Starting phenix.real_space_refine
on Wed Jul  1 23:35:17 2026 by dcliebschner
===============================================================================

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

  Found model, restraint, /net/cci-nas-00/data/ceres_data/8j7r_36046/07_2026/8j7r_36046.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/8j7r_36046/07_2026/8j7r_36046.map

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

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

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    restraint_files = "/net/cci-nas-00/data/ceres_data/8j7r_36046/07_2026/8j7r_36046.cif"
    default_restraint = "/net/cci-nas-00/data/ceres_data/8j7r_36046/07_2026/8j7r_36046.cif"
    real_map_files = "/net/cci-nas-00/data/ceres_data/8j7r_36046/07_2026/8j7r_36046.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/8j7r_36046/07_2026/8j7r_36046.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/8j7r_36046/07_2026/8j7r_36046.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/8j7r_36046/07_2026/8j7r_36046.cif"
  }
  resolution = 3.7
  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=   0.007
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: 6
    Type Number    sf(0)   Gaussians
     P      97      5.49       5
     Mg      3      5.21       5
     S      16      5.16       5
     C    2154      2.51       5
     N     721      2.21       5
     O    1043      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 11 residue(s): 0.00s

  Monomer Library directory:
    "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/chem_data/mon_lib"
  Total number of atoms: 4034
  Number of models: 1
  Model: ""
    Number of chains: 3
    Chain: "B"
      Number of atoms: 1951
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 238, 1951
          Classifications: {'peptide': 238}
          Link IDs: {'PTRANS': 5, 'TRANS': 232}
    Chain: "C"
      Number of atoms: 2079
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 97, 2079
          Classifications: {'RNA': 97}
          Modifications used: {'rna2p_pur': 11, 'rna2p_pyr': 2, 'rna3p_pur': 43, 'rna3p_pyr': 41}
          Link IDs: {'rna2p': 13, 'rna3p': 83}
          Chain breaks: 2
    Chain: "C"
      Number of atoms: 4
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 4, 4
          Unusual residues: {' MG': 3}
          Classifications: {'undetermined': 3, 'water': 1}
          Link IDs: {None: 3}
  Time building chain proxies: 1.16, per 1000 atoms: 0.29
  Number of scatterers: 4034
  At special positions: 0
  Unit cell: (100.98, 91.8, 84.915, 90, 90, 90)
  Space group: P 1 (No. 1)
  Number of sites at special positions: 0
  Number of scattering types: 6
    Type Number    sf(0)
     S      16     16.00
     P      97     15.00
     Mg      3     11.99
     O    1043      8.00
     N     721      7.00
     C    2154      6.00
    sf(0) = scattering factor at diffraction angle 0.

  Number of disulfides: simple=0, symmetry=0

  Automatic linking
    Parameters for automatic linking
      Linking & cutoffs
        Metal                : Auto  - 3.00
        Amino acid           : True  - 1.90
        Carbohydrate         : True  - 1.99
        Ligands              : True  - 1.99
        Small molecules      : False - 1.98
        Amino acid - RNA/DNA : False
      
  Number of custom bonds: simple=0, symmetry=0
  Time building additional restraints: 0.37
  Conformation dependent library (CDL) restraints added in 82.5 milliseconds
  

  472 Ramachandran restraints generated.
    236 Oldfield, 0 Emsley, 236 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  462

  Finding SS restraints...
    Secondary structure from input PDB file:
      12 helices and 1 sheets defined
      85.7% alpha, 0.8% beta
      37 base pairs and 53 stacking pairs defined.
    Time for finding SS restraints: 0.61
  Creating SS restraints...
    Processing helix  chain 'B' and resid 754 through 771
      removed outlier: 3.874A  pdb=" N   GLN B 758 " --> pdb=" O   GLY B 754 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 775 through 785
      removed outlier: 3.724A  pdb=" N   LEU B 779 " --> pdb=" O   MET B 775 " (cutoff:3.500A)
      removed outlier: 3.945A  pdb=" N   LYS B 781 " --> pdb=" O   GLN B 777 " (cutoff:3.500A)
      removed outlier: 4.742A  pdb=" N   GLN B 782 " --> pdb=" O   GLN B 778 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 790 through 808
    Processing helix  chain 'B' and resid 811 through 822
      removed outlier: 3.560A  pdb=" N   LEU B 822 " --> pdb=" O   MET B 818 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 838 through 852
    Processing helix  chain 'B' and resid 853 through 871
      removed outlier: 3.764A  pdb=" N   ASP B 858 " --> pdb=" O   ASP B 854 " (cutoff:3.500A)
      removed outlier: 5.108A  pdb=" N   GLU B 859 " --> pdb=" O   LYS B 855 " (cutoff:3.500A)
      removed outlier: 3.557A  pdb=" N   LYS B 866 " --> pdb=" O   GLU B 862 " (cutoff:3.500A)
      removed outlier: 5.032A  pdb=" N   GLU B 867 " --> pdb=" O   LYS B 863 " (cutoff:3.500A)
      removed outlier: 3.522A  pdb=" N   MET B 868 " --> pdb=" O   LYS B 864 " (cutoff:3.500A)
      removed outlier: 3.734A  pdb=" N   ASP B 869 " --> pdb=" O   GLN B 865 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 873 through 908
      removed outlier: 3.544A  pdb=" N   LEU B 908 " --> pdb=" O   GLU B 904 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 912 through 926
      removed outlier: 3.598A  pdb=" N   MET B 916 " --> pdb=" O   THR B 912 " (cutoff:3.500A)
      removed outlier: 3.631A  pdb=" N   VAL B 921 " --> pdb=" O   HIS B 917 " (cutoff:3.500A)
      removed outlier: 3.622A  pdb=" N   LYS B 922 " --> pdb=" O   ASP B 918 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 928 through 947
      removed outlier: 6.050A  pdb=" N   LYS B 944 " --> pdb=" O   THR B 940 " (cutoff:3.500A)
      removed outlier: 6.222A  pdb=" N   ASP B 945 " --> pdb=" O   THR B 941 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 948 through 950
      No H-bonds generated for 'chain 'B' and resid 948 through 950'
    Processing helix  chain 'B' and resid 951 through 969
      removed outlier: 3.535A  pdb=" N   PHE B 959 " --> pdb=" O   MET B 955 " (cutoff:3.500A)
      removed outlier: 3.889A  pdb=" N   ASN B 960 " --> pdb=" O   ASP B 956 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 972 through 988
    Processing sheet with id=AA1, first strand: chain 'B' and resid 827 through 828

    140 hydrogen bonds defined for protein.
    417 hydrogen bond angles defined for protein.
    Restraints generated for nucleic acids:
      93 hydrogen bonds
      146 hydrogen bond angles
      0 basepair planarities
      37 basepair parallelities
      53 stacking parallelities
  Total time for adding SS restraints: 0.63

