Starting phenix.real_space_refine
on Tue Mar  3 14:48:43 2026 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/7rhy_24471/03_2026/7rhy_24471_neut.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/7rhy_24471/03_2026/7rhy_24471.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=3.91
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    model {
      file = "/net/cci-nas-00/data/ceres_data/7rhy_24471/03_2026/7rhy_24471_neut.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/7rhy_24471/03_2026/7rhy_24471_neut.cif"
    real_map_files = "/net/cci-nas-00/data/ceres_data/7rhy_24471/03_2026/7rhy_24471.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/7rhy_24471/03_2026/7rhy_24471.map"
  }
  resolution = 3.91
  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=   0.001 sd=   0.055
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      49      5.49       5
     S      14      5.16       5
     C    1968      2.51       5
     N     640      2.21       5
     O     722      1.98       5
     H    2957      0.53       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model
  Monomer Library directory:
    "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-5986/lib/python3.9/site-packages/chem_data/mon_lib"
  Total number of atoms: 6350
  Number of models: 1
  Model: ""
    Number of chains: 2
    Chain: "A"
      Number of atoms: 4789
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 301, 4789
          Classifications: {'peptide': 301}
          Link IDs: {'PTRANS': 7, 'TRANS': 293}
          Chain breaks: 1
    Chain: "B"
      Number of atoms: 1561
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 49, 1561
          Classifications: {'DNA': 49}
          Modifications used: {'3*END': 1}
          Link IDs: {'rna3p': 48}
  Time building chain proxies: 1.22, per 1000 atoms: 0.19
  Number of scatterers: 6350
  At special positions: 0
  Unit cell: (59.5055, 74.8617, 92.1375, 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      14     16.00
     P      49     15.00
     O     722      8.00
     N     640      7.00
     C    1968      6.00
     H    2957      1.00
    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: 0.57
  Conformation dependent library (CDL) restraints added in 209.5 milliseconds
  

  594 Ramachandran restraints generated.
    297 Oldfield, 0 Emsley, 297 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  562

  Finding SS restraints...
    Secondary structure from input PDB file:
      17 helices and 1 sheets defined
      67.4% alpha, 3.3% beta
      23 base pairs and 44 stacking pairs defined.
    Time for finding SS restraints: 1.02
  Creating SS restraints...
    Processing helix  chain 'A' and resid 20 through 34
      removed outlier: 3.665A  pdb=" N   MET A  30 " --> pdb=" O   ASN A  26 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 38 through 59
      removed outlier: 3.595A  pdb=" N   MET A  44 " --> pdb=" O   HIS A  40 " (cutoff:3.500A)
      removed outlier: 3.803A  pdb=" N   LEU A  46 " --> pdb=" O   TRP A  42 " (cutoff:3.500A)
      removed outlier: 3.507A  pdb=" N   SER A  47 " --> pdb=" O   LYS A  43 " (cutoff:3.500A)
      removed outlier: 3.750A  pdb=" N   SER A  51 " --> pdb=" O   SER A  47 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 67 through 81
    Processing helix  chain 'A' and resid 84 through 103
      removed outlier: 3.507A  pdb=" N   ILE A  88 " --> pdb=" O   ALA A  84 " (cutoff:3.500A)
      removed outlier: 3.565A  pdb=" N   GLN A  90 " --> pdb=" O   LYS A  86 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 106 through 109
    Processing helix  chain 'A' and resid 110 through 127
    Processing helix  chain 'A' and resid 138 through 150
      removed outlier: 3.651A  pdb=" N   PHE A 142 " --> pdb=" O   GLU A 138 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 154 through 170
      removed outlier: 3.553A  pdb=" N   ASN A 160 " --> pdb=" O   GLN A 156 " (cutoff:3.500A)
      removed outlier: 3.596A  pdb=" N   ASN A 169 " --> pdb=" O   GLY A 165 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 173 through 178
    Processing helix  chain 'A' and resid 179 through 180
      No H-bonds generated for 'chain 'A' and resid 179 through 180'
    Processing helix  chain 'A' and resid 181 through 183
      No H-bonds generated for 'chain 'A' and resid 181 through 183'
    Processing helix  chain 'A' and resid 216 through 229
      removed outlier: 3.916A  pdb=" N   LEU A 220 " --> pdb=" O   GLY A 216 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 230 through 233
      removed outlier: 4.100A  pdb=" N   ASP A 233 " --> pdb=" O   VAL A 230 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'A' and resid 230 through 233'
    Processing helix  chain 'A' and resid 257 through 273
      removed outlier: 3.633A  pdb=" N   GLY A 263 " --> pdb=" O   ARG A 259 " (cutoff:3.500A)
      removed outlier: 3.518A  pdb=" N   PHE A 265 " --> pdb=" O   LEU A 261 " (cutoff:3.500A)
      removed outlier: 3.578A  pdb=" N   ALA A 267 " --> pdb=" O   GLY A 263 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 287 through 302
      removed outlier: 4.174A  pdb=" N   ALA A 291 " --> pdb=" O   SER A 287 " (cutoff:3.500A)
      removed outlier: 4.557A  pdb=" N   ARG A 292 " --> pdb=" O   GLY A 288 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 305 through 314
    Processing helix  chain 'A' and resid 319 through 325
    Processing sheet with id=AA1, first strand: chain 'A' and resid 185 through 187
      removed outlier: 4.177A  pdb=" N   MET A 193 " --> pdb=" O   LEU A 213 " (cutoff:3.500A)
      removed outlier: 3.524A  pdb=" N   VAL A 209 " --> pdb=" O   ILE A 197 " (cutoff:3.500A)

    129 hydrogen bonds defined for protein.
    384 hydrogen bond angles defined for protein.
    Restraints generated for nucleic acids:
      55 hydrogen bonds
      106 hydrogen bond angles
      0 basepair planarities
      23 basepair parallelities
      44 stacking parallelities
  Total time for adding SS restraints: 1.34

