cos tables:1.440
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   14.290
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7424
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      :  0.009   0.090  10273  Z= 0.394
  Angle     :  0.995  12.786  13895  Z= 0.540
  Chirality :  0.056   0.258   1602
  Planarity :  0.008   0.080   1785
  Dihedral  :  9.448  74.097   3870
  Min Nonbonded Distance : 2.231

Molprobity Statistics.
  All-atom Clashscore : 6.91
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.46 %
    Favored  : 93.54 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  1.60 %
    Favored  : 98.40 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 3.23 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.17 %

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: -5.03 (0.18), residues: 1254
  helix: -4.02 (0.11), residues: 639
  sheet: -3.22 (0.69), residues: 48
  loop : -2.32 (0.24), residues: 567

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.008   0.001   ARG A1823 
 TYR   0.023   0.003   TYR A 920 
 PHE   0.033   0.004   PHE A 626 
 TRP   0.029   0.004   TRP A1092 
 HIS   0.013   0.002   HIS A1479 

Details of bonding type rmsd
  covalent geometry    : bond        0.00940 (10272)
  covalent geometry    : angle       0.99380 (13893)
  SS BOND              : bond        0.01770 (    1)
  SS BOND              : angle       3.89403 (    2)
  hydrogen bonds       : bond        0.30636 (  374)
  hydrogen bonds       : angle      10.14728 ( 1080)

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

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

  2508 Ramachandran restraints generated.
    1254 Oldfield, 0 Emsley, 1254 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2508 Ramachandran restraints generated.
    1254 Oldfield, 0 Emsley, 1254 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  322 residues out of total 1139 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 322
  time to evaluate  : 0.487 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: C   30 ILE cc_start: 0.8886 (mm) cc_final: 0.8685 (mm)
REVERT: D    6 LYS cc_start: 0.7924 (ttpt) cc_final: 0.7507 (ttmm)
REVERT: D   18 GLU cc_start: 0.7620 (mm-30) cc_final: 0.7403 (mm-30)
REVERT: D   25 ASN cc_start: 0.6475 (t0) cc_final: 0.5969 (t0)
REVERT: D   63 LYS cc_start: 0.8688 (ttmm) cc_final: 0.8483 (mptt)
REVERT: A  567 LEU cc_start: 0.8974 (mt) cc_final: 0.8483 (tt)
REVERT: A  576 ASN cc_start: 0.8650 (m-40) cc_final: 0.8164 (t0)
REVERT: A  616 LYS cc_start: 0.8256 (tmtp) cc_final: 0.8036 (mtpt)
REVERT: A  667 MET cc_start: 0.7323 (tpp) cc_final: 0.6942 (tpp)
REVERT: A  688 GLN cc_start: 0.8885 (tt0) cc_final: 0.8426 (tp-100)
REVERT: A  880 ASN cc_start: 0.8885 (m-40) cc_final: 0.8625 (t0)
REVERT: A  924 GLU cc_start: 0.8310 (mm-30) cc_final: 0.7980 (mm-30)
REVERT: A 1105 PHE cc_start: 0.7198 (m-80) cc_final: 0.6968 (m-80)
REVERT: A 1534 LEU cc_start: 0.8036 (mt) cc_final: 0.7430 (mt)
REVERT: A 1915 LEU cc_start: 0.9092 (mt) cc_final: 0.8872 (mm)
REVERT: A 1953 LEU cc_start: 0.8284 (mt) cc_final: 0.8017 (pt)
  outliers start: 0
  outliers final: 0
  residues processed: 322
  average time/residue: 0.1240
  time to fit residues: 53.3050
Evaluate side-chains
  199 residues out of total 1139 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 199
  time to evaluate  : 0.429 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 126
   random chunks:
   chunk 108 optimal weight:    1.9990
   chunk 49 optimal weight:    0.8980
   chunk 97 optimal weight:    1.9990
   chunk 113 optimal weight:    2.9990
   chunk 53 optimal weight:    0.9980
   chunk 5 optimal weight:    8.9990
   chunk 33 optimal weight:    1.9990
   chunk 123 optimal weight:    0.7980
   chunk 65 optimal weight:    0.6980
   chunk 62 optimal weight:    0.9980
   chunk 51 optimal weight:    3.9990
   overall best weight:    0.8780

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

Flipped N/Q/H residues before XYZ refinement:
** C  41 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 493 HIS
A 613 HIS
A 651 ASN
A 681 ASN
A 856 HIS
A 881 HIS
A1479 HIS

Total number of N/Q/H flips: 7

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4007 r_free = 0.4007 target = 0.138713 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 33)----------------|
| r_work = 0.3599 r_free = 0.3599 target = 0.109035 restraints weight = 16995.934|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 32)----------------|
| r_work = 0.3628 r_free = 0.3628 target = 0.112224 restraints weight = 8818.078|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 25)----------------|
| r_work = 0.3641 r_free = 0.3641 target = 0.113262 restraints weight = 6131.666|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 30)----------------|
| r_work = 0.3667 r_free = 0.3667 target = 0.115193 restraints weight = 5274.550|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 25)----------------|
| r_work = 0.3667 r_free = 0.3667 target = 0.115173 restraints weight = 4870.413|
|-----------------------------------------------------------------------------|
r_work (final): 0.3653
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3658
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3658 r_free = 0.3658    target_work(ls_wunit_k1) = 0.113         |
| occupancies: max = 1.00  min = 0.45   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3655 r_free = 0.3655    target_work(ls_wunit_k1) = 0.113         |
| occupancies: max = 1.00  min = 0.83   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.3655
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7294
moved from start:          0.3092

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.028  10273  Z= 0.136
  Angle     :  0.630   7.168  13895  Z= 0.329
  Chirality :  0.042   0.128   1602
  Planarity :  0.005   0.053   1785
  Dihedral  :  5.744  24.549   1355
  Min Nonbonded Distance : 2.554

Molprobity Statistics.
  All-atom Clashscore : 9.18
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.43 %
    Favored  : 96.57 %
  Rotamer:
    Outliers :  1.78 %
    Allowed  :  9.77 %
    Favored  : 88.45 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 3.23 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -3.43 (0.21), residues: 1254
  helix: -2.58 (0.16), residues: 666
  sheet: -2.83 (0.74), residues: 48
  loop : -1.58 (0.26), residues: 540

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.001   ARG A1514 
 TYR   0.019   0.002   TYR A 846 
 PHE   0.015   0.002   PHE A1914 
 TRP   0.015   0.001   TRP A1092 
 HIS   0.004   0.001   HIS A 493 

Details of bonding type rmsd
  covalent geometry    : bond        0.00304 (10272)
  covalent geometry    : angle       0.62922 (13893)
  SS BOND              : bond        0.00472 (    1)
  SS BOND              : angle       2.18288 (    2)
  hydrogen bonds       : bond        0.04581 (  374)
  hydrogen bonds       : angle       5.23051 ( 1080)