  Time building geometry restraints manager: 0.51 seconds

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

  Histogram of bond lengths:
        1.21 -     1.34: 914
        1.34 -     1.46: 1387
        1.46 -     1.58: 1779
        1.58 -     1.71: 191
        1.71 -     1.83: 26
  Bond restraints: 4297
  Sorted by residual:
  bond pdb=" N   ILE B 942 "
       pdb=" CA  ILE B 942 "
    ideal  model  delta    sigma   weight residual
    1.459  1.494 -0.035 1.25e-02 6.40e+03 7.90e+00
  bond pdb=" N   GLU B 852 "
       pdb=" CA  GLU B 852 "
    ideal  model  delta    sigma   weight residual
    1.457  1.489 -0.032 1.16e-02 7.43e+03 7.40e+00
  bond pdb=" CA  SER B 812 "
       pdb=" CB  SER B 812 "
    ideal  model  delta    sigma   weight residual
    1.529  1.488  0.041 1.58e-02 4.01e+03 6.88e+00
  bond pdb=" N   VAL B 835 "
       pdb=" CA  VAL B 835 "
    ideal  model  delta    sigma   weight residual
    1.455  1.490 -0.034 1.32e-02 5.74e+03 6.77e+00
  bond pdb=" N   LYS B 756 "
       pdb=" CA  LYS B 756 "
    ideal  model  delta    sigma   weight residual
    1.459  1.490 -0.031 1.23e-02 6.61e+03 6.21e+00
  ... (remaining 4292 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     1.39: 4586
        1.39 -     2.78: 1355
        2.78 -     4.17: 236
        4.17 -     5.56: 67
        5.56 -     6.95: 8
  Bond angle restraints: 6252
  Sorted by residual:
  angle pdb=" O3'   U C 778 "
        pdb=" C3'   U C 778 "
        pdb=" C2'   U C 778 "
      ideal   model   delta    sigma   weight residual
     113.70  120.65   -6.95 1.50e+00 4.44e-01 2.15e+01
  angle pdb=" CA  PHE B 839 "
        pdb=" CB  PHE B 839 "
        pdb=" CG  PHE B 839 "
      ideal   model   delta    sigma   weight residual
     113.80  118.40   -4.60 1.00e+00 1.00e+00 2.12e+01
  angle pdb=" C4'   U C 778 "
        pdb=" C3'   U C 778 "
        pdb=" C2'   U C 778 "
      ideal   model   delta    sigma   weight residual
     102.60   98.18    4.42 1.00e+00 1.00e+00 1.96e+01
  angle pdb=" C3'   U C 778 "
        pdb=" C2'   U C 778 "
        pdb=" O2'   U C 778 "
      ideal   model   delta    sigma   weight residual
     110.70  116.85   -6.15 1.50e+00 4.44e-01 1.68e+01
  angle pdb=" C4'   U C 685 "
        pdb=" C3'   U C 685 "
        pdb=" O3'   U C 685 "
      ideal   model   delta    sigma   weight residual
     113.00  107.18    5.82 1.50e+00 4.44e-01 1.50e+01
  ... (remaining 6247 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.01 -    31.70: 2213
       31.70 -    63.39: 185
       63.39 -    95.08: 12
       95.08 -   126.77: 2
      126.77 -   158.46: 1
  Dihedral angle restraints: 2413
    sinusoidal: 1712
      harmonic: 701
  Sorted by residual:
  dihedral pdb=" C5'   A C 687 "
           pdb=" C4'   A C 687 "
           pdb=" C3'   A C 687 "
           pdb=" O3'   A C 687 "
      ideal   model   delta sinusoidal    sigma   weight residual
     147.00  109.30   37.70     1      8.00e+00 1.56e-02 3.13e+01
  dihedral pdb=" O4'   A C 687 "
           pdb=" C4'   A C 687 "
           pdb=" C3'   A C 687 "
           pdb=" C2'   A C 687 "
      ideal   model   delta sinusoidal    sigma   weight residual
      24.00  -10.27   34.27     1      8.00e+00 1.56e-02 2.60e+01
  dihedral pdb=" C3'   A C 687 "
           pdb=" C4'   A C 687 "
           pdb=" O4'   A C 687 "
           pdb=" C1'   A C 687 "
      ideal   model   delta sinusoidal    sigma   weight residual
      -2.00   29.65  -31.65     1      8.00e+00 1.56e-02 2.23e+01
  ... (remaining 2410 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.109: 494
       0.109 -    0.219: 206
       0.219 -    0.328: 79
       0.328 -    0.437: 0
       0.437 -    0.546: 3
  Chirality restraints: 782
  Sorted by residual:
  chirality pdb=" P     C C 751 "
            pdb=" OP1   C C 751 "
            pdb=" OP2   C C 751 "
            pdb=" O5'   C C 751 "
    both_signs  ideal   model   delta    sigma   weight residual
      True       2.41   -2.96   -0.55 2.00e-01 2.50e+01 7.46e+00
  chirality pdb=" P     G C 682 "
            pdb=" OP1   G C 682 "
            pdb=" OP2   G C 682 "
            pdb=" O5'   G C 682 "
    both_signs  ideal   model   delta    sigma   weight residual
      True       2.41    2.93   -0.52 2.00e-01 2.50e+01 6.85e+00
  chirality pdb=" P     A C 760 "
            pdb=" OP1   A C 760 "
            pdb=" OP2   A C 760 "
            pdb=" O5'   A C 760 "
    both_signs  ideal   model   delta    sigma   weight residual
      True       2.41    2.93   -0.52 2.00e-01 2.50e+01 6.85e+00
  ... (remaining 779 not shown)

  Planarity restraints: 435
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CB  PHE B 839 "   -0.023 2.00e-02 2.50e+03   1.62e-02 4.59e+00
        pdb=" CG  PHE B 839 "    0.032 2.00e-02 2.50e+03
        pdb=" CD1 PHE B 839 "   -0.002 2.00e-02 2.50e+03
        pdb=" CD2 PHE B 839 "    0.006 2.00e-02 2.50e+03
        pdb=" CE1 PHE B 839 "    0.005 2.00e-02 2.50e+03
        pdb=" CE2 PHE B 839 "   -0.004 2.00e-02 2.50e+03
        pdb=" CZ  PHE B 839 "   -0.015 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C1'   A C 704 "    0.029 2.00e-02 2.50e+03   1.19e-02 3.90e+00
        pdb=" N9    A C 704 "   -0.014 2.00e-02 2.50e+03
        pdb=" C8    A C 704 "   -0.008 2.00e-02 2.50e+03
        pdb=" N7    A C 704 "   -0.005 2.00e-02 2.50e+03
        pdb=" C5    A C 704 "   -0.001 2.00e-02 2.50e+03
        pdb=" C6    A C 704 "    0.005 2.00e-02 2.50e+03
        pdb=" N6    A C 704 "    0.010 2.00e-02 2.50e+03
        pdb=" N1    A C 704 "    0.008 2.00e-02 2.50e+03
        pdb=" C2    A C 704 "   -0.007 2.00e-02 2.50e+03
        pdb=" N3    A C 704 "   -0.009 2.00e-02 2.50e+03
        pdb=" C4    A C 704 "   -0.009 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C1'   U C 685 "   -0.023 2.00e-02 2.50e+03   1.20e-02 3.22e+00
        pdb=" N1    U C 685 "    0.025 2.00e-02 2.50e+03
        pdb=" C2    U C 685 "    0.005 2.00e-02 2.50e+03
        pdb=" O2    U C 685 "    0.002 2.00e-02 2.50e+03
        pdb=" N3    U C 685 "   -0.005 2.00e-02 2.50e+03
        pdb=" C4    U C 685 "   -0.007 2.00e-02 2.50e+03
        pdb=" O4    U C 685 "   -0.002 2.00e-02 2.50e+03
        pdb=" C5    U C 685 "   -0.002 2.00e-02 2.50e+03
        pdb=" C6    U C 685 "    0.007 2.00e-02 2.50e+03
  ... (remaining 432 not shown)

  Histogram of nonbonded interaction distances:
        2.22 -     2.76: 652
        2.76 -     3.29: 3912
        3.29 -     3.83: 8122
        3.83 -     4.36: 9493
        4.36 -     4.90: 12509
  Nonbonded interactions: 34688
  Sorted by model distance:
  nonbonded pdb=" O   CYS B 936 "
            pdb=" OG1 THR B 940 "
     model   vdw
     2.220 3.040
  nonbonded pdb=" NZ  LYS B 864 "
            pdb=" O   LEU B 880 "
     model   vdw
     2.424 3.120
  nonbonded pdb=" NE2 GLN B 980 "
            pdb=" OD1 ASP B 984 "
     model   vdw
     2.428 3.120
  nonbonded pdb=" N   GLU B 859 "
            pdb=" OE1 GLU B 859 "
     model   vdw
     2.444 3.120
  nonbonded pdb=" OE1 GLU B 968 "
            pdb=" NZ  LYS B 970 "
     model   vdw
     2.448 3.120
  ... (remaining 34683 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
========== WARNING! ============

  No NCS relation were found !!!

