Starting phenix.real_space_refine
on Sat May  2 14:33:11 2026 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/9u4v_63856/05_2026/9u4v_63856.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/9u4v_63856/05_2026/9u4v_63856.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=3.09
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/cci-nas-00/data/ceres_data/9u4v_63856/05_2026/9u4v_63856.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/9u4v_63856/05_2026/9u4v_63856.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/9u4v_63856/05_2026/9u4v_63856.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/9u4v_63856/05_2026/9u4v_63856.cif"
  }
  resolution = 3.09
  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=   0.020
Set stop_for_unknowns flag
  Set to: True
Assert model is a single copy model
Assert all atoms have isotropic ADPs
Construct map_model_manager
Extract box with map and model
Check model and map are aligned
Set scattering table
  Set to: electron
  Number of scattering types: 5
    Type Number    sf(0)   Gaussians
     P       1      5.49       5
     S      31      5.16       5
     C    4055      2.51       5
     N    1050      2.21       5
     O    1164      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 9 residue(s): 0.01s

  Monomer Library directory:
    "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.1rc2-6044/lib/python3.9/site-packages/chem_data/mon_lib"
  Total number of atoms: 6301
  Number of models: 1
  Model: ""
    Number of chains: 2
    Chain: "A"
      Number of atoms: 5647
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 742, 5647
          Classifications: {'peptide': 742}
          Link IDs: {'PCIS': 1, 'PTRANS': 38, 'TRANS': 702}
          Chain breaks: 1
    Chain: "B"
      Number of atoms: 654
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 83, 654
          Classifications: {'peptide': 83}
          Link IDs: {'PTRANS': 3, 'TRANS': 79}
          Unresolved non-hydrogen bonds: 1
          Unresolved non-hydrogen angles: 2
          Unresolved non-hydrogen dihedrals: 2
          Planarities with less than four sites: {'4HH:plan-3': 1}
          Unresolved non-hydrogen planarities: 1
  Time building chain proxies: 1.45, per 1000 atoms: 0.23
  Number of scatterers: 6301
  At special positions: 0
  Unit cell: (66, 72.6, 137.5, 90, 90, 90)
  Space group: P 1 (No. 1)
  Number of sites at special positions: 0
  Number of scattering types: 5
    Type Number    sf(0)
     S      31     16.00
     P       1     15.00
     O    1164      8.00
     N    1050      7.00
     C    4055      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: 0.56
  Conformation dependent library (CDL) restraints added in 400.3 milliseconds
  

  1632 Ramachandran restraints generated.
    816 Oldfield, 0 Emsley, 816 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  1526

