Starting phenix.real_space_refine (version: 1.21rc1)
on Sun Aug 13 10:37:06 2023 by dcliebschner
===============================================================================

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

  Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7mi8_23842/08_2023/7mi8_23842.pdb
  Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7mi8_23842/08_2023/7mi8_23842.map

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

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

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7mi8_23842/08_2023/7mi8_23842.map"
    default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7mi8_23842/08_2023/7mi8_23842.map"
    model {
      file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7mi8_23842/08_2023/7mi8_23842.pdb"
    }
    default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7mi8_23842/08_2023/7mi8_23842.pdb"
  }
  resolution = 3.7
  write_initial_geo_file = False
  refinement {
    macro_cycles = 10
  }
  qi {
    qm_restraints {
      package {
        program = *test
      }
    }
  }


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
  Anisotropic ADP refinement not supported. Converting 6930 atoms to isotropic.
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      30      5.16       5
     C    4542      2.51       5
     N    1146      2.21       5
     O    1316      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped
    Residue "A ARG 1536": "NH1" <-> "NH2"
    Residue "A PHE 1537": "CD1" <-> "CD2" "CE1" <-> "CE2"
    Residue "A ASP 1543": "OD1" <-> "OD2"
    Residue "A ASP 1544": "OD1" <-> "OD2"
    Residue "A PHE 1578": "CD1" <-> "CD2" "CE1" <-> "CE2"
    Residue "A GLU 1594": "OE1" <-> "OE2"
    Residue "A ASP 1600": "OD1" <-> "OD2"
    Residue "A ASP 1612": "OD1" <-> "OD2"
    Residue "A GLU 1614": "OE1" <-> "OE2"
    Residue "A ASP 1635": "OD1" <-> "OD2"
    Residue "A ASP 1677": "OD1" <-> "OD2"
    Residue "A ASP 1692": "OD1" <-> "OD2"
    Residue "A ASP 1742": "OD1" <-> "OD2"
    Residue "A TYR 1758": "CD1" <-> "CD2" "CE1" <-> "CE2"
    Residue "A PHE 1760": "CD1" <-> "CD2" "CE1" <-> "CE2"
    Residue "A TYR 1771": "CD1" <-> "CD2" "CE1" <-> "CE2"
    Residue "A PHE 1794": "CD1" <-> "CD2" "CE1" <-> "CE2"
    Residue "A ASP 1824": "OD1" <-> "OD2"
    Residue "A PHE 1826": "CD1" <-> "CD2" "CE1" <-> "CE2"
    Residue "A ASP 1827": "OD1" <-> "OD2"
    Residue "A GLU 1855": "OE1" <-> "OE2"
    Residue "A GLU 1884": "OE1" <-> "OE2"
    Residue "A GLU 1910": "OE1" <-> "OE2"
    Residue "A PHE 3638": "CD1" <-> "CD2" "CE1" <-> "CE2"
    Residue "A ASP 3672": "OD1" <-> "OD2"
    Residue "A TYR 3679": "CD1" <-> "CD2" "CE1" <-> "CE2"
    Residue "A TYR 3715": "CD1" <-> "CD2" "CE1" <-> "CE2"
    Residue "A GLU 3717": "OE1" <-> "OE2"
    Residue "A ASP 3731": "OD1" <-> "OD2"
    Residue "A ASP 3739": "OD1" <-> "OD2"
    Residue "A ASP 3742": "OD1" <-> "OD2"
    Residue "A TYR 3746": "CD1" <-> "CD2" "CE1" <-> "CE2"
    Residue "A PHE 3763": "CD1" <-> "CD2" "CE1" <-> "CE2"
    Residue "A PHE 3768": "CD1" <-> "CD2" "CE1" <-> "CE2"
    Residue "A ASP 3770": "OD1" <-> "OD2"
    Residue "A GLU 3771": "OE1" <-> "OE2"
    Residue "A ASP 3776": "OD1" <-> "OD2"
    Residue "A GLU 3782": "OE1" <-> "OE2"
    Residue "A GLU 3791": "OE1" <-> "OE2"
    Residue "A ARG 3792": "NH1" <-> "NH2"
    Residue "A ASP 3795": "OD1" <-> "OD2"
    Residue "A GLU 3802": "OE1" <-> "OE2"
    Residue "A TYR 3854": "CD1" <-> "CD2" "CE1" <-> "CE2"
    Residue "A GLU 3860": "OE1" <-> "OE2"
    Residue "A GLU 3898": "OE1" <-> "OE2"
    Residue "A ASP 3905": "OD1" <-> "OD2"
    Residue "A ASP 3909": "OD1" <-> "OD2"
    Residue "A PHE 3916": "CD1" <-> "CD2" "CE1" <-> "CE2"
    Residue "A PHE 3961": "CD1" <-> "CD2" "CE1" <-> "CE2"
    Residue "A TYR 3994": "CD1" <-> "CD2" "CE1" <-> "CE2"
    Residue "A GLU 4000": "OE1" <-> "OE2"
    Residue "A GLU 4005": "OE1" <-> "OE2"
    Residue "A ASP 4019": "OD1" <-> "OD2"
    Residue "A ARG 4028": "NH1" <-> "NH2"
    Residue "A GLU 4041": "OE1" <-> "OE2"
    Residue "A GLU 4054": "OE1" <-> "OE2"
    Residue "A GLU 4068": "OE1" <-> "OE2"
    Residue "A GLU 4074": "OE1" <-> "OE2"
  Time to flip residues: 0.02s

  Monomer Library directory:
    "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5044/modules/chem_data/mon_lib"
  Total number of atoms: 7034
  Number of models: 1
  Model: ""
    Number of chains: 1
    Chain: "A"
      Number of atoms: 7034
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 868, 7034
          Classifications: {'peptide': 868}
          Link IDs: {'PTRANS': 21, 'TRANS': 846}
          Chain breaks: 2
  Time building chain proxies: 3.84, per 1000 atoms: 0.55
  Number of scatterers: 7034
  At special positions: 0
  Unit cell: (105.672, 117.586, 91.168, 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      30     16.00
     O    1316      8.00
     N    1146      7.00
     C    4542      6.00
    sf(0) = scattering factor at diffraction angle 0.