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

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

  2508 Ramachandran restraints generated.
    1254 Oldfield, 0 Emsley, 1254 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2508 Ramachandran restraints generated.
    1254 Oldfield, 0 Emsley, 1254 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  249 residues out of total 1139 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 20
    poor density    : 229
  time to evaluate  : 0.288 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: C    1 MET cc_start: 0.6752 (ptp) cc_final: 0.6550 (pmm)
REVERT: C    4 PHE cc_start: 0.8382 (m-80) cc_final: 0.7542 (m-80)
REVERT: C   21 ASP cc_start: 0.7008 (t0) cc_final: 0.6352 (t0)
REVERT: D    6 LYS cc_start: 0.8064 (ttpt) cc_final: 0.7718 (ttmm)
REVERT: A  467 MET cc_start: 0.8404 (mmm) cc_final: 0.8125 (mmm)
REVERT: A  491 MET cc_start: 0.8439 (mmm) cc_final: 0.8042 (tpp)
REVERT: A  509 MET cc_start: 0.7983 (mtp) cc_final: 0.7077 (ptp)
REVERT: A  563 LEU cc_start: 0.8640 (OUTLIER) cc_final: 0.8322 (tp)
REVERT: A  567 LEU cc_start: 0.8988 (mt) cc_final: 0.8609 (tt)
REVERT: A  620 GLU cc_start: 0.7489 (mt-10) cc_final: 0.7157 (mt-10)
REVERT: A  688 GLN cc_start: 0.8788 (tt0) cc_final: 0.8520 (tp-100)
REVERT: A  749 MET cc_start: 0.8571 (mpp) cc_final: 0.8349 (ptp)
REVERT: A 1152 ASP cc_start: 0.8323 (t70) cc_final: 0.7872 (p0)
REVERT: A 1470 ASP cc_start: 0.7538 (OUTLIER) cc_final: 0.7004 (t70)
REVERT: A 1489 TYR cc_start: 0.7890 (m-80) cc_final: 0.7624 (m-80)
REVERT: A 1514 ARG cc_start: 0.8271 (mmm160) cc_final: 0.7846 (tmt-80)
REVERT: A 1534 LEU cc_start: 0.7971 (mt) cc_final: 0.7315 (mt)
REVERT: A 1601 GLN cc_start: 0.8552 (mt0) cc_final: 0.8303 (mt0)
REVERT: A 1957 MET cc_start: 0.5038 (mtt) cc_final: 0.4490 (tpt)
  outliers start: 20
  outliers final: 7
  residues processed: 237
  average time/residue: 0.0904
  time to fit residues: 30.6360
Evaluate side-chains
  194 residues out of total 1139 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 9
    poor density    : 185
  time to evaluate  : 0.446 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain D residue   14 THR
Chi-restraints excluded: chain D residue   49 GLN
Chi-restraints excluded: chain A residue  563 LEU
Chi-restraints excluded: chain A residue 1155 SER
Chi-restraints excluded: chain A residue 1457 THR
Chi-restraints excluded: chain A residue 1470 ASP
Chi-restraints excluded: chain A residue 1632 LEU
Chi-restraints excluded: chain A residue 1854 LEU
Chi-restraints excluded: chain A residue 1916 GLN
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 126
   random chunks:
   chunk 55 optimal weight:    5.9990
   chunk 69 optimal weight:    1.9990
   chunk 43 optimal weight:    5.9990
   chunk 54 optimal weight:    0.6980
   chunk 95 optimal weight:    9.9990
   chunk 50 optimal weight:    3.9990
   chunk 87 optimal weight:    9.9990
   chunk 49 optimal weight:    0.5980
   chunk 59 optimal weight:    5.9990
   chunk 86 optimal weight:    5.9990
   chunk 14 optimal weight:    9.9990
   overall best weight:    2.6586

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

Flipped N/Q/H residues before XYZ refinement:
C  25 ASN
** C  41 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** D   2 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 493 HIS
A1505 ASN
A1891 HIS

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3944 r_free = 0.3944 target = 0.134330 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 31)----------------|
| r_work = 0.3519 r_free = 0.3519 target = 0.104094 restraints weight = 17452.901|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 28)----------------|
| r_work = 0.3547 r_free = 0.3547 target = 0.106978 restraints weight = 9188.685|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 23)----------------|
| r_work = 0.3559 r_free = 0.3559 target = 0.107984 restraints weight = 6222.964|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 23)----------------|
| r_work = 0.3570 r_free = 0.3570 target = 0.108721 restraints weight = 5319.213|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 26)----------------|
| r_work = 0.3573 r_free = 0.3573 target = 0.108927 restraints weight = 5002.658|
|-----------------------------------------------------------------------------|
r_work (final): 0.3558
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3557
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3557 r_free = 0.3557    target_work(ls_wunit_k1) = 0.106         |
| occupancies: max = 1.00  min = 0.83   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3557 r_free = 0.3557    target_work(ls_wunit_k1) = 0.106         |
| occupancies: max = 1.00  min = 0.89   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.3557
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7415
moved from start:          0.3576

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.037  10273  Z= 0.222
  Angle     :  0.664   8.359  13895  Z= 0.340
  Chirality :  0.045   0.151   1602
  Planarity :  0.005   0.049   1785
  Dihedral  :  5.548  25.764   1355
  Min Nonbonded Distance : 2.449

Molprobity Statistics.
  All-atom Clashscore : 10.76
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.18 %
    Favored  : 94.82 %
  Rotamer:
    Outliers :  3.37 %
    Allowed  : 11.46 %
    Favored  : 85.17 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 3.23 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -2.76 (0.22), residues: 1254
  helix: -1.94 (0.17), residues: 670
  sheet: -2.57 (0.73), residues: 47
  loop : -1.40 (0.27), residues: 537

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.001   ARG A 514 
 TYR   0.017   0.002   TYR A1962 
 PHE   0.024   0.002   PHE A1542 
 TRP   0.016   0.002   TRP A1092 
 HIS   0.005   0.001   HIS D  68 

Details of bonding type rmsd
  covalent geometry    : bond        0.00515 (10272)
  covalent geometry    : angle       0.66340 (13893)
  SS BOND              : bond        0.00341 (    1)
  SS BOND              : angle       2.23441 (    2)
  hydrogen bonds       : bond        0.04264 (  374)
  hydrogen bonds       : angle       5.08556 ( 1080)

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

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

  2508 Ramachandran restraints generated.
    1254 Oldfield, 0 Emsley, 1254 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2508 Ramachandran restraints generated.
    1254 Oldfield, 0 Emsley, 1254 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  233 residues out of total 1139 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 38
    poor density    : 195
  time to evaluate  : 0.305 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: C    4 PHE cc_start: 0.8416 (m-80) cc_final: 0.7764 (m-10)
REVERT: D    6 LYS cc_start: 0.7938 (ttpt) cc_final: 0.7566 (ttmm)
REVERT: A  467 MET cc_start: 0.8377 (mmm) cc_final: 0.7907 (mmm)
REVERT: A  491 MET cc_start: 0.8418 (mmm) cc_final: 0.7115 (ttp)
REVERT: A  509 MET cc_start: 0.7933 (mtp) cc_final: 0.7723 (mtp)
REVERT: A  528 GLU cc_start: 0.8447 (tp30) cc_final: 0.8207 (tm-30)
REVERT: A  563 LEU cc_start: 0.8654 (OUTLIER) cc_final: 0.8317 (tp)
REVERT: A  620 GLU cc_start: 0.7687 (mt-10) cc_final: 0.7342 (mt-10)
REVERT: A  677 LEU cc_start: 0.8783 (OUTLIER) cc_final: 0.8532 (tt)
REVERT: A  688 GLN cc_start: 0.8757 (tt0) cc_final: 0.8507 (tp-100)
REVERT: A  727 LEU cc_start: 0.7890 (OUTLIER) cc_final: 0.7336 (tt)
REVERT: A 1601 GLN cc_start: 0.8586 (mt0) cc_final: 0.8282 (mt0)
REVERT: A 1695 MET cc_start: 0.7595 (mmm) cc_final: 0.7270 (mmm)
  outliers start: 38
  outliers final: 15
  residues processed: 213
  average time/residue: 0.0844
  time to fit residues: 26.3622
Evaluate side-chains
  192 residues out of total 1139 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 18
    poor density    : 174
  time to evaluate  : 0.357 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain D residue    9 THR
Chi-restraints excluded: chain D residue   13 ILE
Chi-restraints excluded: chain D residue   14 THR
Chi-restraints excluded: chain D residue   66 THR
Chi-restraints excluded: chain A residue  518 VAL
Chi-restraints excluded: chain A residue  563 LEU
Chi-restraints excluded: chain A residue  677 LEU
Chi-restraints excluded: chain A residue  727 LEU
Chi-restraints excluded: chain A residue  827 ASP
Chi-restraints excluded: chain A residue  843 TYR
Chi-restraints excluded: chain A residue 1147 ILE
Chi-restraints excluded: chain A residue 1155 SER
Chi-restraints excluded: chain A residue 1178 ASP
Chi-restraints excluded: chain A residue 1190 LEU
Chi-restraints excluded: chain A residue 1457 THR
Chi-restraints excluded: chain A residue 1632 LEU
Chi-restraints excluded: chain A residue 1787 VAL
Chi-restraints excluded: chain A residue 1834 VAL
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 126
   random chunks:
   chunk 113 optimal weight:    4.9990
   chunk 14 optimal weight:   10.0000
   chunk 11 optimal weight:    6.9990
   chunk 53 optimal weight:    0.9980
   chunk 47 optimal weight:    0.9990
   chunk 13 optimal weight:    8.9990
   chunk 111 optimal weight:    0.7980
   chunk 45 optimal weight:   10.0000
   chunk 61 optimal weight:    0.0050
   chunk 77 optimal weight:    0.9980
   chunk 48 optimal weight:    2.9990
   overall best weight:    0.7596