  Finding SS restraints...
    Secondary structure from input PDB file:
      35 helices and 2 sheets defined
      72.7% alpha, 4.0% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 0.19
  Creating SS restraints...
    Processing helix  chain 'A' and resid 25 through 33
    Processing helix  chain 'A' and resid 33 through 52
      removed outlier: 3.815A  pdb=" N   VAL A  52 " --> pdb=" O   LEU A  48 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 54 through 62
    Processing helix  chain 'A' and resid 71 through 85
    Processing helix  chain 'A' and resid 104 through 121
      removed outlier: 3.530A  pdb=" N   ASP A 121 " --> pdb=" O   LYS A 117 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 137 through 142
    Processing helix  chain 'A' and resid 161 through 178
    Processing helix  chain 'A' and resid 190 through 226
      removed outlier: 4.630A  pdb=" N   ARG A 207 " --> pdb=" O   ASP A 203 " (cutoff:3.500A)
      removed outlier: 4.711A  pdb=" N   VAL A 208 " --> pdb=" O   ARG A 204 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 227 through 255
    Processing helix  chain 'A' and resid 261 through 294
    Processing helix  chain 'A' and resid 296 through 325
      removed outlier: 5.554A  pdb=" N   HIS A 310 " --> pdb=" O   HIS A 306 " (cutoff:3.500A)
      removed outlier: 5.112A  pdb=" N   VAL A 311 " --> pdb=" O   SER A 307 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 331 through 365
      removed outlier: 4.043A  pdb=" N   LEU A 337 " --> pdb=" O   TYR A 333 " (cutoff:3.500A)
      removed outlier: 3.822A  pdb=" N   ILE A 339 " --> pdb=" O   GLN A 335 " (cutoff:3.500A)
      Proline residue:  A 340  - end of helix
      removed outlier: 4.069A  pdb=" N   ALA A 357 " --> pdb=" O   LEU A 353 " (cutoff:3.500A)
      removed outlier: 3.558A  pdb=" N   ARG A 365 " --> pdb=" O   SER A 361 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 378 through 391
    Processing helix  chain 'A' and resid 391 through 405
      removed outlier: 3.534A  pdb=" N   ILE A 395 " --> pdb=" O   TRP A 391 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 406 through 410
    Processing helix  chain 'A' and resid 427 through 438
    Processing helix  chain 'A' and resid 460 through 477
    Processing helix  chain 'A' and resid 694 through 699
    Processing helix  chain 'A' and resid 700 through 711
    Processing helix  chain 'A' and resid 730 through 749
      removed outlier: 3.923A  pdb=" N   ASP A 738 " --> pdb=" O   ILE A 734 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 763 through 798
    Processing helix  chain 'A' and resid 799 through 828
    Processing helix  chain 'A' and resid 834 through 864
      removed outlier: 3.938A  pdb=" N   LEU A 838 " --> pdb=" O   HIS A 834 " (cutoff:3.500A)
      removed outlier: 3.877A  pdb=" N   ALA A 839 " --> pdb=" O   TRP A 835 " (cutoff:3.500A)
      removed outlier: 3.621A  pdb=" N   ALA A 850 " --> pdb=" O   LEU A 846 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 865 through 867
      No H-bonds generated for 'chain 'A' and resid 865 through 867'
    Processing helix  chain 'A' and resid 868 through 896
      removed outlier: 5.108A  pdb=" N   SER A 881 " --> pdb=" O   GLY A 877 " (cutoff:3.500A)
      removed outlier: 5.044A  pdb=" N   VAL A 882 " --> pdb=" O   GLY A 878 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 897 through 900
    Processing helix  chain 'A' and resid 902 through 922
    Processing helix  chain 'A' and resid 922 through 936
      removed outlier: 4.705A  pdb=" N   THR A 928 " --> pdb=" O   ARG A 924 " (cutoff:3.500A)
      Proline residue:  A 929  - end of helix
    Processing helix  chain 'A' and resid 937 through 941
    Processing helix  chain 'B' and resid 4 through 20
      removed outlier: 3.680A  pdb=" N   ILE B   8 " --> pdb=" O   THR B   4 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 23 through 27
    Processing helix  chain 'B' and resid 33 through 38
    Processing helix  chain 'B' and resid 40 through 55
    Processing helix  chain 'B' and resid 60 through 65
      removed outlier: 3.611A  pdb=" N   ALA B  65 " --> pdb=" O   ASP B  61 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 69 through 82
    Processing sheet with id=AA1, first strand: chain 'A' and resid 125 through 129
      removed outlier: 4.129A  pdb=" N   GLN A 152 " --> pdb=" O   GLN A 129 " (cutoff:3.500A)
    Processing sheet with id=AA2, first strand: chain 'A' and resid 480 through 484

    465 hydrogen bonds defined for protein.
    1356 hydrogen bond angles defined for protein.
    Restraints generated for nucleic acids:
      0 hydrogen bonds
      0 hydrogen bond angles
      0 basepair planarities
      0 basepair parallelities
      0 stacking parallelities
  Total time for adding SS restraints: 1.03