  Number of disulfides: simple=0, symmetry=0

  Automatic linking
    Parameters for automatic linking
      Linking & cutoffs
        Metal                : Auto  - 3.50
        Amino acid           : False - 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: 2.60
  Conformation dependent library (CDL) restraints added in 997.2 milliseconds
  

  1724 Ramachandran restraints generated.
    862 Oldfield, 0 Emsley, 862 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  1642

  Finding SS restraints...
    Secondary structure from input PDB file:
      39 helices and 5 sheets defined
      63.4% alpha, 7.4% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 0.67
  Creating SS restraints...
    Processing helix  chain 'A' and resid 1524 through 1534
    Processing helix  chain 'A' and resid 1535 through 1539
      removed outlier: 3.530A  pdb=" N   TYR A1538 " --> pdb=" O   PRO A1535 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 1541 through 1551
      removed outlier: 3.535A  pdb=" N   LYS A1547 " --> pdb=" O   ASP A1543 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 1558 through 1567
      removed outlier: 4.395A  pdb=" N   LYS A1563 " --> pdb=" O   SER A1559 " (cutoff:3.500A)
      removed outlier: 5.127A  pdb=" N   LYS A1564 " --> pdb=" O   LYS A1560 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 1603 through 1632
      removed outlier: 3.811A  pdb=" N   TRP A1607 " --> pdb=" O   GLN A1603 " (cutoff:3.500A)
      removed outlier: 3.871A  pdb=" N   LYS A1616 " --> pdb=" O   ASP A1612 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 1635 through 1641
      removed outlier: 3.965A  pdb=" N   SER A1641 " --> pdb=" O   GLU A1637 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 1644 through 1667
      removed outlier: 3.775A  pdb=" N   LYS A1662 " --> pdb=" O   GLU A1658 " (cutoff:3.500A)
      removed outlier: 3.803A  pdb=" N   GLN A1665 " --> pdb=" O   GLU A1661 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 1668 through 1689
      removed outlier: 3.581A  pdb=" N   TYR A1672 " --> pdb=" O   GLN A1668 " (cutoff:3.500A)
      removed outlier: 3.645A  pdb=" N   GLU A1675 " --> pdb=" O   LYS A1671 " (cutoff:3.500A)
      removed outlier: 3.568A  pdb=" N   ASN A1688 " --> pdb=" O   LEU A1684 " (cutoff:3.500A)
      removed outlier: 3.877A  pdb=" N   LYS A1689 " --> pdb=" O   ASP A1685 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 1691 through 1717
      removed outlier: 4.108A  pdb=" N   LYS A1696 " --> pdb=" O   ASP A1692 " (cutoff:3.500A)
      removed outlier: 4.386A  pdb=" N   LYS A1697 " --> pdb=" O   ASN A1693 " (cutoff:3.500A)
      removed outlier: 3.878A  pdb=" N   GLU A1704 " --> pdb=" O   ALA A1700 " (cutoff:3.500A)
      removed outlier: 3.601A  pdb=" N   ASN A1717 " --> pdb=" O   GLY A1713 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 1720 through 1731
      removed outlier: 4.098A  pdb=" N   LYS A1730 " --> pdb=" O   LEU A1726 " (cutoff:3.500A)
      removed outlier: 3.780A  pdb=" N   VAL A1731 " --> pdb=" O   LEU A1727 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 1742 through 1745
    Processing helix  chain 'A' and resid 1772 through 1788
      removed outlier: 3.949A  pdb=" N   GLN A1788 " --> pdb=" O   ASP A1784 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 1801 through 1813
      removed outlier: 3.570A  pdb=" N   LEU A1813 " --> pdb=" O   PHE A1809 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 1827 through 1842
      removed outlier: 3.683A  pdb=" N   LEU A1831 " --> pdb=" O   ASP A1827 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 1854 through 1875
    Processing helix  chain 'A' and resid 1909 through 1913
      removed outlier: 3.525A  pdb=" N   LYS A1913 " --> pdb=" O   GLU A1910 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 3617 through 3639
      removed outlier: 3.618A  pdb=" N   HIS A3624 " --> pdb=" O   ILE A3620 " (cutoff:3.500A)
      removed outlier: 3.852A  pdb=" N   LYS A3627 " --> pdb=" O   LYS A3623 " (cutoff:3.500A)
      removed outlier: 3.547A  pdb=" N   HIS A3639 " --> pdb=" O   PHE A3635 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 3645 through 3655
      removed outlier: 3.679A  pdb=" N   PHE A3649 " --> pdb=" O   SER A3645 " (cutoff:3.500A)
      removed outlier: 3.739A  pdb=" N   ARG A3655 " --> pdb=" O   SER A3651 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 3670 through 3687
      removed outlier: 3.944A  pdb=" N   TRP A3676 " --> pdb=" O   ASP A3672 " (cutoff:3.500A)
      removed outlier: 3.742A  pdb=" N   SER A3687 " --> pdb=" O   TYR A3683 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 3688 through 3690
      No H-bonds generated for 'chain 'A' and resid 3688 through 3690'
    Processing helix  chain 'A' and resid 3691 through 3711
      removed outlier: 4.425A  pdb=" N   ASP A3709 " --> pdb=" O   LEU A3705 " (cutoff:3.500A)
      removed outlier: 3.679A  pdb=" N   ILE A3710 " --> pdb=" O   TYR A3706 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 3712 through 3727
      removed outlier: 3.595A  pdb=" N   LYS A3716 " --> pdb=" O   SER A3712 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 3745 through 3753
