Starting phenix.real_space_refine
on Wed Sep 17 05:12:09 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/9vid_65084/09_2025/9vid_65084.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/9vid_65084/09_2025/9vid_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 {
    real_map_files = "/net/cci-nas-00/data/ceres_data/9vid_65084/09_2025/9vid_65084.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/9vid_65084/09_2025/9vid_65084.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/9vid_65084/09_2025/9vid_65084.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/9vid_65084/09_2025/9vid_65084.cif"
  }
  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-2.0-5805/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: 1.40, per 1000 atoms: 0.29
  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: 0.39
  Conformation dependent library (CDL) restraints added in 140.1 milliseconds
  
  Enol-peptide restraints added in 476.8 nanoseconds
  

  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: 0.12
  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: 0.83

  Time building geometry restraints manager: 0.46 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=" 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
  bond pdb=" C2C HEM B 201 "
       pdb=" C3C HEM B 201 "
    ideal  model  delta    sigma   weight residual
    1.334  1.418 -0.084 2.00e-02 2.50e+03 1.78e+01
  bond pdb=" C3B HEM C 201 "
       pdb=" CAB HEM C 201 "
    ideal  model  delta    sigma   weight residual
    1.544  1.466  0.078 2.00e-02 2.50e+03 1.54e+01
  bond pdb=" C3B HEM A 201 "
       pdb=" CAB HEM A 201 "
    ideal  model  delta    sigma   weight residual
    1.544  1.466  0.078 2.00e-02 2.50e+03 1.54e+01
  bond pdb=" ND1 HIS C  58 "
       pdb=" CE1 HIS C  58 "
    ideal  model  delta    sigma   weight residual
    1.321  1.360 -0.039 1.00e-02 1.00e+04 1.50e+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 -     3.08: 2912
        3.08 -     3.78: 9018
        3.78 -     4.47: 14798
        4.47 -     5.17: 22560
        5.17 -     5.86: 27407
  Nonbonded interactions: 76695
  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 4.030
  ... (remaining 76690 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: 0.01
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:             1.560
  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:             0.000
  Extract box with map and model:          0.080
  Check model and map are aligned:         0.010
  Set scattering table:                    0.020
  Process input model:                     6.580
  Find NCS groups from input model:        0.040
  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:9.510
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   17.810
-------------------------------------------------------------------------------
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= 0.726
  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 aren 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        0.01225 ( 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  : 0.207 
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: 0.7773 (tp30)
REVERT: A  120 GLU cc_start: 0.8272 (mt-10) cc_final: 0.7173 (mp0)
REVERT: B    7 GLU cc_start: 0.8449 (mt-10) cc_final: 0.8136 (mt-10)
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: 0.6546 (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: 0.6964 (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: 0.7772 (tp30)
REVERT: C  120 GLU cc_start: 0.8270 (mt-10) cc_final: 0.7171 (mp0)
REVERT: D    7 GLU cc_start: 0.8450 (mt-10) cc_final: 0.8137 (mt-10)
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: 0.6548 (mt-10)
REVERT: D   61 GLN cc_start: 0.7932 (mm-40) cc_final: 0.7615 (mm110)
REVERT: D   65 LYS cc_start: 0.8405 (mttp) cc_final: 0.8188 (mttp)
REVERT: D   66 LYS cc_start: 0.7674 (mttt) cc_final: 0.6966 (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: 0.8639
  time to fit residues: 123.7273
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  : 0.177 
-------------------------------------------------------------------------------
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:    0.9980
   chunk 32 optimal weight:    1.9990
   chunk 31 optimal weight:    0.5980
   chunk 25 optimal weight:    0.6980
   chunk 50 optimal weight:    2.9990
   chunk 53 optimal weight:    0.8980
   overall best weight:    0.4496

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

Flipped N/Q/H residues before XYZ refinement:
A  58 HIS
A  67 HIS
A 122 HIS
B  63 HIS
C  58 HIS
C  67 HIS
C 122 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 = 0.3594 r_free = 0.3594 target = 0.146397 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 42)----------------|
| r_work = 0.3419 r_free = 0.3419 target = 0.130966 restraints weight = 3625.036|
|-----------------------------------------------------------------------------|
r_work (start): 0.3419 rms_B_bonded: 0.94
r_work: 0.3279 rms_B_bonded: 1.65 restraints_weight: 0.5000
r_work: 0.3169 rms_B_bonded: 2.81 restraints_weight: 0.2500
r_work (final): 0.3169
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7959
moved from start:          0.2021

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.090   4900  Z= 0.123
  Angle     :  0.579   6.054   6670  Z= 0.279
  Chirality :  0.038   0.117    686
  Planarity :  0.004   0.031    836
  Dihedral  : 11.647  88.694    640
  Min Nonbonded Distance : 2.636

