Starting phenix.real_space_refine
on Sat May  2 12:30:54 2026 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/9vid_65084/05_2026/9vid_65084.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/9vid_65084/05_2026/9vid_65084.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=2.22
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    model {
      file = "/net/cci-nas-00/data/ceres_data/9vid_65084/05_2026/9vid_65084.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/9vid_65084/05_2026/9vid_65084.cif"
    real_map_files = "/net/cci-nas-00/data/ceres_data/9vid_65084/05_2026/9vid_65084.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/9vid_65084/05_2026/9vid_65084.map"
  }
  resolution = 2.22
  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=   0.064
Set stop_for_unknowns flag
  Set to: True
Assert model is a single copy model
Assert all atoms have isotropic ADPs
Construct map_model_manager
Extract box with map and model
Check model and map are aligned
Set scattering table
  Set to: electron
  Number of scattering types: 5
    Type Number    sf(0)   Gaussians
     Fe      4      7.16       5
     S      26      5.16       5
     C    3074      2.51       5
     N     830      2.21       5
     O     812      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 30 residue(s): 0.00s

  Monomer Library directory:
    "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.1rc2-6044/lib/python3.9/site-packages/chem_data/mon_lib"
  Total number of atoms: 4746
  Number of models: 1
  Model: ""
    Number of chains: 4
    Chain: "A"
      Number of atoms: 1109
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 141, 1109
          Classifications: {'peptide': 141}
          Modifications used: {'COO': 1}
          Link IDs: {'PTRANS': 6, 'TRANS': 134}
    Chain: "B"
      Number of atoms: 1174
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 146, 1174
          Classifications: {'peptide': 146}
          Modifications used: {'COO': 1}
          Link IDs: {'PTRANS': 3, 'TRANS': 142}
    Chain: "A"
      Number of atoms: 45
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 2, 45
          Unusual residues: {'CMO': 1, 'HEM': 1}
          Classifications: {'undetermined': 2}
          Link IDs: {None: 1}
    Chain: "B"
      Number of atoms: 45
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 2, 45
          Unusual residues: {'CMO': 1, 'HEM': 1}
          Classifications: {'undetermined': 2}
          Link IDs: {None: 1}
  Restraints were copied for chains:
    C, D
  Time building chain proxies: 0.86, per 1000 atoms: 0.18
  Number of scatterers: 4746
  At special positions: 0
  Unit cell: (72.42, 84.66, 64.26, 90, 90, 90)
  Space group: P 1 (No. 1)
  Number of sites at special positions: 0
  Number of scattering types: 5
    Type Number    sf(0)
     Fe      4     26.01
     S      26     16.00
     O     812      8.00
     N     830      7.00
     C    3074      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=4, symmetry=0
  Number of additional bonds: simple=4, symmetry=0
  Coordination:
  Other bonds:
  Time building additional restraints: 0.25
  Conformation dependent library (CDL) restraints added in 171.1 milliseconds
  

  1132 Ramachandran restraints generated.
    566 Oldfield, 0 Emsley, 566 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  1104

  Finding SS restraints...
    Secondary structure from input PDB file:
      34 helices and 0 sheets defined
      82.9% alpha, 0.0% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 0.07
  Creating SS restraints...
    Processing helix  chain 'A' and resid 3 through 16
      removed outlier: 3.843A  pdb=" N   LYS A  16 " --> pdb=" O   ALA A  12 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 20 through 36
    Processing helix  chain 'A' and resid 37 through 43
      removed outlier: 3.671A  pdb=" N   ILE A  41 " --> pdb=" O   GLN A  38 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 52 through 72
    Processing helix  chain 'A' and resid 75 through 80
    Processing helix  chain 'A' and resid 80 through 89
    Processing helix  chain 'A' and resid 95 through 113
      removed outlier: 4.092A  pdb=" N   LYS A  99 " --> pdb=" O   PRO A  95 " (cutoff:3.500A)
      removed outlier: 3.624A  pdb=" N   PHE A 100 " --> pdb=" O   VAL A  96 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 118 through 137
    Processing helix  chain 'B' and resid 4 through 16
    Processing helix  chain 'B' and resid 19 through 35
    Processing helix  chain 'B' and resid 36 through 46
      removed outlier: 5.515A  pdb=" N   HIS B  44 " --> pdb=" O   TYR B  41 " (cutoff:3.500A)
      removed outlier: 3.628A  pdb=" N   GLY B  46 " --> pdb=" O   GLU B  43 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 50 through 56
    Processing helix  chain 'B' and resid 57 through 72
    Processing helix  chain 'B' and resid 73 through 77
    Processing helix  chain 'B' and resid 80 through 95
      removed outlier: 5.507A  pdb=" N   ASN B  87 " --> pdb=" O   GLY B  83 " (cutoff:3.500A)
      removed outlier: 5.737A  pdb=" N   LEU B  88 " --> pdb=" O   HIS B  84 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 100 through 118
      removed outlier: 4.475A  pdb=" N   LYS B 104 " --> pdb=" O   PRO B 100 " (cutoff:3.500A)
      removed outlier: 3.786A  pdb=" N   LEU B 105 " --> pdb=" O   GLU B 101 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 123 through 142
    Processing helix  chain 'C' and resid 3 through 16
      removed outlier: 3.843A  pdb=" N   LYS C  16 " --> pdb=" O   ALA C  12 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 20 through 36
    Processing helix  chain 'C' and resid 37 through 43
      removed outlier: 3.671A  pdb=" N   ILE C  41 " --> pdb=" O   GLN C  38 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 52 through 72
    Processing helix  chain 'C' and resid 75 through 80
    Processing helix  chain 'C' and resid 80 through 89
    Processing helix  chain 'C' and resid 95 through 113
      removed outlier: 4.092A  pdb=" N   LYS C  99 " --> pdb=" O   PRO C  95 " (cutoff:3.500A)
      removed outlier: 3.624A  pdb=" N   PHE C 100 " --> pdb=" O   VAL C  96 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 118 through 137
    Processing helix  chain 'D' and resid 4 through 16
    Processing helix  chain 'D' and resid 19 through 35
    Processing helix  chain 'D' and resid 36 through 46
      removed outlier: 5.515A  pdb=" N   HIS D  44 " --> pdb=" O   TYR D  41 " (cutoff:3.500A)
      removed outlier: 3.628A  pdb=" N   GLY D  46 " --> pdb=" O   GLU D  43 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 50 through 56
    Processing helix  chain 'D' and resid 57 through 72
    Processing helix  chain 'D' and resid 73 through 77
    Processing helix  chain 'D' and resid 80 through 95
      removed outlier: 5.507A  pdb=" N   ASN D  87 " --> pdb=" O   GLY D  83 " (cutoff:3.500A)
      removed outlier: 5.737A  pdb=" N   LEU D  88 " --> pdb=" O   HIS D  84 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 100 through 118
      removed outlier: 4.475A  pdb=" N   LYS D 104 " --> pdb=" O   PRO D 100 " (cutoff:3.500A)
      removed outlier: 3.786A  pdb=" N   LEU D 105 " --> pdb=" O   GLU D 101 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 123 through 142

    326 hydrogen bonds defined for protein.
    912 hydrogen bond angles defined for protein.
    Restraints generated for nucleic acids:
      0 hydrogen bonds
      0 hydrogen bond angles
      0 basepair planarities
      0 basepair parallelities
      0 stacking parallelities
  Total time for adding SS restraints: 0.40