  Time building geometry restraints manager: 0.79 seconds

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

  Histogram of bond lengths:
        0.84 -     1.03: 2953
        1.03 -     1.23: 29
        1.23 -     1.42: 1533
        1.42 -     1.61: 1974
        1.61 -     1.81: 24
  Bond restraints: 6513
  Sorted by residual:
  bond pdb=" C4'  DG B   9 "
       pdb=" O4'  DG B   9 "
    ideal  model  delta    sigma   weight residual
    1.450  1.415  0.035 2.00e-02 2.50e+03 3.10e+00
  bond pdb=" N   SER A  20 "
       pdb=" CA  SER A  20 "
    ideal  model  delta    sigma   weight residual
    1.458  1.490 -0.032 1.90e-02 2.77e+03 2.88e+00
  bond pdb=" N   SER A  20 "
       pdb=" H   SER A  20 "
    ideal  model  delta    sigma   weight residual
    0.860  0.890 -0.030 2.00e-02 2.50e+03 2.28e+00
  bond pdb=" C2'  DT B  10 "
       pdb=" C1'  DT B  10 "
    ideal  model  delta    sigma   weight residual
    1.525  1.497  0.028 2.00e-02 2.50e+03 1.93e+00
  bond pdb=" C4'  DC B  37 "
       pdb=" O4'  DC B  37 "
    ideal  model  delta    sigma   weight residual
    1.450  1.424  0.026 2.00e-02 2.50e+03 1.71e+00
  ... (remaining 6508 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     1.36: 10812
        1.36 -     2.72: 869
        2.72 -     4.08: 52
        4.08 -     5.44: 10
        5.44 -     6.80: 3
  Bond angle restraints: 11746
  Sorted by residual:
  angle pdb=" C3'  DC B  15 "
        pdb=" O3'  DC B  15 "
        pdb=" P    DA B  16 "
      ideal   model   delta    sigma   weight residual
     120.20  125.87   -5.67 1.50e+00 4.44e-01 1.43e+01
  angle pdb=" C2'  DG B   9 "
        pdb=" C1'  DG B   9 "
        pdb=" N9   DG B   9 "
      ideal   model   delta    sigma   weight residual
     113.50  118.42   -4.92 1.50e+00 4.44e-01 1.07e+01
  angle pdb=" C3'  DT B  10 "
        pdb=" O3'  DT B  10 "
        pdb=" P    DA B  11 "
      ideal   model   delta    sigma   weight residual
     120.20  125.07   -4.87 1.50e+00 4.44e-01 1.05e+01
  angle pdb=" C2'  DG B  14 "
        pdb=" C1'  DG B  14 "
        pdb=" N9   DG B  14 "
      ideal   model   delta    sigma   weight residual
     113.50  118.02   -4.52 1.50e+00 4.44e-01 9.10e+00
  angle pdb=" C2'  DT B  10 "
        pdb=" C1'  DT B  10 "
        pdb=" N1   DT B  10 "
      ideal   model   delta    sigma   weight residual
     113.50  117.70   -4.20 1.50e+00 4.44e-01 7.85e+00
  ... (remaining 11741 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    34.52: 2584
       34.52 -    69.04: 281
       69.04 -   103.57: 2
      103.57 -   138.09: 0
      138.09 -   172.61: 1
  Dihedral angle restraints: 2868
    sinusoidal: 1872
      harmonic: 996
  Sorted by residual:
  dihedral pdb=" CA  ALA A 212 "
           pdb=" C   ALA A 212 "
           pdb=" N   LEU A 213 "
           pdb=" CA  LEU A 213 "
      ideal   model   delta  harmonic     sigma   weight residual
    -180.00 -154.53  -25.47     0      5.00e+00 4.00e-02 2.60e+01
  dihedral pdb=" CA  LYS A 211 "
           pdb=" C   LYS A 211 "
           pdb=" N   ALA A 212 "
           pdb=" CA  ALA A 212 "
      ideal   model   delta  harmonic     sigma   weight residual
    -180.00 -157.59  -22.41     0      5.00e+00 4.00e-02 2.01e+01
  dihedral pdb=" CA  PRO A 250 "
           pdb=" C   PRO A 250 "
           pdb=" N   SER A 251 "
           pdb=" CA  SER A 251 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  160.10   19.90     0      5.00e+00 4.00e-02 1.58e+01
  ... (remaining 2865 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.044: 402
       0.044 -    0.088: 106
       0.088 -    0.132: 40
       0.132 -    0.176: 4
       0.176 -    0.220: 2
  Chirality restraints: 554
  Sorted by residual:
  chirality pdb=" C1'  DT B  10 "
            pdb=" O4'  DT B  10 "
            pdb=" C2'  DT B  10 "
            pdb=" N1   DT B  10 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.47    2.25    0.22 2.00e-01 2.50e+01 1.21e+00
  chirality pdb=" C3'  DC B  15 "
            pdb=" C4'  DC B  15 "
            pdb=" O3'  DC B  15 "
            pdb=" C2'  DC B  15 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.66   -2.47   -0.19 2.00e-01 2.50e+01 8.97e-01
  chirality pdb=" C1'  DC B  21 "
            pdb=" O4'  DC B  21 "
            pdb=" C2'  DC B  21 "
            pdb=" N1   DC B  21 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.47    2.30    0.17 2.00e-01 2.50e+01 6.87e-01
  ... (remaining 551 not shown)

  Planarity restraints: 801
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C1'  DT B  10 "    0.041 2.00e-02 2.50e+03   4.29e-02 5.53e+01
        pdb=" N1   DT B  10 "   -0.119 2.00e-02 2.50e+03
        pdb=" C2   DT B  10 "    0.076 2.00e-02 2.50e+03
        pdb=" O2   DT B  10 "   -0.008 2.00e-02 2.50e+03
        pdb=" N3   DT B  10 "   -0.005 2.00e-02 2.50e+03
        pdb=" C4   DT B  10 "    0.001 2.00e-02 2.50e+03
        pdb=" O4   DT B  10 "    0.002 2.00e-02 2.50e+03
        pdb=" C5   DT B  10 "    0.004 2.00e-02 2.50e+03
        pdb=" C7   DT B  10 "    0.009 2.00e-02 2.50e+03
        pdb=" C6   DT B  10 "   -0.001 2.00e-02 2.50e+03
        pdb=" H3   DT B  10 "   -0.009 2.00e-02 2.50e+03
        pdb=" H6   DT B  10 "    0.009 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C1'  DA B  11 "    0.039 2.00e-02 2.50e+03   2.98e-02 2.88e+01
        pdb=" N9   DA B  11 "   -0.088 2.00e-02 2.50e+03
        pdb=" C8   DA B  11 "    0.046 2.00e-02 2.50e+03
        pdb=" N7   DA B  11 "   -0.002 2.00e-02 2.50e+03
        pdb=" C5   DA B  11 "   -0.001 2.00e-02 2.50e+03
        pdb=" C6   DA B  11 "    0.002 2.00e-02 2.50e+03
        pdb=" N6   DA B  11 "    0.001 2.00e-02 2.50e+03
        pdb=" N1   DA B  11 "    0.002 2.00e-02 2.50e+03
        pdb=" C2   DA B  11 "    0.001 2.00e-02 2.50e+03
        pdb=" N3   DA B  11 "    0.001 2.00e-02 2.50e+03
        pdb=" C4   DA B  11 "   -0.004 2.00e-02 2.50e+03
        pdb=" H8   DA B  11 "   -0.005 2.00e-02 2.50e+03
        pdb=" H2   DA B  11 "    0.006 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C1'  DT B   7 "    0.028 2.00e-02 2.50e+03   2.56e-02 1.97e+01
        pdb=" N1   DT B   7 "   -0.073 2.00e-02 2.50e+03
        pdb=" C2   DT B   7 "    0.041 2.00e-02 2.50e+03
        pdb=" O2   DT B   7 "   -0.007 2.00e-02 2.50e+03
        pdb=" N3   DT B   7 "   -0.003 2.00e-02 2.50e+03
        pdb=" C4   DT B   7 "    0.002 2.00e-02 2.50e+03
        pdb=" O4   DT B   7 "    0.003 2.00e-02 2.50e+03
        pdb=" C5   DT B   7 "    0.004 2.00e-02 2.50e+03
        pdb=" C7   DT B   7 "    0.002 2.00e-02 2.50e+03
        pdb=" C6   DT B   7 "    0.003 2.00e-02 2.50e+03
        pdb=" H3   DT B   7 "   -0.004 2.00e-02 2.50e+03
        pdb=" H6   DT B   7 "    0.004 2.00e-02 2.50e+03
  ... (remaining 798 not shown)