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

Flipped N/Q/H residues before XYZ refinement:
C  25 ASN
** C  41 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
A1916 GLN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3998 r_free = 0.3998 target = 0.138601 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 45)----------------|
| r_work = 0.3527 r_free = 0.3527 target = 0.105093 restraints weight = 17141.799|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 42)----------------|
| r_work = 0.3591 r_free = 0.3591 target = 0.109410 restraints weight = 8921.104|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 40)----------------|
| r_work = 0.3632 r_free = 0.3632 target = 0.112235 restraints weight = 5928.047|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 40)----------------|
| r_work = 0.3659 r_free = 0.3659 target = 0.114135 restraints weight = 4550.027|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 28)----------------|
| r_work = 0.3673 r_free = 0.3673 target = 0.115246 restraints weight = 3824.945|
|-----------------------------------------------------------------------------|
r_work (final): 0.3664
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3664
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3664 r_free = 0.3664    target_work(ls_wunit_k1) = 0.113         |
| occupancies: max = 1.00  min = 0.89   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3664 r_free = 0.3664    target_work(ls_wunit_k1) = 0.113         |
| occupancies: max = 1.00  min = 0.89   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.3664
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7275
moved from start:          0.4022

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.032  10273  Z= 0.114
  Angle     :  0.567   7.168  13895  Z= 0.290
  Chirality :  0.041   0.184   1602
  Planarity :  0.004   0.050   1785
  Dihedral  :  4.978  21.930   1355
  Min Nonbonded Distance : 2.391

Molprobity Statistics.
  All-atom Clashscore : 9.03
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.27 %
    Favored  : 96.73 %
  Rotamer:
    Outliers :  1.51 %
    Allowed  : 14.12 %
    Favored  : 84.37 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 3.23 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -2.06 (0.23), residues: 1254
  helix: -1.34 (0.18), residues: 681
  sheet: -2.37 (0.72), residues: 48
  loop : -1.06 (0.28), residues: 525

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.000   ARG A 514 
 TYR   0.018   0.001   TYR A1962 
 PHE   0.015   0.001   PHE A1914 
 TRP   0.009   0.001   TRP A1874 
 HIS   0.004   0.001   HIS C  68 

Details of bonding type rmsd
  covalent geometry    : bond        0.00265 (10272)
  covalent geometry    : angle       0.56628 (13893)
  SS BOND              : bond        0.00456 (    1)
  SS BOND              : angle       1.78277 (    2)
  hydrogen bonds       : bond        0.03433 (  374)
  hydrogen bonds       : angle       4.60610 ( 1080)

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

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

  2508 Ramachandran restraints generated.
    1254 Oldfield, 0 Emsley, 1254 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2508 Ramachandran restraints generated.
    1254 Oldfield, 0 Emsley, 1254 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  213 residues out of total 1139 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 17
    poor density    : 196
  time to evaluate  : 0.429 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: C    4 PHE cc_start: 0.8337 (m-80) cc_final: 0.7521 (m-80)
REVERT: C   21 ASP cc_start: 0.7086 (t0) cc_final: 0.6803 (t0)
REVERT: D    6 LYS cc_start: 0.7865 (ttpt) cc_final: 0.7557 (ttmm)
REVERT: A  467 MET cc_start: 0.8370 (mmm) cc_final: 0.7927 (mmm)
REVERT: A  491 MET cc_start: 0.8409 (mmm) cc_final: 0.7136 (ttp)
REVERT: A  509 MET cc_start: 0.7913 (mtp) cc_final: 0.7686 (mtp)
REVERT: A  528 GLU cc_start: 0.8569 (tp30) cc_final: 0.8364 (tm-30)
REVERT: A  688 GLN cc_start: 0.8651 (tt0) cc_final: 0.8402 (tp-100)
REVERT: A  689 LEU cc_start: 0.8598 (OUTLIER) cc_final: 0.8357 (mp)
REVERT: A  910 MET cc_start: 0.7600 (mmm) cc_final: 0.7276 (tpt)
REVERT: A 1601 GLN cc_start: 0.8556 (mt0) cc_final: 0.8297 (mt0)
REVERT: A 1695 MET cc_start: 0.7440 (mmm) cc_final: 0.7173 (mmm)
REVERT: A 1957 MET cc_start: 0.5221 (mtt) cc_final: 0.4770 (tpt)
  outliers start: 17
  outliers final: 7
  residues processed: 204
  average time/residue: 0.0881
  time to fit residues: 26.0296
Evaluate side-chains
  180 residues out of total 1139 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 8
    poor density    : 172
  time to evaluate  : 0.404 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain D residue    9 THR
Chi-restraints excluded: chain D residue   14 THR
Chi-restraints excluded: chain D residue   56 LEU
Chi-restraints excluded: chain A residue  689 LEU
Chi-restraints excluded: chain A residue 1155 SER
Chi-restraints excluded: chain A residue 1471 VAL
Chi-restraints excluded: chain A residue 1534 LEU
Chi-restraints excluded: chain A residue 1609 LEU
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 126
   random chunks:
   chunk 61 optimal weight:    7.9990
   chunk 81 optimal weight:    0.5980
   chunk 115 optimal weight:    0.9980
   chunk 85 optimal weight:    0.0980
   chunk 15 optimal weight:    6.9990
   chunk 73 optimal weight:   10.0000
   chunk 51 optimal weight:    6.9990
   chunk 49 optimal weight:    5.9990
   chunk 67 optimal weight:    5.9990
   chunk 77 optimal weight:    2.9990
   chunk 50 optimal weight:    0.9980
   overall best weight:    1.1382

