Starting phenix.real_space_refine
on Thu Jul  2 03:55:06 2026 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/9prc_71807/07_2026/9prc_71807.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/9prc_71807/07_2026/9prc_71807.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=3.5
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    model {
      file = "/net/cci-nas-00/data/ceres_data/9prc_71807/07_2026/9prc_71807.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/9prc_71807/07_2026/9prc_71807.cif"
    real_map_files = "/net/cci-nas-00/data/ceres_data/9prc_71807/07_2026/9prc_71807.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/9prc_71807/07_2026/9prc_71807.map"
  }
  resolution = 3.5
  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=   0.000
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
     P     152      5.49       5
     C    3543      2.51       5
     N    1149      2.21       5
     O    1649      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 9 residue(s): 0.00s

  Monomer Library directory:
    "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/chem_data/mon_lib"
  Total number of atoms: 6493
  Number of models: 1
  Model: ""
    Number of chains: 12
    Chain: "A"
      Number of atoms: 422
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 52, 422
          Classifications: {'peptide': 52}
          Incomplete info: {'truncation_to_alanine': 4}
          Link IDs: {'PTRANS': 1, 'TRANS': 50}
          Unresolved non-hydrogen bonds: 15
          Unresolved non-hydrogen angles: 16
          Unresolved non-hydrogen dihedrals: 14
          Planarities with less than four sites: {'ASP:plan': 1}
          Unresolved non-hydrogen planarities: 3
    Chain: "B"
      Number of atoms: 422
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 52, 422
          Classifications: {'peptide': 52}
          Incomplete info: {'truncation_to_alanine': 4}
          Link IDs: {'PTRANS': 1, 'TRANS': 50}
          Unresolved non-hydrogen bonds: 15
          Unresolved non-hydrogen angles: 16
          Unresolved non-hydrogen dihedrals: 14
          Planarities with less than four sites: {'ASP:plan': 1}
          Unresolved non-hydrogen planarities: 3
    Chain: "C"
      Number of atoms: 412
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 50, 412
          Classifications: {'peptide': 50}
          Incomplete info: {'truncation_to_alanine': 2}
          Link IDs: {'PTRANS': 1, 'TRANS': 48}
          Unresolved non-hydrogen bonds: 8
          Unresolved non-hydrogen angles: 8
          Unresolved non-hydrogen dihedrals: 8
    Chain: "D"
      Number of atoms: 407
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 49, 407
          Classifications: {'peptide': 49}
          Incomplete info: {'truncation_to_alanine': 1}
          Link IDs: {'PTRANS': 1, 'TRANS': 47}
          Unresolved non-hydrogen bonds: 4
          Unresolved non-hydrogen angles: 4
          Unresolved non-hydrogen dihedrals: 4
    Chain: "E"
      Number of atoms: 412
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 50, 412
          Classifications: {'peptide': 50}
          Incomplete info: {'truncation_to_alanine': 2}
          Link IDs: {'PTRANS': 1, 'TRANS': 48}
          Unresolved non-hydrogen bonds: 8
          Unresolved non-hydrogen angles: 8
          Unresolved non-hydrogen dihedrals: 8
    Chain: "F"
      Number of atoms: 407
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 49, 407
          Classifications: {'peptide': 49}
          Incomplete info: {'truncation_to_alanine': 1}
          Link IDs: {'PTRANS': 1, 'TRANS': 47}
          Unresolved non-hydrogen bonds: 4
          Unresolved non-hydrogen angles: 4
          Unresolved non-hydrogen dihedrals: 4
    Chain: "G"
      Number of atoms: 412
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 50, 412
          Classifications: {'peptide': 50}
          Incomplete info: {'truncation_to_alanine': 2}
          Link IDs: {'PTRANS': 1, 'TRANS': 48}
          Unresolved non-hydrogen bonds: 8
          Unresolved non-hydrogen angles: 8
          Unresolved non-hydrogen dihedrals: 8
    Chain: "H"
      Number of atoms: 407
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 49, 407
          Classifications: {'peptide': 49}
          Incomplete info: {'truncation_to_alanine': 1}
          Link IDs: {'PTRANS': 1, 'TRANS': 47}
          Unresolved non-hydrogen bonds: 4
          Unresolved non-hydrogen angles: 4
          Unresolved non-hydrogen dihedrals: 4
    Chain: "J"
      Number of atoms: 756
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 36, 756
          Classifications: {'RNA': 36}
          Modifications used: {'rna3p_pur': 18, 'rna3p_pyr': 18}
          Link IDs: {'rna3p': 35}
          Chain breaks: 1
    Chain: "K"
      Number of atoms: 840
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 40, 840
          Classifications: {'RNA': 40}
          Modifications used: {'rna3p_pur': 20, 'rna3p_pyr': 20}
          Link IDs: {'rna3p': 39}
          Chain breaks: 1
    Chain: "M"
      Number of atoms: 756
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 36, 756
          Classifications: {'RNA': 36}
          Modifications used: {'rna3p_pur': 18, 'rna3p_pyr': 18}
          Link IDs: {'rna3p': 35}
          Chain breaks: 1
    Chain: "P"
      Number of atoms: 840
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 40, 840
          Classifications: {'RNA': 40}
          Modifications used: {'rna2p_pur': 1, 'rna2p_pyr': 4, 'rna3p_pur': 19, 'rna3p_pyr': 16}
          Link IDs: {'rna2p': 4, 'rna3p': 35}
          Chain breaks: 1
  Time building chain proxies: 1.38, per 1000 atoms: 0.21
  Number of scatterers: 6493
  At special positions: 0
  Unit cell: (120.285, 106.434, 85.293, 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)
     P     152     15.00
     O    1649      8.00
     N    1149      7.00
     C    3543      6.00
    sf(0) = scattering factor at diffraction angle 0.

  Number of disulfides: simple=0, symmetry=0

  Automatic linking
    Parameters for automatic linking
      Linking & cutoffs
        Metal                : Auto  - 3.00
        Amino acid           : True  - 1.90
        Carbohydrate         : True  - 1.99
        Ligands              : True  - 1.99
        Small molecules      : False - 1.98
        Amino acid - RNA/DNA : False
      
  Number of custom bonds: simple=0, symmetry=0
  Time building additional restraints: 0.48
  Conformation dependent library (CDL) restraints added in 115.3 milliseconds
  

  770 Ramachandran restraints generated.
    385 Oldfield, 0 Emsley, 385 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  722

  Finding SS restraints...
    Secondary structure from input PDB file:
      16 helices and 0 sheets defined
      96.5% alpha, 0.0% beta
      64 base pairs and 82 stacking pairs defined.
    Time for finding SS restraints: 0.76
  Creating SS restraints...
    Processing helix  chain 'A' and resid 12 through 48
      removed outlier: 3.881A  pdb=" N   VAL A  16 " --> pdb=" O   GLY A  12 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 49 through 60
      removed outlier: 4.224A  pdb=" N   ASN A  53 " --> pdb=" O   PRO A  49 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 13 through 48
    Processing helix  chain 'B' and resid 49 through 59
      removed outlier: 4.133A  pdb=" N   ASN B  53 " --> pdb=" O   PRO B  49 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 13 through 48
      removed outlier: 3.651A  pdb=" N   HIS C  48 " --> pdb=" O   LEU C  44 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 48 through 60
      removed outlier: 3.627A  pdb=" N   GLY C  52 " --> pdb=" O   HIS C  48 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 13 through 48
    Processing helix  chain 'D' and resid 48 through 60
      removed outlier: 3.792A  pdb=" N   GLY D  52 " --> pdb=" O   HIS D  48 " (cutoff:3.500A)
    Processing helix  chain 'E' and resid 13 through 47
      removed outlier: 4.222A  pdb=" N   GLU E  47 " --> pdb=" O   LYS E  43 " (cutoff:3.500A)
    Processing helix  chain 'E' and resid 48 through 59
    Processing helix  chain 'F' and resid 13 through 47
      removed outlier: 4.471A  pdb=" N   GLU F  47 " --> pdb=" O   LYS F  43 " (cutoff:3.500A)
    Processing helix  chain 'F' and resid 48 through 60
    Processing helix  chain 'G' and resid 13 through 48
    Processing helix  chain 'G' and resid 48 through 61
      removed outlier: 3.626A  pdb=" N   GLY G  52 " --> pdb=" O   HIS G  48 " (cutoff:3.500A)
      removed outlier: 4.047A  pdb=" N   LYS G  61 " --> pdb=" O   ILE G  57 " (cutoff:3.500A)
    Processing helix  chain 'H' and resid 13 through 47
    Processing helix  chain 'H' and resid 48 through 60
      removed outlier: 3.532A  pdb=" N   GLY H  52 " --> pdb=" O   HIS H  48 " (cutoff:3.500A)
      removed outlier: 3.598A  pdb=" N   LYS H  60 " --> pdb=" O   GLY H  56 " (cutoff:3.500A)