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

Found NCS groups:
  found none.
Set up NCS constraints
  No NCS constraints will be used in refinement.
Set refine NCS operators
Adjust number of macro_cycles
  Number of macro_cycles: 10
Reset NCS operators
Extract rigid body selections
Check and reset occupancies
  Occupancies: min=1.00 max=1.00 mean=1.00
Load rotamer database and sin/cos tables
Set ADP refinement strategy
  ADPs will be refined as group one per residue
Make a string to write initial .geo file
Internal consistency checks
Time:
  Set random seed:                         0.000
  Set model cs if undefined:               0.000
  Decide on map wrapping:                  0.000
  Normalize map: mean=0, sd=1:             0.160
  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:          0.070
  Check model and map are aligned:         0.010
  Set scattering table:                    0.010
  Process input model:                     6.340
  Find NCS groups from input model:        0.020
  Set up NCS constraints:                  0.000
  Set refine NCS operators:                0.000
  Adjust number of macro_cycles:           0.000
  Reset NCS operators:                     0.000
  Extract rigid body selections:           0.000
  Check and reset occupancies:             0.010
  Load rotamer database and sin/cos tables:1.280
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:    7.900
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7647
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      :  0.010   0.041   4297  Z= 0.658
  Angle     :  1.340   6.949   6252  Z= 0.867
  Chirality :  0.128   0.546    782
  Planarity :  0.005   0.026    435
  Dihedral  : 19.098 158.465   1951
  Min Nonbonded Distance : 2.220

Molprobity Statistics.
  All-atom Clashscore : 9.29
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.54 %
    Favored  : 97.46 %
  Rotamer:
    Outliers :  6.85 %
    Allowed  : 23.29 %
    Favored  : 69.86 %
  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: -0.13 (0.53), residues: 236
  helix:  0.49 (0.37), residues: 177
  sheet:  None (None), residues: 0
  loop : -1.69 (0.81), residues: 59

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.008   0.001   ARG B 762 
 TYR   0.010   0.002   TYR B 815 
 PHE   0.032   0.005   PHE B 839 
 TRP   0.009   0.003   TRP B 990 
 HIS   0.007   0.004   HIS B 917 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00975 /  0.66 ( 4297)
  covalent geometry    : angle       1.33998 /  0.87 ( 6252)
  hydrogen bonds       : bond        0.16528 / 10.88 (  233)
  hydrogen bonds       : angle       6.24283 /  4.44 (  563)

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

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

  472 Ramachandran restraints generated.
    236 Oldfield, 0 Emsley, 236 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  472 Ramachandran restraints generated.
    236 Oldfield, 0 Emsley, 236 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  95 residues out of total 219 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 15
    poor density    : 80
  time to evaluate  : 0.101 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: B  762 ARG cc_start: 0.7668 (mmt90) cc_final: 0.6933 (tpt170)
REVERT: B  775 MET cc_start: 0.8109 (tpt) cc_final: 0.7404 (ttt)
REVERT: B  778 GLN cc_start: 0.8435 (mp10) cc_final: 0.8087 (mp10)
REVERT: B  827 VAL cc_start: 0.8563 (OUTLIER) cc_final: 0.8340 (p)
REVERT: B  838 ASN cc_start: 0.8019 (t0) cc_final: 0.7774 (t0)
REVERT: B  841 LYS cc_start: 0.7643 (OUTLIER) cc_final: 0.7362 (tppt)
REVERT: B  883 GLU cc_start: 0.8687 (mm-30) cc_final: 0.8362 (mt-10)
REVERT: B  930 GLU cc_start: 0.8070 (mp0) cc_final: 0.7662 (tt0)
REVERT: B  944 LYS cc_start: 0.8364 (OUTLIER) cc_final: 0.7992 (tptp)
REVERT: B  949 GLU cc_start: 0.8500 (mm-30) cc_final: 0.7915 (pt0)
REVERT: B  961 GLN cc_start: 0.8328 (tp-100) cc_final: 0.7748 (tm-30)
REVERT: B  968 GLU cc_start: 0.7934 (mm-30) cc_final: 0.7732 (mm-30)
REVERT: B  989 ASN cc_start: 0.9259 (m-40) cc_final: 0.8864 (t0)
  outliers start: 15
  outliers final: 7
  residues processed: 87
  average time/residue: 0.1020
  time to fit residues: 10.3556
Evaluate side-chains
  56 residues out of total 219 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 46
  time to evaluate  : 0.126 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue  783 VAL
Chi-restraints excluded: chain B residue  827 VAL
Chi-restraints excluded: chain B residue  841 LYS
Chi-restraints excluded: chain B residue  845 ASN
Chi-restraints excluded: chain B residue  884 LEU
Chi-restraints excluded: chain B residue  893 ARG
Chi-restraints excluded: chain B residue  899 ILE
Chi-restraints excluded: chain B residue  944 LYS
Chi-restraints excluded: chain B residue  962 MET
Chi-restraints excluded: chain B residue  982 VAL
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 32
   random chunks:
   chunk 24 optimal weight:    9.9990
   chunk 26 optimal weight:   10.0000
   chunk 2 optimal weight:    1.9990
   chunk 16 optimal weight:    0.7980
   chunk 31 optimal weight:    9.9990
   chunk 25 optimal weight:    8.9990
   chunk 19 optimal weight:    6.9990
   chunk 30 optimal weight:   10.0000
   chunk 22 optimal weight:    6.9990
   chunk 13 optimal weight:    3.9990
   chunk 8 optimal weight:    0.9990
   overall best weight:    2.9588

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

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3631 r_free = 0.3631 target = 0.101340 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 40)----------------|
| r_work = 0.3166 r_free = 0.3166 target = 0.075978 restraints weight = 9865.397|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 46)----------------|
| r_work = 0.3213 r_free = 0.3213 target = 0.078476 restraints weight = 4566.532|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 30)----------------|
| r_work = 0.3243 r_free = 0.3243 target = 0.080040 restraints weight = 2972.473|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 28)----------------|
| r_work = 0.3259 r_free = 0.3259 target = 0.080908 restraints weight = 2369.423|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 21)----------------|
| r_work = 0.3269 r_free = 0.3269 target = 0.081410 restraints weight = 2108.116|
|-----------------------------------------------------------------------------|
r_work (final): 0.3254
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7965
moved from start:          0.2778