  Histogram of nonbonded interaction distances:
        1.59 -     2.19: 219
        2.19 -     2.80: 11394
        2.80 -     3.40: 15364
        3.40 -     4.00: 19680
        4.00 -     4.60: 30595
  Nonbonded interactions: 77252
  Sorted by model distance:
  nonbonded pdb=" H   ARG A 181 "
            pdb=" OD2 ASP A 184 "
     model   vdw
     1.593 2.450
  nonbonded pdb=" HG1 THR A  41 "
            pdb=" OP2  DT B  33 "
     model   vdw
     1.605 2.450
  nonbonded pdb="HH21 ARG A 297 "
            pdb=" O   ASN A 327 "
     model   vdw
     1.732 2.450
  nonbonded pdb="HH12 ARG A  61 "
            pdb=" OD1 ASP A  70 "
     model   vdw
     1.744 2.450
  nonbonded pdb=" HG  SER A 287 "
            pdb=" OP1  DA B  36 "
     model   vdw
     1.752 2.450
  ... (remaining 77247 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:             1.130
  Set stop_for_unknowns flag:              0.000
  Assert model is a single copy model:     0.000
  Assert all atoms have isotropic ADPs:    0.010
  Construct map_model_manager:             0.030
  Extract box with map and model:          0.090
  Check model and map are aligned:         0.020
  Set scattering table:                    0.030
  Process input model:                     8.350
  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:             0.000
  Load rotamer database and sin/cos tables:1.330
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   11.010
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7654
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      :  0.005   0.035   3556  Z= 0.222
  Angle     :  0.805   6.800   5012  Z= 0.511
  Chirality :  0.047   0.220    554
  Planarity :  0.011   0.100    474
  Dihedral  : 21.980 172.609   1463
  Min Nonbonded Distance : 2.404

Molprobity Statistics.
  All-atom Clashscore : 3.31
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.02 %
    Favored  : 97.98 %
  Rotamer:
    Outliers :  0.80 %
    Allowed  :  1.60 %
    Favored  : 97.60 %
  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: -1.06 (0.45), residues: 297
  helix: -1.09 (0.33), residues: 183
  sheet:  2.44 (1.61), residues: 10
  loop :  0.10 (0.61), residues: 104

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.025   0.002   ARG A  61 
 TYR   0.010   0.004   TYR A 237 
 PHE   0.009   0.003   PHE A  64 
 TRP   0.007   0.002   TRP A  55 
 HIS   0.005   0.002   HIS A  91 

Details of bonding type rmsd
  covalent geometry    : bond        0.00457 ( 3556)
  covalent geometry    : angle       0.80499 ( 5012)
  hydrogen bonds       : bond        0.14353 (  184)
  hydrogen bonds       : angle       6.36246 (  490)

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

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

  594 Ramachandran restraints generated.
    297 Oldfield, 0 Emsley, 297 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  594 Ramachandran restraints generated.
    297 Oldfield, 0 Emsley, 297 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  81 residues out of total 250 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 2
    poor density    : 79
  time to evaluate  : 0.148 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  170 THR cc_start: 0.9297 (m) cc_final: 0.8995 (p)
REVERT: A  308 GLU cc_start: 0.8446 (tt0) cc_final: 0.8064 (tm-30)
REVERT: A  309 ILE cc_start: 0.8785 (mt) cc_final: 0.8559 (mt)
REVERT: A  316 THR cc_start: 0.8645 (m) cc_final: 0.8385 (p)
  outliers start: 2
  outliers final: 0
  residues processed: 80
  average time/residue: 0.2635
  time to fit residues: 23.3684
Evaluate side-chains
  37 residues out of total 250 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 37
  time to evaluate  : 0.137 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 34
   random chunks:
   chunk 24 optimal weight:    1.9990
   chunk 26 optimal weight:    1.9990
   chunk 2 optimal weight:    1.9990
   chunk 16 optimal weight:    0.9990
   chunk 32 optimal weight:    3.9990
   chunk 31 optimal weight:    1.9990
   chunk 25 optimal weight:    0.9990
   chunk 19 optimal weight:    2.9990
   chunk 30 optimal weight:    1.9990
   chunk 22 optimal weight:    1.9990
   chunk 13 optimal weight:    0.9990
   overall best weight:    1.3990

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

Flipped N/Q/H residues before XYZ refinement:
A  91 HIS

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3743 r_free = 0.3743 target = 0.134677 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 37)----------------|
| r_work = 0.3269 r_free = 0.3269 target = 0.101791 restraints weight = 17729.764|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 43)----------------|
| r_work = 0.3358 r_free = 0.3358 target = 0.107700 restraints weight = 8582.671|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 37)----------------|
| r_work = 0.3417 r_free = 0.3417 target = 0.111691 restraints weight = 5506.812|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 37)----------------|
| r_work = 0.3458 r_free = 0.3458 target = 0.114485 restraints weight = 4055.412|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 40)----------------|
| r_work = 0.3485 r_free = 0.3485 target = 0.116374 restraints weight = 3235.528|
|-----------------------------------------------------------------------------|
r_work (final): 0.3481
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7681
moved from start:          0.3278