    311 hydrogen bonds defined for protein.
    933 hydrogen bond angles defined for protein.
    Restraints generated for nucleic acids:
      128 hydrogen bonds
      256 hydrogen bond angles
      0 basepair planarities
      64 basepair parallelities
      82 stacking parallelities
  Total time for adding SS restraints: 0.90

  Time building geometry restraints manager: 0.67 seconds

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

  Histogram of bond lengths:
        1.21 -     1.29: 729
        1.29 -     1.38: 1447
        1.38 -     1.46: 1511
        1.46 -     1.54: 2899
        1.54 -     1.62: 319
  Bond restraints: 6905
  Sorted by residual:
  bond pdb=" N9    A P  27 "
       pdb=" C4    A P  27 "
    ideal  model  delta    sigma   weight residual
    1.374  1.361  0.013 6.00e-03 2.78e+04 4.65e+00
  bond pdb=" N9    A K  25 "
       pdb=" C4    A K  25 "
    ideal  model  delta    sigma   weight residual
    1.374  1.386 -0.012 6.00e-03 2.78e+04 4.13e+00
  bond pdb=" N7    A M  15 "
       pdb=" C5    A M  15 "
    ideal  model  delta    sigma   weight residual
    1.388  1.379  0.009 6.00e-03 2.78e+04 2.03e+00
  bond pdb=" C5    A J  37 "
       pdb=" C6    A J  37 "
    ideal  model  delta    sigma   weight residual
    1.406  1.393  0.013 9.00e-03 1.23e+04 2.02e+00
  bond pdb=" N7    A K  25 "
       pdb=" C5    A K  25 "
    ideal  model  delta    sigma   weight residual
    1.388  1.380  0.008 6.00e-03 2.78e+04 1.96e+00
  ... (remaining 6900 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     1.89: 9762
        1.89 -     3.78: 143
        3.78 -     5.67: 32
        5.67 -     7.56: 8
        7.56 -     9.45: 2
  Bond angle restraints: 9947
  Sorted by residual:
  angle pdb=" O2    U K  20 "
        pdb=" C2    U K  20 "
        pdb=" N3    U K  20 "
      ideal   model   delta    sigma   weight residual
     122.20  118.37    3.83 7.00e-01 2.04e+00 2.99e+01
  angle pdb=" N1    U P  26 "
        pdb=" C6    U P  26 "
        pdb=" C5    U P  26 "
      ideal   model   delta    sigma   weight residual
     122.70  125.08   -2.38 5.00e-01 4.00e+00 2.28e+01
  angle pdb=" C1'   U P  34 "
        pdb=" N1    U P  34 "
        pdb=" C2    U P  34 "
      ideal   model   delta    sigma   weight residual
     117.70  122.92   -5.22 1.20e+00 6.94e-01 1.89e+01
  angle pdb=" CB  LYS F  26 "
        pdb=" CG  LYS F  26 "
        pdb=" CD  LYS F  26 "
      ideal   model   delta    sigma   weight residual
     111.30  120.75   -9.45 2.30e+00 1.89e-01 1.69e+01
  angle pdb=" C1'   U P  32 "
        pdb=" N1    U P  32 "
        pdb=" C2    U P  32 "
      ideal   model   delta    sigma   weight residual
     117.70  122.59   -4.89 1.20e+00 6.94e-01 1.66e+01
  ... (remaining 9942 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    35.69: 3876
       35.69 -    71.39: 301
       71.39 -   107.08: 14
      107.08 -   142.78: 1
      142.78 -   178.47: 3
  Dihedral angle restraints: 4195
    sinusoidal: 3080
      harmonic: 1115
  Sorted by residual:
  dihedral pdb=" O4'   U P  34 "
           pdb=" C1'   U P  34 "
           pdb=" N1    U P  34 "
           pdb=" C2    U P  34 "
      ideal   model   delta sinusoidal    sigma   weight residual
    -160.00   18.47 -178.47     1      1.50e+01 4.44e-03 8.53e+01
  dihedral pdb=" O4'   U P  32 "
           pdb=" C1'   U P  32 "
           pdb=" N1    U P  32 "
           pdb=" C2    U P  32 "
      ideal   model   delta sinusoidal    sigma   weight residual
     232.00   66.49  165.51     1      1.70e+01 3.46e-03 6.54e+01
  dihedral pdb=" O4'   U P  26 "
           pdb=" C1'   U P  26 "
           pdb=" N1    U P  26 "
           pdb=" C2    U P  26 "
      ideal   model   delta sinusoidal    sigma   weight residual
    -128.00  -24.01 -103.99     1      1.70e+01 3.46e-03 4.13e+01
  ... (remaining 4192 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.034: 1054
       0.034 -    0.068: 137
       0.068 -    0.102: 24
       0.102 -    0.135: 5
       0.135 -    0.169: 5
  Chirality restraints: 1225
  Sorted by residual:
  chirality pdb=" C1'   A P  41 "
            pdb=" O4'   A P  41 "
            pdb=" C2'   A P  41 "
            pdb=" N9    A P  41 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.46    2.29    0.17 2.00e-01 2.50e+01 7.17e-01
  chirality pdb=" C1'   U P  32 "
            pdb=" O4'   U P  32 "
            pdb=" C2'   U P  32 "
            pdb=" N1    U P  32 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.45    2.29    0.15 2.00e-01 2.50e+01 5.82e-01
  chirality pdb=" P     A P  33 "
            pdb=" OP1   A P  33 "
            pdb=" OP2   A P  33 "
            pdb=" O5'   A P  33 "
    both_signs  ideal   model   delta    sigma   weight residual
      True       2.41   -2.56   -0.15 2.00e-01 2.50e+01 5.62e-01
  ... (remaining 1222 not shown)

  Planarity restraints: 705
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CG  GLU D  28 "    0.009 2.00e-02 2.50e+03   1.80e-02 3.22e+00
        pdb=" CD  GLU D  28 "   -0.031 2.00e-02 2.50e+03
        pdb=" OE1 GLU D  28 "    0.011 2.00e-02 2.50e+03
        pdb=" OE2 GLU D  28 "    0.011 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CG  GLU D  15 "   -0.009 2.00e-02 2.50e+03   1.76e-02 3.08e+00
        pdb=" CD  GLU D  15 "    0.030 2.00e-02 2.50e+03
        pdb=" OE1 GLU D  15 "   -0.011 2.00e-02 2.50e+03
        pdb=" OE2 GLU D  15 "   -0.011 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CG  GLU G  28 "    0.009 2.00e-02 2.50e+03   1.73e-02 3.01e+00
        pdb=" CD  GLU G  28 "   -0.030 2.00e-02 2.50e+03
        pdb=" OE1 GLU G  28 "    0.011 2.00e-02 2.50e+03
        pdb=" OE2 GLU G  28 "    0.011 2.00e-02 2.50e+03
  ... (remaining 702 not shown)