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.024   4297  Z= 0.173
  Angle     :  0.623   8.614   6252  Z= 0.312
  Chirality :  0.033   0.215    782
  Planarity :  0.004   0.037    435
  Dihedral  : 16.162 166.956   1436
  Min Nonbonded Distance : 2.489

Molprobity Statistics.
  All-atom Clashscore : 10.14
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.69 %
    Favored  : 98.31 %
  Rotamer:
    Outliers :  7.31 %
    Allowed  : 27.40 %
    Favored  : 65.30 %
  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:  1.53 (0.55), residues: 236
  helix:  1.49 (0.37), residues: 194
  sheet:  None (None), residues: 0
  loop : -1.14 (1.00), residues: 42

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.001   ARG B 877 
 TYR   0.008   0.002   TYR B 815 
 PHE   0.011   0.002   PHE B 959 
 TRP   0.005   0.002   TRP B 990 
 HIS   0.003   0.001   HIS B 917 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00361 /  0.17 ( 4297)
  covalent geometry    : angle       0.62331 /  0.31 ( 6252)
  hydrogen bonds       : bond        0.05375 /  3.81 (  233)
  hydrogen bonds       : angle       3.48107 /  2.50 (  563)

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

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

  472 Ramachandran restraints generated.
    236 Oldfield, 0 Emsley, 236 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  472 Ramachandran restraints generated.
    236 Oldfield, 0 Emsley, 236 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  62 residues out of total 219 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 46
  time to evaluate  : 0.087 
Fit side-chains
   revert: symmetry clash
REVERT: B  762 ARG cc_start: 0.7414 (mmt90) cc_final: 0.7006 (tpt170)
REVERT: B  775 MET cc_start: 0.6417 (tpt) cc_final: 0.5828 (ttt)
REVERT: B  958 TYR cc_start: 0.7669 (m-10) cc_final: 0.6465 (m-10)
REVERT: B  961 GLN cc_start: 0.8458 (OUTLIER) cc_final: 0.7748 (tm-30)
  outliers start: 16
  outliers final: 9
  residues processed: 57
  average time/residue: 0.0625
  time to fit residues: 4.4305
Evaluate side-chains
  44 residues out of total 219 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 34
  time to evaluate  : 0.124 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue  799 ASP
Chi-restraints excluded: chain B residue  827 VAL
Chi-restraints excluded: chain B residue  829 THR
Chi-restraints excluded: chain B residue  834 THR
Chi-restraints excluded: chain B residue  884 LEU
Chi-restraints excluded: chain B residue  899 ILE
Chi-restraints excluded: chain B residue  902 ILE
Chi-restraints excluded: chain B residue  955 MET
Chi-restraints excluded: chain B residue  961 GLN
Chi-restraints excluded: chain B residue  965 ILE
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 32
   random chunks:
   chunk 25 optimal weight:   10.0000
   chunk 17 optimal weight:    0.9990
   chunk 13 optimal weight:    0.9990
   chunk 5 optimal weight:   10.0000
   chunk 27 optimal weight:   10.0000
   chunk 1 optimal weight:    2.9990
   chunk 30 optimal weight:   20.0000
   chunk 21 optimal weight:    6.9990
   chunk 0 optimal weight:    9.9990
   chunk 12 optimal weight:    5.9990
   chunk 18 optimal weight:    0.9980
   overall best weight:    2.3988

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

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3630 r_free = 0.3630 target = 0.101431 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 41)----------------|
| r_work = 0.3163 r_free = 0.3163 target = 0.075919 restraints weight = 9904.683|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 39)----------------|
| r_work = 0.3210 r_free = 0.3210 target = 0.078345 restraints weight = 4606.709|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 46)----------------|
| r_work = 0.3241 r_free = 0.3241 target = 0.079924 restraints weight = 3056.089|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 31)----------------|
| r_work = 0.3254 r_free = 0.3254 target = 0.080691 restraints weight = 2454.170|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 30)----------------|
| r_work = 0.3265 r_free = 0.3265 target = 0.081220 restraints weight = 2212.110|
|-----------------------------------------------------------------------------|
r_work (final): 0.3257
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7971
moved from start:          0.3647

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.028   4297  Z= 0.146
  Angle     :  0.561   7.223   6252  Z= 0.282
  Chirality :  0.031   0.210    782
  Planarity :  0.004   0.035    435
  Dihedral  : 15.180 164.009   1417
  Min Nonbonded Distance : 2.498

Molprobity Statistics.
  All-atom Clashscore : 9.57
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.69 %
    Favored  : 98.31 %
  Rotamer:
    Outliers :  5.94 %
    Allowed  : 31.05 %
    Favored  : 63.01 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  2.17 (0.56), residues: 236
  helix:  1.94 (0.38), residues: 194
  sheet:  None (None), residues: 0
  loop : -0.97 (0.98), residues: 42

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG B 893 
 TYR   0.007   0.001   TYR B 815 
 PHE   0.010   0.001   PHE B 959 
 TRP   0.003   0.001   TRP B 990 
 HIS   0.001   0.001   HIS B 917 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00302 /  0.15 ( 4297)
  covalent geometry    : angle       0.56066 /  0.28 ( 6252)
  hydrogen bonds       : bond        0.04813 /  3.55 (  233)
  hydrogen bonds       : angle       3.11926 /  2.23 (  563)

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

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

  472 Ramachandran restraints generated.
    236 Oldfield, 0 Emsley, 236 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  472 Ramachandran restraints generated.
    236 Oldfield, 0 Emsley, 236 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  51 residues out of total 219 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 38
  time to evaluate  : 0.104 
Fit side-chains
   revert: symmetry clash
REVERT: B  762 ARG cc_start: 0.7840 (mmt90) cc_final: 0.6997 (tpt170)
REVERT: B  775 MET cc_start: 0.6367 (tpt) cc_final: 0.5959 (ttt)
REVERT: B  899 ILE cc_start: 0.8945 (OUTLIER) cc_final: 0.8608 (mm)
REVERT: B  958 TYR cc_start: 0.7713 (m-10) cc_final: 0.6612 (m-10)
REVERT: B  961 GLN cc_start: 0.8511 (OUTLIER) cc_final: 0.7680 (tm-30)
  outliers start: 13
  outliers final: 8
  residues processed: 44
  average time/residue: 0.0528
  time to fit residues: 3.0320
Evaluate side-chains
  42 residues out of total 219 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 32
  time to evaluate  : 0.129 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue  798 ILE
Chi-restraints excluded: chain B residue  799 ASP
Chi-restraints excluded: chain B residue  827 VAL
Chi-restraints excluded: chain B residue  829 THR
Chi-restraints excluded: chain B residue  899 ILE
Chi-restraints excluded: chain B residue  955 MET
Chi-restraints excluded: chain B residue  961 GLN
Chi-restraints excluded: chain B residue  962 MET
Chi-restraints excluded: chain B residue  965 ILE
Chi-restraints excluded: chain B residue  982 VAL
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 32
   random chunks:
   chunk 30 optimal weight:   20.0000
   chunk 18 optimal weight:    5.9990
   chunk 31 optimal weight:   10.0000
   chunk 29 optimal weight:   20.0000
   chunk 3 optimal weight:    4.9990
   chunk 19 optimal weight:    9.9990
   chunk 23 optimal weight:   10.0000
   chunk 8 optimal weight:    6.9990
   chunk 14 optimal weight:    0.8980
   chunk 28 optimal weight:    9.9990
   chunk 15 optimal weight:    3.9990
   overall best weight:    4.5788