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

Flipped N/Q/H residues before XYZ refinement:
C  25 ASN
** C  41 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** D   2 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3994 r_free = 0.3994 target = 0.137892 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.3595 r_free = 0.3595 target = 0.108973 restraints weight = 16808.024|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 28)----------------|
| r_work = 0.3642 r_free = 0.3642 target = 0.113177 restraints weight = 8159.748|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 25)----------------|
| r_work = 0.3650 r_free = 0.3650 target = 0.113944 restraints weight = 5186.613|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 28)----------------|
| r_work = 0.3664 r_free = 0.3664 target = 0.114921 restraints weight = 4606.316|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 27)----------------|
| r_work = 0.3665 r_free = 0.3665 target = 0.115088 restraints weight = 4374.025|
|-----------------------------------------------------------------------------|
r_work (final): 0.3635
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3652
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3652 r_free = 0.3652    target_work(ls_wunit_k1) = 0.113         |
| occupancies: max = 1.00  min = 0.89   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3652 r_free = 0.3652    target_work(ls_wunit_k1) = 0.113         |
| occupancies: max = 1.00  min = 0.87   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.3652
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7322
moved from start:          0.4225

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.034  10273  Z= 0.127
  Angle     :  0.575   8.085  13895  Z= 0.290
  Chirality :  0.042   0.137   1602
  Planarity :  0.004   0.047   1785
  Dihedral  :  4.821  20.982   1355
  Min Nonbonded Distance : 2.412

Molprobity Statistics.
  All-atom Clashscore : 9.18
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.59 %
    Favored  : 96.41 %
  Rotamer:
    Outliers :  1.78 %
    Allowed  : 13.77 %
    Favored  : 84.46 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 3.23 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -1.75 (0.23), residues: 1254
  helix: -1.06 (0.19), residues: 680
  sheet: -2.07 (0.65), residues: 60
  loop : -0.95 (0.28), residues: 514

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.009   0.000   ARG A 514 
 TYR   0.017   0.001   TYR A1962 
 PHE   0.018   0.001   PHE A1929 
 TRP   0.007   0.001   TRP A1874 
 HIS   0.004   0.001   HIS C  68 

Details of bonding type rmsd
  covalent geometry    : bond        0.00299 (10272)
  covalent geometry    : angle       0.57432 (13893)
  SS BOND              : bond        0.00507 (    1)
  SS BOND              : angle       1.82965 (    2)
  hydrogen bonds       : bond        0.03374 (  374)
  hydrogen bonds       : angle       4.57323 ( 1080)

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

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

  2508 Ramachandran restraints generated.
    1254 Oldfield, 0 Emsley, 1254 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2508 Ramachandran restraints generated.
    1254 Oldfield, 0 Emsley, 1254 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  210 residues out of total 1139 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 20
    poor density    : 190
  time to evaluate  : 0.479 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: C    4 PHE cc_start: 0.8322 (m-80) cc_final: 0.7505 (m-80)
REVERT: D    6 LYS cc_start: 0.7956 (ttpt) cc_final: 0.7596 (ttmm)
REVERT: A  467 MET cc_start: 0.8332 (mmm) cc_final: 0.7909 (mmm)
REVERT: A  491 MET cc_start: 0.8393 (mmm) cc_final: 0.7221 (ttp)
REVERT: A  587 ASN cc_start: 0.8190 (m-40) cc_final: 0.7799 (m110)
REVERT: A  690 MET cc_start: 0.7043 (mmt) cc_final: 0.6740 (mmt)
REVERT: A  727 LEU cc_start: 0.7714 (OUTLIER) cc_final: 0.7256 (tt)
REVERT: A  910 MET cc_start: 0.7621 (mmm) cc_final: 0.7386 (tpt)
REVERT: A 1601 GLN cc_start: 0.8551 (mt0) cc_final: 0.8293 (mt0)
REVERT: A 1695 MET cc_start: 0.7482 (mmm) cc_final: 0.7241 (mmm)
REVERT: A 1704 MET cc_start: 0.7503 (mmm) cc_final: 0.7186 (mtt)
REVERT: A 1957 MET cc_start: 0.5430 (mtt) cc_final: 0.4931 (tpt)
  outliers start: 20
  outliers final: 13
  residues processed: 200
  average time/residue: 0.0980
  time to fit residues: 28.4212
Evaluate side-chains
  185 residues out of total 1139 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 171
  time to evaluate  : 0.403 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain D residue    9 THR
Chi-restraints excluded: chain D residue   13 ILE
Chi-restraints excluded: chain A residue  498 MET
Chi-restraints excluded: chain A residue  518 VAL
Chi-restraints excluded: chain A residue  625 CYS
Chi-restraints excluded: chain A residue  671 VAL
Chi-restraints excluded: chain A residue  727 LEU
Chi-restraints excluded: chain A residue 1155 SER
Chi-restraints excluded: chain A residue 1158 ILE
Chi-restraints excluded: chain A residue 1471 VAL
Chi-restraints excluded: chain A residue 1534 LEU
Chi-restraints excluded: chain A residue 1609 LEU
Chi-restraints excluded: chain A residue 1632 LEU
Chi-restraints excluded: chain A residue 1787 VAL
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 126
   random chunks:
   chunk 43 optimal weight:    4.9990
   chunk 39 optimal weight:    5.9990
   chunk 61 optimal weight:    4.9990
   chunk 80 optimal weight:    0.9990
   chunk 55 optimal weight:    0.0980
   chunk 21 optimal weight:    0.6980
   chunk 102 optimal weight:    0.9990
   chunk 6 optimal weight:    9.9990
   chunk 37 optimal weight:    0.6980
   chunk 57 optimal weight:   10.0000
   chunk 16 optimal weight:   10.0000
   overall best weight:    0.6984

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

Flipped N/Q/H residues before XYZ refinement:
** C  31 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** C  41 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** D   2 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4018 r_free = 0.4018 target = 0.140146 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 33)----------------|
| r_work = 0.3631 r_free = 0.3631 target = 0.111720 restraints weight = 16777.875|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 29)----------------|
| r_work = 0.3683 r_free = 0.3683 target = 0.116492 restraints weight = 8128.821|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 26)----------------|
| r_work = 0.3693 r_free = 0.3693 target = 0.117509 restraints weight = 4909.395|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 27)----------------|
| r_work = 0.3703 r_free = 0.3703 target = 0.118014 restraints weight = 4341.785|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 23)----------------|
| r_work = 0.3706 r_free = 0.3706 target = 0.118357 restraints weight = 3955.811|
|-----------------------------------------------------------------------------|
r_work (final): 0.3678
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3691
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3691 r_free = 0.3691    target_work(ls_wunit_k1) = 0.115         |
| occupancies: max = 1.00  min = 0.87   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3691 r_free = 0.3691    target_work(ls_wunit_k1) = 0.115         |
| occupancies: max = 1.00  min = 0.91   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.3691
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7263
moved from start:          0.4467

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.033  10273  Z= 0.108
  Angle     :  0.578  11.066  13895  Z= 0.285
  Chirality :  0.041   0.139   1602
  Planarity :  0.004   0.046   1785
  Dihedral  :  4.585  19.426   1355
  Min Nonbonded Distance : 2.551

Molprobity Statistics.
  All-atom Clashscore : 8.79
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.51 %
    Favored  : 96.49 %
  Rotamer:
    Outliers :  1.51 %
    Allowed  : 15.10 %
    Favored  : 83.39 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 3.23 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -1.26 (0.23), residues: 1254
  helix: -0.64 (0.19), residues: 682
  sheet: -1.73 (0.68), residues: 59
  loop : -0.78 (0.28), residues: 513

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.007   0.000   ARG A1514 
 TYR   0.015   0.001   TYR A1962 
 PHE   0.019   0.001   PHE A1544 
 TRP   0.007   0.001   TRP A1874 
 HIS   0.004   0.001   HIS A1191 

Details of bonding type rmsd
  covalent geometry    : bond        0.00255 (10272)
  covalent geometry    : angle       0.57775 (13893)
  SS BOND              : bond        0.00543 (    1)
  SS BOND              : angle       1.72632 (    2)
  hydrogen bonds       : bond        0.03063 (  374)
  hydrogen bonds       : angle       4.40629 ( 1080)