Molprobity Statistics.
  All-atom Clashscore : 3.41
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  0.71 %
    Favored  : 99.29 %
  Rotamer:
    Outliers :  1.46 %
    Allowed  :  9.38 %
    Favored  : 89.17 %
  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 aren not related in a simple way.
  whole:  3.29 (0.35), residues: 566
  helix:  2.14 (0.24), residues: 412
  sheet:  None (None), residues: 0
  loop :  2.67 (0.57), residues: 154

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.007   0.001   ARG A  56 
 TYR   0.011   0.001   TYR A 140 
 PHE   0.012   0.001   PHE D 130 
 TRP   0.014   0.002   TRP A  14 
 HIS   0.005   0.001   HIS A 113 

Details of bonding type rmsd
  covalent geometry    : bond        0.00272 ( 4896)
  covalent geometry    : angle       0.57933 ( 6670)
  hydrogen bonds       : bond        0.04308 (  326)
  hydrogen bonds       : angle       4.00063 (  912)
  Misc. bond           : bond        0.06525 (    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
  135 residues out of total 480 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 7
    poor density    : 128
  time to evaluate  : 0.191 
Fit side-chains
REVERT: A   27 GLU cc_start: 0.8756 (tt0) cc_final: 0.8344 (tt0)
REVERT: A   30 GLU cc_start: 0.8500 (mt-10) cc_final: 0.8275 (mm-30)
REVERT: B   40 ARG cc_start: 0.7554 (ttp80) cc_final: 0.6936 (ttp-110)
REVERT: B  125 GLU cc_start: 0.8152 (mt-10) cc_final: 0.7812 (mp0)
REVERT: C   27 GLU cc_start: 0.8747 (tt0) cc_final: 0.8336 (tt0)
REVERT: C   30 GLU cc_start: 0.8505 (mt-10) cc_final: 0.8277 (mm-30)
REVERT: D   40 ARG cc_start: 0.7546 (ttp80) cc_final: 0.6925 (ttp-110)
REVERT: D  125 GLU cc_start: 0.8148 (mt-10) cc_final: 0.7813 (mp0)
  outliers start: 7
  outliers final: 0
  residues processed: 130
  average time/residue: 0.8389
  time to fit residues: 111.6884
Evaluate side-chains
  108 residues out of total 480 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 108
  time to evaluate  : 0.106 
-------------------------------------------------------------------------------
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:    0.5980
   chunk 3 optimal weight:    0.7980
   chunk 29 optimal weight:    0.0770
   chunk 33 optimal weight:    4.9990
   chunk 35 optimal weight:    1.9990
   chunk 39 optimal weight:    0.8980
   chunk 36 optimal weight:    0.7980
   chunk 34 optimal weight:    0.5980
   chunk 47 optimal weight:    1.9990
   chunk 42 optimal weight:    0.5980
   overall best weight:    0.5338

-------------------------------------------------------------------------------
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
D  22 GLN
D  61 GLN
D  80 ASN

Total number of N/Q/H flips: 9

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3572 r_free = 0.3572 target = 0.144930 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 41)----------------|
| r_work = 0.3406 r_free = 0.3406 target = 0.130193 restraints weight = 3671.776|
|-----------------------------------------------------------------------------|
r_work (start): 0.3406 rms_B_bonded: 0.89
r_work: 0.3273 rms_B_bonded: 1.56 restraints_weight: 0.5000
r_work: 0.3167 rms_B_bonded: 2.66 restraints_weight: 0.2500
r_work (final): 0.3167
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7951
moved from start:          0.2315

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.114   4900  Z= 0.125
  Angle     :  0.601   9.170   6670  Z= 0.276
  Chirality :  0.038   0.116    686
  Planarity :  0.004   0.035    836
  Dihedral  : 10.834  89.423    640
  Min Nonbonded Distance : 2.637

Molprobity Statistics.
  All-atom Clashscore : 3.09
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  0.35 %
    Favored  : 99.65 %
  Rotamer:
    Outliers :  0.62 %
    Allowed  : 12.92 %
    Favored  : 86.46 %
  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 aren not related in a simple way.
  whole:  3.70 (0.35), residues: 566
  helix:  2.51 (0.25), residues: 412
  sheet:  None (None), residues: 0
  loop :  2.57 (0.56), residues: 154