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.032   3556  Z= 0.221
  Angle     :  0.667   4.971   5012  Z= 0.396
  Chirality :  0.040   0.132    554
  Planarity :  0.004   0.030    474
  Dihedral  : 25.420 171.230    889
  Min Nonbonded Distance : 2.477

Molprobity Statistics.
  All-atom Clashscore : 4.57
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.03 %
    Favored  : 96.97 %
  Rotamer:
    Outliers :  2.80 %
    Allowed  :  9.60 %
    Favored  : 87.60 %
  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: -0.04 (0.47), residues: 297
  helix:  0.10 (0.37), residues: 186
  sheet:  1.01 (1.56), residues: 10
  loop : -0.08 (0.61), residues: 101

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.007   0.001   ARG A 101 
 TYR   0.014   0.002   TYR A  77 
 PHE   0.017   0.003   PHE A  37 
 TRP   0.008   0.001   TRP A  42 
 HIS   0.003   0.001   HIS A 269 

Details of bonding type rmsd
  covalent geometry    : bond        0.00472 ( 3556)
  covalent geometry    : angle       0.66679 ( 5012)
  hydrogen bonds       : bond        0.07132 (  184)
  hydrogen bonds       : angle       4.94441 (  490)

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

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

  594 Ramachandran restraints generated.
    297 Oldfield, 0 Emsley, 297 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  594 Ramachandran restraints generated.
    297 Oldfield, 0 Emsley, 297 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  52 residues out of total 250 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 7
    poor density    : 45
  time to evaluate  : 0.134 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   28 MET cc_start: 0.4917 (mmt) cc_final: 0.4710 (mmt)
REVERT: A  170 THR cc_start: 0.9298 (m) cc_final: 0.9063 (p)
REVERT: A  176 GLU cc_start: 0.7665 (mt-10) cc_final: 0.7310 (mt-10)
REVERT: A  316 THR cc_start: 0.8649 (m) cc_final: 0.8431 (p)
  outliers start: 7
  outliers final: 6
  residues processed: 50
  average time/residue: 0.1145
  time to fit residues: 7.1725
Evaluate side-chains
  41 residues out of total 250 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 6
    poor density    : 35
  time to evaluate  : 0.152 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   48 VAL
Chi-restraints excluded: chain A residue   63 TRP
Chi-restraints excluded: chain A residue   96 ASN
Chi-restraints excluded: chain A residue  166 ILE
Chi-restraints excluded: chain A residue  287 SER
Chi-restraints excluded: chain A residue  323 ASN
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 34
   random chunks:
   chunk 24 optimal weight:    1.9990
   chunk 9 optimal weight:    4.9990
   chunk 31 optimal weight:    1.9990
   chunk 8 optimal weight:    2.9990
   chunk 3 optimal weight:    0.9980
   chunk 19 optimal weight:    0.9990
   chunk 30 optimal weight:    1.9990
   chunk 29 optimal weight:    0.6980
   chunk 26 optimal weight:    1.9990
   chunk 21 optimal weight:    0.8980
   chunk 14 optimal weight:    0.9980
   overall best weight:    0.9182

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3762 r_free = 0.3762 target = 0.136047 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.3288 r_free = 0.3288 target = 0.102999 restraints weight = 17551.568|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 42)----------------|
| r_work = 0.3379 r_free = 0.3379 target = 0.109077 restraints weight = 8308.678|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 38)----------------|
| r_work = 0.3437 r_free = 0.3437 target = 0.113126 restraints weight = 5259.349|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 39)----------------|
| r_work = 0.3477 r_free = 0.3477 target = 0.115942 restraints weight = 3856.769|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 32)----------------|
| r_work = 0.3500 r_free = 0.3500 target = 0.117609 restraints weight = 3075.811|
|-----------------------------------------------------------------------------|
r_work (final): 0.3496
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7660
moved from start:          0.3807

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.038   3556  Z= 0.169
  Angle     :  0.603   6.298   5012  Z= 0.360
  Chirality :  0.037   0.120    554
  Planarity :  0.004   0.031    474
  Dihedral  : 25.207 170.876    889
  Min Nonbonded Distance : 2.430

Molprobity Statistics.
  All-atom Clashscore : 3.31
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.37 %
    Favored  : 96.63 %
  Rotamer:
    Outliers :  1.60 %
    Allowed  : 12.80 %
    Favored  : 85.60 %
  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:  0.71 (0.49), residues: 297
  helix:  0.87 (0.39), residues: 185
  sheet:  0.88 (1.71), residues: 10
  loop : -0.14 (0.61), residues: 102

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG A 101 
 TYR   0.010   0.001   TYR A  77 
 PHE   0.013   0.002   PHE A  37 
 TRP   0.005   0.001   TRP A  42 
 HIS   0.002   0.001   HIS A 269 

Details of bonding type rmsd
  covalent geometry    : bond        0.00356 ( 3556)
  covalent geometry    : angle       0.60315 ( 5012)
  hydrogen bonds       : bond        0.05399 (  184)
  hydrogen bonds       : angle       4.41706 (  490)

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

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

  594 Ramachandran restraints generated.
    297 Oldfield, 0 Emsley, 297 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  594 Ramachandran restraints generated.
    297 Oldfield, 0 Emsley, 297 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  40 residues out of total 250 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 4
    poor density    : 36
  time to evaluate  : 0.135 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  176 GLU cc_start: 0.7575 (mt-10) cc_final: 0.7255 (mt-10)
  outliers start: 4
  outliers final: 4
  residues processed: 38
  average time/residue: 0.0652
  time to fit residues: 3.7301
Evaluate side-chains
  37 residues out of total 250 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 4
    poor density    : 33
  time to evaluate  : 0.141 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   48 VAL
Chi-restraints excluded: chain A residue   63 TRP
Chi-restraints excluded: chain A residue   96 ASN
Chi-restraints excluded: chain A residue  166 ILE
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 34
   random chunks:
   chunk 12 optimal weight:    0.5980
   chunk 8 optimal weight:    2.9990
   chunk 9 optimal weight:    2.9990
   chunk 23 optimal weight:    0.9980
   chunk 31 optimal weight:    1.9990
   chunk 22 optimal weight:    0.9990
   chunk 29 optimal weight:    0.8980
   chunk 16 optimal weight:    1.9990
   chunk 19 optimal weight:    1.9990
   chunk 3 optimal weight:    1.9990
   chunk 28 optimal weight:    1.9990
   overall best weight:    1.0984