  Time building geometry restraints manager: 0.33 seconds

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

  Histogram of bond lengths:
        1.21 -     1.39: 1930
        1.39 -     1.57: 2914
        1.57 -     1.75: 0
        1.75 -     1.93: 36
        1.93 -     2.11: 16
  Bond restraints: 4896
  Sorted by residual:
  bond pdb=" C   CMO C 202 "
       pdb=" O   CMO C 202 "
    ideal  model  delta    sigma   weight residual
    1.141  1.278 -0.137 2.00e-02 2.50e+03 4.71e+01
  bond pdb=" C   CMO A 202 "
       pdb=" O   CMO A 202 "
    ideal  model  delta    sigma   weight residual
    1.141  1.278 -0.137 2.00e-02 2.50e+03 4.71e+01
  bond pdb=" C   CMO D 202 "
       pdb=" O   CMO D 202 "
    ideal  model  delta    sigma   weight residual
    1.141  1.254 -0.113 2.00e-02 2.50e+03 3.19e+01
  bond pdb=" C   CMO B 202 "
       pdb=" O   CMO B 202 "
    ideal  model  delta    sigma   weight residual
    1.141  1.254 -0.113 2.00e-02 2.50e+03 3.19e+01
  bond pdb=" C2C HEM D 201 "
       pdb=" C3C HEM D 201 "
    ideal  model  delta    sigma   weight residual
    1.334  1.418 -0.084 2.00e-02 2.50e+03 1.78e+01
  ... (remaining 4891 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     1.53: 4850
        1.53 -     3.07: 1450
        3.07 -     4.60: 296
        4.60 -     6.13: 56
        6.13 -     7.67: 18
  Bond angle restraints: 6670
  Sorted by residual:
  angle pdb=" CA  ASP A  94 "
        pdb=" CB  ASP A  94 "
        pdb=" CG  ASP A  94 "
      ideal   model   delta    sigma   weight residual
     112.60  119.31   -6.71 1.00e+00 1.00e+00 4.50e+01
  angle pdb=" CA  ASP C  94 "
        pdb=" CB  ASP C  94 "
        pdb=" CG  ASP C  94 "
      ideal   model   delta    sigma   weight residual
     112.60  119.31   -6.71 1.00e+00 1.00e+00 4.50e+01
  angle pdb=" CA  HIS C 122 "
        pdb=" CB  HIS C 122 "
        pdb=" CG  HIS C 122 "
      ideal   model   delta    sigma   weight residual
     113.80  119.20   -5.40 1.00e+00 1.00e+00 2.92e+01
  angle pdb=" CA  HIS A 122 "
        pdb=" CB  HIS A 122 "
        pdb=" CG  HIS A 122 "
      ideal   model   delta    sigma   weight residual
     113.80  119.20   -5.40 1.00e+00 1.00e+00 2.92e+01
  angle pdb=" CA  ASP B   4 "
        pdb=" CB  ASP B   4 "
        pdb=" CG  ASP B   4 "
      ideal   model   delta    sigma   weight residual
     112.60  117.54   -4.94 1.00e+00 1.00e+00 2.44e+01
  ... (remaining 6665 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.01 -    17.95: 2544
       17.95 -    35.89: 188
       35.89 -    53.83: 32
       53.83 -    71.77: 24
       71.77 -    89.71: 14
  Dihedral angle restraints: 2802
    sinusoidal: 1114
      harmonic: 1688
  Sorted by residual:
  dihedral pdb=" CA  PHE A  46 "
           pdb=" C   PHE A  46 "
           pdb=" N   ASP A  47 "
           pdb=" CA  ASP A  47 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  158.74   21.26     0      5.00e+00 4.00e-02 1.81e+01
  dihedral pdb=" CA  PHE C  46 "
           pdb=" C   PHE C  46 "
           pdb=" N   ASP C  47 "
           pdb=" CA  ASP C  47 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  158.74   21.26     0      5.00e+00 4.00e-02 1.81e+01
  dihedral pdb=" C   GLU B  43 "
           pdb=" N   GLU B  43 "
           pdb=" CA  GLU B  43 "
           pdb=" CB  GLU B  43 "
      ideal   model   delta  harmonic     sigma   weight residual
    -122.60 -132.68   10.08     0      2.50e+00 1.60e-01 1.63e+01
  ... (remaining 2799 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.070: 392
       0.070 -    0.140: 220
       0.140 -    0.210: 48
       0.210 -    0.281: 16
       0.281 -    0.351: 10
  Chirality restraints: 686
  Sorted by residual:
  chirality pdb=" CA  PRO B 100 "
            pdb=" N   PRO B 100 "
            pdb=" C   PRO B 100 "
            pdb=" CB  PRO B 100 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.72    2.37    0.35 2.00e-01 2.50e+01 3.08e+00
  chirality pdb=" CA  PRO D 100 "
            pdb=" N   PRO D 100 "
            pdb=" C   PRO D 100 "
            pdb=" CB  PRO D 100 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.72    2.37    0.35 2.00e-01 2.50e+01 3.08e+00
  chirality pdb=" CA  GLU B  43 "
            pdb=" N   GLU B  43 "
            pdb=" C   GLU B  43 "
            pdb=" CB  GLU B  43 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.19    0.32 2.00e-01 2.50e+01 2.54e+00
  ... (remaining 683 not shown)

  Planarity restraints: 836
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CD  ARG D  40 "    0.518 9.50e-02 1.11e+02   2.34e-01 3.96e+01
        pdb=" NE  ARG D  40 "   -0.016 2.00e-02 2.50e+03
        pdb=" CZ  ARG D  40 "   -0.050 2.00e-02 2.50e+03
        pdb=" NH1 ARG D  40 "    0.011 2.00e-02 2.50e+03
        pdb=" NH2 ARG D  40 "    0.032 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CD  ARG B  40 "   -0.518 9.50e-02 1.11e+02   2.34e-01 3.96e+01
        pdb=" NE  ARG B  40 "    0.016 2.00e-02 2.50e+03
        pdb=" CZ  ARG B  40 "    0.050 2.00e-02 2.50e+03
        pdb=" NH1 ARG B  40 "   -0.011 2.00e-02 2.50e+03
        pdb=" NH2 ARG B  40 "   -0.032 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CB  TRP A  14 "    0.058 2.00e-02 2.50e+03   3.04e-02 2.31e+01
        pdb=" CG  TRP A  14 "   -0.032 2.00e-02 2.50e+03
        pdb=" CD1 TRP A  14 "   -0.024 2.00e-02 2.50e+03
        pdb=" CD2 TRP A  14 "   -0.002 2.00e-02 2.50e+03
        pdb=" NE1 TRP A  14 "   -0.008 2.00e-02 2.50e+03
        pdb=" CE2 TRP A  14 "    0.009 2.00e-02 2.50e+03
        pdb=" CE3 TRP A  14 "   -0.023 2.00e-02 2.50e+03
        pdb=" CZ2 TRP A  14 "    0.016 2.00e-02 2.50e+03
        pdb=" CZ3 TRP A  14 "   -0.037 2.00e-02 2.50e+03
        pdb=" CH2 TRP A  14 "    0.044 2.00e-02 2.50e+03
  ... (remaining 833 not shown)

  Histogram of nonbonded interaction distances:
        2.39 -     2.89: 1492
        2.89 -     3.39: 4694
        3.39 -     3.89: 8572
        3.89 -     4.40: 9694
        4.40 -     4.90: 15534
  Nonbonded interactions: 39986
  Sorted by model distance:
  nonbonded pdb=" OD2 ASP A  94 "
            pdb=" OH  TYR D  41 "
     model   vdw
     2.386 3.040
  nonbonded pdb=" OH  TYR B  41 "
            pdb=" OD2 ASP C  94 "
     model   vdw
     2.386 3.040
  nonbonded pdb=" O   VAL A  93 "
            pdb=" OH  TYR A 140 "
     model   vdw
     2.386 3.040
  nonbonded pdb=" O   VAL C  93 "
            pdb=" OH  TYR C 140 "
     model   vdw
     2.386 3.040
  nonbonded pdb=" NE2 HIS A  58 "
            pdb=" C   CMO A 202 "
     model   vdw
     2.390 3.350
  ... (remaining 39981 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'
  selection = chain 'C'
}
ncs_group {
  reference = chain 'B'
  selection = chain 'D'
}

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 individual isotropic
Make a string to write initial .geo file
Internal consistency checks
Time:
  Set random seed:                         0.000
  Set model cs if undefined:               0.000
  Decide on map wrapping:                  0.000
  Normalize map: mean=0, sd=1:             1.330
  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:          0.040
  Check model and map are aligned:         0.010
  Set scattering table:                    0.000
  Process input model:                     4.080
  Find NCS groups from input model:        0.020
  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:4.870
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   10.370
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7476
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      :  0.013   0.163   4900  Z= 0.745
  Angle     :  1.542   7.667   6670  Z= 1.016
  Chirality :  0.096   0.351    686
  Planarity :  0.019   0.234    836
  Dihedral  : 16.078  89.705   1698
  Min Nonbonded Distance : 2.386

Molprobity Statistics.
  All-atom Clashscore : 1.71
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.77 %
    Favored  : 98.23 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  3.33 %
    Favored  : 96.67 %
  Cbeta Deviations :  0.36 %
  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: -0.11 (0.32), residues: 566
  helix: -0.33 (0.21), residues: 432
  sheet:  None (None), residues: 0
  loop :  1.57 (0.61), residues: 134

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.045   0.007   ARG D  40 
 TYR   0.028   0.009   TYR C  24 
 PHE   0.036   0.011   PHE B 130 
 TRP   0.058   0.018   TRP C  14 
 HIS   0.019   0.006   HIS A  87 