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.001   ARG C  56 
 TYR   0.013   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        0.00281 ( 4896)
  covalent geometry    : angle       0.60072 ( 6670)
  hydrogen bonds       : bond        0.04348 (  326)
  hydrogen bonds       : angle       3.87335 (  912)
  Misc. bond           : bond        0.11187 (    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: 3
    poor density    : 109
  time to evaluate  : 0.175 
Fit side-chains
REVERT: A   27 GLU cc_start: 0.8707 (tt0) cc_final: 0.8311 (tt0)
REVERT: B  125 GLU cc_start: 0.8113 (mt-10) cc_final: 0.7810 (mp0)
REVERT: C   27 GLU cc_start: 0.8702 (tt0) cc_final: 0.8313 (tt0)
REVERT: D  125 GLU cc_start: 0.8104 (mt-10) cc_final: 0.7814 (mp0)
  outliers start: 3
  outliers final: 0
  residues processed: 110
  average time/residue: 0.8273
  time to fit residues: 93.3104
Evaluate side-chains
  106 residues out of total 480 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 106
  time to evaluate  : 0.182 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 56
   random chunks:
   chunk 1 optimal weight:    0.0980
   chunk 17 optimal weight:    0.6980
   chunk 3 optimal weight:    0.6980
   chunk 42 optimal weight:    0.7980
   chunk 55 optimal weight:    4.9990
   chunk 2 optimal weight:    1.9990
   chunk 25 optimal weight:    2.9990
   chunk 22 optimal weight:    0.8980
   chunk 0 optimal weight:    0.5980
   chunk 30 optimal weight:    4.9990
   chunk 36 optimal weight:    0.7980
   overall best weight:    0.5780

-------------------------------------------------------------------------------
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 = 0.3563 r_free = 0.3563 target = 0.143866 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 42)----------------|
| r_work = 0.3401 r_free = 0.3401 target = 0.129410 restraints weight = 3682.921|
|-----------------------------------------------------------------------------|
r_work (start): 0.3403 rms_B_bonded: 0.88
r_work: 0.3271 rms_B_bonded: 1.56 restraints_weight: 0.5000
r_work: 0.3167 rms_B_bonded: 2.64 restraints_weight: 0.2500
r_work (final): 0.3167
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7964
moved from start:          0.2479

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= 0.121
  Angle     :  0.575   6.575   6670  Z= 0.269
  Chirality :  0.038   0.116    686
  Planarity :  0.004   0.038    836
  Dihedral  : 10.071  89.322    640
  Min Nonbonded Distance : 2.625

Molprobity Statistics.
  All-atom Clashscore : 3.41
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  0.35 %
    Favored  : 99.65 %
  Rotamer:
    Outliers :  1.67 %
    Allowed  : 12.50 %
    Favored  : 85.83 %
  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 aren not related in a simple way.
  whole:  3.72 (0.35), residues: 566
  helix:  2.54 (0.25), residues: 412
  sheet:  None (None), residues: 0
  loop :  2.51 (0.56), residues: 154

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG A  56 
 TYR   0.010   0.001   TYR C 140 
 PHE   0.010   0.001   PHE D 130 
 TRP   0.010   0.002   TRP D  15 
 HIS   0.005   0.001   HIS C 112 

Details of bonding type rmsd
  covalent geometry    : bond        0.00270 ( 4896)
  covalent geometry    : angle       0.57533 ( 6670)
  hydrogen bonds       : bond        0.04277 (  326)
  hydrogen bonds       : angle       3.87378 (  912)
  Misc. bond           : bond        0.08329 (    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  : 0.237 
Fit side-chains
REVERT: A    4 MET cc_start: 0.7553 (mmp) cc_final: 0.7351 (mmm)
REVERT: B   76 LYS cc_start: 0.8425 (mttt) cc_final: 0.7960 (mtmt)
REVERT: B  125 GLU cc_start: 0.8091 (mt-10) cc_final: 0.7741 (mp0)
REVERT: C    4 MET cc_start: 0.7546 (mmp) cc_final: 0.7345 (mmm)
REVERT: D   76 LYS cc_start: 0.8427 (mttt) cc_final: 0.7965 (mtmt)
REVERT: D  125 GLU cc_start: 0.8090 (mt-10) cc_final: 0.7741 (mp0)
  outliers start: 8
  outliers final: 0
  residues processed: 110
  average time/residue: 0.8402
  time to fit residues: 94.8744
Evaluate side-chains
  104 residues out of total 480 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 104
  time to evaluate  : 0.178 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
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:    2.9990
   chunk 52 optimal weight:    0.9990
   chunk 54 optimal weight:    1.9990
   chunk 55 optimal weight:    1.9990
   chunk 9 optimal weight:    2.9990
   chunk 10 optimal weight:    0.9980
   chunk 40 optimal weight:    0.5980
   chunk 50 optimal weight:    0.5980
   chunk 3 optimal weight:    0.6980
   chunk 12 optimal weight:    0.5980
   overall best weight:    0.6980