  Histogram of nonbonded interaction distances:
        2.21 -     2.75: 838
        2.75 -     3.29: 6294
        3.29 -     3.82: 12980
        3.82 -     4.36: 13699
        4.36 -     4.90: 19686
  Nonbonded interactions: 53497
  Sorted by model distance:
  nonbonded pdb=" O4    U P  12 "
            pdb=" N6    A P  33 "
     model   vdw
     2.208 3.120
  nonbonded pdb=" OD1 ASN D  53 "
            pdb=" O2'   U J  32 "
     model   vdw
     2.212 3.040
  nonbonded pdb=" OE2 GLU B  31 "
            pdb=" NH1 ARG B  35 "
     model   vdw
     2.246 3.120
  nonbonded pdb=" OE2 GLU B  29 "
            pdb=" NH1 ARG B  32 "
     model   vdw
     2.287 3.120
  nonbonded pdb=" O2    U P  10 "
            pdb=" N6    A P  35 "
     model   vdw
     2.302 3.120
  ... (remaining 53492 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 'A' and resid 12 through 60)
  selection = (chain 'B' and resid 12 through 60)
  selection = (chain 'C' and resid 12 through 60)
  selection = chain 'D'
  selection = (chain 'E' and resid 12 through 60)
  selection = chain 'F'
  selection = (chain 'G' and resid 12 through 60)
  selection = chain 'H'
}
ncs_group {
  reference = chain 'J'
  selection = (chain 'K' and resid 5 through 44)
  selection = chain 'M'
  selection = (chain 'P' and resid 5 through 44)
}

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:             6.430
  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:          0.170
  Check model and map are aligned:         0.020
  Set scattering table:                    0.010
  Process input model:                     7.180
  Find NCS groups from input model:        0.060
  Set up NCS constraints:                  0.010
  Set refine NCS operators:                0.000
  Adjust number of macro_cycles:           0.000
  Reset NCS operators:                     0.000
  Extract rigid body selections:           0.000
  Check and reset occupancies:             0.000
  Load rotamer database and sin/cos tables:1.010
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   14.900
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7566
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      :  0.004   0.041   6905  Z= 0.228
  Angle     :  0.597   9.447   9947  Z= 0.447
  Chirality :  0.027   0.169   1225
  Planarity :  0.004   0.034    705
  Dihedral  : 19.631 178.472   3473
  Min Nonbonded Distance : 2.208

Molprobity Statistics.
  All-atom Clashscore : 16.17
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  0.78 %
    Favored  : 99.22 %
  Rotamer:
    Outliers :  2.62 %
    Allowed  : 37.21 %
    Favored  : 60.17 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  5.49 (0.40), residues: 385
  helix:  3.77 (0.25), residues: 369
  sheet:  None (None), residues: 0
  loop : -2.31 (1.03), residues: 16

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.007   0.001   ARG F  32 
 TRP   0.016   0.002   TRP H  20 
 HIS   0.011   0.002   HIS D  48 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00362 /  0.23 ( 6905)
  covalent geometry    : angle       0.59705 /  0.45 ( 9947)
  hydrogen bonds       : bond        0.07560 /  4.56 (  439)
  hydrogen bonds       : angle       3.57558 /  2.59 ( 1189)

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

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

  770 Ramachandran restraints generated.
    385 Oldfield, 0 Emsley, 385 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  770 Ramachandran restraints generated.
    385 Oldfield, 0 Emsley, 385 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  115 residues out of total 361 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 9
    poor density    : 106
  time to evaluate  : 0.186 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: B   28 GLU cc_start: 0.7602 (tm-30) cc_final: 0.7302 (tm-30)
REVERT: B   29 GLU cc_start: 0.8013 (mm-30) cc_final: 0.7600 (mm-30)
REVERT: E   45 GLU cc_start: 0.8032 (tp30) cc_final: 0.7684 (tm-30)
REVERT: E   55 LYS cc_start: 0.6364 (tptm) cc_final: 0.5896 (tptm)
REVERT: F   42 LYS cc_start: 0.8368 (tppt) cc_final: 0.8126 (mmtm)
REVERT: G   46 ASP cc_start: 0.7738 (t0) cc_final: 0.7383 (t0)
REVERT: H   18 GLU cc_start: 0.7717 (tp30) cc_final: 0.7216 (tp30)
  outliers start: 9
  outliers final: 6
  residues processed: 114
  average time/residue: 0.1526
  time to fit residues: 20.4235
Evaluate side-chains
  110 residues out of total 361 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 6
    poor density    : 104
  time to evaluate  : 0.201 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   34 LEU
Chi-restraints excluded: chain C residue   38 LYS
Chi-restraints excluded: chain D residue   57 ILE
Chi-restraints excluded: chain E residue   41 ILE
Chi-restraints excluded: chain F residue   51 LEU
Chi-restraints excluded: chain H residue   51 LEU
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 51
   random chunks:
   chunk 24 optimal weight:    0.8980
   chunk 48 optimal weight:   10.0000
   chunk 26 optimal weight:    1.9990
   chunk 2 optimal weight:    2.9990
   chunk 16 optimal weight:    0.7980
   chunk 32 optimal weight:    0.0770
   chunk 31 optimal weight:    0.9990
   chunk 25 optimal weight:    0.9990
   chunk 50 optimal weight:   10.0000
   chunk 19 optimal weight:    0.6980
   chunk 30 optimal weight:    0.6980
   overall best weight:    0.6338

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
B  53 ASN
F  53 ASN
** G  48 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4160 r_free = 0.4160 target = 0.124213 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 40)----------------|
| r_work = 0.3806 r_free = 0.3806 target = 0.101074 restraints weight = 18264.936|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 30)----------------|
| r_work = 0.3832 r_free = 0.3832 target = 0.102751 restraints weight = 9007.738|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 47)----------------|
| r_work = 0.3853 r_free = 0.3853 target = 0.103935 restraints weight = 5722.210|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 32)----------------|
| r_work = 0.3863 r_free = 0.3863 target = 0.104624 restraints weight = 4315.701|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 31)----------------|
| r_work = 0.3868 r_free = 0.3868 target = 0.104953 restraints weight = 3666.143|
|-----------------------------------------------------------------------------|
r_work (final): 0.3828
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7529
moved from start:          0.0576

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.026   6905  Z= 0.133
  Angle     :  0.467   5.722   9947  Z= 0.262
  Chirality :  0.027   0.240   1225
  Planarity :  0.003   0.028    705
  Dihedral  : 17.615 173.681   2543
  Min Nonbonded Distance : 2.446

Molprobity Statistics.
  All-atom Clashscore : 12.89
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  0.52 %
    Favored  : 99.48 %
  Rotamer:
    Outliers :  3.78 %
    Allowed  : 32.85 %
    Favored  : 63.37 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  5.45 (0.39), residues: 385
  helix:  3.73 (0.24), residues: 369
  sheet:  None (None), residues: 0
  loop : -2.13 (1.05), residues: 16

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.007   0.001   ARG B  32 
 TRP   0.011   0.001   TRP H  20 
 HIS   0.007   0.002   HIS D  48 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00276 /  0.13 ( 6905)
  covalent geometry    : angle       0.46738 /  0.26 ( 9947)
  hydrogen bonds       : bond        0.04919 /  3.31 (  439)
  hydrogen bonds       : angle       3.15810 /  2.31 ( 1189)