Details of bonding type rmsd
  covalent geometry    : bond        0.01272 ( 4896)
  covalent geometry    : angle       1.54171 ( 6670)
  hydrogen bonds       : bond        0.20355 (  326)
  hydrogen bonds       : angle       6.38875 (  912)
  Misc. bond           : bond        0.11954 (    4)

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

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

  1132 Ramachandran restraints generated.
    566 Oldfield, 0 Emsley, 566 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1132 Ramachandran restraints generated.
    566 Oldfield, 0 Emsley, 566 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  140 residues out of total 480 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 140
  time to evaluate  : 0.097 
Fit side-chains
REVERT: A   27 GLU cc_start: 0.8605 (tt0) cc_final: 0.8341 (tt0)
REVERT: A   68 GLU cc_start: 0.8145 (mm-30) cc_final: 0.7941 (mm-30)
REVERT: A   85 GLU cc_start: 0.8034 (tp30) cc_final: 0.7776 (tp30)
REVERT: A  120 GLU cc_start: 0.8272 (mt-10) cc_final: 0.7153 (mp0)
REVERT: B    7 GLU cc_start: 0.8449 (mt-10) cc_final: 0.8137 (mt-10)
REVERT: B   28 LEU cc_start: 0.7963 (tp) cc_final: 0.7581 (mm)
REVERT: B   40 ARG cc_start: 0.7505 (ttp80) cc_final: 0.6521 (ttp-110)
REVERT: B   43 GLU cc_start: 0.7030 (pt0) cc_final: 0.6514 (mt-10)
REVERT: B   61 GLN cc_start: 0.7926 (mm-40) cc_final: 0.7607 (mm110)
REVERT: B   65 LYS cc_start: 0.8398 (mttp) cc_final: 0.8181 (mttp)
REVERT: B   66 LYS cc_start: 0.7671 (mttt) cc_final: 0.6965 (mmtm)
REVERT: B   82 LYS cc_start: 0.7350 (tttt) cc_final: 0.7006 (tttm)
REVERT: B  125 GLU cc_start: 0.7673 (mt-10) cc_final: 0.6842 (mp0)
REVERT: C   27 GLU cc_start: 0.8607 (tt0) cc_final: 0.8343 (tt0)
REVERT: C   68 GLU cc_start: 0.8140 (mm-30) cc_final: 0.7936 (mm-30)
REVERT: C   85 GLU cc_start: 0.8031 (tp30) cc_final: 0.7775 (tp30)
REVERT: C  120 GLU cc_start: 0.8270 (mt-10) cc_final: 0.7152 (mp0)
REVERT: D    7 GLU cc_start: 0.8450 (mt-10) cc_final: 0.8137 (mt-10)
REVERT: D   28 LEU cc_start: 0.7965 (tp) cc_final: 0.7584 (mm)
REVERT: D   40 ARG cc_start: 0.7506 (ttp80) cc_final: 0.6479 (ttp-110)
REVERT: D   43 GLU cc_start: 0.7029 (pt0) cc_final: 0.6516 (mt-10)
REVERT: D   61 GLN cc_start: 0.7932 (mm-40) cc_final: 0.7615 (mm110)
REVERT: D   65 LYS cc_start: 0.8404 (mttp) cc_final: 0.8188 (mttp)
REVERT: D   66 LYS cc_start: 0.7674 (mttt) cc_final: 0.6968 (mmtm)
REVERT: D   82 LYS cc_start: 0.7352 (tttt) cc_final: 0.7007 (tttm)
REVERT: D  125 GLU cc_start: 0.7669 (mt-10) cc_final: 0.6840 (mp0)
  outliers start: 0
  outliers final: 0
  residues processed: 140
  average time/residue: 0.4869
  time to fit residues: 69.8684
Evaluate side-chains
  128 residues out of total 480 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 128
  time to evaluate  : 0.094 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 56
   random chunks:
   chunk 54 optimal weight:    0.0770
   chunk 24 optimal weight:    1.9990
   chunk 48 optimal weight:    0.8980
   chunk 26 optimal weight:    0.0770
   chunk 2 optimal weight:    0.7980
   chunk 16 optimal weight:    0.9990
   chunk 32 optimal weight:    1.9990
   chunk 31 optimal weight:    0.9990
   chunk 25 optimal weight:    0.7980
   chunk 50 optimal weight:    2.9990
   chunk 53 optimal weight:    0.5980
   overall best weight:    0.4696

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

Flipped N/Q/H residues before XYZ refinement:
A  67 HIS
A 122 HIS
B  52 HIS
B  63 HIS
C  67 HIS
C 122 HIS
D  52 HIS
D  63 HIS

Total number of N/Q/H flips: 8

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3580 r_free = 0.3580 target = 0.145362 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 46)----------------|
| r_work = 0.3404 r_free = 0.3404 target = 0.130111 restraints weight = 3587.093|
|-----------------------------------------------------------------------------|
r_work (start): 0.3406 rms_B_bonded: 0.91
r_work: 0.3269 rms_B_bonded: 1.59 restraints_weight: 0.5000
r_work: 0.3159 rms_B_bonded: 2.71 restraints_weight: 0.2500
r_work (final): 0.3159
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7953
moved from start:          0.1974

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.039   4900  Z= 0.121
  Angle     :  0.563   5.837   6670  Z= 0.275
  Chirality :  0.038   0.116    686
  Planarity :  0.004   0.030    836
  Dihedral  : 11.646  89.691    640
  Min Nonbonded Distance : 2.629

Molprobity Statistics.
  All-atom Clashscore : 3.41
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.06 %
    Favored  : 98.94 %
  Rotamer:
    Outliers :  1.46 %
    Allowed  :  9.79 %
    Favored  : 88.75 %
  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:  3.41 (0.35), residues: 566
  helix:  2.21 (0.24), residues: 410
  sheet:  None (None), residues: 0
  loop :  2.76 (0.57), residues: 156

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.007   0.001   ARG A  56 
 TYR   0.012   0.001   TYR A 140 
 PHE   0.012   0.001   PHE D 130 
 TRP   0.014   0.003   TRP A  14 
 HIS   0.004   0.001   HIS A 113 

Details of bonding type rmsd
  covalent geometry    : bond        0.00274 ( 4896)
  covalent geometry    : angle       0.56277 ( 6670)
  hydrogen bonds       : bond        0.04295 (  326)
  hydrogen bonds       : angle       4.00489 (  912)
  Misc. bond           : bond        0.02791 (    4)

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

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

  1132 Ramachandran restraints generated.
    566 Oldfield, 0 Emsley, 566 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1132 Ramachandran restraints generated.
    566 Oldfield, 0 Emsley, 566 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  137 residues out of total 480 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 7
    poor density    : 130
  time to evaluate  : 0.232 
Fit side-chains
REVERT: A   27 GLU cc_start: 0.8719 (tt0) cc_final: 0.8365 (tt0)
REVERT: A   30 GLU cc_start: 0.8360 (mt-10) cc_final: 0.8106 (mm-30)
REVERT: A  120 GLU cc_start: 0.8396 (mt-10) cc_final: 0.7682 (mp0)
REVERT: B   28 LEU cc_start: 0.8368 (tp) cc_final: 0.8128 (mm)
REVERT: B   40 ARG cc_start: 0.7487 (ttp80) cc_final: 0.6847 (ttp-110)
REVERT: B  125 GLU cc_start: 0.8039 (mt-10) cc_final: 0.7753 (mp0)
REVERT: C   27 GLU cc_start: 0.8713 (tt0) cc_final: 0.8359 (tt0)
REVERT: C   30 GLU cc_start: 0.8364 (mt-10) cc_final: 0.8108 (mm-30)
REVERT: C  120 GLU cc_start: 0.8407 (mt-10) cc_final: 0.7689 (mp0)
REVERT: D   28 LEU cc_start: 0.8369 (tp) cc_final: 0.8127 (mm)
REVERT: D   40 ARG cc_start: 0.7485 (ttp80) cc_final: 0.6845 (ttp-110)
REVERT: D  125 GLU cc_start: 0.8040 (mt-10) cc_final: 0.7757 (mp0)
  outliers start: 7
  outliers final: 0
  residues processed: 132
  average time/residue: 0.5455
  time to fit residues: 73.7325
Evaluate side-chains
  112 residues out of total 480 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 112
  time to evaluate  : 0.094 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 56
   random chunks:
   chunk 11 optimal weight:    3.9990
   chunk 7 optimal weight:    0.7980
   chunk 3 optimal weight:    0.6980
   chunk 29 optimal weight:    0.0980
   chunk 33 optimal weight:    2.9990
   chunk 35 optimal weight:    0.6980
   chunk 39 optimal weight:    0.6980
   chunk 36 optimal weight:    0.3980
   chunk 34 optimal weight:    0.9980
   chunk 47 optimal weight:    4.9990
   chunk 42 optimal weight:    0.7980
   overall best weight:    0.5180