-------------------------------------------------------------------------------
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 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 = 0.3568 r_free = 0.3568 target = 0.143539 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 45)----------------|
| r_work = 0.3390 r_free = 0.3390 target = 0.128367 restraints weight = 3658.239|
|-----------------------------------------------------------------------------|
r_work (start): 0.3392 rms_B_bonded: 0.90
r_work: 0.3256 rms_B_bonded: 1.58 restraints_weight: 0.5000
r_work: 0.3147 rms_B_bonded: 2.68 restraints_weight: 0.2500
r_work (final): 0.3147
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7963
moved from start:          0.2525

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.111   4900  Z= 0.128
  Angle     :  0.582   6.366   6670  Z= 0.276
  Chirality :  0.039   0.118    686
  Planarity :  0.004   0.038    836
  Dihedral  : 10.246  89.799    640
  Min Nonbonded Distance : 2.633

Molprobity Statistics.
  All-atom Clashscore : 3.84
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  0.35 %
    Favored  : 99.65 %
  Rotamer:
    Outliers :  2.08 %
    Allowed  : 13.96 %
    Favored  : 83.96 %
  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 aren not related in a simple way.
  whole:  3.59 (0.35), residues: 566
  helix:  2.49 (0.25), residues: 410
  sheet:  None (None), residues: 0
  loop :  2.36 (0.56), residues: 156

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG A  31 
 TYR   0.009   0.001   TYR A 140 
 PHE   0.010   0.001   PHE B 130 
 TRP   0.011   0.002   TRP D  15 
 HIS   0.005   0.001   HIS C 112 

Details of bonding type rmsd
  covalent geometry    : bond        0.00285 ( 4896)
  covalent geometry    : angle       0.58174 ( 6670)
  hydrogen bonds       : bond        0.04565 (  326)
  hydrogen bonds       : angle       3.91344 (  912)
  Misc. bond           : bond        0.08201 (    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
  118 residues out of total 480 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 108
  time to evaluate  : 0.190 
Fit side-chains
REVERT: A   27 GLU cc_start: 0.8410 (tt0) cc_final: 0.8200 (tt0)
REVERT: B   76 LYS cc_start: 0.8413 (mttt) cc_final: 0.7906 (mtmt)
REVERT: B  125 GLU cc_start: 0.8089 (mt-10) cc_final: 0.7709 (mp0)
REVERT: C   27 GLU cc_start: 0.8406 (tt0) cc_final: 0.8196 (tt0)
REVERT: D   76 LYS cc_start: 0.8413 (mttt) cc_final: 0.7912 (mtmt)
REVERT: D  125 GLU cc_start: 0.8080 (mt-10) cc_final: 0.7707 (mp0)
  outliers start: 10
  outliers final: 4
  residues processed: 114
  average time/residue: 0.8110
  time to fit residues: 94.7981
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  : 0.112 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   18 SER
Chi-restraints excluded: chain B residue   28 LEU
Chi-restraints excluded: chain C residue   18 SER
Chi-restraints excluded: chain D residue   28 LEU
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 56
   random chunks:
   chunk 53 optimal weight:    3.9990
   chunk 3 optimal weight:    0.5980
   chunk 16 optimal weight:    3.9990
   chunk 22 optimal weight:    0.5980
   chunk 33 optimal weight:    3.9990
   chunk 38 optimal weight:    3.9990
   chunk 42 optimal weight:    0.9980
   chunk 23 optimal weight:    0.0000
   chunk 6 optimal weight:    1.9990
   chunk 4 optimal weight:    2.9990
   chunk 51 optimal weight:    9.9990
   overall best weight:    0.8386

-------------------------------------------------------------------------------
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 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 = 0.3558 r_free = 0.3558 target = 0.142650 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 50)----------------|
| r_work = 0.3377 r_free = 0.3377 target = 0.127422 restraints weight = 3679.700|
|-----------------------------------------------------------------------------|
r_work (start): 0.3379 rms_B_bonded: 0.90
r_work: 0.3245 rms_B_bonded: 1.57 restraints_weight: 0.5000
r_work: 0.3135 rms_B_bonded: 2.67 restraints_weight: 0.2500
r_work (final): 0.3135
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7974
moved from start:          0.2475

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.114   4900  Z= 0.137
  Angle     :  0.602   6.303   6670  Z= 0.287
  Chirality :  0.040   0.120    686
  Planarity :  0.004   0.038    836
  Dihedral  : 10.357  89.523    640
  Min Nonbonded Distance : 2.632

Molprobity Statistics.
  All-atom Clashscore : 4.27
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  0.35 %
    Favored  : 99.65 %
  Rotamer:
    Outliers :  2.50 %
    Allowed  : 14.17 %
    Favored  : 83.33 %
  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 aren not related in a simple way.
  whole:  3.56 (0.35), residues: 566
  helix:  2.42 (0.24), residues: 410
  sheet:  None (None), residues: 0
  loop :  2.46 (0.57), residues: 156