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

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

  770 Ramachandran restraints generated.
    385 Oldfield, 0 Emsley, 385 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  770 Ramachandran restraints generated.
    385 Oldfield, 0 Emsley, 385 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  123 residues out of total 361 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 110
  time to evaluate  : 0.124 
Fit side-chains
   revert: symmetry clash
REVERT: B   28 GLU cc_start: 0.7606 (tm-30) cc_final: 0.7322 (tm-30)
REVERT: B   48 HIS cc_start: 0.8022 (m90) cc_final: 0.7784 (m170)
REVERT: D   13 ARG cc_start: 0.6127 (ttm170) cc_final: 0.5461 (ptm160)
REVERT: D   18 GLU cc_start: 0.7861 (OUTLIER) cc_final: 0.7570 (tm-30)
REVERT: E   45 GLU cc_start: 0.8110 (tp30) cc_final: 0.7758 (tm-30)
REVERT: E   55 LYS cc_start: 0.6541 (tptm) cc_final: 0.6036 (tptm)
REVERT: F   28 GLU cc_start: 0.7115 (tp30) cc_final: 0.6819 (tp30)
REVERT: F   32 ARG cc_start: 0.7920 (mtm110) cc_final: 0.7659 (mtm110)
REVERT: F   42 LYS cc_start: 0.8516 (tppt) cc_final: 0.8273 (mmtm)
REVERT: G   46 ASP cc_start: 0.7945 (t0) cc_final: 0.7607 (t0)
REVERT: H   18 GLU cc_start: 0.7824 (tp30) cc_final: 0.7261 (tp30)
  outliers start: 13
  outliers final: 9
  residues processed: 118
  average time/residue: 0.1495
  time to fit residues: 20.7880
Evaluate side-chains
  115 residues out of total 361 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 105
  time to evaluate  : 0.182 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   34 LEU
Chi-restraints excluded: chain C residue   38 LYS
Chi-restraints excluded: chain D residue   18 GLU
Chi-restraints excluded: chain D residue   54 ILE
Chi-restraints excluded: chain E residue   54 ILE
Chi-restraints excluded: chain F residue   51 LEU
Chi-restraints excluded: chain G residue   47 GLU
Chi-restraints excluded: chain G residue   57 ILE
Chi-restraints excluded: chain H residue   39 LYS
Chi-restraints excluded: chain H residue   51 LEU
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 51
   random chunks:
   chunk 29 optimal weight:    0.5980
   chunk 46 optimal weight:    6.9990
   chunk 32 optimal weight:    0.8980
   chunk 14 optimal weight:    0.5980
   chunk 16 optimal weight:    0.8980
   chunk 24 optimal weight:    0.9990
   chunk 3 optimal weight:    3.9990
   chunk 27 optimal weight:    0.9990
   chunk 28 optimal weight:    0.4980
   chunk 31 optimal weight:    0.5980
   chunk 10 optimal weight:    0.0770
   overall best weight:    0.4738

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
** B  48 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** G  48 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4147 r_free = 0.4147 target = 0.123730 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.3772 r_free = 0.3772 target = 0.100300 restraints weight = 18286.294|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 32)----------------|
| r_work = 0.3804 r_free = 0.3804 target = 0.102157 restraints weight = 9214.775|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 37)----------------|
| r_work = 0.3826 r_free = 0.3826 target = 0.103438 restraints weight = 5844.212|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 25)----------------|
| r_work = 0.3836 r_free = 0.3836 target = 0.104094 restraints weight = 4386.711|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 41)----------------|
| r_work = 0.3848 r_free = 0.3848 target = 0.104755 restraints weight = 3758.182|
|-----------------------------------------------------------------------------|
r_work (final): 0.3843
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7485
moved from start:          0.0908

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.031   6905  Z= 0.123
  Angle     :  0.444   6.802   9947  Z= 0.246
  Chirality :  0.026   0.191   1225
  Planarity :  0.003   0.031    705
  Dihedral  : 17.398 168.002   2539
  Min Nonbonded Distance : 2.473

Molprobity Statistics.
  All-atom Clashscore : 12.37
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  0.26 %
    Favored  : 99.74 %
  Rotamer:
    Outliers :  5.23 %
    Allowed  : 32.85 %
    Favored  : 61.92 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  5.64 (0.39), residues: 385
  helix:  3.85 (0.24), residues: 369
  sheet:  None (None), residues: 0
  loop : -2.01 (1.08), residues: 16

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG D  24 
 TRP   0.011   0.001   TRP H  20 
 HIS   0.010   0.002   HIS D  48 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00254 /  0.12 ( 6905)
  covalent geometry    : angle       0.44414 /  0.25 ( 9947)
  hydrogen bonds       : bond        0.04604 /  3.09 (  439)
  hydrogen bonds       : angle       3.04854 /  2.24 ( 1189)

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

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

  770 Ramachandran restraints generated.
    385 Oldfield, 0 Emsley, 385 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  770 Ramachandran restraints generated.
    385 Oldfield, 0 Emsley, 385 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  130 residues out of total 361 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 18
    poor density    : 112
  time to evaluate  : 0.224 
Fit side-chains
   revert: symmetry clash
REVERT: B   28 GLU cc_start: 0.7563 (tm-30) cc_final: 0.7287 (tm-30)
REVERT: C   47 GLU cc_start: 0.6386 (OUTLIER) cc_final: 0.6070 (mp0)
REVERT: D   18 GLU cc_start: 0.7762 (OUTLIER) cc_final: 0.7507 (tm-30)
REVERT: E   45 GLU cc_start: 0.8041 (tp30) cc_final: 0.7763 (tm-30)
REVERT: E   55 LYS cc_start: 0.6467 (tptm) cc_final: 0.5979 (tptm)
REVERT: F   42 LYS cc_start: 0.8433 (tppt) cc_final: 0.8188 (mmtm)
REVERT: G   46 ASP cc_start: 0.7949 (t0) cc_final: 0.7627 (t0)
REVERT: H   18 GLU cc_start: 0.7825 (tp30) cc_final: 0.7232 (tp30)
  outliers start: 18
  outliers final: 12
  residues processed: 124
  average time/residue: 0.1400
  time to fit residues: 20.4185
Evaluate side-chains
  120 residues out of total 361 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 106
  time to evaluate  : 0.167 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   34 LEU
Chi-restraints excluded: chain C residue   38 LYS
Chi-restraints excluded: chain C residue   47 GLU
Chi-restraints excluded: chain D residue   18 GLU
Chi-restraints excluded: chain D residue   47 GLU
Chi-restraints excluded: chain D residue   54 ILE
Chi-restraints excluded: chain D residue   57 ILE
Chi-restraints excluded: chain E residue   54 ILE
Chi-restraints excluded: chain F residue   51 LEU
Chi-restraints excluded: chain G residue   47 GLU
Chi-restraints excluded: chain G residue   57 ILE
Chi-restraints excluded: chain H residue   35 ARG
Chi-restraints excluded: chain H residue   39 LYS
Chi-restraints excluded: chain H residue   51 LEU
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 51
   random chunks:
   chunk 18 optimal weight:    0.9980
   chunk 38 optimal weight:    6.9990
   chunk 24 optimal weight:    1.9990
   chunk 27 optimal weight:    2.9990
   chunk 31 optimal weight:    1.9990
   chunk 5 optimal weight:    0.5980
   chunk 8 optimal weight:    0.4980
   chunk 4 optimal weight:    0.9990
   chunk 7 optimal weight:    0.7980
   chunk 28 optimal weight:    0.8980
   chunk 45 optimal weight:    6.9990
   overall best weight:    0.7580

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
** D  48 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4161 r_free = 0.4161 target = 0.124417 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 40)----------------|
| r_work = 0.3800 r_free = 0.3800 target = 0.101018 restraints weight = 18858.982|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 35)----------------|
| r_work = 0.3832 r_free = 0.3832 target = 0.102903 restraints weight = 9362.305|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 41)----------------|
| r_work = 0.3853 r_free = 0.3853 target = 0.104165 restraints weight = 5900.367|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 29)----------------|
| r_work = 0.3864 r_free = 0.3864 target = 0.104861 restraints weight = 4438.864|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 45)----------------|
| r_work = 0.3874 r_free = 0.3874 target = 0.105462 restraints weight = 3794.002|
|-----------------------------------------------------------------------------|
r_work (final): 0.3833
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7514
moved from start:          0.1047

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.034   6905  Z= 0.138
  Angle     :  0.457   6.543   9947  Z= 0.253
  Chirality :  0.027   0.179   1225
  Planarity :  0.003   0.030    705
  Dihedral  : 17.328 165.320   2539
  Min Nonbonded Distance : 2.474

Molprobity Statistics.
  All-atom Clashscore : 12.63
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  0.78 %
    Favored  : 99.22 %
  Rotamer:
    Outliers :  4.36 %
    Allowed  : 34.88 %
    Favored  : 60.76 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  5.62 (0.39), residues: 385
  helix:  3.84 (0.24), residues: 369
  sheet:  None (None), residues: 0
  loop : -2.09 (1.08), residues: 16

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.006   0.000   ARG F  32 
 TRP   0.014   0.001   TRP F  50 
 HIS   0.009   0.002   HIS D  48 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00294 /  0.14 ( 6905)
  covalent geometry    : angle       0.45693 /  0.25 ( 9947)
  hydrogen bonds       : bond        0.04737 /  3.21 (  439)
  hydrogen bonds       : angle       3.05513 /  2.23 ( 1189)