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

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

  2508 Ramachandran restraints generated.
    1254 Oldfield, 0 Emsley, 1254 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2508 Ramachandran restraints generated.
    1254 Oldfield, 0 Emsley, 1254 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  202 residues out of total 1139 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 17
    poor density    : 185
  time to evaluate  : 0.413 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: C    4 PHE cc_start: 0.8297 (m-80) cc_final: 0.7485 (m-80)
REVERT: D    6 LYS cc_start: 0.8019 (ttpt) cc_final: 0.7645 (ttmm)
REVERT: A  467 MET cc_start: 0.8323 (mmm) cc_final: 0.7931 (mmm)
REVERT: A  491 MET cc_start: 0.8381 (mmm) cc_final: 0.7729 (ttp)
REVERT: A  587 ASN cc_start: 0.8058 (m-40) cc_final: 0.7672 (m110)
REVERT: A  690 MET cc_start: 0.7093 (mmt) cc_final: 0.6793 (mmt)
REVERT: A  924 GLU cc_start: 0.7942 (mm-30) cc_final: 0.7710 (mm-30)
REVERT: A 1695 MET cc_start: 0.7424 (mmm) cc_final: 0.7212 (mmm)
REVERT: A 1940 ARG cc_start: 0.7103 (tpt-90) cc_final: 0.6888 (ttt90)
REVERT: A 1957 MET cc_start: 0.5250 (mtt) cc_final: 0.5019 (tmm)
  outliers start: 17
  outliers final: 14
  residues processed: 193
  average time/residue: 0.0903
  time to fit residues: 26.1421
Evaluate side-chains
  184 residues out of total 1139 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 170
  time to evaluate  : 0.390 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain D residue    9 THR
Chi-restraints excluded: chain A residue  498 MET
Chi-restraints excluded: chain A residue  518 VAL
Chi-restraints excluded: chain A residue  532 VAL
Chi-restraints excluded: chain A residue  606 LEU
Chi-restraints excluded: chain A residue  625 CYS
Chi-restraints excluded: chain A residue  671 VAL
Chi-restraints excluded: chain A residue 1155 SER
Chi-restraints excluded: chain A residue 1471 VAL
Chi-restraints excluded: chain A residue 1534 LEU
Chi-restraints excluded: chain A residue 1609 LEU
Chi-restraints excluded: chain A residue 1726 MET
Chi-restraints excluded: chain A residue 1787 VAL
Chi-restraints excluded: chain A residue 1953 LEU
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 126
   random chunks:
   chunk 84 optimal weight:    3.9990
   chunk 43 optimal weight:    1.9990
   chunk 92 optimal weight:    4.9990
   chunk 120 optimal weight:    0.9990
   chunk 49 optimal weight:    5.9990
   chunk 65 optimal weight:    0.7980
   chunk 48 optimal weight:    1.9990
   chunk 124 optimal weight:    1.9990
   chunk 119 optimal weight:   50.0000
   chunk 47 optimal weight:    0.6980
   chunk 25 optimal weight:    6.9990
   overall best weight:    1.2986

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

Flipped N/Q/H residues before XYZ refinement:
C  25 ASN
C  41 GLN
** D   2 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3981 r_free = 0.3981 target = 0.136181 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 43)----------------|
| r_work = 0.3518 r_free = 0.3518 target = 0.103120 restraints weight = 17032.281|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 34)----------------|
| r_work = 0.3580 r_free = 0.3580 target = 0.107313 restraints weight = 8917.800|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 44)----------------|
| r_work = 0.3621 r_free = 0.3621 target = 0.110176 restraints weight = 5936.769|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 43)----------------|
| r_work = 0.3647 r_free = 0.3647 target = 0.112008 restraints weight = 4555.900|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 32)----------------|
| r_work = 0.3662 r_free = 0.3662 target = 0.113171 restraints weight = 3834.638|
|-----------------------------------------------------------------------------|
r_work (final): 0.3660
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3660
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3660 r_free = 0.3660    target_work(ls_wunit_k1) = 0.113         |
| occupancies: max = 1.00  min = 0.91   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3660 r_free = 0.3660    target_work(ls_wunit_k1) = 0.113         |
| occupancies: max = 1.00  min = 0.92   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.3660
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7288
moved from start:          0.4586

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.034  10273  Z= 0.135
  Angle     :  0.606  11.173  13895  Z= 0.299
  Chirality :  0.042   0.160   1602
  Planarity :  0.004   0.047   1785
  Dihedral  :  4.621  19.873   1355
  Min Nonbonded Distance : 2.526

Molprobity Statistics.
  All-atom Clashscore : 9.48
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.07 %
    Favored  : 95.93 %
  Rotamer:
    Outliers :  1.87 %
    Allowed  : 15.81 %
    Favored  : 82.33 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 3.23 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -1.12 (0.24), residues: 1254
  helix: -0.53 (0.20), residues: 682
  sheet: -1.39 (0.73), residues: 56
  loop : -0.75 (0.28), residues: 516

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.000   ARG A1514 
 TYR   0.015   0.001   TYR A1962 
 PHE   0.016   0.002   PHE A1914 
 TRP   0.007   0.001   TRP A1092 
 HIS   0.004   0.001   HIS C  68 

Details of bonding type rmsd
  covalent geometry    : bond        0.00323 (10272)
  covalent geometry    : angle       0.60556 (13893)
  SS BOND              : bond        0.00561 (    1)
  SS BOND              : angle       1.99861 (    2)
  hydrogen bonds       : bond        0.03225 (  374)
  hydrogen bonds       : angle       4.44071 ( 1080)

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

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

  2508 Ramachandran restraints generated.
    1254 Oldfield, 0 Emsley, 1254 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2508 Ramachandran restraints generated.
    1254 Oldfield, 0 Emsley, 1254 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  204 residues out of total 1139 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 21
    poor density    : 183
  time to evaluate  : 0.408 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: C    4 PHE cc_start: 0.8291 (m-80) cc_final: 0.7472 (m-80)
REVERT: D    6 LYS cc_start: 0.7963 (ttpt) cc_final: 0.7625 (ttmm)
REVERT: D   34 GLU cc_start: 0.8071 (mp0) cc_final: 0.7797 (mp0)
REVERT: A  467 MET cc_start: 0.8338 (mmm) cc_final: 0.7962 (mmm)
REVERT: A  491 MET cc_start: 0.8405 (mmm) cc_final: 0.7215 (ttp)
REVERT: A  528 GLU cc_start: 0.8183 (tm-30) cc_final: 0.7728 (tm-30)
REVERT: A  587 ASN cc_start: 0.8129 (m-40) cc_final: 0.7683 (m110)
REVERT: A  690 MET cc_start: 0.7223 (mmt) cc_final: 0.6964 (mmt)
REVERT: A  727 LEU cc_start: 0.7620 (OUTLIER) cc_final: 0.7181 (tt)
REVERT: A  824 MET cc_start: 0.7495 (mmp) cc_final: 0.6825 (mmm)
REVERT: A  924 GLU cc_start: 0.7954 (mm-30) cc_final: 0.7695 (mm-30)
REVERT: A 1695 MET cc_start: 0.7483 (mmm) cc_final: 0.7267 (mmm)
REVERT: A 1940 ARG cc_start: 0.7286 (tpt-90) cc_final: 0.6930 (ttt90)
  outliers start: 21
  outliers final: 17
  residues processed: 191
  average time/residue: 0.0895
  time to fit residues: 25.2599
Evaluate side-chains
  188 residues out of total 1139 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 18
    poor density    : 170
  time to evaluate  : 0.323 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain D residue    9 THR
Chi-restraints excluded: chain D residue   13 ILE
Chi-restraints excluded: chain A residue  498 MET
Chi-restraints excluded: chain A residue  518 VAL
Chi-restraints excluded: chain A residue  606 LEU
Chi-restraints excluded: chain A residue  625 CYS
Chi-restraints excluded: chain A residue  671 VAL
Chi-restraints excluded: chain A residue  727 LEU
Chi-restraints excluded: chain A residue  918 SER
Chi-restraints excluded: chain A residue 1155 SER
Chi-restraints excluded: chain A residue 1158 ILE
Chi-restraints excluded: chain A residue 1471 VAL
Chi-restraints excluded: chain A residue 1534 LEU
Chi-restraints excluded: chain A residue 1609 LEU
Chi-restraints excluded: chain A residue 1744 VAL
Chi-restraints excluded: chain A residue 1787 VAL
Chi-restraints excluded: chain A residue 1854 LEU
Chi-restraints excluded: chain A residue 1953 LEU
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 126
   random chunks:
   chunk 81 optimal weight:    4.9990
   chunk 37 optimal weight:    1.9990
   chunk 97 optimal weight:    7.9990
   chunk 8 optimal weight:    0.3980
   chunk 115 optimal weight:    0.0270
   chunk 78 optimal weight:    3.9990
   chunk 56 optimal weight:    3.9990
   chunk 52 optimal weight:    3.9990
   chunk 41 optimal weight:    3.9990
   chunk 68 optimal weight:    0.9980
   chunk 64 optimal weight:    0.0670
   overall best weight:    0.6978