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.001   ARG A  31 
 TYR   0.009   0.001   TYR C 140 
 PHE   0.010   0.001   PHE D 130 
 TRP   0.012   0.002   TRP D  15 
 HIS   0.005   0.001   HIS C  58 

Details of bonding type rmsd
  covalent geometry    : bond        0.00301 ( 4896)
  covalent geometry    : angle       0.60239 ( 6670)
  hydrogen bonds       : bond        0.04846 (  326)
  hydrogen bonds       : angle       3.96904 (  912)
  Misc. bond           : bond        0.08398 (    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
  118 residues out of total 480 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 106
  time to evaluate  : 0.180 
Fit side-chains
REVERT: B   13 ASP cc_start: 0.8463 (OUTLIER) cc_final: 0.7937 (m-30)
REVERT: B   76 LYS cc_start: 0.8420 (mttt) cc_final: 0.7899 (mtmt)
REVERT: B  125 GLU cc_start: 0.8086 (mt-10) cc_final: 0.7711 (mp0)
REVERT: D   13 ASP cc_start: 0.8459 (OUTLIER) cc_final: 0.7933 (m-30)
REVERT: D   76 LYS cc_start: 0.8427 (mttt) cc_final: 0.7911 (mtmt)
REVERT: D  125 GLU cc_start: 0.8080 (mt-10) cc_final: 0.7710 (mp0)
  outliers start: 12
  outliers final: 2
  residues processed: 110
  average time/residue: 0.7952
  time to fit residues: 89.6779
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  : 0.187 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue   13 ASP
Chi-restraints excluded: chain B residue   28 LEU
Chi-restraints excluded: chain D residue   13 ASP
Chi-restraints excluded: chain D residue   28 LEU
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 56
   random chunks:
   chunk 49 optimal weight:    0.6980
   chunk 21 optimal weight:    0.7980
   chunk 46 optimal weight:    0.5980
   chunk 16 optimal weight:    3.9990
   chunk 26 optimal weight:    0.9990
   chunk 39 optimal weight:    3.9990
   chunk 9 optimal weight:    1.9990
   chunk 48 optimal weight:    0.7980
   chunk 23 optimal weight:    1.9990
   chunk 42 optimal weight:    1.9990
   chunk 5 optimal weight:    1.9990
   overall best weight:    0.7782

-------------------------------------------------------------------------------
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 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 = 0.3565 r_free = 0.3565 target = 0.143361 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 50)----------------|
| r_work = 0.3386 r_free = 0.3386 target = 0.128249 restraints weight = 3611.224|
|-----------------------------------------------------------------------------|
r_work (start): 0.3388 rms_B_bonded: 0.89
r_work: 0.3254 rms_B_bonded: 1.57 restraints_weight: 0.5000
r_work: 0.3146 rms_B_bonded: 2.66 restraints_weight: 0.2500
r_work (final): 0.3146
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7968
moved from start:          0.2513

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.116   4900  Z= 0.132
  Angle     :  0.592   6.200   6670  Z= 0.282
  Chirality :  0.040   0.119    686
  Planarity :  0.004   0.038    836
  Dihedral  : 10.306  89.831    640
  Min Nonbonded Distance : 2.633

Molprobity Statistics.
  All-atom Clashscore : 4.16
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  0.71 %
    Favored  : 99.29 %
  Rotamer:
    Outliers :  2.92 %
    Allowed  : 15.00 %
    Favored  : 82.08 %
  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 aren not related in a simple way.
  whole:  3.53 (0.35), residues: 566
  helix:  2.43 (0.24), residues: 410
  sheet:  None (None), residues: 0
  loop :  2.37 (0.57), residues: 156