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3760 r_free = 0.3760 target = 0.134475 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 36)----------------|
| r_work = 0.3283 r_free = 0.3283 target = 0.101734 restraints weight = 17009.149|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 28)----------------|
| r_work = 0.3369 r_free = 0.3369 target = 0.107548 restraints weight = 7977.923|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 35)----------------|
| r_work = 0.3427 r_free = 0.3427 target = 0.111560 restraints weight = 5050.495|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 33)----------------|
| r_work = 0.3466 r_free = 0.3466 target = 0.114196 restraints weight = 3689.442|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 27)----------------|
| r_work = 0.3491 r_free = 0.3491 target = 0.115972 restraints weight = 2969.744|
|-----------------------------------------------------------------------------|
r_work (final): 0.3496
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7692
moved from start:          0.4156

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.036   3556  Z= 0.184
  Angle     :  0.612   6.530   5012  Z= 0.362
  Chirality :  0.038   0.118    554
  Planarity :  0.003   0.031    474
  Dihedral  : 25.159 169.812    889
  Min Nonbonded Distance : 2.487

Molprobity Statistics.
  All-atom Clashscore : 4.41
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.70 %
    Favored  : 96.30 %
  Rotamer:
    Outliers :  2.00 %
    Allowed  : 14.40 %
    Favored  : 83.60 %
  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:  0.86 (0.49), residues: 297
  helix:  1.13 (0.39), residues: 186
  sheet:  0.53 (1.58), residues: 10
  loop : -0.35 (0.61), residues: 101

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG A 101 
 TYR   0.010   0.001   TYR A 273 
 PHE   0.010   0.002   PHE A  64 
 TRP   0.006   0.001   TRP A  42 
 HIS   0.003   0.001   HIS A 269 

Details of bonding type rmsd
  covalent geometry    : bond        0.00390 ( 3556)
  covalent geometry    : angle       0.61151 ( 5012)
  hydrogen bonds       : bond        0.05778 (  184)
  hydrogen bonds       : angle       4.32762 (  490)

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

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

  594 Ramachandran restraints generated.
    297 Oldfield, 0 Emsley, 297 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  594 Ramachandran restraints generated.
    297 Oldfield, 0 Emsley, 297 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  41 residues out of total 250 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 5
    poor density    : 36
  time to evaluate  : 0.151 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  176 GLU cc_start: 0.7624 (mt-10) cc_final: 0.7300 (mt-10)
REVERT: A  323 ASN cc_start: 0.8276 (OUTLIER) cc_final: 0.7888 (t0)
  outliers start: 5
  outliers final: 4
  residues processed: 38
  average time/residue: 0.0863
  time to fit residues: 4.4255
Evaluate side-chains
  38 residues out of total 250 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 5
    poor density    : 33
  time to evaluate  : 0.139 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   48 VAL
Chi-restraints excluded: chain A residue   63 TRP
Chi-restraints excluded: chain A residue   96 ASN
Chi-restraints excluded: chain A residue  166 ILE
Chi-restraints excluded: chain A residue  323 ASN
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 34
   random chunks:
   chunk 28 optimal weight:    2.9990
   chunk 23 optimal weight:    0.9980
   chunk 26 optimal weight:    0.8980
   chunk 13 optimal weight:    2.9990
   chunk 15 optimal weight:    0.5980
   chunk 19 optimal weight:    0.7980
   chunk 20 optimal weight:    2.9990
   chunk 9 optimal weight:    2.9990
   chunk 31 optimal weight:    1.9990
   chunk 32 optimal weight:    4.9990
   chunk 18 optimal weight:    2.9990
   overall best weight:    1.0582

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3759 r_free = 0.3759 target = 0.134283 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.3279 r_free = 0.3279 target = 0.101431 restraints weight = 17305.534|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 39)----------------|
| r_work = 0.3366 r_free = 0.3366 target = 0.107283 restraints weight = 8130.923|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 39)----------------|
| r_work = 0.3424 r_free = 0.3424 target = 0.111220 restraints weight = 5155.651|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 36)----------------|
| r_work = 0.3463 r_free = 0.3463 target = 0.113868 restraints weight = 3796.552|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 37)----------------|
| r_work = 0.3490 r_free = 0.3490 target = 0.115696 restraints weight = 3045.976|
|-----------------------------------------------------------------------------|
r_work (final): 0.3490
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7701
moved from start:          0.4462

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.037   3556  Z= 0.178
  Angle     :  0.589   6.969   5012  Z= 0.353
  Chirality :  0.037   0.116    554
  Planarity :  0.003   0.032    474
  Dihedral  : 25.107 169.522    889
  Min Nonbonded Distance : 2.482

Molprobity Statistics.
  All-atom Clashscore : 4.41
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.39 %
    Favored  : 94.61 %
  Rotamer:
    Outliers :  2.40 %
    Allowed  : 14.80 %
    Favored  : 82.80 %
  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:  0.98 (0.50), residues: 297
  helix:  1.34 (0.39), residues: 185
  sheet:  0.65 (1.65), residues: 10
  loop : -0.56 (0.61), residues: 102

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG A 101 
 TYR   0.011   0.001   TYR A 273 
 PHE   0.012   0.002   PHE A  37 
 TRP   0.006   0.001   TRP A  42 
 HIS   0.002   0.001   HIS A 269 

Details of bonding type rmsd
  covalent geometry    : bond        0.00377 ( 3556)
  covalent geometry    : angle       0.58915 ( 5012)
  hydrogen bonds       : bond        0.05386 (  184)
  hydrogen bonds       : angle       4.15097 (  490)

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

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

  594 Ramachandran restraints generated.
    297 Oldfield, 0 Emsley, 297 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  594 Ramachandran restraints generated.
    297 Oldfield, 0 Emsley, 297 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  39 residues out of total 250 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 6
    poor density    : 33
  time to evaluate  : 0.142 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
  outliers start: 6
  outliers final: 5
  residues processed: 37
  average time/residue: 0.0698
  time to fit residues: 3.8063
Evaluate side-chains
  36 residues out of total 250 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 5
    poor density    : 31
  time to evaluate  : 0.139 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   48 VAL
Chi-restraints excluded: chain A residue   63 TRP
Chi-restraints excluded: chain A residue   96 ASN
Chi-restraints excluded: chain A residue  166 ILE
Chi-restraints excluded: chain A residue  284 LEU
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 34
   random chunks:
   chunk 25 optimal weight:    2.9990
   chunk 21 optimal weight:    0.9990
   chunk 17 optimal weight:    3.9990
   chunk 31 optimal weight:    1.9990
   chunk 12 optimal weight:    0.9980
   chunk 27 optimal weight:    3.9990
   chunk 11 optimal weight:    0.8980
   chunk 15 optimal weight:    0.7980
   chunk 7 optimal weight:    1.9990
   chunk 4 optimal weight:    0.6980
   chunk 22 optimal weight:    0.6980
   overall best weight:    0.8180