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

Flipped N/Q/H residues before XYZ refinement:
** D   2 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4002 r_free = 0.4002 target = 0.137653 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 32)----------------|
| r_work = 0.3580 r_free = 0.3580 target = 0.107006 restraints weight = 16976.023|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 28)----------------|
| r_work = 0.3620 r_free = 0.3620 target = 0.110067 restraints weight = 7631.600|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 27)----------------|
| r_work = 0.3636 r_free = 0.3636 target = 0.111582 restraints weight = 5457.583|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 28)----------------|
| r_work = 0.3649 r_free = 0.3649 target = 0.112282 restraints weight = 4648.548|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 28)----------------|
| r_work = 0.3649 r_free = 0.3649 target = 0.112464 restraints weight = 4420.846|
|-----------------------------------------------------------------------------|
r_work (final): 0.3662
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3662
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3662 r_free = 0.3662    target_work(ls_wunit_k1) = 0.112         |
| occupancies: max = 1.00  min = 0.92   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3661 r_free = 0.3661    target_work(ls_wunit_k1) = 0.112         |
| occupancies: max = 1.00  min = 0.93   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.3661
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7290
moved from start:          0.4815

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.030  10273  Z= 0.109
  Angle     :  0.596  12.256  13895  Z= 0.293
  Chirality :  0.041   0.142   1602
  Planarity :  0.004   0.048   1785
  Dihedral  :  4.454  18.263   1355
  Min Nonbonded Distance : 2.531

Molprobity Statistics.
  All-atom Clashscore : 8.84
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.71 %
    Favored  : 97.29 %
  Rotamer:
    Outliers :  1.95 %
    Allowed  : 16.07 %
    Favored  : 81.97 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 3.23 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -0.88 (0.24), residues: 1254
  helix: -0.32 (0.20), residues: 681
  sheet: -1.27 (0.67), residues: 70
  loop : -0.64 (0.29), residues: 503

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.000   ARG A1514 
 TYR   0.023   0.001   TYR A1962 
 PHE   0.014   0.001   PHE A1929 
 TRP   0.006   0.001   TRP A1485 
 HIS   0.003   0.001   HIS C  68 

Details of bonding type rmsd
  covalent geometry    : bond        0.00257 (10272)
  covalent geometry    : angle       0.59562 (13893)
  SS BOND              : bond        0.00571 (    1)
  SS BOND              : angle       1.85677 (    2)
  hydrogen bonds       : bond        0.03017 (  374)
  hydrogen bonds       : angle       4.33543 ( 1080)

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

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

  2508 Ramachandran restraints generated.
    1254 Oldfield, 0 Emsley, 1254 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2508 Ramachandran restraints generated.
    1254 Oldfield, 0 Emsley, 1254 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  198 residues out of total 1139 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 22
    poor density    : 176
  time to evaluate  : 0.432 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: C    4 PHE cc_start: 0.8271 (m-80) cc_final: 0.7440 (m-80)
REVERT: C   67 LEU cc_start: 0.7771 (pp) cc_final: 0.7544 (pp)
REVERT: D    6 LYS cc_start: 0.7999 (ttpt) cc_final: 0.7342 (tmtt)
REVERT: D   34 GLU cc_start: 0.8112 (mp0) cc_final: 0.7795 (mp0)
REVERT: A  467 MET cc_start: 0.8275 (mmm) cc_final: 0.8002 (mmm)
REVERT: A  491 MET cc_start: 0.8401 (mmm) cc_final: 0.7758 (ttp)
REVERT: A  528 GLU cc_start: 0.8157 (tm-30) cc_final: 0.7828 (tm-30)
REVERT: A  587 ASN cc_start: 0.8061 (m-40) cc_final: 0.7642 (m110)
REVERT: A  667 MET cc_start: 0.7266 (tpt) cc_final: 0.6791 (tpp)
REVERT: A  690 MET cc_start: 0.7283 (mmt) cc_final: 0.6941 (mmt)
REVERT: A  727 LEU cc_start: 0.7648 (OUTLIER) cc_final: 0.7225 (tt)
REVERT: A  824 MET cc_start: 0.7592 (mmp) cc_final: 0.7030 (mmt)
REVERT: A  924 GLU cc_start: 0.7906 (mm-30) cc_final: 0.7644 (mm-30)
  outliers start: 22
  outliers final: 17
  residues processed: 187
  average time/residue: 0.0981
  time to fit residues: 26.6946
Evaluate side-chains
  187 residues out of total 1139 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 18
    poor density    : 169
  time to evaluate  : 0.412 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain D residue    9 THR
Chi-restraints excluded: chain D residue   66 THR
Chi-restraints excluded: chain A residue  498 MET
Chi-restraints excluded: chain A residue  518 VAL
Chi-restraints excluded: chain A residue  606 LEU
Chi-restraints excluded: chain A residue  625 CYS
Chi-restraints excluded: chain A residue  671 VAL
Chi-restraints excluded: chain A residue  727 LEU
Chi-restraints excluded: chain A residue  830 LEU
Chi-restraints excluded: chain A residue 1155 SER
Chi-restraints excluded: chain A residue 1158 ILE
Chi-restraints excluded: chain A residue 1471 VAL
Chi-restraints excluded: chain A residue 1534 LEU
Chi-restraints excluded: chain A residue 1609 LEU
Chi-restraints excluded: chain A residue 1744 VAL
Chi-restraints excluded: chain A residue 1787 VAL
Chi-restraints excluded: chain A residue 1854 LEU
Chi-restraints excluded: chain A residue 1953 LEU
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 126
   random chunks:
   chunk 81 optimal weight:    3.9990
   chunk 106 optimal weight:    4.9990
   chunk 29 optimal weight:    0.9990
   chunk 53 optimal weight:    3.9990
   chunk 84 optimal weight:    0.9980
   chunk 58 optimal weight:    4.9990
   chunk 114 optimal weight:    0.7980
   chunk 47 optimal weight:    0.6980
   chunk 33 optimal weight:    7.9990
   chunk 82 optimal weight:    3.9990
   chunk 3 optimal weight:    7.9990
   overall best weight:    1.4984