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

Flipped N/Q/H residues before XYZ refinement:
A  71 ASN
A 122 HIS
B  22 GLN
B  61 GLN
B  80 ASN
C  71 ASN
C 122 HIS
D  22 GLN
D  61 GLN
D  80 ASN

Total number of N/Q/H flips: 10

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3558 r_free = 0.3558 target = 0.144155 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 47)----------------|
| r_work = 0.3382 r_free = 0.3382 target = 0.128634 restraints weight = 3619.835|
|-----------------------------------------------------------------------------|
r_work (start): 0.3381 rms_B_bonded: 0.94
r_work: 0.3246 rms_B_bonded: 1.63 restraints_weight: 0.5000
r_work: 0.3142 rms_B_bonded: 2.74 restraints_weight: 0.2500
r_work (final): 0.3142
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7971
moved from start:          0.2280

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.077   4900  Z= 0.119
  Angle     :  0.548   6.095   6670  Z= 0.264
  Chirality :  0.038   0.116    686
  Planarity :  0.004   0.037    836
  Dihedral  : 10.697  89.611    640
  Min Nonbonded Distance : 2.636

Molprobity Statistics.
  All-atom Clashscore : 2.45
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  0.71 %
    Favored  : 99.29 %
  Rotamer:
    Outliers :  0.83 %
    Allowed  : 12.92 %
    Favored  : 86.25 %
  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:  3.80 (0.35), residues: 566
  helix:  2.58 (0.25), residues: 412
  sheet:  None (None), residues: 0
  loop :  2.63 (0.56), residues: 154

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.001   ARG A  56 
 TYR   0.012   0.001   TYR C 140 
 PHE   0.010   0.001   PHE D 130 
 TRP   0.010   0.002   TRP B  15 
 HIS   0.004   0.001   HIS A 112 

Details of bonding type rmsd
  covalent geometry    : bond        0.00273 ( 4896)
  covalent geometry    : angle       0.54795 ( 6670)
  hydrogen bonds       : bond        0.04284 (  326)
  hydrogen bonds       : angle       3.87197 (  912)
  Misc. bond           : bond        0.05527 (    4)

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

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

  1132 Ramachandran restraints generated.
    566 Oldfield, 0 Emsley, 566 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1132 Ramachandran restraints generated.
    566 Oldfield, 0 Emsley, 566 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  112 residues out of total 480 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 4
    poor density    : 108
  time to evaluate  : 0.101 
Fit side-chains
REVERT: A   27 GLU cc_start: 0.8715 (tt0) cc_final: 0.8302 (tt0)
REVERT: A   30 GLU cc_start: 0.8386 (mt-10) cc_final: 0.8168 (mm-30)
REVERT: A  120 GLU cc_start: 0.8397 (mt-10) cc_final: 0.7718 (mp0)
REVERT: B   40 ARG cc_start: 0.7539 (ttp80) cc_final: 0.6837 (ttp-110)
REVERT: B  125 GLU cc_start: 0.8130 (mt-10) cc_final: 0.7781 (mp0)
REVERT: C   27 GLU cc_start: 0.8706 (tt0) cc_final: 0.8297 (tt0)
REVERT: C   30 GLU cc_start: 0.8391 (mt-10) cc_final: 0.8168 (mm-30)
REVERT: C  120 GLU cc_start: 0.8399 (mt-10) cc_final: 0.7716 (mp0)
REVERT: D   40 ARG cc_start: 0.7544 (ttp80) cc_final: 0.6842 (ttp-110)
REVERT: D  125 GLU cc_start: 0.8132 (mt-10) cc_final: 0.7786 (mp0)
  outliers start: 4
  outliers final: 2
  residues processed: 110
  average time/residue: 0.7698
  time to fit residues: 86.7914
Evaluate side-chains
  112 residues out of total 480 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 2
    poor density    : 110
  time to evaluate  : 0.189 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue   31 MET
Chi-restraints excluded: chain D residue   31 MET
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 56
   random chunks:
   chunk 1 optimal weight:    0.7980
   chunk 17 optimal weight:    0.5980
   chunk 3 optimal weight:    0.9990
   chunk 42 optimal weight:    0.6980
   chunk 55 optimal weight:    4.9990
   chunk 2 optimal weight:    0.9980
   chunk 25 optimal weight:    2.9990
   chunk 22 optimal weight:    1.9990
   chunk 0 optimal weight:    0.5980
   chunk 30 optimal weight:    4.9990
   chunk 36 optimal weight:    1.9990
   overall best weight:    0.7380

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

Flipped N/Q/H residues before XYZ refinement:
A  71 ASN
A 122 HIS
B  22 GLN
B  80 ASN
C  71 ASN
C 122 HIS
D  22 GLN
D  80 ASN

Total number of N/Q/H flips: 8

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3559 r_free = 0.3559 target = 0.143133 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 44)----------------|
| r_work = 0.3377 r_free = 0.3377 target = 0.127516 restraints weight = 3583.360|
|-----------------------------------------------------------------------------|
r_work (start): 0.3378 rms_B_bonded: 0.91
r_work: 0.3239 rms_B_bonded: 1.58 restraints_weight: 0.5000
r_work: 0.3129 rms_B_bonded: 2.66 restraints_weight: 0.2500
r_work (final): 0.3129
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7969
moved from start:          0.2313

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.093   4900  Z= 0.134
  Angle     :  0.571   6.298   6670  Z= 0.276
  Chirality :  0.039   0.118    686
  Planarity :  0.004   0.039    836
  Dihedral  : 10.311  89.783    640
  Min Nonbonded Distance : 2.627

Molprobity Statistics.
  All-atom Clashscore : 2.77
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  0.35 %
    Favored  : 99.65 %
  Rotamer:
    Outliers :  1.67 %
    Allowed  : 13.33 %
    Favored  : 85.00 %
  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:  3.68 (0.35), residues: 566
  helix:  2.52 (0.25), residues: 410
  sheet:  None (None), residues: 0
  loop :  2.48 (0.56), residues: 156

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.001   ARG A  56 
 TYR   0.010   0.001   TYR A 140 
 PHE   0.010   0.001   PHE D 130 
 TRP   0.011   0.002   TRP D  15 
 HIS   0.006   0.001   HIS C 112 

Details of bonding type rmsd
  covalent geometry    : bond        0.00303 ( 4896)
  covalent geometry    : angle       0.57103 ( 6670)
  hydrogen bonds       : bond        0.04749 (  326)
  hydrogen bonds       : angle       3.93738 (  912)
  Misc. bond           : bond        0.06579 (    4)

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

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

  1132 Ramachandran restraints generated.
    566 Oldfield, 0 Emsley, 566 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1132 Ramachandran restraints generated.
    566 Oldfield, 0 Emsley, 566 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  114 residues out of total 480 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 8
    poor density    : 106
  time to evaluate  : 0.191 
Fit side-chains
REVERT: A   30 GLU cc_start: 0.8387 (mt-10) cc_final: 0.8163 (mm-30)
REVERT: A  120 GLU cc_start: 0.8429 (mt-10) cc_final: 0.7724 (mp0)
REVERT: B   28 LEU cc_start: 0.8485 (tp) cc_final: 0.8211 (mm)
REVERT: B   40 ARG cc_start: 0.7576 (ttp80) cc_final: 0.6824 (ttp-110)
REVERT: B   76 LYS cc_start: 0.8419 (mttt) cc_final: 0.7936 (mtmt)
REVERT: B  125 GLU cc_start: 0.8068 (mt-10) cc_final: 0.7675 (mp0)
REVERT: C   30 GLU cc_start: 0.8387 (mt-10) cc_final: 0.8163 (mm-30)
REVERT: C  120 GLU cc_start: 0.8427 (mt-10) cc_final: 0.7721 (mp0)
REVERT: D   28 LEU cc_start: 0.8480 (tp) cc_final: 0.8205 (mm)
REVERT: D   40 ARG cc_start: 0.7578 (ttp80) cc_final: 0.6825 (ttp-110)
REVERT: D   76 LYS cc_start: 0.8425 (mttt) cc_final: 0.7943 (mtmt)
REVERT: D  125 GLU cc_start: 0.8061 (mt-10) cc_final: 0.7676 (mp0)
  outliers start: 8
  outliers final: 4
  residues processed: 110
  average time/residue: 0.9169
  time to fit residues: 103.2635
Evaluate side-chains
  110 residues out of total 480 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 4
    poor density    : 106
  time to evaluate  : 0.136 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue   31 MET
Chi-restraints excluded: chain B residue   43 GLU
Chi-restraints excluded: chain D residue   31 MET
Chi-restraints excluded: chain D residue   43 GLU
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 56
   random chunks:
   chunk 42 optimal weight:    1.9990
   chunk 24 optimal weight:    0.9980
   chunk 52 optimal weight:    3.9990
   chunk 54 optimal weight:    0.8980
   chunk 55 optimal weight:    0.8980
   chunk 9 optimal weight:    2.9990
   chunk 10 optimal weight:    2.9990
   chunk 40 optimal weight:    0.5980
   chunk 50 optimal weight:    0.9990
   chunk 3 optimal weight:    0.6980
   chunk 12 optimal weight:    4.9990
   overall best weight:    0.8180