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

Flipped N/Q/H residues before XYZ refinement:
A  90 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3770 r_free = 0.3770 target = 0.135157 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 35)----------------|
| r_work = 0.3295 r_free = 0.3295 target = 0.102357 restraints weight = 17080.398|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 36)----------------|
| r_work = 0.3380 r_free = 0.3380 target = 0.108119 restraints weight = 7913.199|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 45)----------------|
| r_work = 0.3438 r_free = 0.3438 target = 0.112128 restraints weight = 5009.590|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 38)----------------|
| r_work = 0.3477 r_free = 0.3477 target = 0.114849 restraints weight = 3677.726|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 36)----------------|
| r_work = 0.3503 r_free = 0.3503 target = 0.116689 restraints weight = 2940.895|
|-----------------------------------------------------------------------------|
r_work (final): 0.3504
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7675
moved from start:          0.4652

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.037   3556  Z= 0.158
  Angle     :  0.574   7.222   5012  Z= 0.344
  Chirality :  0.036   0.117    554
  Planarity :  0.003   0.032    474
  Dihedral  : 25.102 169.757    889
  Min Nonbonded Distance : 2.463

Molprobity Statistics.
  All-atom Clashscore : 4.25
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.37 %
    Favored  : 96.63 %
  Rotamer:
    Outliers :  2.80 %
    Allowed  : 15.60 %
    Favored  : 81.60 %
  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:  1.20 (0.50), residues: 297
  helix:  1.61 (0.40), residues: 185
  sheet:  0.56 (1.46), residues: 10
  loop : -0.67 (0.61), residues: 102

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG A 101 
 TYR   0.010   0.001   TYR A 273 
 PHE   0.010   0.002   PHE A  37 
 TRP   0.007   0.001   TRP A  42 
 HIS   0.002   0.001   HIS A 269 

Details of bonding type rmsd
  covalent geometry    : bond        0.00335 ( 3556)
  covalent geometry    : angle       0.57370 ( 5012)
  hydrogen bonds       : bond        0.05023 (  184)
  hydrogen bonds       : angle       3.98310 (  490)

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

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

  594 Ramachandran restraints generated.
    297 Oldfield, 0 Emsley, 297 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  594 Ramachandran restraints generated.
    297 Oldfield, 0 Emsley, 297 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  42 residues out of total 250 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 7
    poor density    : 35
  time to evaluate  : 0.095 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  176 GLU cc_start: 0.7584 (mt-10) cc_final: 0.7256 (mt-10)
  outliers start: 7
  outliers final: 6
  residues processed: 38
  average time/residue: 0.0559
  time to fit residues: 3.1693
Evaluate side-chains
  40 residues out of total 250 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 6
    poor density    : 34
  time to evaluate  : 0.143 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   48 VAL
Chi-restraints excluded: chain A residue   63 TRP
Chi-restraints excluded: chain A residue   96 ASN
Chi-restraints excluded: chain A residue  166 ILE
Chi-restraints excluded: chain A residue  284 LEU
Chi-restraints excluded: chain A residue  299 MET
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 34
   random chunks:
   chunk 19 optimal weight:    1.9990
   chunk 15 optimal weight:    0.9980
   chunk 10 optimal weight:    0.7980
   chunk 3 optimal weight:    0.9980
   chunk 17 optimal weight:    1.9990
   chunk 24 optimal weight:    2.9990
   chunk 30 optimal weight:    2.9990
   chunk 18 optimal weight:    1.9990
   chunk 21 optimal weight:    0.6980
   chunk 13 optimal weight:    1.9990
   chunk 2 optimal weight:    0.9980
   overall best weight:    0.8980

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3761 r_free = 0.3761 target = 0.134482 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 37)----------------|
| r_work = 0.3280 r_free = 0.3280 target = 0.101669 restraints weight = 17084.992|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 32)----------------|
| r_work = 0.3367 r_free = 0.3367 target = 0.107469 restraints weight = 7950.204|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 36)----------------|
| r_work = 0.3427 r_free = 0.3427 target = 0.111498 restraints weight = 5023.953|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 35)----------------|
| r_work = 0.3466 r_free = 0.3466 target = 0.114137 restraints weight = 3669.726|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 25)----------------|
| r_work = 0.3488 r_free = 0.3488 target = 0.115725 restraints weight = 2947.092|
|-----------------------------------------------------------------------------|
r_work (final): 0.3485
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7689
moved from start:          0.4781

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.037   3556  Z= 0.165
  Angle     :  0.575   7.338   5012  Z= 0.345
  Chirality :  0.037   0.117    554
  Planarity :  0.003   0.032    474
  Dihedral  : 25.118 169.559    889
  Min Nonbonded Distance : 2.468

Molprobity Statistics.
  All-atom Clashscore : 5.04
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.71 %
    Favored  : 95.29 %
  Rotamer:
    Outliers :  2.80 %
    Allowed  : 16.40 %
    Favored  : 80.80 %
  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:  1.31 (0.50), residues: 297
  helix:  1.71 (0.40), residues: 186
  sheet:  0.62 (1.39), residues: 10
  loop : -0.67 (0.61), residues: 101

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG A 101 
 TYR   0.010   0.001   TYR A 273 
 PHE   0.009   0.002   PHE A  37 
 TRP   0.005   0.001   TRP A  42 
 HIS   0.002   0.001   HIS A 269 

Details of bonding type rmsd
  covalent geometry    : bond        0.00349 ( 3556)
  covalent geometry    : angle       0.57516 ( 5012)
  hydrogen bonds       : bond        0.05077 (  184)
  hydrogen bonds       : angle       3.99973 (  490)

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

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

  594 Ramachandran restraints generated.
    297 Oldfield, 0 Emsley, 297 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  594 Ramachandran restraints generated.
    297 Oldfield, 0 Emsley, 297 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  43 residues out of total 250 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 7
    poor density    : 36
  time to evaluate  : 0.120 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
  outliers start: 7
  outliers final: 6
  residues processed: 39
  average time/residue: 0.0639
  time to fit residues: 3.7059
Evaluate side-chains
  40 residues out of total 250 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 6
    poor density    : 34
  time to evaluate  : 0.120 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   48 VAL
Chi-restraints excluded: chain A residue   63 TRP
Chi-restraints excluded: chain A residue   78 LEU
Chi-restraints excluded: chain A residue   96 ASN
Chi-restraints excluded: chain A residue  166 ILE
Chi-restraints excluded: chain A residue  284 LEU
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 34
   random chunks:
   chunk 3 optimal weight:    0.9990
   chunk 12 optimal weight:    0.9980
   chunk 1 optimal weight:    2.9990
   chunk 10 optimal weight:    0.8980
   chunk 33 optimal weight:    1.9990
   chunk 4 optimal weight:    0.9990
   chunk 26 optimal weight:    1.9990
   chunk 19 optimal weight:    2.9990
   chunk 8 optimal weight:    0.8980
   chunk 30 optimal weight:    2.9990
   chunk 23 optimal weight:    0.9980
   overall best weight:    0.9582