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

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

  770 Ramachandran restraints generated.
    385 Oldfield, 0 Emsley, 385 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  770 Ramachandran restraints generated.
    385 Oldfield, 0 Emsley, 385 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  121 residues out of total 361 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 15
    poor density    : 106
  time to evaluate  : 0.265 
Fit side-chains
   revert: symmetry clash
REVERT: B   28 GLU cc_start: 0.7571 (tm-30) cc_final: 0.7324 (tm-30)
REVERT: C   47 GLU cc_start: 0.6352 (OUTLIER) cc_final: 0.6020 (mp0)
REVERT: D   18 GLU cc_start: 0.7781 (OUTLIER) cc_final: 0.7495 (tm-30)
REVERT: E   55 LYS cc_start: 0.6507 (tptm) cc_final: 0.5982 (tptm)
REVERT: F   42 LYS cc_start: 0.8518 (tppt) cc_final: 0.8063 (mmtm)
REVERT: G   46 ASP cc_start: 0.7974 (t0) cc_final: 0.7642 (t0)
REVERT: H   18 GLU cc_start: 0.7811 (tp30) cc_final: 0.7221 (tp30)
  outliers start: 15
  outliers final: 12
  residues processed: 115
  average time/residue: 0.1477
  time to fit residues: 20.2183
Evaluate side-chains
  118 residues out of total 361 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 104
  time to evaluate  : 0.178 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   34 LEU
Chi-restraints excluded: chain C residue   38 LYS
Chi-restraints excluded: chain C residue   44 LEU
Chi-restraints excluded: chain C residue   47 GLU
Chi-restraints excluded: chain D residue   18 GLU
Chi-restraints excluded: chain D residue   47 GLU
Chi-restraints excluded: chain D residue   54 ILE
Chi-restraints excluded: chain D residue   57 ILE
Chi-restraints excluded: chain F residue   37 VAL
Chi-restraints excluded: chain F residue   51 LEU
Chi-restraints excluded: chain G residue   47 GLU
Chi-restraints excluded: chain G residue   57 ILE
Chi-restraints excluded: chain H residue   39 LYS
Chi-restraints excluded: chain H residue   51 LEU
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 51
   random chunks:
   chunk 38 optimal weight:    6.9990
   chunk 39 optimal weight:    7.9990
   chunk 23 optimal weight:    0.0030
   chunk 35 optimal weight:    0.9990
   chunk 11 optimal weight:    2.9990
   chunk 5 optimal weight:    0.9990
   chunk 47 optimal weight:   10.0000
   chunk 20 optimal weight:    0.9990
   chunk 34 optimal weight:    0.7980
   chunk 21 optimal weight:    1.9990
   chunk 24 optimal weight:    0.7980
   overall best weight:    0.7194

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
** G  48 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4209 r_free = 0.4209 target = 0.124758 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.3866 r_free = 0.3866 target = 0.102616 restraints weight = 19539.412|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 27)----------------|
| r_work = 0.3894 r_free = 0.3894 target = 0.104445 restraints weight = 9765.348|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 43)----------------|
| r_work = 0.3914 r_free = 0.3914 target = 0.105697 restraints weight = 6179.440|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 29)----------------|
| r_work = 0.3924 r_free = 0.3924 target = 0.106377 restraints weight = 4625.583|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 38)----------------|
| r_work = 0.3935 r_free = 0.3935 target = 0.106962 restraints weight = 3956.650|
|-----------------------------------------------------------------------------|
r_work (final): 0.3919
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7509
moved from start:          0.1173

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.035   6905  Z= 0.134
  Angle     :  0.461   7.201   9947  Z= 0.255
  Chirality :  0.027   0.178   1225
  Planarity :  0.003   0.026    705
  Dihedral  : 17.274 164.018   2539
  Min Nonbonded Distance : 2.479

Molprobity Statistics.
  All-atom Clashscore : 12.89
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  0.78 %
    Favored  : 99.22 %
  Rotamer:
    Outliers :  5.81 %
    Allowed  : 34.01 %
    Favored  : 60.17 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  5.54 (0.39), residues: 385
  helix:  3.79 (0.24), residues: 369
  sheet:  None (None), residues: 0
  loop : -2.04 (1.10), residues: 16

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG A  32 
 TRP   0.009   0.001   TRP H  20 
 HIS   0.008   0.001   HIS D  48 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00285 /  0.13 ( 6905)
  covalent geometry    : angle       0.46084 /  0.26 ( 9947)
  hydrogen bonds       : bond        0.04718 /  3.21 (  439)
  hydrogen bonds       : angle       3.04866 /  2.24 ( 1189)

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

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

  770 Ramachandran restraints generated.
    385 Oldfield, 0 Emsley, 385 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  770 Ramachandran restraints generated.
    385 Oldfield, 0 Emsley, 385 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  128 residues out of total 361 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 20
    poor density    : 108
  time to evaluate  : 0.178 
Fit side-chains
   revert: symmetry clash
REVERT: B   28 GLU cc_start: 0.7564 (tm-30) cc_final: 0.7311 (tm-30)
REVERT: C   47 GLU cc_start: 0.6405 (OUTLIER) cc_final: 0.6084 (mp0)
REVERT: D   13 ARG cc_start: 0.6180 (ttm170) cc_final: 0.5567 (ptm160)
REVERT: D   18 GLU cc_start: 0.7717 (OUTLIER) cc_final: 0.7441 (tm-30)
REVERT: E   55 LYS cc_start: 0.6441 (tptm) cc_final: 0.5865 (tptm)
REVERT: F   42 LYS cc_start: 0.8444 (tppt) cc_final: 0.8207 (mmtm)
REVERT: G   46 ASP cc_start: 0.7926 (t0) cc_final: 0.7608 (t0)
REVERT: H   18 GLU cc_start: 0.7797 (tp30) cc_final: 0.7232 (tp30)
  outliers start: 20
  outliers final: 11
  residues processed: 122
  average time/residue: 0.1439
  time to fit residues: 20.8914
Evaluate side-chains
  116 residues out of total 361 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 103
  time to evaluate  : 0.135 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   34 LEU
Chi-restraints excluded: chain C residue   38 LYS
Chi-restraints excluded: chain C residue   47 GLU
Chi-restraints excluded: chain D residue   18 GLU
Chi-restraints excluded: chain D residue   47 GLU
Chi-restraints excluded: chain D residue   54 ILE
Chi-restraints excluded: chain D residue   57 ILE
Chi-restraints excluded: chain E residue   41 ILE
Chi-restraints excluded: chain F residue   37 VAL
Chi-restraints excluded: chain F residue   51 LEU
Chi-restraints excluded: chain G residue   47 GLU
Chi-restraints excluded: chain G residue   57 ILE
Chi-restraints excluded: chain H residue   51 LEU
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 51
   random chunks:
   chunk 21 optimal weight:    0.6980
   chunk 10 optimal weight:    1.9990
   chunk 23 optimal weight:    1.9990
   chunk 31 optimal weight:    0.8980
   chunk 40 optimal weight:   10.0000
   chunk 39 optimal weight:    8.9990
   chunk 17 optimal weight:    0.8980
   chunk 37 optimal weight:    8.9990
   chunk 18 optimal weight:    0.8980
   chunk 34 optimal weight:    1.9990
   chunk 45 optimal weight:    6.9990
   overall best weight:    1.0782

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
** D  48 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** G  48 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4143 r_free = 0.4143 target = 0.123149 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 42)----------------|
| r_work = 0.3773 r_free = 0.3773 target = 0.099793 restraints weight = 18669.081|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 35)----------------|
| r_work = 0.3804 r_free = 0.3804 target = 0.101605 restraints weight = 9456.359|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 36)----------------|
| r_work = 0.3825 r_free = 0.3825 target = 0.102826 restraints weight = 6054.284|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 41)----------------|
| r_work = 0.3839 r_free = 0.3839 target = 0.103626 restraints weight = 4592.789|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 24)----------------|
| r_work = 0.3845 r_free = 0.3845 target = 0.104024 restraints weight = 3899.446|
|-----------------------------------------------------------------------------|
r_work (final): 0.3810
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7549
moved from start:          0.1277