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

Flipped N/Q/H residues before XYZ refinement:
A  71 ASN
B  22 GLN
B  80 ASN
C  71 ASN
D  22 GLN
D  80 ASN

Total number of N/Q/H flips: 6

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3547 r_free = 0.3547 target = 0.142231 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.3365 r_free = 0.3365 target = 0.126817 restraints weight = 3613.548|
|-----------------------------------------------------------------------------|
r_work (start): 0.3367 rms_B_bonded: 0.90
r_work: 0.3232 rms_B_bonded: 1.56 restraints_weight: 0.5000
r_work: 0.3123 rms_B_bonded: 2.64 restraints_weight: 0.2500
r_work (final): 0.3123
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7981
moved from start:          0.2323

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.095   4900  Z= 0.137
  Angle     :  0.580   6.216   6670  Z= 0.279
  Chirality :  0.040   0.119    686
  Planarity :  0.005   0.040    836
  Dihedral  : 10.378  89.836    640
  Min Nonbonded Distance : 2.636

Molprobity Statistics.
  All-atom Clashscore : 2.88
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.06 %
    Favored  : 98.94 %
  Rotamer:
    Outliers :  2.50 %
    Allowed  : 12.92 %
    Favored  : 84.58 %
  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:  3.59 (0.35), residues: 566
  helix:  2.46 (0.24), residues: 410
  sheet:  None (None), residues: 0
  loop :  2.43 (0.56), residues: 156

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.001   ARG A  56 
 TYR   0.009   0.001   TYR A 140 
 PHE   0.010   0.002   PHE D 130 
 TRP   0.012   0.002   TRP D  15 
 HIS   0.005   0.001   HIS C 112 

Details of bonding type rmsd
  covalent geometry    : bond        0.00309 ( 4896)
  covalent geometry    : angle       0.57961 ( 6670)
  hydrogen bonds       : bond        0.04812 (  326)
  hydrogen bonds       : angle       3.94908 (  912)
  Misc. bond           : bond        0.06762 (    4)

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

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

  1132 Ramachandran restraints generated.
    566 Oldfield, 0 Emsley, 566 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1132 Ramachandran restraints generated.
    566 Oldfield, 0 Emsley, 566 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  120 residues out of total 480 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 108
  time to evaluate  : 0.176 
Fit side-chains
REVERT: A   27 GLU cc_start: 0.8449 (tt0) cc_final: 0.8208 (tt0)
REVERT: A   30 GLU cc_start: 0.8404 (OUTLIER) cc_final: 0.8200 (mm-30)
REVERT: A  120 GLU cc_start: 0.8443 (mt-10) cc_final: 0.7743 (mp0)
REVERT: B   13 ASP cc_start: 0.8452 (OUTLIER) cc_final: 0.7928 (m-30)
REVERT: B   28 LEU cc_start: 0.8407 (tp) cc_final: 0.8180 (mm)
REVERT: B   40 ARG cc_start: 0.7577 (ttp80) cc_final: 0.6827 (ttp-110)
REVERT: B   76 LYS cc_start: 0.8453 (mttt) cc_final: 0.7975 (mtmt)
REVERT: B  125 GLU cc_start: 0.8067 (mt-10) cc_final: 0.7694 (mp0)
REVERT: C   27 GLU cc_start: 0.8444 (tt0) cc_final: 0.8203 (tt0)
REVERT: C   30 GLU cc_start: 0.8408 (OUTLIER) cc_final: 0.8204 (mm-30)
REVERT: C  120 GLU cc_start: 0.8441 (mt-10) cc_final: 0.7729 (mp0)
REVERT: D   13 ASP cc_start: 0.8450 (OUTLIER) cc_final: 0.7927 (m-30)
REVERT: D   28 LEU cc_start: 0.8403 (tp) cc_final: 0.8175 (mm)
REVERT: D   40 ARG cc_start: 0.7577 (ttp80) cc_final: 0.6827 (ttp-110)
REVERT: D   76 LYS cc_start: 0.8455 (mttt) cc_final: 0.7979 (mtmt)
REVERT: D  125 GLU cc_start: 0.8060 (mt-10) cc_final: 0.7694 (mp0)
  outliers start: 12
  outliers final: 6
  residues processed: 112
  average time/residue: 0.8981
  time to fit residues: 103.0202
Evaluate side-chains
  116 residues out of total 480 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 106
  time to evaluate  : 0.179 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   30 GLU
Chi-restraints excluded: chain B residue    9 LYS
Chi-restraints excluded: chain B residue   13 ASP
Chi-restraints excluded: chain B residue   31 MET
Chi-restraints excluded: chain B residue   43 GLU
Chi-restraints excluded: chain C residue   30 GLU
Chi-restraints excluded: chain D residue    9 LYS
Chi-restraints excluded: chain D residue   13 ASP
Chi-restraints excluded: chain D residue   31 MET
Chi-restraints excluded: chain D residue   43 GLU
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 56
   random chunks:
   chunk 53 optimal weight:    0.0570
   chunk 3 optimal weight:    0.6980
   chunk 16 optimal weight:    4.9990
   chunk 22 optimal weight:    1.9990
   chunk 33 optimal weight:    0.6980
   chunk 38 optimal weight:    0.8980
   chunk 42 optimal weight:    1.9990
   chunk 23 optimal weight:    3.9990
   chunk 6 optimal weight:    1.9990
   chunk 4 optimal weight:    0.5980
   chunk 51 optimal weight:   20.0000
   overall best weight:    0.5898

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

Flipped N/Q/H residues before XYZ refinement:
A 122 HIS
B  22 GLN
B  80 ASN
** C  58 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
D  22 GLN
D  80 ASN

Total number of N/Q/H flips: 5

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3565 r_free = 0.3565 target = 0.143844 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 53)----------------|
| r_work = 0.3384 r_free = 0.3384 target = 0.128361 restraints weight = 3653.786|
|-----------------------------------------------------------------------------|
r_work (start): 0.3383 rms_B_bonded: 0.91
r_work: 0.3252 rms_B_bonded: 1.58 restraints_weight: 0.5000
r_work: 0.3145 rms_B_bonded: 2.67 restraints_weight: 0.2500
r_work (final): 0.3145
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7958
moved from start:          0.2463

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.083   4900  Z= 0.121
  Angle     :  0.548   6.024   6670  Z= 0.262
  Chirality :  0.038   0.115    686
  Planarity :  0.004   0.040    836
  Dihedral  : 10.078  89.287    640
  Min Nonbonded Distance : 2.635

Molprobity Statistics.
  All-atom Clashscore : 3.20
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.06 %
    Favored  : 98.94 %
  Rotamer:
    Outliers :  2.29 %
    Allowed  : 14.58 %
    Favored  : 83.12 %
  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:  3.80 (0.35), residues: 566
  helix:  2.61 (0.25), residues: 412
  sheet:  None (None), residues: 0
  loop :  2.52 (0.56), residues: 154

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG A  56 
 TYR   0.008   0.001   TYR C 140 
 PHE   0.010   0.001   PHE D 130 
 TRP   0.011   0.002   TRP B  15 
 HIS   0.004   0.001   HIS C 112 

Details of bonding type rmsd
  covalent geometry    : bond        0.00280 ( 4896)
  covalent geometry    : angle       0.54784 ( 6670)
  hydrogen bonds       : bond        0.04259 (  326)
  hydrogen bonds       : angle       3.82792 (  912)
  Misc. bond           : bond        0.06007 (    4)