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
B 810 ASN
B 961 GLN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3587 r_free = 0.3587 target = 0.098898 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 33)----------------|
| r_work = 0.3110 r_free = 0.3110 target = 0.073587 restraints weight = 9896.126|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 28)----------------|
| r_work = 0.3156 r_free = 0.3156 target = 0.075978 restraints weight = 4614.275|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 29)----------------|
| r_work = 0.3185 r_free = 0.3185 target = 0.077473 restraints weight = 3038.860|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 29)----------------|
| r_work = 0.3200 r_free = 0.3200 target = 0.078283 restraints weight = 2453.073|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 26)----------------|
| r_work = 0.3208 r_free = 0.3208 target = 0.078721 restraints weight = 2202.580|
|-----------------------------------------------------------------------------|
r_work (final): 0.3184
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8031
moved from start:          0.4247

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.028   4297  Z= 0.231
  Angle     :  0.661   8.720   6252  Z= 0.325
  Chirality :  0.035   0.231    782
  Planarity :  0.004   0.033    435
  Dihedral  : 15.058 163.225   1415
  Min Nonbonded Distance : 2.515

Molprobity Statistics.
  All-atom Clashscore : 10.14
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.12 %
    Favored  : 97.88 %
  Rotamer:
    Outliers :  6.85 %
    Allowed  : 30.14 %
    Favored  : 63.01 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  1.96 (0.56), residues: 236
  helix:  1.80 (0.37), residues: 194
  sheet:  None (None), residues: 0
  loop : -1.02 (1.00), residues: 42

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.001   ARG B 820 
 TYR   0.007   0.002   TYR B 815 
 PHE   0.009   0.002   PHE B 959 
 TRP   0.010   0.003   TRP B 990 
 HIS   0.002   0.001   HIS B 917 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00486 /  0.23 ( 4297)
  covalent geometry    : angle       0.66094 /  0.32 ( 6252)
  hydrogen bonds       : bond        0.05923 /  4.39 (  233)
  hydrogen bonds       : angle       3.34135 /  2.38 (  563)

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

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

  472 Ramachandran restraints generated.
    236 Oldfield, 0 Emsley, 236 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  472 Ramachandran restraints generated.
    236 Oldfield, 0 Emsley, 236 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  47 residues out of total 219 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 15
    poor density    : 32
  time to evaluate  : 0.105 
Fit side-chains
   revert: symmetry clash
REVERT: B  775 MET cc_start: 0.6474 (tpt) cc_final: 0.5984 (ttt)
REVERT: B  958 TYR cc_start: 0.7834 (m-10) cc_final: 0.6771 (m-80)
  outliers start: 15
  outliers final: 9
  residues processed: 42
  average time/residue: 0.0559
  time to fit residues: 3.1017
Evaluate side-chains
  38 residues out of total 219 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 9
    poor density    : 29
  time to evaluate  : 0.104 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue  798 ILE
Chi-restraints excluded: chain B residue  799 ASP
Chi-restraints excluded: chain B residue  827 VAL
Chi-restraints excluded: chain B residue  829 THR
Chi-restraints excluded: chain B residue  834 THR
Chi-restraints excluded: chain B residue  899 ILE
Chi-restraints excluded: chain B residue  927 HIS
Chi-restraints excluded: chain B residue  965 ILE
Chi-restraints excluded: chain B residue  982 VAL
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 32
   random chunks:
   chunk 26 optimal weight:   20.0000
   chunk 30 optimal weight:   20.0000
   chunk 24 optimal weight:   10.0000
   chunk 22 optimal weight:    1.9990
   chunk 17 optimal weight:    4.9990
   chunk 2 optimal weight:    7.9990
   chunk 15 optimal weight:    1.9990
   chunk 12 optimal weight:    6.9990
   chunk 0 optimal weight:   10.0000
   chunk 31 optimal weight:    8.9990
   chunk 1 optimal weight:    3.9990
   overall best weight:    3.9990

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
B 960 ASN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3602 r_free = 0.3602 target = 0.099527 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 42)----------------|
| r_work = 0.3125 r_free = 0.3125 target = 0.074170 restraints weight = 9975.193|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 36)----------------|
| r_work = 0.3172 r_free = 0.3172 target = 0.076568 restraints weight = 4740.103|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 42)----------------|
| r_work = 0.3202 r_free = 0.3202 target = 0.078118 restraints weight = 3152.265|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 30)----------------|
| r_work = 0.3215 r_free = 0.3215 target = 0.078843 restraints weight = 2539.266|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 26)----------------|
| r_work = 0.3225 r_free = 0.3225 target = 0.079369 restraints weight = 2288.271|
|-----------------------------------------------------------------------------|
r_work (final): 0.3216
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8024
moved from start:          0.4593

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.026   4297  Z= 0.201
  Angle     :  0.618   8.167   6252  Z= 0.305
  Chirality :  0.033   0.222    782
  Planarity :  0.004   0.030    435
  Dihedral  : 14.719 162.848   1415
  Min Nonbonded Distance : 2.507

Molprobity Statistics.
  All-atom Clashscore : 9.43
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.69 %
    Favored  : 98.31 %
  Rotamer:
    Outliers :  6.39 %
    Allowed  : 30.59 %
    Favored  : 63.01 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  2.03 (0.56), residues: 236
  helix:  1.80 (0.37), residues: 195
  sheet:  None (None), residues: 0
  loop : -0.81 (1.03), residues: 41

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG B 877 
 TYR   0.006   0.002   TYR B 815 
 PHE   0.008   0.002   PHE B 959 
 TRP   0.008   0.002   TRP B 990 
 HIS   0.003   0.001   HIS B 917 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00425 /  0.20 ( 4297)
  covalent geometry    : angle       0.61839 /  0.31 ( 6252)
  hydrogen bonds       : bond        0.05470 /  4.00 (  233)
  hydrogen bonds       : angle       3.20542 /  2.29 (  563)

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

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

  472 Ramachandran restraints generated.
    236 Oldfield, 0 Emsley, 236 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  472 Ramachandran restraints generated.
    236 Oldfield, 0 Emsley, 236 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  45 residues out of total 219 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 31
  time to evaluate  : 0.112 
Fit side-chains
   revert: symmetry clash
REVERT: B  775 MET cc_start: 0.6326 (tpt) cc_final: 0.5972 (ttt)
REVERT: B  958 TYR cc_start: 0.7835 (m-10) cc_final: 0.6644 (m-10)
  outliers start: 14
  outliers final: 11
  residues processed: 41
  average time/residue: 0.0589
  time to fit residues: 3.2222
Evaluate side-chains
  39 residues out of total 219 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 28
  time to evaluate  : 0.103 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue  798 ILE
Chi-restraints excluded: chain B residue  799 ASP
Chi-restraints excluded: chain B residue  806 ILE
Chi-restraints excluded: chain B residue  827 VAL
Chi-restraints excluded: chain B residue  829 THR
Chi-restraints excluded: chain B residue  834 THR
Chi-restraints excluded: chain B residue  899 ILE
Chi-restraints excluded: chain B residue  902 ILE
Chi-restraints excluded: chain B residue  912 THR
Chi-restraints excluded: chain B residue  965 ILE
Chi-restraints excluded: chain B residue  982 VAL
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 32
   random chunks:
   chunk 26 optimal weight:   20.0000
   chunk 21 optimal weight:   10.0000
   chunk 4 optimal weight:    0.9980
   chunk 19 optimal weight:    8.9990
   chunk 8 optimal weight:    5.9990
   chunk 23 optimal weight:   10.0000
   chunk 15 optimal weight:    0.2980
   chunk 31 optimal weight:   10.0000
   chunk 17 optimal weight:    5.9990
   chunk 5 optimal weight:    6.9990
   chunk 9 optimal weight:    0.7980
   overall best weight:    2.8184