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.032   6905  Z= 0.165
  Angle     :  0.487   7.038   9947  Z= 0.270
  Chirality :  0.028   0.173   1225
  Planarity :  0.003   0.027    705
  Dihedral  : 17.312 163.645   2539
  Min Nonbonded Distance : 2.464

Molprobity Statistics.
  All-atom Clashscore : 14.10
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  0.78 %
    Favored  : 99.22 %
  Rotamer:
    Outliers :  5.81 %
    Allowed  : 34.30 %
    Favored  : 59.88 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  5.51 (0.39), residues: 385
  helix:  3.77 (0.24), residues: 369
  sheet:  None (None), residues: 0
  loop : -2.16 (1.10), residues: 16

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.006   0.000   ARG F  32 
 TRP   0.008   0.001   TRP B  20 
 HIS   0.007   0.002   HIS D  48 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00355 /  0.16 ( 6905)
  covalent geometry    : angle       0.48733 /  0.27 ( 9947)
  hydrogen bonds       : bond        0.05163 /  3.55 (  439)
  hydrogen bonds       : angle       3.10741 /  2.28 ( 1189)

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

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

  770 Ramachandran restraints generated.
    385 Oldfield, 0 Emsley, 385 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  770 Ramachandran restraints generated.
    385 Oldfield, 0 Emsley, 385 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  125 residues out of total 361 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 20
    poor density    : 105
  time to evaluate  : 0.190 
Fit side-chains
   revert: symmetry clash
REVERT: B   28 GLU cc_start: 0.7609 (tm-30) cc_final: 0.7391 (tm-30)
REVERT: C   47 GLU cc_start: 0.6503 (OUTLIER) cc_final: 0.6164 (mp0)
REVERT: E   55 LYS cc_start: 0.6504 (tptm) cc_final: 0.5974 (tptm)
REVERT: F   42 LYS cc_start: 0.8449 (tppt) cc_final: 0.8232 (mmtm)
REVERT: G   46 ASP cc_start: 0.7957 (t0) cc_final: 0.7628 (t0)
REVERT: H   18 GLU cc_start: 0.7836 (tp30) cc_final: 0.7253 (tp30)
  outliers start: 20
  outliers final: 14
  residues processed: 118
  average time/residue: 0.1438
  time to fit residues: 20.0649
Evaluate side-chains
  117 residues out of total 361 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 15
    poor density    : 102
  time to evaluate  : 0.197 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   34 LEU
Chi-restraints excluded: chain C residue   38 LYS
Chi-restraints excluded: chain C residue   44 LEU
Chi-restraints excluded: chain C residue   47 GLU
Chi-restraints excluded: chain D residue   47 GLU
Chi-restraints excluded: chain D residue   54 ILE
Chi-restraints excluded: chain D residue   57 ILE
Chi-restraints excluded: chain E residue   41 ILE
Chi-restraints excluded: chain F residue   37 VAL
Chi-restraints excluded: chain F residue   51 LEU
Chi-restraints excluded: chain G residue   27 LEU
Chi-restraints excluded: chain G residue   47 GLU
Chi-restraints excluded: chain G residue   57 ILE
Chi-restraints excluded: chain H residue   35 ARG
Chi-restraints excluded: chain H residue   51 LEU
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 51
   random chunks:
   chunk 31 optimal weight:    0.8980
   chunk 41 optimal weight:    9.9990
   chunk 9 optimal weight:    0.9980
   chunk 45 optimal weight:    6.9990
   chunk 46 optimal weight:    6.9990
   chunk 8 optimal weight:    2.9990
   chunk 35 optimal weight:    0.9990
   chunk 1 optimal weight:    1.9990
   chunk 39 optimal weight:    6.9990
   chunk 11 optimal weight:    2.9990
   chunk 3 optimal weight:    0.4980
   overall best weight:    1.0784

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
B  53 ASN
** D  48 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** G  48 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4144 r_free = 0.4144 target = 0.123297 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 40)----------------|
| r_work = 0.3780 r_free = 0.3780 target = 0.100118 restraints weight = 18637.112|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 30)----------------|
| r_work = 0.3809 r_free = 0.3809 target = 0.101847 restraints weight = 9693.787|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 32)----------------|
| r_work = 0.3828 r_free = 0.3828 target = 0.102996 restraints weight = 6301.957|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 44)----------------|
| r_work = 0.3842 r_free = 0.3842 target = 0.103790 restraints weight = 4816.518|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 33)----------------|
| r_work = 0.3849 r_free = 0.3849 target = 0.104225 restraints weight = 4105.023|
|-----------------------------------------------------------------------------|
r_work (final): 0.3809
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7539
moved from start:          0.1323

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.052   6905  Z= 0.165
  Angle     :  0.500   7.640   9947  Z= 0.275
  Chirality :  0.028   0.175   1225
  Planarity :  0.003   0.027    705
  Dihedral  : 17.317 163.315   2539
  Min Nonbonded Distance : 2.460

Molprobity Statistics.
  All-atom Clashscore : 14.18
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  0.78 %
    Favored  : 99.22 %
  Rotamer:
    Outliers :  4.65 %
    Allowed  : 35.76 %
    Favored  : 59.59 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  5.47 (0.39), residues: 385
  helix:  3.75 (0.24), residues: 369
  sheet:  None (None), residues: 0
  loop : -2.18 (1.13), residues: 16

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.007   0.000   ARG F  32 
 TRP   0.009   0.001   TRP H  20 
 HIS   0.007   0.002   HIS D  48 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00358 /  0.16 ( 6905)
  covalent geometry    : angle       0.49995 /  0.27 ( 9947)
  hydrogen bonds       : bond        0.05184 /  3.56 (  439)
  hydrogen bonds       : angle       3.12370 /  2.29 ( 1189)

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

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

  770 Ramachandran restraints generated.
    385 Oldfield, 0 Emsley, 385 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  770 Ramachandran restraints generated.
    385 Oldfield, 0 Emsley, 385 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  121 residues out of total 361 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 105
  time to evaluate  : 0.176 
Fit side-chains
   revert: symmetry clash
REVERT: C   47 GLU cc_start: 0.6562 (OUTLIER) cc_final: 0.6229 (mp0)
REVERT: E   55 LYS cc_start: 0.6446 (tptm) cc_final: 0.5925 (tptm)
REVERT: F   42 LYS cc_start: 0.8351 (tppt) cc_final: 0.8135 (mmtm)
REVERT: G   46 ASP cc_start: 0.7896 (t0) cc_final: 0.7575 (t0)
REVERT: H   18 GLU cc_start: 0.7793 (tp30) cc_final: 0.7260 (tp30)
  outliers start: 16
  outliers final: 14
  residues processed: 115
  average time/residue: 0.1509
  time to fit residues: 20.4729
Evaluate side-chains
  117 residues out of total 361 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 15
    poor density    : 102
  time to evaluate  : 0.184 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   34 LEU
Chi-restraints excluded: chain C residue   37 VAL
Chi-restraints excluded: chain C residue   38 LYS
Chi-restraints excluded: chain C residue   44 LEU
Chi-restraints excluded: chain C residue   47 GLU
Chi-restraints excluded: chain D residue   47 GLU
Chi-restraints excluded: chain D residue   54 ILE
Chi-restraints excluded: chain D residue   57 ILE
Chi-restraints excluded: chain E residue   41 ILE
Chi-restraints excluded: chain F residue   37 VAL
Chi-restraints excluded: chain F residue   51 LEU
Chi-restraints excluded: chain G residue   47 GLU
Chi-restraints excluded: chain G residue   57 ILE
Chi-restraints excluded: chain H residue   51 LEU
Chi-restraints excluded: chain H residue   58 LEU
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 51
   random chunks:
   chunk 15 optimal weight:    1.9990
   chunk 7 optimal weight:    0.9980
   chunk 1 optimal weight:    0.8980
   chunk 19 optimal weight:    0.1980
   chunk 45 optimal weight:    6.9990
   chunk 31 optimal weight:    0.8980
   chunk 44 optimal weight:    8.9990
   chunk 17 optimal weight:    0.8980
   chunk 39 optimal weight:    7.9990
   chunk 36 optimal weight:    2.9990
   chunk 12 optimal weight:    0.3980
   overall best weight:    0.6580