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3762 r_free = 0.3762 target = 0.134473 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 41)----------------|
| r_work = 0.3276 r_free = 0.3276 target = 0.101381 restraints weight = 17214.942|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 37)----------------|
| r_work = 0.3365 r_free = 0.3365 target = 0.107242 restraints weight = 8080.115|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 39)----------------|
| r_work = 0.3424 r_free = 0.3424 target = 0.111224 restraints weight = 5107.696|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 35)----------------|
| r_work = 0.3463 r_free = 0.3463 target = 0.113923 restraints weight = 3753.944|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 36)----------------|
| r_work = 0.3491 r_free = 0.3491 target = 0.115775 restraints weight = 3001.537|
|-----------------------------------------------------------------------------|
r_work (final): 0.3491
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7700
moved from start:          0.4895

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.037   3556  Z= 0.169
  Angle     :  0.580   7.832   5012  Z= 0.347
  Chirality :  0.037   0.117    554
  Planarity :  0.003   0.032    474
  Dihedral  : 25.164 169.463    889
  Min Nonbonded Distance : 2.469

Molprobity Statistics.
  All-atom Clashscore : 5.51
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.38 %
    Favored  : 95.62 %
  Rotamer:
    Outliers :  2.80 %
    Allowed  : 16.40 %
    Favored  : 80.80 %
  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:  1.31 (0.50), residues: 297
  helix:  1.74 (0.40), residues: 186
  sheet:  0.59 (1.25), residues: 10
  loop : -0.72 (0.61), residues: 101

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG A  81 
 TYR   0.010   0.001   TYR A 273 
 PHE   0.010   0.002   PHE A  37 
 TRP   0.004   0.001   TRP A  42 
 HIS   0.002   0.001   HIS A 269 

Details of bonding type rmsd
  covalent geometry    : bond        0.00357 ( 3556)
  covalent geometry    : angle       0.57958 ( 5012)
  hydrogen bonds       : bond        0.05127 (  184)
  hydrogen bonds       : angle       4.01401 (  490)

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

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

  594 Ramachandran restraints generated.
    297 Oldfield, 0 Emsley, 297 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  594 Ramachandran restraints generated.
    297 Oldfield, 0 Emsley, 297 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  43 residues out of total 250 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 7
    poor density    : 36
  time to evaluate  : 0.148 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
  outliers start: 7
  outliers final: 7
  residues processed: 39
  average time/residue: 0.0622
  time to fit residues: 3.6070
Evaluate side-chains
  41 residues out of total 250 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 7
    poor density    : 34
  time to evaluate  : 0.156 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   48 VAL
Chi-restraints excluded: chain A residue   63 TRP
Chi-restraints excluded: chain A residue   78 LEU
Chi-restraints excluded: chain A residue   96 ASN
Chi-restraints excluded: chain A residue  166 ILE
Chi-restraints excluded: chain A residue  284 LEU
Chi-restraints excluded: chain A residue  299 MET
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 34
   random chunks:
   chunk 2 optimal weight:    0.9980
   chunk 12 optimal weight:    0.0670
   chunk 14 optimal weight:    0.9980
   chunk 21 optimal weight:    1.9990
   chunk 10 optimal weight:    1.9990
   chunk 29 optimal weight:    1.9990
   chunk 18 optimal weight:    4.9990
   chunk 32 optimal weight:    4.9990
   chunk 9 optimal weight:    0.8980
   chunk 26 optimal weight:    2.9990
   chunk 7 optimal weight:    0.9980
   overall best weight:    0.7918

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3773 r_free = 0.3773 target = 0.135276 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 37)----------------|
| r_work = 0.3287 r_free = 0.3287 target = 0.102150 restraints weight = 17517.749|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 38)----------------|
| r_work = 0.3376 r_free = 0.3376 target = 0.108038 restraints weight = 8194.144|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 29)----------------|
| r_work = 0.3435 r_free = 0.3435 target = 0.112041 restraints weight = 5198.759|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 37)----------------|
| r_work = 0.3475 r_free = 0.3475 target = 0.114736 restraints weight = 3819.537|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 42)----------------|
| r_work = 0.3502 r_free = 0.3502 target = 0.116562 restraints weight = 3062.167|
|-----------------------------------------------------------------------------|
r_work (final): 0.3505
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7686
moved from start:          0.5004

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.037   3556  Z= 0.157
  Angle     :  0.582   8.096   5012  Z= 0.348
  Chirality :  0.036   0.114    554
  Planarity :  0.003   0.032    474
  Dihedral  : 25.175 169.433    889
  Min Nonbonded Distance : 2.469

Molprobity Statistics.
  All-atom Clashscore : 5.20
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.70 %
    Favored  : 96.30 %
  Rotamer:
    Outliers :  2.80 %
    Allowed  : 16.40 %
    Favored  : 80.80 %
  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:  1.48 (0.50), residues: 297
  helix:  1.88 (0.40), residues: 186
  sheet:  0.66 (1.21), residues: 10
  loop : -0.69 (0.61), residues: 101

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG A 101 
 TYR   0.009   0.001   TYR A 273 
 PHE   0.009   0.002   PHE A  37 
 TRP   0.004   0.000   TRP A  42 
 HIS   0.002   0.001   HIS A 269 

Details of bonding type rmsd
  covalent geometry    : bond        0.00332 ( 3556)
  covalent geometry    : angle       0.58160 ( 5012)
  hydrogen bonds       : bond        0.04828 (  184)
  hydrogen bonds       : angle       3.97155 (  490)