      removed outlier: 3.546A  pdb=" N   THR A3753 " --> pdb=" O   ASP A3749 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 3756 through 3768
      removed outlier: 4.409A  pdb=" N   PHE A3763 " --> pdb=" O   ALA A3759 " (cutoff:3.500A)
      removed outlier: 4.323A  pdb=" N   LYS A3764 " --> pdb=" O   LEU A3760 " (cutoff:3.500A)
      removed outlier: 3.870A  pdb=" N   PHE A3767 " --> pdb=" O   PHE A3763 " (cutoff:3.500A)
      removed outlier: 3.985A  pdb=" N   PHE A3768 " --> pdb=" O   LYS A3764 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 3773 through 3781
    Processing helix  chain 'A' and resid 3796 through 3808
      removed outlier: 3.524A  pdb=" N   GLU A3802 " --> pdb=" O   PHE A3798 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 3818 through 3836
      removed outlier: 4.471A  pdb=" N   ILE A3834 " --> pdb=" O   SER A3830 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 3847 through 3854
      removed outlier: 3.633A  pdb=" N   THR A3853 " --> pdb=" O   SER A3849 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 3854 through 3861
      removed outlier: 4.641A  pdb=" N   GLU A3861 " --> pdb=" O   LYS A3857 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 3864 through 3870
      removed outlier: 3.917A  pdb=" N   HIS A3868 " --> pdb=" O   ALA A3864 " (cutoff:3.500A)
      removed outlier: 4.417A  pdb=" N   LYS A3870 " --> pdb=" O   GLU A3866 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 3885 through 3892
    Processing helix  chain 'A' and resid 3902 through 3913
      removed outlier: 3.664A  pdb=" N   SER A3913 " --> pdb=" O   ASP A3909 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 3922 through 3944
      removed outlier: 3.899A  pdb=" N   VAL A3926 " --> pdb=" O   GLY A3922 " (cutoff:3.500A)
      removed outlier: 3.603A  pdb=" N   TYR A3927 " --> pdb=" O   VAL A3923 " (cutoff:3.500A)
      removed outlier: 3.969A  pdb=" N   ARG A3944 " --> pdb=" O   THR A3940 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 3957 through 3974
      removed outlier: 4.058A  pdb=" N   PHE A3961 " --> pdb=" O   ASN A3957 " (cutoff:3.500A)
      removed outlier: 3.700A  pdb=" N   THR A3974 " --> pdb=" O   ASN A3970 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 3981 through 3992
      removed outlier: 4.116A  pdb=" N   ARG A3986 " --> pdb=" O   TRP A3982 " (cutoff:3.500A)
      removed outlier: 4.446A  pdb=" N   ASP A3987 " --> pdb=" O   ALA A3983 " (cutoff:3.500A)
      removed outlier: 3.530A  pdb=" N   HIS A3988 " --> pdb=" O   GLN A3984 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 4000 through 4015
      removed outlier: 3.524A  pdb=" N   HIS A4013 " --> pdb=" O   LYS A4009 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 4037 through 4051
    Processing helix  chain 'A' and resid 4057 through 4062
    Processing helix  chain 'A' and resid 4066 through 4091
      removed outlier: 3.692A  pdb=" N   ILE A4070 " --> pdb=" O   PRO A4066 " (cutoff:3.500A)
    Processing sheet with id=AA1, first strand: chain 'A' and resid 1569 through 1574
      removed outlier: 6.819A  pdb=" N   ARG A1583 " --> pdb=" O   GLU A1570 " (cutoff:3.500A)
      removed outlier: 5.106A  pdb=" N   ILE A1572 " --> pdb=" O   GLY A1581 " (cutoff:3.500A)
      removed outlier: 7.069A  pdb=" N   GLY A1581 " --> pdb=" O   ILE A1572 " (cutoff:3.500A)
      removed outlier: 7.073A  pdb=" N   PHE A1574 " --> pdb=" O   ILE A1579 " (cutoff:3.500A)
      removed outlier: 7.096A  pdb=" N   ILE A1579 " --> pdb=" O   PHE A1574 " (cutoff:3.500A)
    Processing sheet with id=AA2, first strand: chain 'A' and resid 1733 through 1736
    Processing sheet with id=AA3, first strand: chain 'A' and resid 1818 through 1820
      removed outlier: 7.009A  pdb=" N   GLY A1792 " --> pdb=" O   ILE A1896 " (cutoff:3.500A)
      removed outlier: 8.267A  pdb=" N   LEU A1898 " --> pdb=" O   GLY A1792 " (cutoff:3.500A)
      removed outlier: 6.830A  pdb=" N   PHE A1794 " --> pdb=" O   LEU A1898 " (cutoff:3.500A)
      removed outlier: 7.041A  pdb=" N   GLY A1791 " --> pdb=" O   ARG A1917 " (cutoff:3.500A)
      removed outlier: 8.068A  pdb=" N   PHE A1919 " --> pdb=" O   GLY A1791 " (cutoff:3.500A)
      removed outlier: 7.170A  pdb=" N   CYS A1793 " --> pdb=" O   PHE A1919 " (cutoff:3.500A)
    Processing sheet with id=AA4, first strand: chain 'A' and resid 1878 through 1881
    Processing sheet with id=AA5, first strand: chain 'A' and resid 3812 through 3815
      removed outlier: 3.840A  pdb=" N   GLN A3842 " --> pdb=" O   ILE A3814 " (cutoff:3.500A)
      removed outlier: 6.317A  pdb=" N   ILE A3839 " --> pdb=" O   PHE A3874 " (cutoff:3.500A)
      removed outlier: 7.873A  pdb=" N   THR A3876 " --> pdb=" O   ILE A3839 " (cutoff:3.500A)
      removed outlier: 6.777A  pdb=" N   LEU A3841 " --> pdb=" O   THR A3876 " (cutoff:3.500A)
      removed outlier: 8.665A  pdb=" N   HIS A3878 " --> pdb=" O   LEU A3841 " (cutoff:3.500A)
      removed outlier: 3.525A  pdb=" N   CYS A3877 " --> pdb=" O   MET A3788 " (cutoff:3.500A)
      removed outlier: 6.910A  pdb=" N   TYR A3785 " --> pdb=" O   ASP A3893 " (cutoff:3.500A)
      removed outlier: 7.895A  pdb=" N   VAL A3895 " --> pdb=" O   TYR A3785 " (cutoff:3.500A)
      removed outlier: 5.921A  pdb=" N   THR A3787 " --> pdb=" O   VAL A3895 " (cutoff:3.500A)