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

Flipped N/Q/H residues before XYZ refinement:
** D   2 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 707 ASN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3979 r_free = 0.3979 target = 0.136074 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 33)----------------|
| r_work = 0.3546 r_free = 0.3546 target = 0.104682 restraints weight = 17120.529|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 27)----------------|
| r_work = 0.3592 r_free = 0.3592 target = 0.108582 restraints weight = 8870.772|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 28)----------------|
| r_work = 0.3610 r_free = 0.3610 target = 0.110146 restraints weight = 5878.203|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 26)----------------|
| r_work = 0.3625 r_free = 0.3625 target = 0.111013 restraints weight = 4842.630|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 27)----------------|
| r_work = 0.3622 r_free = 0.3622 target = 0.110916 restraints weight = 4432.566|
|-----------------------------------------------------------------------------|
r_work (final): 0.3630
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3628
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3628 r_free = 0.3628    target_work(ls_wunit_k1) = 0.111         |
| occupancies: max = 1.00  min = 0.93   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3628 r_free = 0.3628    target_work(ls_wunit_k1) = 0.111         |
| occupancies: max = 1.00  min = 0.90   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.3628
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7325
moved from start:          0.4862

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.037  10273  Z= 0.149
  Angle     :  0.650  11.965  13895  Z= 0.314
  Chirality :  0.043   0.212   1602
  Planarity :  0.004   0.047   1785
  Dihedral  :  4.544  20.813   1355
  Min Nonbonded Distance : 2.511

Molprobity Statistics.
  All-atom Clashscore : 9.92
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.99 %
    Favored  : 96.01 %
  Rotamer:
    Outliers :  1.69 %
    Allowed  : 16.52 %
    Favored  : 81.79 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 3.23 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -0.84 (0.24), residues: 1254
  helix: -0.32 (0.20), residues: 673
  sheet: -1.20 (0.67), residues: 69
  loop : -0.58 (0.29), residues: 512

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARG A 514 
 TYR   0.019   0.001   TYR A1962 
 PHE   0.020   0.002   PHE A1544 
 TRP   0.007   0.001   TRP A1092 
 HIS   0.003   0.001   HIS C  68 

Details of bonding type rmsd
  covalent geometry    : bond        0.00361 (10272)
  covalent geometry    : angle       0.64973 (13893)
  SS BOND              : bond        0.00554 (    1)
  SS BOND              : angle       2.09536 (    2)
  hydrogen bonds       : bond        0.03248 (  374)
  hydrogen bonds       : angle       4.47723 ( 1080)

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

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

  2508 Ramachandran restraints generated.
    1254 Oldfield, 0 Emsley, 1254 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2508 Ramachandran restraints generated.
    1254 Oldfield, 0 Emsley, 1254 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  194 residues out of total 1139 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 19
    poor density    : 175
  time to evaluate  : 0.416 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: C    4 PHE cc_start: 0.8294 (m-80) cc_final: 0.7439 (m-80)
REVERT: C   14 THR cc_start: 0.8691 (p) cc_final: 0.8306 (t)
REVERT: D    6 LYS cc_start: 0.7957 (ttpt) cc_final: 0.7596 (ttmm)
REVERT: D   34 GLU cc_start: 0.8179 (mp0) cc_final: 0.7800 (mp0)
REVERT: A  467 MET cc_start: 0.8339 (mmm) cc_final: 0.7991 (mmm)
REVERT: A  491 MET cc_start: 0.8442 (mmm) cc_final: 0.7804 (ttp)
REVERT: A  528 GLU cc_start: 0.8192 (tm-30) cc_final: 0.7829 (tm-30)
REVERT: A  587 ASN cc_start: 0.8123 (m-40) cc_final: 0.7712 (m-40)
REVERT: A  667 MET cc_start: 0.7245 (tpt) cc_final: 0.6725 (tpp)
REVERT: A  690 MET cc_start: 0.7343 (mmt) cc_final: 0.6836 (mmt)
REVERT: A  727 LEU cc_start: 0.7659 (OUTLIER) cc_final: 0.7206 (tt)
REVERT: A  824 MET cc_start: 0.7808 (mmp) cc_final: 0.7235 (mmt)
REVERT: A  924 GLU cc_start: 0.7981 (mm-30) cc_final: 0.7704 (mm-30)
REVERT: A 1562 MET cc_start: 0.7850 (mtm) cc_final: 0.7452 (mtp)
  outliers start: 19
  outliers final: 17
  residues processed: 183
  average time/residue: 0.0954
  time to fit residues: 25.5687
Evaluate side-chains
  187 residues out of total 1139 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 18
    poor density    : 169
  time to evaluate  : 0.410 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain D residue    9 THR
Chi-restraints excluded: chain D residue   13 ILE
Chi-restraints excluded: chain A residue  498 MET
Chi-restraints excluded: chain A residue  518 VAL
Chi-restraints excluded: chain A residue  606 LEU
Chi-restraints excluded: chain A residue  625 CYS
Chi-restraints excluded: chain A residue  671 VAL
Chi-restraints excluded: chain A residue  727 LEU
Chi-restraints excluded: chain A residue  830 LEU
Chi-restraints excluded: chain A residue 1147 ILE
Chi-restraints excluded: chain A residue 1158 ILE
Chi-restraints excluded: chain A residue 1471 VAL
Chi-restraints excluded: chain A residue 1534 LEU
Chi-restraints excluded: chain A residue 1609 LEU
Chi-restraints excluded: chain A residue 1632 LEU
Chi-restraints excluded: chain A residue 1744 VAL
Chi-restraints excluded: chain A residue 1787 VAL
Chi-restraints excluded: chain A residue 1953 LEU
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 126
   random chunks:
   chunk 55 optimal weight:    0.1980
   chunk 111 optimal weight:    2.9990
   chunk 78 optimal weight:    2.9990
   chunk 36 optimal weight:    1.9990
   chunk 46 optimal weight:    0.3980
   chunk 60 optimal weight:    0.7980
   chunk 34 optimal weight:    0.7980
   chunk 17 optimal weight:    2.9990
   chunk 83 optimal weight:    0.7980
   chunk 2 optimal weight:    9.9990
   chunk 94 optimal weight:    6.9990
   overall best weight:    0.5980

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

Flipped N/Q/H residues before XYZ refinement:
** D   2 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4024 r_free = 0.4024 target = 0.140131 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 33)----------------|
| r_work = 0.3598 r_free = 0.3598 target = 0.108799 restraints weight = 16744.146|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 31)----------------|
| r_work = 0.3643 r_free = 0.3643 target = 0.112792 restraints weight = 8671.783|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 28)----------------|
| r_work = 0.3667 r_free = 0.3667 target = 0.114707 restraints weight = 5600.008|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 27)----------------|
| r_work = 0.3683 r_free = 0.3683 target = 0.115740 restraints weight = 4515.987|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 28)----------------|
| r_work = 0.3683 r_free = 0.3683 target = 0.115860 restraints weight = 4044.865|
|-----------------------------------------------------------------------------|
r_work (final): 0.3680
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3673
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3673 r_free = 0.3673    target_work(ls_wunit_k1) = 0.113         |
| occupancies: max = 1.00  min = 0.90   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3672 r_free = 0.3672    target_work(ls_wunit_k1) = 0.113         |
| occupancies: max = 1.00  min = 0.93   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.3672
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7241
moved from start:          0.5057

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.040  10273  Z= 0.110
  Angle     :  0.622  11.764  13895  Z= 0.302
  Chirality :  0.042   0.209   1602
  Planarity :  0.004   0.049   1785
  Dihedral  :  4.374  18.153   1355
  Min Nonbonded Distance : 2.513