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

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

  1132 Ramachandran restraints generated.
    566 Oldfield, 0 Emsley, 566 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1132 Ramachandran restraints generated.
    566 Oldfield, 0 Emsley, 566 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  121 residues out of total 480 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 110
  time to evaluate  : 0.182 
Fit side-chains
REVERT: A   27 GLU cc_start: 0.8446 (tt0) cc_final: 0.8220 (tt0)
REVERT: A   30 GLU cc_start: 0.8388 (OUTLIER) cc_final: 0.8156 (mm-30)
REVERT: A  120 GLU cc_start: 0.8378 (mt-10) cc_final: 0.7697 (mp0)
REVERT: B   28 LEU cc_start: 0.8369 (tp) cc_final: 0.8148 (mm)
REVERT: B   40 ARG cc_start: 0.7532 (ttp80) cc_final: 0.6787 (ttp-110)
REVERT: B   76 LYS cc_start: 0.8422 (mttt) cc_final: 0.7914 (mtmt)
REVERT: B  125 GLU cc_start: 0.8047 (mt-10) cc_final: 0.7683 (mp0)
REVERT: C   27 GLU cc_start: 0.8444 (tt0) cc_final: 0.8219 (tt0)
REVERT: C   30 GLU cc_start: 0.8392 (OUTLIER) cc_final: 0.8160 (mm-30)
REVERT: C  120 GLU cc_start: 0.8379 (mt-10) cc_final: 0.7692 (mp0)
REVERT: D   28 LEU cc_start: 0.8368 (tp) cc_final: 0.8145 (mm)
REVERT: D   40 ARG cc_start: 0.7538 (ttp80) cc_final: 0.6789 (ttp-110)
REVERT: D   76 LYS cc_start: 0.8421 (mttt) cc_final: 0.7910 (mtmt)
REVERT: D  125 GLU cc_start: 0.8036 (mt-10) cc_final: 0.7682 (mp0)
  outliers start: 11
  outliers final: 6
  residues processed: 115
  average time/residue: 0.8329
  time to fit residues: 98.1766
Evaluate side-chains
  116 residues out of total 480 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 8
    poor density    : 108
  time to evaluate  : 0.177 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue    2 LEU
Chi-restraints excluded: chain A residue   30 GLU
Chi-restraints excluded: chain B residue   31 MET
Chi-restraints excluded: chain B residue   43 GLU
Chi-restraints excluded: chain C residue    2 LEU
Chi-restraints excluded: chain C residue   30 GLU
Chi-restraints excluded: chain D residue   31 MET
Chi-restraints excluded: chain D residue   43 GLU
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 56
   random chunks:
   chunk 49 optimal weight:    1.9990
   chunk 21 optimal weight:    0.5980
   chunk 46 optimal weight:    0.8980
   chunk 16 optimal weight:    4.9990
   chunk 26 optimal weight:    0.8980
   chunk 39 optimal weight:    2.9990
   chunk 9 optimal weight:    1.9990
   chunk 48 optimal weight:    1.9990
   chunk 23 optimal weight:    1.9990
   chunk 42 optimal weight:    1.9990
   chunk 5 optimal weight:    0.6980
   overall best weight:    1.0182

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

Flipped N/Q/H residues before XYZ refinement:
A 122 HIS
B  22 GLN
B  80 ASN
D  22 GLN
D  80 ASN

Total number of N/Q/H flips: 5

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3540 r_free = 0.3540 target = 0.141454 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 51)----------------|
| r_work = 0.3354 r_free = 0.3354 target = 0.125885 restraints weight = 3592.455|
|-----------------------------------------------------------------------------|
r_work (start): 0.3357 rms_B_bonded: 0.90
r_work: 0.3220 rms_B_bonded: 1.57 restraints_weight: 0.5000
r_work: 0.3111 rms_B_bonded: 2.64 restraints_weight: 0.2500
r_work (final): 0.3111
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7986
moved from start:          0.2341

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.106   4900  Z= 0.153
  Angle     :  0.606   6.388   6670  Z= 0.293
  Chirality :  0.041   0.121    686
  Planarity :  0.005   0.040    836
  Dihedral  : 10.592  89.103    640
  Min Nonbonded Distance : 2.634

Molprobity Statistics.
  All-atom Clashscore : 2.77
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  0.88 %
    Favored  : 99.12 %
  Rotamer:
    Outliers :  2.71 %
    Allowed  : 15.00 %
    Favored  : 82.29 %
  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:  3.18 (0.35), residues: 566
  helix:  2.21 (0.24), residues: 420
  sheet:  None (None), residues: 0
  loop :  2.07 (0.56), residues: 146

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.001   ARG A  31 
 TYR   0.010   0.002   TYR A 140 
 PHE   0.010   0.002   PHE D 130 
 TRP   0.013   0.003   TRP B  15 
 HIS   0.005   0.001   HIS A 112 

Details of bonding type rmsd
  covalent geometry    : bond        0.00343 ( 4896)
  covalent geometry    : angle       0.60601 ( 6670)
  hydrogen bonds       : bond        0.05237 (  326)
  hydrogen bonds       : angle       4.00711 (  912)
  Misc. bond           : bond        0.07514 (    4)

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

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

  1132 Ramachandran restraints generated.
    566 Oldfield, 0 Emsley, 566 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1132 Ramachandran restraints generated.
    566 Oldfield, 0 Emsley, 566 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  121 residues out of total 480 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 108
  time to evaluate  : 0.175 
Fit side-chains
REVERT: A   27 GLU cc_start: 0.8431 (tt0) cc_final: 0.8159 (tt0)
REVERT: A   30 GLU cc_start: 0.8397 (OUTLIER) cc_final: 0.8182 (mm-30)
REVERT: A  120 GLU cc_start: 0.8459 (mt-10) cc_final: 0.7744 (mp0)
REVERT: B   28 LEU cc_start: 0.8366 (tp) cc_final: 0.8136 (mm)
REVERT: B   40 ARG cc_start: 0.7569 (ttp80) cc_final: 0.6821 (ttp-110)
REVERT: B   76 LYS cc_start: 0.8454 (mmtt) cc_final: 0.7925 (mtmt)
REVERT: B  125 GLU cc_start: 0.8065 (mt-10) cc_final: 0.7687 (mp0)
REVERT: C   27 GLU cc_start: 0.8428 (tt0) cc_final: 0.8157 (tt0)
REVERT: C   30 GLU cc_start: 0.8400 (OUTLIER) cc_final: 0.8183 (mm-30)
REVERT: C  120 GLU cc_start: 0.8463 (mt-10) cc_final: 0.7737 (mp0)
REVERT: D   28 LEU cc_start: 0.8364 (tp) cc_final: 0.8132 (mm)
REVERT: D   40 ARG cc_start: 0.7575 (ttp80) cc_final: 0.6824 (ttp-110)
REVERT: D   76 LYS cc_start: 0.8457 (mmtt) cc_final: 0.7929 (mtmt)
REVERT: D  125 GLU cc_start: 0.8050 (mt-10) cc_final: 0.7687 (mp0)
  outliers start: 13
  outliers final: 8
  residues processed: 113
  average time/residue: 0.8411
  time to fit residues: 97.3691
Evaluate side-chains
  118 residues out of total 480 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 108
  time to evaluate  : 0.176 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue    2 LEU
Chi-restraints excluded: chain A residue   30 GLU
Chi-restraints excluded: chain B residue    9 LYS
Chi-restraints excluded: chain B residue   31 MET
Chi-restraints excluded: chain B residue   43 GLU
Chi-restraints excluded: chain C residue    2 LEU
Chi-restraints excluded: chain C residue   30 GLU
Chi-restraints excluded: chain D residue    9 LYS
Chi-restraints excluded: chain D residue   31 MET
Chi-restraints excluded: chain D residue   43 GLU
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 56
   random chunks:
   chunk 32 optimal weight:    2.9990
   chunk 5 optimal weight:    0.9990
   chunk 34 optimal weight:    1.9990
   chunk 49 optimal weight:    2.9990
   chunk 26 optimal weight:    0.1980
   chunk 17 optimal weight:    0.9980
   chunk 24 optimal weight:    1.9990
   chunk 42 optimal weight:    1.9990
   chunk 3 optimal weight:    0.0370
   chunk 6 optimal weight:    1.9990
   chunk 9 optimal weight:    1.9990
   overall best weight:    0.8462

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

Flipped N/Q/H residues before XYZ refinement:
A 122 HIS
B  61 GLN
B  80 ASN
** C  58 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
D  61 GLN
D  80 ASN

Total number of N/Q/H flips: 5

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3548 r_free = 0.3548 target = 0.142041 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 46)----------------|
| r_work = 0.3363 r_free = 0.3363 target = 0.126571 restraints weight = 3645.731|
|-----------------------------------------------------------------------------|
r_work (start): 0.3365 rms_B_bonded: 0.91
r_work: 0.3229 rms_B_bonded: 1.58 restraints_weight: 0.5000
r_work: 0.3121 rms_B_bonded: 2.67 restraints_weight: 0.2500
r_work (final): 0.3121
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7982
moved from start:          0.2380