    371 hydrogen bonds defined for protein.
    1092 hydrogen bond angles defined for protein.
    Restraints generated for nucleic acids:
      0 hydrogen bonds
      0 hydrogen bond angles
      0 basepair planarities
      0 basepair parallelities
      0 stacking parallelities
  Total time for adding SS restraints: 2.09

  Time building geometry restraints manager: 2.80 seconds

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

  Histogram of bond lengths:
        1.22 -     1.34: 2215
        1.34 -     1.46: 1502
        1.46 -     1.58: 3424
        1.58 -     1.70: 0
        1.70 -     1.81: 46
  Bond restraints: 7187
  Sorted by residual:
  bond pdb=" CB  ASP A4019 "
       pdb=" CG  ASP A4019 "
    ideal  model  delta    sigma   weight residual
    1.516  1.565 -0.049 2.50e-02 1.60e+03 3.89e+00
  bond pdb=" CG  LEU A1702 "
       pdb=" CD2 LEU A1702 "
    ideal  model  delta    sigma   weight residual
    1.521  1.467  0.054 3.30e-02 9.18e+02 2.66e+00
  bond pdb=" CB  MET A3788 "
       pdb=" CG  MET A3788 "
    ideal  model  delta    sigma   weight residual
    1.520  1.477  0.043 3.00e-02 1.11e+03 2.06e+00
  bond pdb=" CG  LEU A1545 "
       pdb=" CD1 LEU A1545 "
    ideal  model  delta    sigma   weight residual
    1.521  1.476  0.045 3.30e-02 9.18e+02 1.86e+00
  bond pdb=" CA  THR A3737 "
       pdb=" CB  THR A3737 "
    ideal  model  delta    sigma   weight residual
    1.530  1.553 -0.023 1.69e-02 3.50e+03 1.79e+00
  ... (remaining 7182 not shown)

  Histogram of bond angle deviations from ideal:
       97.04 -   104.46: 73
      104.46 -   111.88: 3306
      111.88 -   119.30: 2680
      119.30 -   126.72: 3553
      126.72 -   134.14: 100
  Bond angle restraints: 9712
  Sorted by residual:
  angle pdb=" C   LEU A3736 "
        pdb=" N   THR A3737 "
        pdb=" CA  THR A3737 "
      ideal   model   delta    sigma   weight residual
     121.54  132.65  -11.11 1.91e+00 2.74e-01 3.38e+01
  angle pdb=" N   THR A3737 "
        pdb=" CA  THR A3737 "
        pdb=" C   THR A3737 "
      ideal   model   delta    sigma   weight residual
     110.80  100.37   10.43 2.13e+00 2.20e-01 2.40e+01
  angle pdb=" CA  LEU A1882 "
        pdb=" CB  LEU A1882 "
        pdb=" CG  LEU A1882 "
      ideal   model   delta    sigma   weight residual
     116.30  132.64  -16.34 3.50e+00 8.16e-02 2.18e+01
  angle pdb=" CA  LEU A1741 "
        pdb=" CB  LEU A1741 "
        pdb=" CG  LEU A1741 "
      ideal   model   delta    sigma   weight residual
     116.30  131.52  -15.22 3.50e+00 8.16e-02 1.89e+01
  angle pdb=" CA  LEU A4033 "
        pdb=" CB  LEU A4033 "
        pdb=" CG  LEU A4033 "
      ideal   model   delta    sigma   weight residual
     116.30  130.64  -14.34 3.50e+00 8.16e-02 1.68e+01
  ... (remaining 9707 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    17.89: 3923
       17.89 -    35.79: 272
       35.79 -    53.68: 59
       53.68 -    71.57: 14
       71.57 -    89.46: 12
  Dihedral angle restraints: 4280
    sinusoidal: 1742
      harmonic: 2538
  Sorted by residual:
  dihedral pdb=" CA  GLU A3809 "
           pdb=" C   GLU A3809 "
           pdb=" N   SER A3810 "
           pdb=" CA  SER A3810 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  160.61   19.39     0      5.00e+00 4.00e-02 1.50e+01
  dihedral pdb=" CB  GLU A4068 "
           pdb=" CG  GLU A4068 "
           pdb=" CD  GLU A4068 "
           pdb=" OE1 GLU A4068 "
      ideal   model   delta sinusoidal    sigma   weight residual
       0.00   88.58  -88.58     1      3.00e+01 1.11e-03 1.04e+01
  dihedral pdb=" CA  ASP A1742 "
           pdb=" C   ASP A1742 "
           pdb=" N   ASP A1743 "
           pdb=" CA  ASP A1743 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00 -164.24  -15.76     0      5.00e+00 4.00e-02 9.94e+00
  ... (remaining 4277 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.046: 706
       0.046 -    0.092: 268
       0.092 -    0.137: 89
       0.137 -    0.183: 13
       0.183 -    0.229: 6
  Chirality restraints: 1082
  Sorted by residual:
  chirality pdb=" CA  ASP A4019 "
            pdb=" N   ASP A4019 "
            pdb=" C   ASP A4019 "
            pdb=" CB  ASP A4019 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.28    0.23 2.00e-01 2.50e+01 1.31e+00
  chirality pdb=" CA  PHE A1794 "
            pdb=" N   PHE A1794 "
            pdb=" C   PHE A1794 "
            pdb=" CB  PHE A1794 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.29    0.22 2.00e-01 2.50e+01 1.16e+00
  chirality pdb=" CB  THR A1740 "
            pdb=" CA  THR A1740 "
            pdb=" OG1 THR A1740 "
            pdb=" CG2 THR A1740 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.55    2.36    0.19 2.00e-01 2.50e+01 8.82e-01
  ... (remaining 1079 not shown)

  Planarity restraints: 1225
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  ILE A3801 "   -0.016 2.00e-02 2.50e+03   3.19e-02 1.02e+01
        pdb=" C   ILE A3801 "    0.055 2.00e-02 2.50e+03
        pdb=" O   ILE A3801 "   -0.021 2.00e-02 2.50e+03
        pdb=" N   GLU A3802 "   -0.018 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  MET A1562 "   -0.016 2.00e-02 2.50e+03   3.15e-02 9.95e+00
        pdb=" C   MET A1562 "    0.055 2.00e-02 2.50e+03
        pdb=" O   MET A1562 "   -0.020 2.00e-02 2.50e+03
        pdb=" N   LYS A1563 "   -0.019 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CB  HIS A1554 "    0.018 2.00e-02 2.50e+03   2.49e-02 9.32e+00
        pdb=" CG  HIS A1554 "   -0.053 2.00e-02 2.50e+03
        pdb=" ND1 HIS A1554 "    0.016 2.00e-02 2.50e+03
        pdb=" CD2 HIS A1554 "    0.019 2.00e-02 2.50e+03
        pdb=" CE1 HIS A1554 "    0.000 2.00e-02 2.50e+03
        pdb=" NE2 HIS A1554 "   -0.001 2.00e-02 2.50e+03
  ... (remaining 1222 not shown)

  Histogram of nonbonded interaction distances:
        2.23 -     2.76: 1217
        2.76 -     3.30: 6889
        3.30 -     3.83: 11188
        3.83 -     4.37: 13130
        4.37 -     4.90: 22444
  Nonbonded interactions: 54868
  Sorted by model distance:
  nonbonded pdb=" O   LEU A1687 "
            pdb=" OG  SER A1690 "
     model   vdw
     2.226 2.440
  nonbonded pdb=" O   LEU A3736 "
            pdb=" OG1 THR A3737 "
     model   vdw
     2.251 2.440
  nonbonded pdb=" O   ASN A3761 "
            pdb=" ND2 ASN A3765 "
     model   vdw
     2.282 2.520
  nonbonded pdb=" O   LYS A3805 "
            pdb=" NZ  LYS A3808 "
     model   vdw
     2.300 2.520
  nonbonded pdb=" NZ  LYS A3735 "
            pdb=" O   THR A3737 "
     model   vdw
     2.338 2.520
  ... (remaining 54863 not shown)

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

  No NCS relation were found !!!