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

Details of bonding type rmsd
  covalent geometry    : bond        0.00292 ( 4896)
  covalent geometry    : angle       0.59161 ( 6670)
  hydrogen bonds       : bond        0.04685 (  326)
  hydrogen bonds       : angle       3.94164 (  912)
  Misc. bond           : bond        0.08536 (    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
  120 residues out of total 480 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 106
  time to evaluate  : 0.181 
Fit side-chains
REVERT: B   13 ASP cc_start: 0.8450 (OUTLIER) cc_final: 0.7916 (m-30)
REVERT: B   76 LYS cc_start: 0.8429 (mttt) cc_final: 0.7908 (mtmt)
REVERT: B  125 GLU cc_start: 0.8078 (mt-10) cc_final: 0.7709 (mp0)
REVERT: D   13 ASP cc_start: 0.8450 (OUTLIER) cc_final: 0.7920 (m-30)
REVERT: D   76 LYS cc_start: 0.8434 (mttt) cc_final: 0.7921 (mtmt)
REVERT: D  125 GLU cc_start: 0.8074 (mt-10) cc_final: 0.7712 (mp0)
  outliers start: 14
  outliers final: 6
  residues processed: 114
  average time/residue: 0.7724
  time to fit residues: 90.3846
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  : 0.192 
-------------------------------------------------------------------------------
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   13 ASP
Chi-restraints excluded: chain B residue   28 LEU
Chi-restraints excluded: chain C residue    2 LEU
Chi-restraints excluded: chain C residue   18 SER
Chi-restraints excluded: chain D residue   13 ASP
Chi-restraints excluded: chain D residue   28 LEU
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 56
   random chunks:
   chunk 32 optimal weight:    0.4980
   chunk 5 optimal weight:    3.9990
   chunk 34 optimal weight:    1.9990
   chunk 49 optimal weight:    0.8980
   chunk 26 optimal weight:    0.7980
   chunk 17 optimal weight:    0.8980
   chunk 24 optimal weight:    0.0670
   chunk 42 optimal weight:    1.9990
   chunk 3 optimal weight:    0.6980
   chunk 6 optimal weight:    0.8980
   chunk 9 optimal weight:    0.9990
   overall best weight:    0.5918

-------------------------------------------------------------------------------
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 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 = 0.3577 r_free = 0.3577 target = 0.144443 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 43)----------------|
| r_work = 0.3399 r_free = 0.3399 target = 0.129379 restraints weight = 3673.828|
|-----------------------------------------------------------------------------|
r_work (start): 0.3402 rms_B_bonded: 0.90
r_work: 0.3269 rms_B_bonded: 1.58 restraints_weight: 0.5000
r_work: 0.3161 rms_B_bonded: 2.68 restraints_weight: 0.2500
r_work (final): 0.3161
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7954
moved from start:          0.2577

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.110   4900  Z= 0.121
  Angle     :  0.572   6.269   6670  Z= 0.270
  Chirality :  0.038   0.116    686
  Planarity :  0.004   0.038    836
  Dihedral  : 10.129  89.541    640
  Min Nonbonded Distance : 2.633

Molprobity Statistics.
  All-atom Clashscore : 4.05
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  0.35 %
    Favored  : 99.65 %
  Rotamer:
    Outliers :  2.92 %
    Allowed  : 14.17 %
    Favored  : 82.92 %
  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 aren not related in a simple way.
  whole:  3.63 (0.35), residues: 566
  helix:  2.52 (0.25), residues: 410
  sheet:  None (None), residues: 0
  loop :  2.34 (0.56), residues: 156

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   0.011   0.002   TRP D  15 
 HIS   0.004   0.001   HIS D  63 

Details of bonding type rmsd
  covalent geometry    : bond        0.00270 ( 4896)
  covalent geometry    : angle       0.57166 ( 6670)
  hydrogen bonds       : bond        0.04272 (  326)
  hydrogen bonds       : angle       3.86451 (  912)
  Misc. bond           : bond        0.08276 (    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
  122 residues out of total 480 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 108
  time to evaluate  : 0.190 
Fit side-chains
REVERT: B   43 GLU cc_start: 0.6763 (OUTLIER) cc_final: 0.6041 (mt-10)
REVERT: B   76 LYS cc_start: 0.8419 (mmtt) cc_final: 0.7910 (mtmt)
REVERT: B  125 GLU cc_start: 0.8079 (mt-10) cc_final: 0.7706 (mp0)
REVERT: D   43 GLU cc_start: 0.6762 (OUTLIER) cc_final: 0.6032 (mt-10)
REVERT: D   76 LYS cc_start: 0.8427 (mmtt) cc_final: 0.7921 (mtmt)
REVERT: D  125 GLU cc_start: 0.8075 (mt-10) cc_final: 0.7705 (mp0)
  outliers start: 14
  outliers final: 6
  residues processed: 116
  average time/residue: 0.7931
  time to fit residues: 94.4702
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  : 0.270 
-------------------------------------------------------------------------------
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   28 LEU
Chi-restraints excluded: chain B residue   43 GLU
Chi-restraints excluded: chain C residue    2 LEU
Chi-restraints excluded: chain C residue   18 SER
Chi-restraints excluded: chain D residue   28 LEU
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:    0.6980
   chunk 45 optimal weight:    0.8980
   chunk 26 optimal weight:    0.7980
   chunk 39 optimal weight:    1.9990
   chunk 34 optimal weight:    1.9990
   chunk 20 optimal weight:    4.9990
   chunk 40 optimal weight:    0.6980
   chunk 19 optimal weight:    0.5980
   chunk 28 optimal weight:    0.8980
   chunk 46 optimal weight:    0.7980
   chunk 36 optimal weight:    0.6980
   overall best weight:    0.6980