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.102   4900  Z= 0.141
  Angle     :  0.584   6.139   6670  Z= 0.282
  Chirality :  0.040   0.118    686
  Planarity :  0.004   0.040    836
  Dihedral  : 10.461  89.702    640
  Min Nonbonded Distance : 2.635

Molprobity Statistics.
  All-atom Clashscore : 2.88
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.06 %
    Favored  : 98.94 %
  Rotamer:
    Outliers :  2.29 %
    Allowed  : 15.42 %
    Favored  : 82.29 %
  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:  3.57 (0.35), residues: 566
  helix:  2.46 (0.24), residues: 410
  sheet:  None (None), residues: 0
  loop :  2.40 (0.57), residues: 156

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.001   ARG C  31 
 TYR   0.008   0.001   TYR A 140 
 PHE   0.010   0.002   PHE D 130 
 TRP   0.012   0.002   TRP B  15 
 HIS   0.005   0.001   HIS A  58 

Details of bonding type rmsd
  covalent geometry    : bond        0.00318 ( 4896)
  covalent geometry    : angle       0.58444 ( 6670)
  hydrogen bonds       : bond        0.04865 (  326)
  hydrogen bonds       : angle       3.94726 (  912)
  Misc. bond           : bond        0.07291 (    4)

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

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

  1132 Ramachandran restraints generated.
    566 Oldfield, 0 Emsley, 566 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1132 Ramachandran restraints generated.
    566 Oldfield, 0 Emsley, 566 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  117 residues out of total 480 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 106
  time to evaluate  : 0.193 
Fit side-chains
REVERT: A   27 GLU cc_start: 0.8457 (tt0) cc_final: 0.8189 (tt0)
REVERT: A   30 GLU cc_start: 0.8389 (OUTLIER) cc_final: 0.8176 (mm-30)
REVERT: A  120 GLU cc_start: 0.8453 (mt-10) cc_final: 0.7732 (mp0)
REVERT: B   28 LEU cc_start: 0.8357 (tp) cc_final: 0.8134 (mm)
REVERT: B   40 ARG cc_start: 0.7555 (ttp80) cc_final: 0.6816 (ttp-110)
REVERT: B   76 LYS cc_start: 0.8454 (mmtt) cc_final: 0.7933 (mtmt)
REVERT: B  125 GLU cc_start: 0.8065 (mt-10) cc_final: 0.7688 (mp0)
REVERT: C   27 GLU cc_start: 0.8454 (tt0) cc_final: 0.8185 (tt0)
REVERT: C   30 GLU cc_start: 0.8392 (OUTLIER) cc_final: 0.8175 (mm-30)
REVERT: C  120 GLU cc_start: 0.8453 (mt-10) cc_final: 0.7725 (mp0)
REVERT: D   28 LEU cc_start: 0.8356 (tp) cc_final: 0.8133 (mm)
REVERT: D   40 ARG cc_start: 0.7561 (ttp80) cc_final: 0.6820 (ttp-110)
REVERT: D   76 LYS cc_start: 0.8457 (mmtt) cc_final: 0.7936 (mtmt)
REVERT: D  125 GLU cc_start: 0.8052 (mt-10) cc_final: 0.7685 (mp0)
  outliers start: 11
  outliers final: 7
  residues processed: 111
  average time/residue: 0.8030
  time to fit residues: 91.2841
Evaluate side-chains
  115 residues out of total 480 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 9
    poor density    : 106
  time to evaluate  : 0.135 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue    2 LEU
Chi-restraints excluded: chain A residue   30 GLU
Chi-restraints excluded: chain B residue   31 MET
Chi-restraints excluded: chain B residue   43 GLU
Chi-restraints excluded: chain C residue    2 LEU
Chi-restraints excluded: chain C residue   30 GLU
Chi-restraints excluded: chain D residue    9 LYS
Chi-restraints excluded: chain D residue   31 MET
Chi-restraints excluded: chain D residue   43 GLU
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 56
   random chunks:
   chunk 3 optimal weight:    0.0060
   chunk 45 optimal weight:    0.7980
   chunk 26 optimal weight:    0.9990
   chunk 39 optimal weight:    2.9990
   chunk 34 optimal weight:    1.9990
   chunk 20 optimal weight:    5.9990
   chunk 40 optimal weight:    2.9990
   chunk 19 optimal weight:    0.5980
   chunk 28 optimal weight:    1.9990
   chunk 46 optimal weight:    0.1980
   chunk 36 optimal weight:    0.8980
   overall best weight:    0.4996

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

Flipped N/Q/H residues before XYZ refinement:
** A  58 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
A 122 HIS
B  22 GLN
B  80 ASN
** C  58 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
C 122 HIS
D  22 GLN
D  80 ASN

Total number of N/Q/H flips: 6

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3575 r_free = 0.3575 target = 0.144457 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 40)----------------|
| r_work = 0.3389 r_free = 0.3389 target = 0.128714 restraints weight = 3613.600|
|-----------------------------------------------------------------------------|
r_work (start): 0.3388 rms_B_bonded: 0.95
r_work: 0.3254 rms_B_bonded: 1.63 restraints_weight: 0.5000
r_work: 0.3145 rms_B_bonded: 2.77 restraints_weight: 0.2500
r_work (final): 0.3145
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7949
moved from start:          0.2533

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.071   4900  Z= 0.116
  Angle     :  0.544   5.890   6670  Z= 0.258
  Chirality :  0.037   0.114    686
  Planarity :  0.004   0.040    836
  Dihedral  : 10.111  88.953    640
  Min Nonbonded Distance : 2.636

Molprobity Statistics.
  All-atom Clashscore : 3.41
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.06 %
    Favored  : 98.94 %
  Rotamer:
    Outliers :  1.88 %
    Allowed  : 16.46 %
    Favored  : 81.67 %
  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:  3.83 (0.35), residues: 566
  helix:  2.66 (0.25), residues: 412
  sheet:  None (None), residues: 0
  loop :  2.45 (0.56), residues: 154

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG A  31 
 TYR   0.008   0.001   TYR C 140 
 PHE   0.010   0.001   PHE D 130 
 TRP   0.010   0.002   TRP D  15 
 HIS   0.004   0.001   HIS B  63 

Details of bonding type rmsd
  covalent geometry    : bond        0.00272 ( 4896)
  covalent geometry    : angle       0.54442 ( 6670)
  hydrogen bonds       : bond        0.04062 (  326)
  hydrogen bonds       : angle       3.78966 (  912)
  Misc. bond           : bond        0.05213 (    4)

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

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

  1132 Ramachandran restraints generated.
    566 Oldfield, 0 Emsley, 566 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1132 Ramachandran restraints generated.
    566 Oldfield, 0 Emsley, 566 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  119 residues out of total 480 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 9
    poor density    : 110
  time to evaluate  : 0.163 
Fit side-chains
REVERT: A   27 GLU cc_start: 0.8448 (tt0) cc_final: 0.8236 (tt0)
REVERT: A   30 GLU cc_start: 0.8393 (mt-10) cc_final: 0.8157 (mm-30)
REVERT: A  120 GLU cc_start: 0.8378 (mt-10) cc_final: 0.7676 (mp0)
REVERT: B   22 GLN cc_start: 0.8494 (tt0) cc_final: 0.8279 (tt0)
REVERT: B   28 LEU cc_start: 0.8296 (tp) cc_final: 0.8080 (mm)
REVERT: B   40 ARG cc_start: 0.7516 (ttp80) cc_final: 0.6765 (ttp-110)
REVERT: B   76 LYS cc_start: 0.8420 (mmtt) cc_final: 0.7903 (mtmt)
REVERT: B  125 GLU cc_start: 0.8060 (mt-10) cc_final: 0.7672 (mp0)
REVERT: C   27 GLU cc_start: 0.8441 (tt0) cc_final: 0.8230 (tt0)
REVERT: C   30 GLU cc_start: 0.8393 (mt-10) cc_final: 0.8157 (mm-30)
REVERT: C  120 GLU cc_start: 0.8375 (mt-10) cc_final: 0.7673 (mp0)
REVERT: D   22 GLN cc_start: 0.8495 (tt0) cc_final: 0.8279 (tt0)
REVERT: D   28 LEU cc_start: 0.8291 (tp) cc_final: 0.8073 (mm)
REVERT: D   40 ARG cc_start: 0.7524 (ttp80) cc_final: 0.6767 (ttp-110)
REVERT: D   76 LYS cc_start: 0.8426 (mmtt) cc_final: 0.7908 (mtmt)
REVERT: D  125 GLU cc_start: 0.8051 (mt-10) cc_final: 0.7671 (mp0)
  outliers start: 9
  outliers final: 7
  residues processed: 115
  average time/residue: 0.8281
  time to fit residues: 97.5600
Evaluate side-chains
  119 residues out of total 480 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 7
    poor density    : 112
  time to evaluate  : 0.179 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue    2 LEU
Chi-restraints excluded: chain A residue   18 SER
Chi-restraints excluded: chain B residue   31 MET
Chi-restraints excluded: chain B residue   43 GLU
Chi-restraints excluded: chain C residue    2 LEU
Chi-restraints excluded: chain D residue   31 MET
Chi-restraints excluded: chain D residue   43 GLU
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 56
   random chunks:
   chunk 47 optimal weight:    0.8980
   chunk 14 optimal weight:    0.9980
   chunk 39 optimal weight:    1.9990
   chunk 32 optimal weight:    1.9990
   chunk 21 optimal weight:    4.9990
   chunk 45 optimal weight:    4.9990
   chunk 29 optimal weight:    0.8980
   chunk 36 optimal weight:    0.9990
   chunk 28 optimal weight:    0.6980
   chunk 46 optimal weight:    3.9990
   chunk 12 optimal weight:    0.6980
   overall best weight:    0.8380