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

Found NCS groups:
  found none.
Set up NCS constraints
  No NCS constraints will be used in refinement.
Set refine NCS operators
Adjust number of macro_cycles
  Number of macro_cycles: 10
Reset NCS operators
Extract rigid body selections
Check and reset occupancies
  Occupancies: min=1.00 max=1.00 mean=1.00
Load rotamer database and sin/cos tables
Set ADP refinement strategy
  ADPs will be refined as group one per residue
Make a string to write initial .geo file
Internal consistency checks
Time:
  Set random seed:                         0.000
  Set model cs if undefined:               0.000
  Decide on map wrapping:                  0.000
  Normalize map: mean=0, sd=1:             2.040
  Set stop_for_unknowns flag:              0.000
  Assert model is a single copy model:     0.000
  Assert all atoms have isotropic ADPs:    0.070
  Construct map_model_manager:             0.010
  Extract box with map and model:          10.800
  Check model and map are aligned:         0.100
  Set scattering table:                    0.060
  Process input model:                     21.220
  Find NCS groups from input model:        0.200
  Set up NCS constraints:                  0.030
  Set refine NCS operators:                0.000
  Adjust number of macro_cycles:           0.000
  Reset NCS operators:                     0.000
  Extract rigid body selections:           0.000
  Check and reset occupancies:             0.000
  Load rotamer database and sin/cos tables:2.610
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   37.140
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8311
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      :  0.006   0.054   7187  Z= 0.384
  Angle     :  0.967  16.338   9712  Z= 0.524
  Chirality :  0.054   0.229   1082
  Planarity :  0.007   0.033   1225
  Dihedral  : 14.131  89.462   2638
  Min Nonbonded Distance : 2.226

Molprobity Statistics.
  All-atom Clashscore : 5.27
  Ramachandran Plot:
    Outliers :  0.12 %
    Allowed  :  2.44 %
    Favored  : 97.45 %
  Rotamer Outliers :  0.38 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -3.11 (0.21), residues: 862
  helix: -2.18 (0.15), residues: 481
  sheet: -0.68 (0.68), residues: 61
  loop : -1.86 (0.28), residues: 320

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

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

  1724 Ramachandran restraints generated.
    862 Oldfield, 0 Emsley, 862 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1724 Ramachandran restraints generated.
    862 Oldfield, 0 Emsley, 862 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  182 residues out of total 782 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 3
    poor density    : 179
  time to evaluate  : 0.838 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
  outliers start: 3
  outliers final: 1
  residues processed: 181
  average time/residue: 0.2413
  time to fit residues: 55.6146
Evaluate side-chains
  96 residues out of total 782 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 1
    poor density    : 95
  time to evaluate  : 0.858 
Switching outliers to nearest non-outliers
  outliers start: 1
  outliers final: 0
  residues processed: 1
  average time/residue: 0.0649
  time to fit residues: 1.2192
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 86
   random chunks:
   chunk 72 optimal weight:    4.9990
   chunk 65 optimal weight:    0.9980
   chunk 36 optimal weight:    5.9990
   chunk 22 optimal weight:    0.8980
   chunk 43 optimal weight:    6.9990
   chunk 34 optimal weight:    1.9990
   chunk 67 optimal weight:    0.0370
   chunk 26 optimal weight:    4.9990
   chunk 40 optimal weight:    6.9990
   chunk 50 optimal weight:    0.9990
   chunk 78 optimal weight:    0.7980
   overall best weight:    0.7460

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

Flipped N/Q/H residues before XYZ refinement:
** A1554 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
A1555 HIS
A1646 GLN
A1693 ASN
A1869 GLN
** A1899 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
A3773 ASN
** A3784 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
A3856 HIS
A3948 HIS

Total number of N/Q/H flips: 7

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8286
moved from start:          0.1929

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd. rmsZ for bonds and angles.
  Bond      :  0.003   0.027   7187  Z= 0.168
  Angle     :  0.595  12.407   9712  Z= 0.309
  Chirality :  0.040   0.170   1082
  Planarity :  0.004   0.031   1225
  Dihedral  :  4.008  21.083    923
  Min Nonbonded Distance : 2.178

Molprobity Statistics.
  All-atom Clashscore : 8.40
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.44 %
    Favored  : 97.56 %
  Rotamer Outliers :  1.79 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -0.51 (0.27), residues: 862
  helix:  0.44 (0.22), residues: 478
  sheet: -0.29 (0.69), residues: 61
  loop : -1.45 (0.30), residues: 323

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

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

  1724 Ramachandran restraints generated.
    862 Oldfield, 0 Emsley, 862 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1724 Ramachandran restraints generated.
    862 Oldfield, 0 Emsley, 862 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  122 residues out of total 782 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 14
    poor density    : 108
  time to evaluate  : 0.838 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
  outliers start: 14
  outliers final: 5
  residues processed: 116
  average time/residue: 0.1792
  time to fit residues: 28.8679
Evaluate side-chains
  95 residues out of total 782 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 5
    poor density    : 90
  time to evaluate  : 0.838 
Switching outliers to nearest non-outliers
  outliers start: 5
  outliers final: 0
  residues processed: 5
  average time/residue: 0.0751
  time to fit residues: 1.8097
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 86
   random chunks:
   chunk 43 optimal weight:    3.9990
   chunk 24 optimal weight:    5.9990
   chunk 64 optimal weight:   10.0000
   chunk 53 optimal weight:    4.9990
   chunk 21 optimal weight:   10.0000
   chunk 78 optimal weight:    0.8980
   chunk 84 optimal weight:    1.9990
   chunk 69 optimal weight:    9.9990
   chunk 77 optimal weight:    3.9990
   chunk 26 optimal weight:    5.9990
   chunk 62 optimal weight:    5.9990
   overall best weight:    3.1788