-------------------------------------------------------------------------------
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 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 = 0.3569 r_free = 0.3569 target = 0.143719 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 45)----------------|
| r_work = 0.3391 r_free = 0.3391 target = 0.128660 restraints weight = 3632.421|
|-----------------------------------------------------------------------------|
r_work (start): 0.3394 rms_B_bonded: 0.90
r_work: 0.3260 rms_B_bonded: 1.57 restraints_weight: 0.5000
r_work: 0.3152 rms_B_bonded: 2.66 restraints_weight: 0.2500
r_work (final): 0.3152
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7962
moved from start:          0.2552

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.109   4900  Z= 0.128
  Angle     :  0.588   6.180   6670  Z= 0.279
  Chirality :  0.039   0.118    686
  Planarity :  0.004   0.038    836
  Dihedral  : 10.266  89.942    640
  Min Nonbonded Distance : 2.632

Molprobity Statistics.
  All-atom Clashscore : 4.16
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  0.71 %
    Favored  : 99.29 %
  Rotamer:
    Outliers :  2.50 %
    Allowed  : 15.00 %
    Favored  : 82.50 %
  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 aren not related in a simple way.
  whole:  3.53 (0.35), residues: 566
  helix:  2.44 (0.24), residues: 410
  sheet:  None (None), residues: 0
  loop :  2.33 (0.56), residues: 156

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG C  31 
 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   0.005   0.001   HIS A  58 

Details of bonding type rmsd
  covalent geometry    : bond        0.00284 ( 4896)
  covalent geometry    : angle       0.58827 ( 6670)
  hydrogen bonds       : bond        0.04538 (  326)
  hydrogen bonds       : angle       3.90658 (  912)
  Misc. bond           : bond        0.08049 (    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
  122 residues out of total 480 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 110
  time to evaluate  : 0.206 
Fit side-chains
REVERT: B   43 GLU cc_start: 0.6784 (OUTLIER) cc_final: 0.6099 (mt-10)
REVERT: B   76 LYS cc_start: 0.8419 (mmtt) cc_final: 0.7907 (mtmt)
REVERT: B  125 GLU cc_start: 0.8084 (mt-10) cc_final: 0.7714 (mp0)
REVERT: D   43 GLU cc_start: 0.6778 (OUTLIER) cc_final: 0.6085 (mt-10)
REVERT: D   76 LYS cc_start: 0.8426 (mmtt) cc_final: 0.7917 (mtmt)
REVERT: D  125 GLU cc_start: 0.8079 (mt-10) cc_final: 0.7714 (mp0)
  outliers start: 12
  outliers final: 6
  residues processed: 116
  average time/residue: 0.7872
  time to fit residues: 93.7187
Evaluate side-chains
  118 residues out of total 480 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 8
    poor density    : 110
  time to evaluate  : 0.181 
-------------------------------------------------------------------------------
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   28 LEU
Chi-restraints excluded: chain B residue   43 GLU
Chi-restraints excluded: chain C residue    2 LEU
Chi-restraints excluded: chain C residue   18 SER
Chi-restraints excluded: chain D residue   28 LEU
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:    0.6980
   chunk 14 optimal weight:    2.9990
   chunk 39 optimal weight:    1.9990
   chunk 32 optimal weight:    0.3980
   chunk 21 optimal weight:    1.9990
   chunk 45 optimal weight:    0.5980
   chunk 29 optimal weight:    0.0270
   chunk 36 optimal weight:    2.9990
   chunk 28 optimal weight:    0.6980
   chunk 46 optimal weight:    2.9990
   chunk 12 optimal weight:    0.8980
   overall best weight:    0.4838

-------------------------------------------------------------------------------
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  61 GLN
B  80 ASN
C 122 HIS
D  22 GLN
D  61 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 = 0.3588 r_free = 0.3588 target = 0.145413 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 46)----------------|
| r_work = 0.3415 r_free = 0.3415 target = 0.130562 restraints weight = 3628.769|
|-----------------------------------------------------------------------------|
r_work (start): 0.3417 rms_B_bonded: 0.89
r_work: 0.3287 rms_B_bonded: 1.56 restraints_weight: 0.5000
r_work: 0.3179 rms_B_bonded: 2.66 restraints_weight: 0.2500
r_work (final): 0.3179
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7940
moved from start:          0.2662

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.103   4900  Z= 0.114
  Angle     :  0.565   6.057   6670  Z= 0.266
  Chirality :  0.038   0.115    686
  Planarity :  0.004   0.038    836
  Dihedral  : 10.061  89.131    640
  Min Nonbonded Distance : 2.634