Molprobity Statistics.
  All-atom Clashscore : 9.28
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.63 %
    Favored  : 97.37 %
  Rotamer:
    Outliers :  1.51 %
    Allowed  : 17.23 %
    Favored  : 81.26 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 3.23 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -0.60 (0.24), residues: 1254
  helix: -0.10 (0.20), residues: 667
  sheet: -1.13 (0.66), residues: 72
  loop : -0.48 (0.29), residues: 515

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.007   0.000   ARG A1940 
 TYR   0.017   0.001   TYR A1962 
 PHE   0.014   0.001   PHE A1929 
 TRP   0.006   0.001   TRP A1485 
 HIS   0.004   0.001   HIS C  68 

Details of bonding type rmsd
  covalent geometry    : bond        0.00262 (10272)
  covalent geometry    : angle       0.62127 (13893)
  SS BOND              : bond        0.00530 (    1)
  SS BOND              : angle       1.59495 (    2)
  hydrogen bonds       : bond        0.02995 (  374)
  hydrogen bonds       : angle       4.33563 ( 1080)

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

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

  2508 Ramachandran restraints generated.
    1254 Oldfield, 0 Emsley, 1254 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2508 Ramachandran restraints generated.
    1254 Oldfield, 0 Emsley, 1254 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  196 residues out of total 1139 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 17
    poor density    : 179
  time to evaluate  : 0.306 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: C    4 PHE cc_start: 0.8288 (m-80) cc_final: 0.7319 (m-80)
REVERT: C   14 THR cc_start: 0.8698 (p) cc_final: 0.8289 (t)
REVERT: D    2 GLN cc_start: 0.8106 (tm-30) cc_final: 0.7882 (tm-30)
REVERT: D    6 LYS cc_start: 0.7925 (ttpt) cc_final: 0.7294 (tmtt)
REVERT: D   34 GLU cc_start: 0.8158 (mp0) cc_final: 0.7807 (mp0)
REVERT: A  467 MET cc_start: 0.8282 (mmm) cc_final: 0.8028 (mmm)
REVERT: A  491 MET cc_start: 0.8399 (OUTLIER) cc_final: 0.7576 (ttp)
REVERT: A  496 ASP cc_start: 0.8687 (m-30) cc_final: 0.8401 (m-30)
REVERT: A  528 GLU cc_start: 0.8223 (tm-30) cc_final: 0.7896 (tm-30)
REVERT: A  587 ASN cc_start: 0.7876 (m-40) cc_final: 0.7495 (m110)
REVERT: A  667 MET cc_start: 0.7230 (tpt) cc_final: 0.6741 (tpp)
REVERT: A  690 MET cc_start: 0.7338 (mmt) cc_final: 0.6966 (mmt)
REVERT: A  727 LEU cc_start: 0.7547 (OUTLIER) cc_final: 0.7139 (tt)
REVERT: A  824 MET cc_start: 0.7735 (mmp) cc_final: 0.7153 (mmt)
REVERT: A  924 GLU cc_start: 0.7826 (mm-30) cc_final: 0.7583 (mm-30)
REVERT: A 1695 MET cc_start: 0.7434 (tpp) cc_final: 0.7140 (mmm)
  outliers start: 17
  outliers final: 15
  residues processed: 187
  average time/residue: 0.0851
  time to fit residues: 23.4145
Evaluate side-chains
  188 residues out of total 1139 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 17
    poor density    : 171
  time to evaluate  : 0.320 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain D residue    9 THR
Chi-restraints excluded: chain D residue   66 THR
Chi-restraints excluded: chain A residue  491 MET
Chi-restraints excluded: chain A residue  498 MET
Chi-restraints excluded: chain A residue  518 VAL
Chi-restraints excluded: chain A residue  606 LEU
Chi-restraints excluded: chain A residue  625 CYS
Chi-restraints excluded: chain A residue  671 VAL
Chi-restraints excluded: chain A residue  727 LEU
Chi-restraints excluded: chain A residue  830 LEU
Chi-restraints excluded: chain A residue 1158 ILE
Chi-restraints excluded: chain A residue 1471 VAL
Chi-restraints excluded: chain A residue 1534 LEU
Chi-restraints excluded: chain A residue 1609 LEU
Chi-restraints excluded: chain A residue 1744 VAL
Chi-restraints excluded: chain A residue 1787 VAL
Chi-restraints excluded: chain A residue 1953 LEU
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 126
   random chunks:
   chunk 30 optimal weight:    0.5980
   chunk 97 optimal weight:    0.9990
   chunk 39 optimal weight:    0.7980
   chunk 23 optimal weight:    0.8980
   chunk 103 optimal weight:    0.9990
   chunk 118 optimal weight:    5.9990
   chunk 65 optimal weight:    0.7980
   chunk 82 optimal weight:    3.9990
   chunk 115 optimal weight:    0.8980
   chunk 93 optimal weight:    6.9990
   chunk 12 optimal weight:    0.9990
   overall best weight:    0.7980

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

Flipped N/Q/H residues before XYZ refinement:
** D   2 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 856 HIS

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4005 r_free = 0.4005 target = 0.137881 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 37)----------------|
| r_work = 0.3572 r_free = 0.3572 target = 0.106360 restraints weight = 17067.112|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 28)----------------|
| r_work = 0.3627 r_free = 0.3627 target = 0.110763 restraints weight = 8035.671|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 32)----------------|
| r_work = 0.3657 r_free = 0.3657 target = 0.113294 restraints weight = 5083.531|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 24)----------------|
| r_work = 0.3663 r_free = 0.3663 target = 0.113516 restraints weight = 4160.952|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 26)----------------|
| r_work = 0.3665 r_free = 0.3665 target = 0.113789 restraints weight = 3933.944|
|-----------------------------------------------------------------------------|
r_work (final): 0.3666
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3666
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3666 r_free = 0.3666    target_work(ls_wunit_k1) = 0.113         |
| occupancies: max = 1.00  min = 0.93   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3666 r_free = 0.3666    target_work(ls_wunit_k1) = 0.113         |
| occupancies: max = 1.00  min = 0.90   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.3666
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7260
moved from start:          0.5141

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.040  10273  Z= 0.115
  Angle     :  0.628  12.461  13895  Z= 0.302
  Chirality :  0.042   0.207   1602
  Planarity :  0.004   0.047   1785
  Dihedral  :  4.300  17.521   1355
  Min Nonbonded Distance : 2.505

Molprobity Statistics.
  All-atom Clashscore : 9.62
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.19 %
    Favored  : 96.81 %
  Rotamer:
    Outliers :  1.51 %
    Allowed  : 17.05 %
    Favored  : 81.44 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 3.23 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -0.54 (0.24), residues: 1254
  helix: -0.03 (0.20), residues: 672
  sheet: -1.74 (0.67), residues: 65
  loop : -0.42 (0.29), residues: 517

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.006   0.000   ARG A1940 
 TYR   0.014   0.001   TYR A1962 
 PHE   0.013   0.001   PHE A1929 
 TRP   0.006   0.001   TRP A1485 
 HIS   0.003   0.001   HIS C  68 

Details of bonding type rmsd
  covalent geometry    : bond        0.00277 (10272)
  covalent geometry    : angle       0.62784 (13893)
  SS BOND              : bond        0.00527 (    1)
  SS BOND              : angle       1.78035 (    2)
  hydrogen bonds       : bond        0.02987 (  374)
  hydrogen bonds       : angle       4.34816 ( 1080)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 2105.24 seconds
wall clock time: 37 minutes 0.50 seconds (2220.50 seconds total)