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

Flipped N/Q/H residues before XYZ refinement:
** A1554 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
A1788 GLN
A1869 GLN
** A1899 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
A3714 GLN
** A3784 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
A3856 HIS

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8417
moved from start:          0.2508

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd. rmsZ for bonds and angles.
  Bond      :  0.005   0.038   7187  Z= 0.344
  Angle     :  0.646  11.015   9712  Z= 0.341
  Chirality :  0.043   0.270   1082
  Planarity :  0.004   0.027   1225
  Dihedral  :  4.326  21.767    923
  Min Nonbonded Distance : 2.108

Molprobity Statistics.
  All-atom Clashscore : 11.18
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.02 %
    Favored  : 96.98 %
  Rotamer Outliers :  2.81 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.30 (0.27), residues: 862
  helix:  1.16 (0.23), residues: 485
  sheet: -0.23 (0.64), residues: 73
  loop : -1.23 (0.31), residues: 304

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

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

  1724 Ramachandran restraints generated.
    862 Oldfield, 0 Emsley, 862 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1724 Ramachandran restraints generated.
    862 Oldfield, 0 Emsley, 862 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  111 residues out of total 782 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 22
    poor density    : 89
  time to evaluate  : 0.831 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
  outliers start: 22
  outliers final: 14
  residues processed: 101
  average time/residue: 0.1523
  time to fit residues: 22.5169
Evaluate side-chains
  97 residues out of total 782 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 14
    poor density    : 83
  time to evaluate  : 0.831 
Switching outliers to nearest non-outliers
  outliers start: 14
  outliers final: 0
  residues processed: 14
  average time/residue: 0.0699
  time to fit residues: 2.9299
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 86
   random chunks:
   chunk 77 optimal weight:    2.9990
   chunk 58 optimal weight:    7.9990
   chunk 40 optimal weight:    6.9990
   chunk 8 optimal weight:    0.9980
   chunk 37 optimal weight:    3.9990
   chunk 52 optimal weight:    3.9990
   chunk 78 optimal weight:    1.9990
   chunk 83 optimal weight:    7.9990
   chunk 41 optimal weight:    0.9990
   chunk 74 optimal weight:    3.9990
   chunk 22 optimal weight:    0.7980
   overall best weight:    1.5586

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

Flipped N/Q/H residues before XYZ refinement:
** A1554 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** A1899 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A3784 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
A3856 HIS

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8383
moved from start:          0.2685

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd. rmsZ for bonds and angles.
  Bond      :  0.003   0.038   7187  Z= 0.200
  Angle     :  0.562   9.769   9712  Z= 0.291
  Chirality :  0.040   0.219   1082
  Planarity :  0.003   0.028   1225
  Dihedral  :  4.141  22.106    923
  Min Nonbonded Distance : 2.147

Molprobity Statistics.
  All-atom Clashscore : 9.12
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.67 %
    Favored  : 97.33 %
  Rotamer Outliers :  2.05 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.64 (0.28), residues: 862
  helix:  1.49 (0.23), residues: 485
  sheet: -0.34 (0.62), residues: 73
  loop : -1.11 (0.32), residues: 304

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

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

  1724 Ramachandran restraints generated.
    862 Oldfield, 0 Emsley, 862 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1724 Ramachandran restraints generated.
    862 Oldfield, 0 Emsley, 862 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  104 residues out of total 782 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 16
    poor density    : 88
  time to evaluate  : 0.840 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
  outliers start: 16
  outliers final: 11
  residues processed: 96
  average time/residue: 0.1484
  time to fit residues: 21.0530
Evaluate side-chains
  90 residues out of total 782 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 11
    poor density    : 79
  time to evaluate  : 0.805 
Switching outliers to nearest non-outliers
  outliers start: 11
  outliers final: 0
  residues processed: 11
  average time/residue: 0.0731
  time to fit residues: 2.5529
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 86
   random chunks:
   chunk 69 optimal weight:   10.0000
   chunk 47 optimal weight:    3.9990
   chunk 1 optimal weight:    3.9990
   chunk 61 optimal weight:    2.9990
   chunk 34 optimal weight:    3.9990
   chunk 70 optimal weight:    1.9990
   chunk 57 optimal weight:    1.9990
   chunk 0 optimal weight:    5.9990
   chunk 42 optimal weight:    0.6980
   chunk 74 optimal weight:    1.9990
   chunk 20 optimal weight:    3.9990
   overall best weight:    1.9388

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

Flipped N/Q/H residues before XYZ refinement:
** A1554 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
A1840 GLN
** A1899 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A3784 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
A3856 HIS

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8398
moved from start:          0.2921

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd. rmsZ for bonds and angles.
  Bond      :  0.004   0.032   7187  Z= 0.230
  Angle     :  0.585   8.456   9712  Z= 0.299
  Chirality :  0.041   0.259   1082
  Planarity :  0.003   0.032   1225
  Dihedral  :  4.146  21.856    923
  Min Nonbonded Distance : 2.149

Molprobity Statistics.
  All-atom Clashscore : 9.90
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.02 %
    Favored  : 96.98 %
  Rotamer Outliers :  1.79 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.80 (0.28), residues: 862
  helix:  1.66 (0.23), residues: 482
  sheet: -0.37 (0.57), residues: 79
  loop : -1.08 (0.33), residues: 301

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

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

  1724 Ramachandran restraints generated.
    862 Oldfield, 0 Emsley, 862 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1724 Ramachandran restraints generated.
    862 Oldfield, 0 Emsley, 862 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  101 residues out of total 782 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 14
    poor density    : 87
  time to evaluate  : 0.892 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
  outliers start: 14
  outliers final: 5
  residues processed: 95
  average time/residue: 0.1562
  time to fit residues: 21.7232
Evaluate side-chains
  82 residues out of total 782 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 5
    poor density    : 77
  time to evaluate  : 0.821 
Switching outliers to nearest non-outliers
  outliers start: 5
  outliers final: 0
  residues processed: 5
  average time/residue: 0.0730
  time to fit residues: 1.8262
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 86
   random chunks:
   chunk 27 optimal weight:    0.9990
   chunk 74 optimal weight:    0.9980
   chunk 16 optimal weight:    2.9990
   chunk 48 optimal weight:    0.0970
   chunk 20 optimal weight:    3.9990
   chunk 83 optimal weight:    6.9990
   chunk 69 optimal weight:    8.9990
   chunk 38 optimal weight:    4.9990
   chunk 6 optimal weight:    2.9990
   chunk 43 optimal weight:    3.9990
   chunk 80 optimal weight:    3.9990
   overall best weight:    1.6184