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
B 810 ASN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3622 r_free = 0.3622 target = 0.100910 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 40)----------------|
| r_work = 0.3154 r_free = 0.3154 target = 0.075496 restraints weight = 10039.841|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 29)----------------|
| r_work = 0.3202 r_free = 0.3202 target = 0.077988 restraints weight = 4711.000|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 44)----------------|
| r_work = 0.3232 r_free = 0.3232 target = 0.079563 restraints weight = 3096.783|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 28)----------------|
| r_work = 0.3248 r_free = 0.3248 target = 0.080429 restraints weight = 2465.620|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 22)----------------|
| r_work = 0.3256 r_free = 0.3256 target = 0.080864 restraints weight = 2193.296|
|-----------------------------------------------------------------------------|
r_work (final): 0.3245
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7993
moved from start:          0.4735

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.022   4297  Z= 0.155
  Angle     :  0.576   9.231   6252  Z= 0.284
  Chirality :  0.031   0.211    782
  Planarity :  0.003   0.030    435
  Dihedral  : 14.430 162.736   1415
  Min Nonbonded Distance : 2.506

Molprobity Statistics.
  All-atom Clashscore : 8.45
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.69 %
    Favored  : 98.31 %
  Rotamer:
    Outliers :  6.85 %
    Allowed  : 29.68 %
    Favored  : 63.47 %
  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:  2.55 (0.56), residues: 236
  helix:  2.15 (0.37), residues: 195
  sheet:  None (None), residues: 0
  loop : -0.61 (1.07), residues: 41

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.001   0.000   ARG B 976 
 TYR   0.007   0.001   TYR B 815 
 PHE   0.006   0.001   PHE B 959 
 TRP   0.006   0.002   TRP B 990 
 HIS   0.003   0.001   HIS B 917 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00325 /  0.16 ( 4297)
  covalent geometry    : angle       0.57557 /  0.28 ( 6252)
  hydrogen bonds       : bond        0.05011 /  3.65 (  233)
  hydrogen bonds       : angle       3.00607 /  2.13 (  563)

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

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

  472 Ramachandran restraints generated.
    236 Oldfield, 0 Emsley, 236 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  472 Ramachandran restraints generated.
    236 Oldfield, 0 Emsley, 236 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  51 residues out of total 219 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 15
    poor density    : 36
  time to evaluate  : 0.109 
Fit side-chains
   revert: symmetry clash
REVERT: B  775 MET cc_start: 0.6372 (tpt) cc_final: 0.6036 (ttt)
REVERT: B  776 PHE cc_start: 0.7518 (t80) cc_final: 0.7288 (t80)
REVERT: B  791 GLU cc_start: 0.8108 (OUTLIER) cc_final: 0.7849 (tt0)
REVERT: B  955 MET cc_start: 0.7797 (OUTLIER) cc_final: 0.7383 (ttt)
REVERT: B  958 TYR cc_start: 0.7810 (m-10) cc_final: 0.6639 (m-10)
  outliers start: 15
  outliers final: 10
  residues processed: 45
  average time/residue: 0.0504
  time to fit residues: 3.1041
Evaluate side-chains
  40 residues out of total 219 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 28
  time to evaluate  : 0.100 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue  791 GLU
Chi-restraints excluded: chain B residue  798 ILE
Chi-restraints excluded: chain B residue  799 ASP
Chi-restraints excluded: chain B residue  806 ILE
Chi-restraints excluded: chain B residue  827 VAL
Chi-restraints excluded: chain B residue  829 THR
Chi-restraints excluded: chain B residue  834 THR
Chi-restraints excluded: chain B residue  899 ILE
Chi-restraints excluded: chain B residue  927 HIS
Chi-restraints excluded: chain B residue  955 MET
Chi-restraints excluded: chain B residue  965 ILE
Chi-restraints excluded: chain B residue  982 VAL
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 32
   random chunks:
   chunk 5 optimal weight:    4.9990
   chunk 18 optimal weight:    4.9990
   chunk 21 optimal weight:    2.9990
   chunk 3 optimal weight:    6.9990
   chunk 20 optimal weight:    0.8980
   chunk 15 optimal weight:    0.4980
   chunk 24 optimal weight:   10.0000
   chunk 9 optimal weight:    0.3980
   chunk 23 optimal weight:   10.0000
   chunk 17 optimal weight:    2.9990
   chunk 4 optimal weight:    0.6980
   overall best weight:    1.0982

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
B 810 ASN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3648 r_free = 0.3648 target = 0.102293 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 43)----------------|
| r_work = 0.3184 r_free = 0.3184 target = 0.076830 restraints weight = 10080.824|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 44)----------------|
| r_work = 0.3232 r_free = 0.3232 target = 0.079363 restraints weight = 4705.196|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 29)----------------|
| r_work = 0.3264 r_free = 0.3264 target = 0.080961 restraints weight = 3063.476|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 47)----------------|
| r_work = 0.3282 r_free = 0.3282 target = 0.081888 restraints weight = 2434.862|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 30)----------------|
| r_work = 0.3290 r_free = 0.3290 target = 0.082333 restraints weight = 2161.720|
|-----------------------------------------------------------------------------|
r_work (final): 0.3278
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7927
moved from start:          0.4960

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.020   4297  Z= 0.101
  Angle     :  0.496   6.634   6252  Z= 0.249
  Chirality :  0.029   0.188    782
  Planarity :  0.003   0.030    435
  Dihedral  : 14.079 162.022   1415
  Min Nonbonded Distance : 2.492

Molprobity Statistics.
  All-atom Clashscore : 7.04
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.54 %
    Favored  : 97.46 %
  Rotamer:
    Outliers :  5.48 %
    Allowed  : 32.42 %
    Favored  : 62.10 %
  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:  3.09 (0.56), residues: 236
  helix:  2.52 (0.37), residues: 195
  sheet:  None (None), residues: 0
  loop : -0.38 (1.07), residues: 41

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.006   0.000   ARG B 877 
 TYR   0.007   0.002   TYR B 815 
 PHE   0.009   0.001   PHE B 776 
 TRP   0.003   0.001   TRP B 990 
 HIS   0.002   0.001   HIS B 917 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00198 /  0.10 ( 4297)
  covalent geometry    : angle       0.49575 /  0.25 ( 6252)
  hydrogen bonds       : bond        0.04158 /  3.04 (  233)
  hydrogen bonds       : angle       2.78923 /  1.97 (  563)