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
** D  48 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** G  48 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4209 r_free = 0.4209 target = 0.124867 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 38)----------------|
| r_work = 0.3867 r_free = 0.3867 target = 0.102707 restraints weight = 19451.923|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 35)----------------|
| r_work = 0.3896 r_free = 0.3896 target = 0.104553 restraints weight = 9570.733|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 38)----------------|
| r_work = 0.3916 r_free = 0.3916 target = 0.105789 restraints weight = 5995.241|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 48)----------------|
| r_work = 0.3929 r_free = 0.3929 target = 0.106593 restraints weight = 4491.880|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 28)----------------|
| r_work = 0.3935 r_free = 0.3935 target = 0.106996 restraints weight = 3782.529|
|-----------------------------------------------------------------------------|
r_work (final): 0.3918
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7518
moved from start:          0.1474

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.042   6905  Z= 0.136
  Angle     :  0.503   8.040   9947  Z= 0.274
  Chirality :  0.027   0.173   1225
  Planarity :  0.003   0.027    705
  Dihedral  : 17.245 162.545   2539
  Min Nonbonded Distance : 2.489

Molprobity Statistics.
  All-atom Clashscore : 12.97
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  0.52 %
    Favored  : 99.48 %
  Rotamer:
    Outliers :  5.23 %
    Allowed  : 36.05 %
    Favored  : 58.72 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  5.60 (0.39), residues: 385
  helix:  3.83 (0.24), residues: 369
  sheet:  None (None), residues: 0
  loop : -2.17 (1.12), residues: 16

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.010   0.000   ARG F  32 
 TRP   0.011   0.001   TRP H  20 
 HIS   0.006   0.001   HIS D  48 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00297 /  0.14 ( 6905)
  covalent geometry    : angle       0.50289 /  0.27 ( 9947)
  hydrogen bonds       : bond        0.04870 /  3.31 (  439)
  hydrogen bonds       : angle       3.01249 /  2.21 ( 1189)

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

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

  770 Ramachandran restraints generated.
    385 Oldfield, 0 Emsley, 385 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  770 Ramachandran restraints generated.
    385 Oldfield, 0 Emsley, 385 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  123 residues out of total 361 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 18
    poor density    : 105
  time to evaluate  : 0.175 
Fit side-chains
   revert: symmetry clash
REVERT: C   47 GLU cc_start: 0.6514 (OUTLIER) cc_final: 0.6168 (mp0)
REVERT: C   58 LEU cc_start: 0.8947 (mt) cc_final: 0.8705 (mp)
REVERT: E   55 LYS cc_start: 0.6455 (tptm) cc_final: 0.5984 (tptm)
REVERT: F   42 LYS cc_start: 0.8388 (tppt) cc_final: 0.8170 (mmtm)
REVERT: G   46 ASP cc_start: 0.7911 (t0) cc_final: 0.7603 (t0)
REVERT: H   18 GLU cc_start: 0.7823 (tp30) cc_final: 0.7259 (tp30)
  outliers start: 18
  outliers final: 12
  residues processed: 116
  average time/residue: 0.1435
  time to fit residues: 19.7060
Evaluate side-chains
  114 residues out of total 361 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 101
  time to evaluate  : 0.124 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   34 LEU
Chi-restraints excluded: chain C residue   38 LYS
Chi-restraints excluded: chain C residue   47 GLU
Chi-restraints excluded: chain D residue   43 LYS
Chi-restraints excluded: chain D residue   47 GLU
Chi-restraints excluded: chain D residue   54 ILE
Chi-restraints excluded: chain D residue   57 ILE
Chi-restraints excluded: chain E residue   41 ILE
Chi-restraints excluded: chain F residue   51 LEU
Chi-restraints excluded: chain F residue   54 ILE
Chi-restraints excluded: chain G residue   47 GLU
Chi-restraints excluded: chain G residue   57 ILE
Chi-restraints excluded: chain H residue   58 LEU
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 51
   random chunks:
   chunk 8 optimal weight:    0.5980
   chunk 44 optimal weight:    9.9990
   chunk 28 optimal weight:    1.9990
   chunk 26 optimal weight:    0.6980
   chunk 11 optimal weight:    0.7980
   chunk 45 optimal weight:    5.9990
   chunk 34 optimal weight:    1.9990
   chunk 25 optimal weight:    0.9980
   chunk 29 optimal weight:    0.8980
   chunk 27 optimal weight:    0.6980
   chunk 5 optimal weight:    0.1980
   overall best weight:    0.5980

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
** D  48 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** G  48 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4210 r_free = 0.4210 target = 0.125018 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 34)----------------|
| r_work = 0.3872 r_free = 0.3872 target = 0.102963 restraints weight = 19794.124|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 31)----------------|
| r_work = 0.3900 r_free = 0.3900 target = 0.104798 restraints weight = 9792.892|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 47)----------------|
| r_work = 0.3920 r_free = 0.3920 target = 0.106062 restraints weight = 6119.259|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 31)----------------|
| r_work = 0.3930 r_free = 0.3930 target = 0.106799 restraints weight = 4559.199|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 38)----------------|
| r_work = 0.3940 r_free = 0.3940 target = 0.107353 restraints weight = 3868.213|
|-----------------------------------------------------------------------------|
r_work (final): 0.3921
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7505
moved from start:          0.1527

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.035   6905  Z= 0.130
  Angle     :  0.512   8.802   9947  Z= 0.276
  Chirality :  0.026   0.165   1225
  Planarity :  0.003   0.028    705
  Dihedral  : 17.185 162.498   2537
  Min Nonbonded Distance : 2.503

Molprobity Statistics.
  All-atom Clashscore : 12.89
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  0.52 %
    Favored  : 99.48 %
  Rotamer:
    Outliers :  4.65 %
    Allowed  : 36.34 %
    Favored  : 59.01 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  5.65 (0.39), residues: 385
  helix:  3.86 (0.24), residues: 369
  sheet:  None (None), residues: 0
  loop : -2.17 (1.13), residues: 16

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.009   0.000   ARG F  32 
 TRP   0.011   0.001   TRP H  20 
 HIS   0.006   0.001   HIS D  48 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00282 /  0.13 ( 6905)
  covalent geometry    : angle       0.51204 /  0.28 ( 9947)
  hydrogen bonds       : bond        0.04808 /  3.28 (  439)
  hydrogen bonds       : angle       3.00337 /  2.20 ( 1189)

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

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

  770 Ramachandran restraints generated.
    385 Oldfield, 0 Emsley, 385 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  770 Ramachandran restraints generated.
    385 Oldfield, 0 Emsley, 385 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  124 residues out of total 361 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 108
  time to evaluate  : 0.194 
Fit side-chains
   revert: symmetry clash
REVERT: A   28 GLU cc_start: 0.7756 (tm-30) cc_final: 0.7542 (tm-30)
REVERT: C   47 GLU cc_start: 0.6417 (OUTLIER) cc_final: 0.6116 (mp0)
REVERT: C   58 LEU cc_start: 0.8932 (mt) cc_final: 0.8688 (mp)
REVERT: D   13 ARG cc_start: 0.6404 (OUTLIER) cc_final: 0.6020 (ptm160)
REVERT: F   28 GLU cc_start: 0.6972 (tp30) cc_final: 0.6696 (tp30)
REVERT: F   42 LYS cc_start: 0.8373 (tppt) cc_final: 0.8161 (mmtm)
REVERT: G   46 ASP cc_start: 0.7902 (t0) cc_final: 0.7597 (t0)
REVERT: H   18 GLU cc_start: 0.7811 (tp30) cc_final: 0.7245 (tp30)
  outliers start: 16
  outliers final: 12
  residues processed: 118
  average time/residue: 0.1526
  time to fit residues: 21.3974
Evaluate side-chains
  119 residues out of total 361 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 105
  time to evaluate  : 0.184 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   34 LEU
Chi-restraints excluded: chain C residue   38 LYS
Chi-restraints excluded: chain C residue   47 GLU
Chi-restraints excluded: chain D residue   13 ARG
Chi-restraints excluded: chain D residue   47 GLU
Chi-restraints excluded: chain D residue   54 ILE
Chi-restraints excluded: chain D residue   57 ILE
Chi-restraints excluded: chain E residue   41 ILE
Chi-restraints excluded: chain F residue   37 VAL
Chi-restraints excluded: chain F residue   51 LEU
Chi-restraints excluded: chain F residue   54 ILE
Chi-restraints excluded: chain G residue   47 GLU
Chi-restraints excluded: chain G residue   57 ILE
Chi-restraints excluded: chain H residue   58 LEU
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 51
   random chunks:
   chunk 21 optimal weight:    0.8980
   chunk 47 optimal weight:   10.0000
   chunk 9 optimal weight:    1.9990
   chunk 46 optimal weight:    6.9990
   chunk 0 optimal weight:    2.9990
   chunk 23 optimal weight:    1.9990
   chunk 45 optimal weight:    5.9990
   chunk 32 optimal weight:    0.7980
   chunk 6 optimal weight:    1.9990
   chunk 35 optimal weight:    0.6980
   chunk 20 optimal weight:    0.7980
   overall best weight:    1.0382