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

Flipped N/Q/H residues before XYZ refinement:
** A1554 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** A3784 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
A3856 HIS

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8389
moved from start:          0.3073

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd. rmsZ for bonds and angles.
  Bond      :  0.003   0.030   7187  Z= 0.208
  Angle     :  0.598   8.968   9712  Z= 0.300
  Chirality :  0.041   0.306   1082
  Planarity :  0.003   0.049   1225
  Dihedral  :  4.153  21.663    923
  Min Nonbonded Distance : 2.166

Molprobity Statistics.
  All-atom Clashscore : 9.76
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.78 %
    Favored  : 97.22 %
  Rotamer Outliers :  1.41 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.89 (0.28), residues: 862
  helix:  1.75 (0.23), residues: 480
  sheet: -0.33 (0.57), residues: 79
  loop : -1.06 (0.33), residues: 303

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

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

  1724 Ramachandran restraints generated.
    862 Oldfield, 0 Emsley, 862 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1724 Ramachandran restraints generated.
    862 Oldfield, 0 Emsley, 862 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  95 residues out of total 782 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 11
    poor density    : 84
  time to evaluate  : 0.918 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
  outliers start: 11
  outliers final: 4
  residues processed: 93
  average time/residue: 0.1482
  time to fit residues: 20.5041
Evaluate side-chains
  84 residues out of total 782 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 4
    poor density    : 80
  time to evaluate  : 0.810 
Switching outliers to nearest non-outliers
  outliers start: 4
  outliers final: 0
  residues processed: 4
  average time/residue: 0.0752
  time to fit residues: 1.6391
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 86
   random chunks:
   chunk 9 optimal weight:    4.9990
   chunk 47 optimal weight:    0.8980
   chunk 60 optimal weight:    0.9980
   chunk 70 optimal weight:    1.9990
   chunk 46 optimal weight:    1.9990
   chunk 82 optimal weight:    9.9990
   chunk 51 optimal weight:    8.9990
   chunk 50 optimal weight:    4.9990
   chunk 38 optimal weight:    3.9990
   chunk 33 optimal weight:    4.9990
   chunk 49 optimal weight:    0.6980
   overall best weight:    1.3184

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

Flipped N/Q/H residues before XYZ refinement:
A1533 GLN
A1668 GLN
** A3784 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
A3856 HIS

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8380
moved from start:          0.3226

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd. rmsZ for bonds and angles.
  Bond      :  0.003   0.032   7187  Z= 0.185
  Angle     :  0.581   9.119   9712  Z= 0.292
  Chirality :  0.040   0.283   1082
  Planarity :  0.003   0.053   1225
  Dihedral  :  4.075  21.561    923
  Min Nonbonded Distance : 2.172

Molprobity Statistics.
  All-atom Clashscore : 9.04
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.25 %
    Favored  : 96.75 %
  Rotamer Outliers :  0.90 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.92 (0.28), residues: 862
  helix:  1.77 (0.23), residues: 483
  sheet: -0.23 (0.57), residues: 79
  loop : -1.08 (0.33), residues: 300

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

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

  1724 Ramachandran restraints generated.
    862 Oldfield, 0 Emsley, 862 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1724 Ramachandran restraints generated.
    862 Oldfield, 0 Emsley, 862 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  99 residues out of total 782 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 7
    poor density    : 92
  time to evaluate  : 0.823 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
  outliers start: 7
  outliers final: 3
  residues processed: 95
  average time/residue: 0.1479
  time to fit residues: 20.9767
Evaluate side-chains
  83 residues out of total 782 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 3
    poor density    : 80
  time to evaluate  : 0.880 
Switching outliers to nearest non-outliers
  outliers start: 3
  outliers final: 0
  residues processed: 3
  average time/residue: 0.0715
  time to fit residues: 1.5777
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 86
   random chunks:
   chunk 24 optimal weight:    0.7980
   chunk 16 optimal weight:    2.9990
   chunk 52 optimal weight:    3.9990
   chunk 56 optimal weight:    8.9990
   chunk 40 optimal weight:    1.9990
   chunk 7 optimal weight:    5.9990
   chunk 65 optimal weight:    4.9990
   chunk 75 optimal weight:    5.9990
   chunk 79 optimal weight:    6.9990
   chunk 72 optimal weight:    0.6980
   chunk 77 optimal weight:    6.9990
   overall best weight:    2.0986

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

Flipped N/Q/H residues before XYZ refinement:
** A3784 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8407
moved from start:          0.3355

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd. rmsZ for bonds and angles.
  Bond      :  0.004   0.036   7187  Z= 0.248
  Angle     :  0.604   9.742   9712  Z= 0.307
  Chirality :  0.041   0.306   1082
  Planarity :  0.003   0.044   1225
  Dihedral  :  4.163  21.715    923
  Min Nonbonded Distance : 2.156

Molprobity Statistics.
  All-atom Clashscore : 9.54
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.60 %
    Favored  : 96.40 %
  Rotamer Outliers :  1.15 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.88 (0.28), residues: 862
  helix:  1.75 (0.23), residues: 485
  sheet: -0.31 (0.57), residues: 79
  loop : -1.13 (0.33), residues: 298