Molprobity Statistics.
  All-atom Clashscore : 4.16
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  0.71 %
    Favored  : 99.29 %
  Rotamer:
    Outliers :  2.50 %
    Allowed  : 15.00 %
    Favored  : 82.50 %
  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 aren not related in a simple way.
  whole:  3.65 (0.35), residues: 566
  helix:  2.53 (0.25), residues: 412
  sheet:  None (None), residues: 0
  loop :  2.37 (0.56), residues: 154

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG A  31 
 TYR   0.007   0.001   TYR C 140 
 PHE   0.010   0.001   PHE B 130 
 TRP   0.010   0.002   TRP B  15 
 HIS   0.004   0.001   HIS D  63 

Details of bonding type rmsd
  covalent geometry    : bond        0.00261 ( 4896)
  covalent geometry    : angle       0.56465 ( 6670)
  hydrogen bonds       : bond        0.04013 (  326)
  hydrogen bonds       : angle       3.79103 (  912)
  Misc. bond           : bond        0.07873 (    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: 12
    poor density    : 108
  time to evaluate  : 0.184 
Fit side-chains
REVERT: B   43 GLU cc_start: 0.6715 (OUTLIER) cc_final: 0.6004 (mt-10)
REVERT: B   76 LYS cc_start: 0.8409 (mmtt) cc_final: 0.7904 (mtmt)
REVERT: B  125 GLU cc_start: 0.8060 (mt-10) cc_final: 0.7713 (mp0)
REVERT: D   43 GLU cc_start: 0.6712 (OUTLIER) cc_final: 0.5992 (mt-10)
REVERT: D   76 LYS cc_start: 0.8417 (mmtt) cc_final: 0.7915 (mtmt)
REVERT: D  125 GLU cc_start: 0.8062 (mt-10) cc_final: 0.7715 (mp0)
  outliers start: 12
  outliers final: 6
  residues processed: 114
  average time/residue: 0.7861
  time to fit residues: 92.0143
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  : 0.173 
-------------------------------------------------------------------------------
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   28 LEU
Chi-restraints excluded: chain B residue   43 GLU
Chi-restraints excluded: chain C residue    2 LEU
Chi-restraints excluded: chain C residue   18 SER
Chi-restraints excluded: chain D residue   28 LEU
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:    0.5980
   chunk 9 optimal weight:    1.9990
   chunk 18 optimal weight:    0.0970
   chunk 50 optimal weight:    0.9980
   chunk 28 optimal weight:    2.9990
   chunk 34 optimal weight:    0.3980
   chunk 4 optimal weight:    2.9990
   chunk 20 optimal weight:    0.6980
   chunk 25 optimal weight:    2.9990
   chunk 42 optimal weight:    1.9990
   chunk 8 optimal weight:    4.9990
   overall best weight:    0.5578

-------------------------------------------------------------------------------
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 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 = 0.3892 r_free = 0.3892 target = 0.176114 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 32)----------------|
| r_work = 0.3766 r_free = 0.3766 target = 0.161981 restraints weight = 3990.549|
|-----------------------------------------------------------------------------|
r_work (start): 0.3749 rms_B_bonded: 0.79
r_work: 0.3652 rms_B_bonded: 1.39 restraints_weight: 0.5000
r_work: 0.3554 rms_B_bonded: 2.51 restraints_weight: 0.2500
r_work (final): 0.3554
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8128
moved from start:          0.2636

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.101   4900  Z= 0.119
  Angle     :  0.576   6.142   6670  Z= 0.273
  Chirality :  0.038   0.116    686
  Planarity :  0.004   0.038    836
  Dihedral  : 10.181  89.747    640
  Min Nonbonded Distance : 2.634

Molprobity Statistics.
  All-atom Clashscore : 4.05
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  0.35 %
    Favored  : 99.65 %
  Rotamer:
    Outliers :  2.50 %
    Allowed  : 14.58 %
    Favored  : 82.92 %
  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 aren not related in a simple way.
  whole:  3.58 (0.35), residues: 566
  helix:  2.51 (0.25), residues: 410
  sheet:  None (None), residues: 0
  loop :  2.23 (0.55), residues: 156

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 B  15 
 HIS   0.004   0.001   HIS D  63 

Details of bonding type rmsd
  covalent geometry    : bond        0.00269 ( 4896)
  covalent geometry    : angle       0.57640 ( 6670)
  hydrogen bonds       : bond        0.04224 (  326)
  hydrogen bonds       : angle       3.83618 (  912)
  Misc. bond           : bond        0.07601 (    4)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 2520.01 seconds
wall clock time: 43 minutes 45.37 seconds (2625.37 seconds total)