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
** D  48 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** G  48 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4155 r_free = 0.4155 target = 0.123742 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 40)----------------|
| r_work = 0.3787 r_free = 0.3787 target = 0.100147 restraints weight = 18337.188|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 38)----------------|
| r_work = 0.3818 r_free = 0.3818 target = 0.101973 restraints weight = 9090.830|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 41)----------------|
| r_work = 0.3840 r_free = 0.3840 target = 0.103196 restraints weight = 5768.514|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 19)----------------|
| r_work = 0.3849 r_free = 0.3849 target = 0.103784 restraints weight = 4356.533|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 45)----------------|
| r_work = 0.3861 r_free = 0.3861 target = 0.104463 restraints weight = 3760.978|
|-----------------------------------------------------------------------------|
r_work (final): 0.3814
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7529
moved from start:          0.1591

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.036   6905  Z= 0.161
  Angle     :  0.526   8.904   9947  Z= 0.286
  Chirality :  0.028   0.161   1225
  Planarity :  0.004   0.029    705
  Dihedral  : 17.200 162.944   2537
  Min Nonbonded Distance : 2.489

Molprobity Statistics.
  All-atom Clashscore : 14.53
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  0.78 %
    Favored  : 99.22 %
  Rotamer:
    Outliers :  5.52 %
    Allowed  : 35.76 %
    Favored  : 58.72 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  5.59 (0.39), residues: 385
  helix:  3.83 (0.24), residues: 369
  sheet:  None (None), residues: 0
  loop : -2.22 (1.13), residues: 16

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.010   0.000   ARG F  32 
 TRP   0.018   0.002   TRP C  50 
 HIS   0.005   0.002   HIS D  48 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00353 /  0.16 ( 6905)
  covalent geometry    : angle       0.52629 /  0.29 ( 9947)
  hydrogen bonds       : bond        0.05191 /  3.56 (  439)
  hydrogen bonds       : angle       3.09771 /  2.27 ( 1189)

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

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

  770 Ramachandran restraints generated.
    385 Oldfield, 0 Emsley, 385 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  770 Ramachandran restraints generated.
    385 Oldfield, 0 Emsley, 385 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  127 residues out of total 361 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 19
    poor density    : 108
  time to evaluate  : 0.187 
Fit side-chains
   revert: symmetry clash
REVERT: C   18 GLU cc_start: 0.7907 (tp30) cc_final: 0.7401 (tp30)
REVERT: C   47 GLU cc_start: 0.6501 (OUTLIER) cc_final: 0.6149 (mp0)
REVERT: D   13 ARG cc_start: 0.6485 (OUTLIER) cc_final: 0.5988 (ptm160)
REVERT: E   55 LYS cc_start: 0.6424 (tptm) cc_final: 0.5949 (tptm)
REVERT: F   28 GLU cc_start: 0.6925 (tp30) cc_final: 0.6524 (tp30)
REVERT: F   32 ARG cc_start: 0.7737 (mtm110) cc_final: 0.7295 (mtm110)
REVERT: F   42 LYS cc_start: 0.8352 (tppt) cc_final: 0.8137 (mmtm)
REVERT: G   46 ASP cc_start: 0.7856 (t0) cc_final: 0.7541 (t0)
REVERT: H   18 GLU cc_start: 0.7767 (tp30) cc_final: 0.7231 (tp30)
  outliers start: 19
  outliers final: 15
  residues processed: 121
  average time/residue: 0.1468
  time to fit residues: 20.9217
Evaluate side-chains
  122 residues out of total 361 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 17
    poor density    : 105
  time to evaluate  : 0.188 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   34 LEU
Chi-restraints excluded: chain C residue   38 LYS
Chi-restraints excluded: chain C residue   44 LEU
Chi-restraints excluded: chain C residue   47 GLU
Chi-restraints excluded: chain D residue   13 ARG
Chi-restraints excluded: chain D residue   47 GLU
Chi-restraints excluded: chain D residue   54 ILE
Chi-restraints excluded: chain D residue   57 ILE
Chi-restraints excluded: chain E residue   41 ILE
Chi-restraints excluded: chain F residue   37 VAL
Chi-restraints excluded: chain F residue   51 LEU
Chi-restraints excluded: chain G residue   15 GLU
Chi-restraints excluded: chain G residue   27 LEU
Chi-restraints excluded: chain G residue   47 GLU
Chi-restraints excluded: chain G residue   57 ILE
Chi-restraints excluded: chain H residue   35 ARG
Chi-restraints excluded: chain H residue   58 LEU
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 51
   random chunks:
   chunk 7 optimal weight:    0.9990
   chunk 45 optimal weight:    6.9990
   chunk 35 optimal weight:    0.9990
   chunk 37 optimal weight:    8.9990
   chunk 46 optimal weight:    6.9990
   chunk 20 optimal weight:    0.8980
   chunk 13 optimal weight:    0.9990
   chunk 14 optimal weight:    0.0870
   chunk 16 optimal weight:    0.7980
   chunk 32 optimal weight:    4.9990
   chunk 50 optimal weight:   10.0000
   overall best weight:    0.7562

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
** D  48 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** G  48 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4206 r_free = 0.4206 target = 0.124755 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 40)----------------|
| r_work = 0.3867 r_free = 0.3867 target = 0.102607 restraints weight = 19425.759|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 41)----------------|
| r_work = 0.3895 r_free = 0.3895 target = 0.104451 restraints weight = 9603.704|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 46)----------------|
| r_work = 0.3915 r_free = 0.3915 target = 0.105692 restraints weight = 6045.176|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 37)----------------|
| r_work = 0.3928 r_free = 0.3928 target = 0.106512 restraints weight = 4528.954|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 37)----------------|
| r_work = 0.3936 r_free = 0.3936 target = 0.107047 restraints weight = 3799.383|
|-----------------------------------------------------------------------------|
r_work (final): 0.3920
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7518
moved from start:          0.1623

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.038   6905  Z= 0.143
  Angle     :  0.535   8.691   9947  Z= 0.288
  Chirality :  0.027   0.164   1225
  Planarity :  0.004   0.029    705
  Dihedral  : 17.165 162.596   2537
  Min Nonbonded Distance : 2.519

Molprobity Statistics.
  All-atom Clashscore : 13.66
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  0.52 %
    Favored  : 99.48 %
  Rotamer:
    Outliers :  4.94 %
    Allowed  : 36.92 %
    Favored  : 58.14 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  5.65 (0.38), residues: 385
  helix:  3.86 (0.24), residues: 369
  sheet:  None (None), residues: 0
  loop : -2.19 (1.13), residues: 16

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.010   0.001   ARG F  32 
 TRP   0.015   0.002   TRP C  50 
 HIS   0.005   0.001   HIS D  48 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00318 /  0.14 ( 6905)
  covalent geometry    : angle       0.53471 /  0.29 ( 9947)
  hydrogen bonds       : bond        0.04933 /  3.36 (  439)
  hydrogen bonds       : angle       3.05264 /  2.23 ( 1189)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 1454.89 seconds
wall clock time: 25 minutes 53.95 seconds (1553.95 seconds total)