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

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

  1724 Ramachandran restraints generated.
    862 Oldfield, 0 Emsley, 862 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1724 Ramachandran restraints generated.
    862 Oldfield, 0 Emsley, 862 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  91 residues out of total 782 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 9
    poor density    : 82
  time to evaluate  : 0.823 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
  outliers start: 9
  outliers final: 5
  residues processed: 88
  average time/residue: 0.1737
  time to fit residues: 22.1536
Evaluate side-chains
  81 residues out of total 782 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 5
    poor density    : 76
  time to evaluate  : 0.844 
Switching outliers to nearest non-outliers
  outliers start: 5
  outliers final: 0
  residues processed: 5
  average time/residue: 0.0725
  time to fit residues: 1.8592
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 86
   random chunks:
   chunk 79 optimal weight:    8.9990
   chunk 46 optimal weight:    3.9990
   chunk 33 optimal weight:    5.9990
   chunk 60 optimal weight:    0.9990
   chunk 23 optimal weight:    5.9990
   chunk 69 optimal weight:    1.9990
   chunk 73 optimal weight:    2.9990
   chunk 76 optimal weight:    4.9990
   chunk 50 optimal weight:    2.9990
   chunk 81 optimal weight:    5.9990
   chunk 49 optimal weight:    1.9990
   overall best weight:    2.1990

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

Flipped N/Q/H residues before XYZ refinement:
** A3784 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8411
moved from start:          0.3457

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd. rmsZ for bonds and angles.
  Bond      :  0.004   0.036   7187  Z= 0.256
  Angle     :  0.633  12.365   9712  Z= 0.320
  Chirality :  0.043   0.361   1082
  Planarity :  0.003   0.053   1225
  Dihedral  :  4.242  21.507    923
  Min Nonbonded Distance : 2.152

Molprobity Statistics.
  All-atom Clashscore : 10.40
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.36 %
    Favored  : 96.64 %
  Rotamer Outliers :  0.51 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.87 (0.28), residues: 862
  helix:  1.77 (0.23), residues: 482
  sheet: -0.19 (0.58), residues: 82
  loop : -1.19 (0.33), residues: 298

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

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

  1724 Ramachandran restraints generated.
    862 Oldfield, 0 Emsley, 862 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1724 Ramachandran restraints generated.
    862 Oldfield, 0 Emsley, 862 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  83 residues out of total 782 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 4
    poor density    : 79
  time to evaluate  : 0.822 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
  outliers start: 4
  outliers final: 3
  residues processed: 81
  average time/residue: 0.1600
  time to fit residues: 19.1660
Evaluate side-chains
  81 residues out of total 782 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 3
    poor density    : 78
  time to evaluate  : 0.903 
Switching outliers to nearest non-outliers
  outliers start: 3
  outliers final: 0
  residues processed: 3
  average time/residue: 0.0719
  time to fit residues: 1.5999
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 86
   random chunks:
   chunk 38 optimal weight:    0.2980
   chunk 56 optimal weight:    3.9990
   chunk 85 optimal weight:    4.9990
   chunk 78 optimal weight:    1.9990
   chunk 68 optimal weight:    2.9990
   chunk 7 optimal weight:    5.9990
   chunk 52 optimal weight:    4.9990
   chunk 41 optimal weight:    0.9990
   chunk 54 optimal weight:    0.9980
   chunk 72 optimal weight:    0.8980
   chunk 20 optimal weight:    6.9990
   overall best weight:    1.0384

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

Flipped N/Q/H residues before XYZ refinement:
** A3784 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8377
moved from start:          0.3531

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd. rmsZ for bonds and angles.
  Bond      :  0.003   0.033   7187  Z= 0.176
  Angle     :  0.630  11.515   9712  Z= 0.312
  Chirality :  0.041   0.303   1082
  Planarity :  0.003   0.049   1225
  Dihedral  :  4.117  21.535    923
  Min Nonbonded Distance : 2.196

Molprobity Statistics.
  All-atom Clashscore : 10.11
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.36 %
    Favored  : 96.64 %
  Rotamer Outliers :  0.13 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.01 (0.29), residues: 862
  helix:  1.88 (0.23), residues: 482
  sheet: -0.23 (0.59), residues: 79
  loop : -1.10 (0.33), residues: 301

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

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

  1724 Ramachandran restraints generated.
    862 Oldfield, 0 Emsley, 862 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1724 Ramachandran restraints generated.
    862 Oldfield, 0 Emsley, 862 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  87 residues out of total 782 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 1
    poor density    : 86
  time to evaluate  : 0.867 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
  outliers start: 1
  outliers final: 0
  residues processed: 87
  average time/residue: 0.1749
  time to fit residues: 22.3606
Evaluate side-chains
  79 residues out of total 782 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 0
    poor density    : 79
  time to evaluate  : 0.849 
Switching outliers to nearest non-outliers
  outliers start: 0
  outliers final: 0
  residues processed: 0
  time to fit residues: 1.1549
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 86
   random chunks:
   chunk 62 optimal weight:    4.9990
   chunk 10 optimal weight:    0.7980
   chunk 18 optimal weight:    0.8980
   chunk 68 optimal weight:    3.9990
   chunk 28 optimal weight:    5.9990
   chunk 70 optimal weight:    0.8980
   chunk 8 optimal weight:    0.4980
   chunk 12 optimal weight:    1.9990
   chunk 59 optimal weight:    4.9990
   chunk 3 optimal weight:    1.9990
   chunk 49 optimal weight:    2.9990
   overall best weight:    1.0182

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

Flipped N/Q/H residues before XYZ refinement:
A1840 GLN
** A3784 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3462 r_free = 0.3462 target = 0.097849 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 37)----------------|
| r_work = 0.3117 r_free = 0.3117 target = 0.078932 restraints weight = 19014.294|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 31)----------------|
| r_work = 0.3168 r_free = 0.3168 target = 0.081647 restraints weight = 10271.987|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 33)----------------|
| r_work = 0.3201 r_free = 0.3201 target = 0.083484 restraints weight = 6939.631|
|-----------------------------------------------------------------------------|
r_work (final): 0.3200
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8477
moved from start:          0.3631

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd. rmsZ for bonds and angles.
  Bond      :  0.003   0.035   7187  Z= 0.175
  Angle     :  0.627  11.614   9712  Z= 0.312
  Chirality :  0.041   0.290   1082
  Planarity :  0.003   0.051   1225
  Dihedral  :  4.052  21.263    923
  Min Nonbonded Distance : 2.191

Molprobity Statistics.
  All-atom Clashscore : 9.90
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.36 %
    Favored  : 96.64 %
  Rotamer Outliers :  0.51 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.04 (0.29), residues: 862
  helix:  1.91 (0.24), residues: 482
  sheet: -0.13 (0.60), residues: 79
  loop : -1.12 (0.33), residues: 301
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 1720.78 seconds
wall clock time: 32 minutes 2.40 seconds (1922.40 seconds total)