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

Flipped N/Q/H residues before XYZ refinement:
** A  58 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
A 122 HIS
** B  61 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
B  80 ASN
** C  58 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
C 122 HIS
** D  61 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
D  80 ASN

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3550 r_free = 0.3550 target = 0.141964 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 46)----------------|
| r_work = 0.3364 r_free = 0.3364 target = 0.126579 restraints weight = 3593.421|
|-----------------------------------------------------------------------------|
r_work (start): 0.3367 rms_B_bonded: 0.90
r_work: 0.3231 rms_B_bonded: 1.57 restraints_weight: 0.5000
r_work: 0.3122 rms_B_bonded: 2.65 restraints_weight: 0.2500
r_work (final): 0.3122
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7973
moved from start:          0.2434

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.093   4900  Z= 0.141
  Angle     :  0.592   6.241   6670  Z= 0.284
  Chirality :  0.040   0.120    686
  Planarity :  0.004   0.040    836
  Dihedral  : 10.483  89.489    640
  Min Nonbonded Distance : 2.634

Molprobity Statistics.
  All-atom Clashscore : 3.84
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.06 %
    Favored  : 98.94 %
  Rotamer:
    Outliers :  2.08 %
    Allowed  : 16.67 %
    Favored  : 81.25 %
  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:  3.64 (0.35), residues: 566
  helix:  2.51 (0.24), residues: 412
  sheet:  None (None), residues: 0
  loop :  2.40 (0.57), residues: 154

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.001   ARG C  31 
 TYR   0.009   0.001   TYR A 140 
 PHE   0.010   0.002   PHE D 130 
 TRP   0.012   0.002   TRP D  15 
 HIS   0.005   0.001   HIS D  63 

Details of bonding type rmsd
  covalent geometry    : bond        0.00319 ( 4896)
  covalent geometry    : angle       0.59178 ( 6670)
  hydrogen bonds       : bond        0.04865 (  326)
  hydrogen bonds       : angle       3.92772 (  912)
  Misc. bond           : bond        0.06602 (    4)

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

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

  1132 Ramachandran restraints generated.
    566 Oldfield, 0 Emsley, 566 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1132 Ramachandran restraints generated.
    566 Oldfield, 0 Emsley, 566 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  120 residues out of total 480 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 110
  time to evaluate  : 0.222 
Fit side-chains
REVERT: A   27 GLU cc_start: 0.8468 (tt0) cc_final: 0.8196 (tt0)
REVERT: A   30 GLU cc_start: 0.8389 (mt-10) cc_final: 0.8170 (mm-30)
REVERT: A  120 GLU cc_start: 0.8422 (mt-10) cc_final: 0.7705 (mp0)
REVERT: B   28 LEU cc_start: 0.8350 (tp) cc_final: 0.8126 (mm)
REVERT: B   40 ARG cc_start: 0.7542 (ttp80) cc_final: 0.6797 (ttp-110)
REVERT: B   76 LYS cc_start: 0.8427 (mmtt) cc_final: 0.7901 (mtmt)
REVERT: B  125 GLU cc_start: 0.8058 (mt-10) cc_final: 0.7680 (mp0)
REVERT: C   27 GLU cc_start: 0.8464 (tt0) cc_final: 0.8192 (tt0)
REVERT: C   30 GLU cc_start: 0.8390 (mt-10) cc_final: 0.8170 (mm-30)
REVERT: C  120 GLU cc_start: 0.8422 (mt-10) cc_final: 0.7701 (mp0)
REVERT: D   28 LEU cc_start: 0.8345 (tp) cc_final: 0.8121 (mm)
REVERT: D   40 ARG cc_start: 0.7550 (ttp80) cc_final: 0.6803 (ttp-110)
REVERT: D   76 LYS cc_start: 0.8433 (mmtt) cc_final: 0.7907 (mtmt)
REVERT: D  125 GLU cc_start: 0.8052 (mt-10) cc_final: 0.7683 (mp0)
  outliers start: 10
  outliers final: 7
  residues processed: 116
  average time/residue: 0.8655
  time to fit residues: 102.8479
Evaluate side-chains
  117 residues out of total 480 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 7
    poor density    : 110
  time to evaluate  : 0.175 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue    1 VAL
Chi-restraints excluded: chain A residue    2 LEU
Chi-restraints excluded: chain B residue   31 MET
Chi-restraints excluded: chain B residue   43 GLU
Chi-restraints excluded: chain C residue    2 LEU
Chi-restraints excluded: chain D residue   31 MET
Chi-restraints excluded: chain D residue   43 GLU
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 56
   random chunks:
   chunk 47 optimal weight:    0.7980
   chunk 9 optimal weight:    1.9990
   chunk 18 optimal weight:    3.9990
   chunk 50 optimal weight:    0.8980
   chunk 28 optimal weight:    2.9990
   chunk 34 optimal weight:    1.9990
   chunk 4 optimal weight:    0.3980
   chunk 20 optimal weight:    3.9990
   chunk 25 optimal weight:    6.9990
   chunk 42 optimal weight:    0.9980
   chunk 8 optimal weight:    4.9990
   overall best weight:    1.0182

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

Flipped N/Q/H residues before XYZ refinement:
** A  58 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
A 122 HIS
B  22 GLN
** B  61 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
B  80 ASN
** C  58 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
C 122 HIS
D  22 GLN
** D  61 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
D  80 ASN

Total number of N/Q/H flips: 6

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3543 r_free = 0.3543 target = 0.141260 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 34)----------------|
| r_work = 0.3356 r_free = 0.3356 target = 0.125819 restraints weight = 3624.465|
|-----------------------------------------------------------------------------|
r_work (start): 0.3358 rms_B_bonded: 0.90
r_work: 0.3221 rms_B_bonded: 1.57 restraints_weight: 0.5000
r_work: 0.3112 rms_B_bonded: 2.65 restraints_weight: 0.2500
r_work (final): 0.3112
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7989
moved from start:          0.2398

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.105   4900  Z= 0.153
  Angle     :  0.615   6.204   6670  Z= 0.297
  Chirality :  0.041   0.121    686
  Planarity :  0.005   0.040    836
  Dihedral  : 10.611  89.307    640
  Min Nonbonded Distance : 2.631

Molprobity Statistics.
  All-atom Clashscore : 3.84
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.06 %
    Favored  : 98.94 %
  Rotamer:
    Outliers :  2.71 %
    Allowed  : 16.04 %
    Favored  : 81.25 %
  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:  3.18 (0.35), residues: 566
  helix:  2.19 (0.24), residues: 422
  sheet:  None (None), residues: 0
  loop :  2.13 (0.57), residues: 144

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.001   ARG C  31 
 TYR   0.009   0.001   TYR A 140 
 PHE   0.010   0.002   PHE C  98 
 TRP   0.013   0.003   TRP D  15 
 HIS   0.005   0.001   HIS A  58 

Details of bonding type rmsd
  covalent geometry    : bond        0.00345 ( 4896)
  covalent geometry    : angle       0.61502 ( 6670)
  hydrogen bonds       : bond        0.05171 (  326)
  hydrogen bonds       : angle       3.98469 (  912)
  Misc. bond           : bond        0.07469 (    4)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 2274.25 seconds
wall clock time: 39 minutes 51.51 seconds (2391.51 seconds total)