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

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

  594 Ramachandran restraints generated.
    297 Oldfield, 0 Emsley, 297 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  594 Ramachandran restraints generated.
    297 Oldfield, 0 Emsley, 297 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  40 residues out of total 250 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 7
    poor density    : 33
  time to evaluate  : 0.100 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  176 GLU cc_start: 0.7544 (mt-10) cc_final: 0.7238 (mt-10)
  outliers start: 7
  outliers final: 7
  residues processed: 37
  average time/residue: 0.0636
  time to fit residues: 3.4491
Evaluate side-chains
  40 residues out of total 250 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 7
    poor density    : 33
  time to evaluate  : 0.117 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   48 VAL
Chi-restraints excluded: chain A residue   63 TRP
Chi-restraints excluded: chain A residue   78 LEU
Chi-restraints excluded: chain A residue   96 ASN
Chi-restraints excluded: chain A residue  166 ILE
Chi-restraints excluded: chain A residue  284 LEU
Chi-restraints excluded: chain A residue  299 MET
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 34
   random chunks:
   chunk 15 optimal weight:    0.9980
   chunk 21 optimal weight:    1.9990
   chunk 13 optimal weight:    0.0870
   chunk 19 optimal weight:    0.5980
   chunk 27 optimal weight:    0.8980
   chunk 20 optimal weight:    0.5980
   chunk 30 optimal weight:    1.9990
   chunk 1 optimal weight:    1.9990
   chunk 9 optimal weight:    0.9980
   chunk 4 optimal weight:    0.8980
   chunk 8 optimal weight:    0.9990
   overall best weight:    0.6158

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3791 r_free = 0.3791 target = 0.136637 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 35)----------------|
| r_work = 0.3308 r_free = 0.3308 target = 0.103624 restraints weight = 17008.109|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 39)----------------|
| r_work = 0.3397 r_free = 0.3397 target = 0.109503 restraints weight = 7963.849|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 37)----------------|
| r_work = 0.3454 r_free = 0.3454 target = 0.113450 restraints weight = 5061.224|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 36)----------------|
| r_work = 0.3495 r_free = 0.3495 target = 0.116212 restraints weight = 3734.081|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 36)----------------|
| r_work = 0.3523 r_free = 0.3523 target = 0.118082 restraints weight = 2982.507|
|-----------------------------------------------------------------------------|
r_work (final): 0.3526
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7650
moved from start:          0.5124

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.037   3556  Z= 0.146
  Angle     :  0.572   8.446   5012  Z= 0.342
  Chirality :  0.036   0.116    554
  Planarity :  0.003   0.032    474
  Dihedral  : 25.173 169.269    889
  Min Nonbonded Distance : 2.460

Molprobity Statistics.
  All-atom Clashscore : 5.04
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.70 %
    Favored  : 96.30 %
  Rotamer:
    Outliers :  2.80 %
    Allowed  : 16.80 %
    Favored  : 80.40 %
  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:  1.70 (0.51), residues: 297
  helix:  2.03 (0.40), residues: 187
  sheet:  0.88 (1.30), residues: 10
  loop : -0.59 (0.61), residues: 100

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG A  81 
 TYR   0.009   0.001   TYR A 273 
 PHE   0.008   0.001   PHE A  37 
 TRP   0.003   0.000   TRP A  42 
 HIS   0.002   0.000   HIS A 269 

Details of bonding type rmsd
  covalent geometry    : bond        0.00311 ( 3556)
  covalent geometry    : angle       0.57210 ( 5012)
  hydrogen bonds       : bond        0.04395 (  184)
  hydrogen bonds       : angle       3.84416 (  490)

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

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

  594 Ramachandran restraints generated.
    297 Oldfield, 0 Emsley, 297 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  594 Ramachandran restraints generated.
    297 Oldfield, 0 Emsley, 297 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  42 residues out of total 250 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 7
    poor density    : 35
  time to evaluate  : 0.138 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   48 VAL cc_start: 0.8280 (OUTLIER) cc_final: 0.8048 (t)
REVERT: A  176 GLU cc_start: 0.7540 (mt-10) cc_final: 0.7230 (mt-10)
  outliers start: 7
  outliers final: 5
  residues processed: 37
  average time/residue: 0.0620
  time to fit residues: 3.4057
Evaluate side-chains
  41 residues out of total 250 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 6
    poor density    : 35
  time to evaluate  : 0.135 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   48 VAL
Chi-restraints excluded: chain A residue   63 TRP
Chi-restraints excluded: chain A residue   96 ASN
Chi-restraints excluded: chain A residue  166 ILE
Chi-restraints excluded: chain A residue  284 LEU
Chi-restraints excluded: chain A residue  299 MET
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 34
   random chunks:
   chunk 10 optimal weight:    0.8980
   chunk 18 optimal weight:    1.9990
   chunk 28 optimal weight:    2.9990
   chunk 7 optimal weight:    1.9990
   chunk 21 optimal weight:    0.8980
   chunk 19 optimal weight:    0.9990
   chunk 0 optimal weight:    4.9990
   chunk 26 optimal weight:    1.9990
   chunk 29 optimal weight:    0.8980
   chunk 24 optimal weight:    0.7980
   chunk 2 optimal weight:    0.6980
   overall best weight:    0.8380

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3778 r_free = 0.3778 target = 0.135611 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.3292 r_free = 0.3292 target = 0.102828 restraints weight = 17075.122|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 41)----------------|
| r_work = 0.3381 r_free = 0.3381 target = 0.108678 restraints weight = 7985.922|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 37)----------------|
| r_work = 0.3439 r_free = 0.3439 target = 0.112605 restraints weight = 5055.085|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 37)----------------|
| r_work = 0.3480 r_free = 0.3480 target = 0.115359 restraints weight = 3718.060|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 32)----------------|
| r_work = 0.3508 r_free = 0.3508 target = 0.117215 restraints weight = 2966.986|
|-----------------------------------------------------------------------------|
r_work (final): 0.3511
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7677
moved from start:          0.5194

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.036   3556  Z= 0.161
  Angle     :  0.580   8.033   5012  Z= 0.347
  Chirality :  0.037   0.115    554
  Planarity :  0.003   0.032    474
  Dihedral  : 25.195 169.149    889
  Min Nonbonded Distance : 2.470

Molprobity Statistics.
  All-atom Clashscore : 5.51
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.71 %
    Favored  : 95.29 %
  Rotamer:
    Outliers :  2.40 %
    Allowed  : 17.20 %
    Favored  : 80.40 %
  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:  1.69 (0.51), residues: 297
  helix:  2.05 (0.40), residues: 186
  sheet:  1.06 (1.35), residues: 10
  loop : -0.64 (0.61), residues: 101

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG A  81 
 TYR   0.009   0.001   TYR A 273 
 PHE   0.008   0.002   PHE A  37 
 TRP   0.003   0.000   TRP A  42 
 HIS   0.002   0.001   HIS A 269 

Details of bonding type rmsd
  covalent geometry    : bond        0.00342 ( 3556)
  covalent geometry    : angle       0.57992 ( 5012)
  hydrogen bonds       : bond        0.04786 (  184)
  hydrogen bonds       : angle       3.94870 (  490)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 1442.69 seconds
wall clock time: 25 minutes 5.98 seconds (1505.98 seconds total)