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

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

  472 Ramachandran restraints generated.
    236 Oldfield, 0 Emsley, 236 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  472 Ramachandran restraints generated.
    236 Oldfield, 0 Emsley, 236 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  45 residues out of total 219 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 33
  time to evaluate  : 0.064 
Fit side-chains
   revert: symmetry clash
REVERT: B  775 MET cc_start: 0.6468 (tpt) cc_final: 0.6145 (ttt)
REVERT: B  791 GLU cc_start: 0.8153 (OUTLIER) cc_final: 0.7806 (tt0)
REVERT: B  899 ILE cc_start: 0.8860 (OUTLIER) cc_final: 0.8394 (mm)
REVERT: B  958 TYR cc_start: 0.7750 (m-10) cc_final: 0.6541 (m-10)
  outliers start: 12
  outliers final: 6
  residues processed: 41
  average time/residue: 0.0405
  time to fit residues: 2.3168
Evaluate side-chains
  37 residues out of total 219 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 8
    poor density    : 29
  time to evaluate  : 0.100 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue  791 GLU
Chi-restraints excluded: chain B residue  798 ILE
Chi-restraints excluded: chain B residue  799 ASP
Chi-restraints excluded: chain B residue  827 VAL
Chi-restraints excluded: chain B residue  829 THR
Chi-restraints excluded: chain B residue  834 THR
Chi-restraints excluded: chain B residue  899 ILE
Chi-restraints excluded: chain B residue  982 VAL
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 32
   random chunks:
   chunk 5 optimal weight:    9.9990
   chunk 28 optimal weight:   10.0000
   chunk 10 optimal weight:    4.9990
   chunk 30 optimal weight:   20.0000
   chunk 13 optimal weight:    6.9990
   chunk 1 optimal weight:    5.9990
   chunk 11 optimal weight:    7.9990
   chunk 24 optimal weight:   10.0000
   chunk 23 optimal weight:   10.0000
   chunk 22 optimal weight:    9.9990
   chunk 12 optimal weight:    0.6980
   overall best weight:    5.3388

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
B 774 GLN
B 810 ASN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3604 r_free = 0.3604 target = 0.099914 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 44)----------------|
| r_work = 0.3131 r_free = 0.3131 target = 0.074348 restraints weight = 10109.657|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 36)----------------|
| r_work = 0.3178 r_free = 0.3178 target = 0.076819 restraints weight = 4651.905|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 38)----------------|
| r_work = 0.3208 r_free = 0.3208 target = 0.078353 restraints weight = 3076.984|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 25)----------------|
| r_work = 0.3223 r_free = 0.3223 target = 0.079177 restraints weight = 2480.419|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 26)----------------|
| r_work = 0.3229 r_free = 0.3229 target = 0.079484 restraints weight = 2219.806|
|-----------------------------------------------------------------------------|
r_work (final): 0.3221
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8028
moved from start:          0.4995

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.006   0.036   4297  Z= 0.260
  Angle     :  0.678   9.894   6252  Z= 0.329
  Chirality :  0.035   0.238    782
  Planarity :  0.004   0.024    435
  Dihedral  : 14.561 161.012   1415
  Min Nonbonded Distance : 2.511

Molprobity Statistics.
  All-atom Clashscore : 10.84
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.39 %
    Favored  : 96.61 %
  Rotamer:
    Outliers :  6.39 %
    Allowed  : 31.51 %
    Favored  : 62.10 %
  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:  2.28 (0.55), residues: 236
  helix:  2.04 (0.37), residues: 197
  sheet:  None (None), residues: 0
  loop : -1.27 (0.97), residues: 39

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.007   0.001   ARG B 877 
 TYR   0.005   0.002   TYR B 815 
 PHE   0.011   0.002   PHE B 959 
 TRP   0.009   0.003   TRP B 990 
 HIS   0.005   0.002   HIS B 917 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00551 /  0.26 ( 4297)
  covalent geometry    : angle       0.67821 /  0.33 ( 6252)
  hydrogen bonds       : bond        0.06032 /  4.37 (  233)
  hydrogen bonds       : angle       3.22543 /  2.29 (  563)

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

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

  472 Ramachandran restraints generated.
    236 Oldfield, 0 Emsley, 236 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  472 Ramachandran restraints generated.
    236 Oldfield, 0 Emsley, 236 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  41 residues out of total 219 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 27
  time to evaluate  : 0.104 
Fit side-chains
   revert: symmetry clash
REVERT: B  775 MET cc_start: 0.6795 (tpt) cc_final: 0.6433 (ttt)
REVERT: B  958 TYR cc_start: 0.7877 (m-10) cc_final: 0.6742 (m-80)
  outliers start: 14
  outliers final: 11
  residues processed: 39
  average time/residue: 0.0409
  time to fit residues: 2.3397
Evaluate side-chains
  35 residues out of total 219 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 24
  time to evaluate  : 0.105 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue  772 THR
Chi-restraints excluded: chain B residue  798 ILE
Chi-restraints excluded: chain B residue  799 ASP
Chi-restraints excluded: chain B residue  827 VAL
Chi-restraints excluded: chain B residue  829 THR
Chi-restraints excluded: chain B residue  834 THR
Chi-restraints excluded: chain B residue  899 ILE
Chi-restraints excluded: chain B residue  927 HIS
Chi-restraints excluded: chain B residue  965 ILE
Chi-restraints excluded: chain B residue  982 VAL
Chi-restraints excluded: chain B residue  985 LEU
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 32
   random chunks:
   chunk 31 optimal weight:   10.0000
   chunk 14 optimal weight:    0.8980
   chunk 15 optimal weight:    0.9990
   chunk 3 optimal weight:    6.9990
   chunk 22 optimal weight:    1.9990
   chunk 16 optimal weight:    1.9990
   chunk 18 optimal weight:    0.9990
   chunk 5 optimal weight:    7.9990
   chunk 0 optimal weight:   10.0000
   chunk 20 optimal weight:    1.9990
   chunk 13 optimal weight:    7.9990
   overall best weight:    1.3788

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
B 810 ASN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3632 r_free = 0.3632 target = 0.101299 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 44)----------------|
| r_work = 0.3155 r_free = 0.3155 target = 0.075497 restraints weight = 10129.593|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 38)----------------|
| r_work = 0.3206 r_free = 0.3206 target = 0.078024 restraints weight = 4660.265|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 36)----------------|
| r_work = 0.3238 r_free = 0.3238 target = 0.079648 restraints weight = 3047.293|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 30)----------------|
| r_work = 0.3257 r_free = 0.3257 target = 0.080588 restraints weight = 2427.314|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 20)----------------|
| r_work = 0.3263 r_free = 0.3263 target = 0.080909 restraints weight = 2156.292|
|-----------------------------------------------------------------------------|
r_work (final): 0.3252
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7953
moved from start:          0.5141

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.020   4297  Z= 0.113
  Angle     :  0.543  10.270   6252  Z= 0.267
  Chirality :  0.030   0.200    782
  Planarity :  0.003   0.029    435
  Dihedral  : 14.091 161.994   1415
  Min Nonbonded Distance : 2.497

Molprobity Statistics.
  All-atom Clashscore : 7.60
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.12 %
    Favored  : 97.88 %
  Rotamer:
    Outliers :  4.57 %
    Allowed  : 33.33 %
    Favored  : 62.10 %
  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:  2.88 (0.56), residues: 236
  helix:  2.40 (0.37), residues: 195
  sheet:  None (None), residues: 0
  loop : -0.55 (1.05), residues: 41

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.000   ARG B 877 
 TYR   0.007   0.001   TYR B 815 
 PHE   0.010   0.001   PHE B 776 
 TRP   0.003   0.001   TRP B 990 
 HIS   0.001   0.000   HIS B 917 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00230 /  0.11 ( 4297)
  covalent geometry    : angle       0.54311 /  0.27 ( 6252)
  hydrogen bonds       : bond        0.04454 /  3.25 (  233)
  hydrogen bonds       : angle       2.84650 /  2.01 (  563)

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

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

  472 Ramachandran restraints generated.
    236 Oldfield, 0 Emsley, 236 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  472 Ramachandran restraints generated.
    236 Oldfield, 0 Emsley, 236 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  35 residues out of total 219 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 25
  time to evaluate  : 0.106 
Fit side-chains
   revert: symmetry clash
REVERT: B  775 MET cc_start: 0.6726 (tpt) cc_final: 0.6401 (ttt)
REVERT: B  868 MET cc_start: 0.7672 (ttm) cc_final: 0.7051 (tmm)
REVERT: B  899 ILE cc_start: 0.8915 (OUTLIER) cc_final: 0.8461 (mm)
REVERT: B  958 TYR cc_start: 0.7748 (m-10) cc_final: 0.6497 (m-10)
  outliers start: 10
  outliers final: 6
  residues processed: 32
  average time/residue: 0.0437
  time to fit residues: 2.0273
Evaluate side-chains
  31 residues out of total 219 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 7
    poor density    : 24
  time to evaluate  : 0.103 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue  798 ILE
Chi-restraints excluded: chain B residue  799 ASP
Chi-restraints excluded: chain B residue  827 VAL
Chi-restraints excluded: chain B residue  829 THR
Chi-restraints excluded: chain B residue  834 THR
Chi-restraints excluded: chain B residue  899 ILE
Chi-restraints excluded: chain B residue  965 ILE
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 32
   random chunks:
   chunk 18 optimal weight:    0.9990
   chunk 20 optimal weight:    0.3980
   chunk 14 optimal weight:    0.9990
   chunk 9 optimal weight:    0.8980
   chunk 27 optimal weight:   10.0000
   chunk 2 optimal weight:    0.0060
   chunk 30 optimal weight:   20.0000
   chunk 15 optimal weight:    0.6980
   chunk 7 optimal weight:    1.9990
   chunk 17 optimal weight:    0.1980
   chunk 16 optimal weight:    2.9990
   overall best weight:    0.4396

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
B 810 ASN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3720 r_free = 0.3720 target = 0.106359 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.3264 r_free = 0.3264 target = 0.080862 restraints weight = 10000.233|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 46)----------------|
| r_work = 0.3314 r_free = 0.3314 target = 0.083470 restraints weight = 4709.820|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 38)----------------|
| r_work = 0.3344 r_free = 0.3344 target = 0.085077 restraints weight = 3083.426|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 36)----------------|
| r_work = 0.3363 r_free = 0.3363 target = 0.086079 restraints weight = 2457.466|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 24)----------------|
| r_work = 0.3370 r_free = 0.3370 target = 0.086461 restraints weight = 2163.314|
|-----------------------------------------------------------------------------|
r_work (final): 0.3361
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7830
moved from start:          0.5629

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.023   4297  Z= 0.092
  Angle     :  0.502  12.684   6252  Z= 0.243
  Chirality :  0.028   0.168    782
  Planarity :  0.003   0.035    435
  Dihedral  : 13.798 161.024   1415
  Min Nonbonded Distance : 2.488

Molprobity Statistics.
  All-atom Clashscore : 8.31
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.54 %
    Favored  : 97.46 %
  Rotamer:
    Outliers :  1.83 %
    Allowed  : 36.07 %
    Favored  : 62.10 %
  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:  3.38 (0.56), residues: 236
  helix:  2.77 (0.37), residues: 195
  sheet:  None (None), residues: 0
  loop : -0.57 (0.99), residues: 41

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARG B 877 
 TYR   0.006   0.002   TYR B 958 
 PHE   0.010   0.001   PHE B 839 
 TRP   0.002   0.001   TRP B 990 
 HIS   0.001   0.000   HIS B 917 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00182 /  0.09 ( 4297)
  covalent geometry    : angle       0.50246 /  0.24 ( 6252)
  hydrogen bonds       : bond        0.03536 /  2.52 (  233)
  hydrogen bonds       : angle       2.62724 /  1.85 (  563)

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

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

  472 Ramachandran restraints generated.
    236 Oldfield, 0 Emsley, 236 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  472 Ramachandran restraints generated.
    236 Oldfield, 0 Emsley, 236 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  40 residues out of total 219 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 4
    poor density    : 36
  time to evaluate  : 0.143 
Fit side-chains
REVERT: B  775 MET cc_start: 0.6597 (tpt) cc_final: 0.6143 (ttt)
REVERT: B  868 MET cc_start: 0.7623 (ttm) cc_final: 0.6913 (tmm)
REVERT: B  958 TYR cc_start: 0.7610 (m-10) cc_final: 0.6476 (m-10)
  outliers start: 4
  outliers final: 4
  residues processed: 38
  average time/residue: 0.0437
  time to fit residues: 2.3560
Evaluate side-chains
  34 residues out of total 219 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 4
    poor density    : 30
  time to evaluate  : 0.107 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue  798 ILE
Chi-restraints excluded: chain B residue  799 ASP
Chi-restraints excluded: chain B residue  829 THR
Chi-restraints excluded: chain B residue  834 THR
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 32
   random chunks:
   chunk 21 optimal weight:    3.9990
   chunk 23 optimal weight:   10.0000
   chunk 24 optimal weight:   10.0000
   chunk 17 optimal weight:    0.3980
   chunk 4 optimal weight:    5.9990
   chunk 9 optimal weight:    1.9990
   chunk 31 optimal weight:   10.0000
   chunk 20 optimal weight:    0.9990
   chunk 29 optimal weight:   20.0000
   chunk 5 optimal weight:    0.9980
   chunk 27 optimal weight:    7.9990
   overall best weight:    1.6786

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
B 785 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3667 r_free = 0.3667 target = 0.103428 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 38)----------------|
| r_work = 0.3191 r_free = 0.3191 target = 0.077199 restraints weight = 10070.048|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 35)----------------|
| r_work = 0.3238 r_free = 0.3238 target = 0.079682 restraints weight = 4917.684|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 39)----------------|
| r_work = 0.3269 r_free = 0.3269 target = 0.081257 restraints weight = 3265.758|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 42)----------------|
| r_work = 0.3287 r_free = 0.3287 target = 0.082175 restraints weight = 2629.719|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 23)----------------|
| r_work = 0.3289 r_free = 0.3289 target = 0.082321 restraints weight = 2330.128|
|-----------------------------------------------------------------------------|
r_work (final): 0.3281
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7920
moved from start:          0.5612

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.017   4297  Z= 0.112
  Angle     :  0.499   6.228   6252  Z= 0.248
  Chirality :  0.029   0.192    782
  Planarity :  0.003   0.027    435
  Dihedral  : 13.791 160.511   1412
  Min Nonbonded Distance : 2.514

Molprobity Statistics.
  All-atom Clashscore : 7.60
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.54 %
    Favored  : 97.46 %
  Rotamer:
    Outliers :  3.65 %
    Allowed  : 35.62 %
    Favored  : 60.73 %
  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:  3.19 (0.56), residues: 236
  helix:  2.64 (0.37), residues: 195
  sheet:  None (None), residues: 0
  loop : -0.66 (0.98), residues: 41

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.000   ARG B 877 
 TYR   0.003   0.001   TYR B 815 
 PHE   0.007   0.001   PHE B 776 
 TRP   0.002   0.001   TRP B 990 
 HIS   0.002   0.001   HIS B 917 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00230 /  0.11 ( 4297)
  covalent geometry    : angle       0.49861 /  0.25 ( 6252)
  hydrogen bonds       : bond        0.04024 /  2.94 (  233)
  hydrogen bonds       : angle       2.70545 /  1.93 (  563)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 732.46 seconds
wall clock time: 13 minutes 19.00 seconds (799.00 seconds total)