  Time building geometry restraints manager: 0.75 seconds

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

  Histogram of bond lengths:
        1.18 -     1.31: 1039
        1.31 -     1.44: 1598
        1.44 -     1.56: 3732
        1.56 -     1.69: 1
        1.69 -     1.82: 59
  Bond restraints: 6429
  Sorted by residual:
  bond pdb=" CL3 4HH B  41 "
       pdb=" NN  4HH B  41 "
    ideal  model  delta    sigma   weight residual
    1.335  1.452 -0.117 2.00e-02 2.50e+03 3.42e+01
  bond pdb=" CQ  4HH B  41 "
       pdb=" NR  4HH B  41 "
    ideal  model  delta    sigma   weight residual
    1.345  1.452 -0.107 2.00e-02 2.50e+03 2.86e+01
  bond pdb=" OG  4HH B  41 "
       pdb=" P   4HH B  41 "
    ideal  model  delta    sigma   weight residual
    1.642  1.558  0.084 2.00e-02 2.50e+03 1.77e+01
  bond pdb=" CL3 4HH B  41 "
       pdb=" ON  4HH B  41 "
    ideal  model  delta    sigma   weight residual
    1.226  1.185  0.041 2.00e-02 2.50e+03 4.28e+00
  bond pdb=" O1P 4HH B  41 "
       pdb=" P   4HH B  41 "
    ideal  model  delta    sigma   weight residual
    1.500  1.460  0.040 2.00e-02 2.50e+03 3.98e+00
  ... (remaining 6424 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     7.35: 8753
        7.35 -    14.69: 2
       14.69 -    22.04: 2
       22.04 -    29.38: 1
       29.38 -    36.73: 1
  Bond angle restraints: 8759
  Sorted by residual:
  angle pdb=" CB  4HH B  41 "
        pdb=" OG  4HH B  41 "
        pdb=" P   4HH B  41 "
      ideal   model   delta    sigma   weight residual
     117.42  154.15  -36.73 3.00e+00 1.11e-01 1.50e+02
  angle pdb=" OG  4HH B  41 "
        pdb=" P   4HH B  41 "
        pdb=" O3P 4HH B  41 "
      ideal   model   delta    sigma   weight residual
      92.93  116.75  -23.82 3.00e+00 1.11e-01 6.30e+01
  angle pdb=" OG  4HH B  41 "
        pdb=" P   4HH B  41 "
        pdb=" O1P 4HH B  41 "
      ideal   model   delta    sigma   weight residual
     110.27   92.65   17.62 3.00e+00 1.11e-01 3.45e+01
  angle pdb=" O1P 4HH B  41 "
        pdb=" P   4HH B  41 "
        pdb=" O2P 4HH B  41 "
      ideal   model   delta    sigma   weight residual
     119.62  104.33   15.29 3.00e+00 1.11e-01 2.60e+01
  angle pdb=" C   GLN A 826 "
        pdb=" N   HIS A 827 "
        pdb=" CA  HIS A 827 "
      ideal   model   delta    sigma   weight residual
     121.54  114.09    7.45 1.91e+00 2.74e-01 1.52e+01
  ... (remaining 8754 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    22.50: 3629
       22.50 -    45.00: 205
       45.00 -    67.49: 18
       67.49 -    89.99: 9
       89.99 -   112.49: 3
  Dihedral angle restraints: 3864
    sinusoidal: 1494
      harmonic: 2370
  Sorted by residual:
  dihedral pdb=" CA  MET A 451 "
           pdb=" C   MET A 451 "
           pdb=" N   ILE A 452 "
           pdb=" CA  ILE A 452 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  157.86   22.14     0      5.00e+00 4.00e-02 1.96e+01
  dihedral pdb=" NR  4HH B  41 "
           pdb=" CS  4HH B  41 "
           pdb=" CT  4HH B  41 "
           pdb=" SU  4HH B  41 "
      ideal   model   delta sinusoidal    sigma   weight residual
     179.08  -68.43 -112.49     1      3.00e+01 1.11e-03 1.47e+01
  dihedral pdb=" CB  GLU B  46 "
           pdb=" CG  GLU B  46 "
           pdb=" CD  GLU B  46 "
           pdb=" OE1 GLU B  46 "
      ideal   model   delta sinusoidal    sigma   weight residual
       0.00   92.34  -92.34     1      3.00e+01 1.11e-03 1.11e+01
  ... (remaining 3861 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.054: 847
       0.054 -    0.109: 178
       0.109 -    0.163: 16
       0.163 -    0.218: 1
       0.218 -    0.272: 1
  Chirality restraints: 1043
  Sorted by residual:
  chirality pdb=" CB  ILE B  39 "
            pdb=" CA  ILE B  39 "
            pdb=" CG1 ILE B  39 "
            pdb=" CG2 ILE B  39 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.64    2.37    0.27 2.00e-01 2.50e+01 1.85e+00
  chirality pdb=" CA  PHE A 767 "
            pdb=" N   PHE A 767 "
            pdb=" C   PHE A 767 "
            pdb=" CB  PHE A 767 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.33    0.18 2.00e-01 2.50e+01 8.50e-01
  chirality pdb=" CG  LEU B  42 "
            pdb=" CB  LEU B  42 "
            pdb=" CD1 LEU B  42 "
            pdb=" CD2 LEU B  42 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.59   -2.73    0.14 2.00e-01 2.50e+01 4.98e-01
  ... (remaining 1040 not shown)

  Planarity restraints: 1109
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   TRP A 941 "    0.037 5.00e-02 4.00e+02   5.64e-02 5.09e+00
        pdb=" N   PRO A 942 "   -0.098 5.00e-02 4.00e+02
        pdb=" CA  PRO A 942 "    0.032 5.00e-02 4.00e+02
        pdb=" CD  PRO A 942 "    0.028 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   GLU B  23 "    0.032 5.00e-02 4.00e+02   4.93e-02 3.89e+00
        pdb=" N   PRO B  24 "   -0.085 5.00e-02 4.00e+02
        pdb=" CA  PRO B  24 "    0.026 5.00e-02 4.00e+02
        pdb=" CD  PRO B  24 "    0.027 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  SER A 352 "   -0.009 2.00e-02 2.50e+03   1.79e-02 3.22e+00
        pdb=" C   SER A 352 "    0.031 2.00e-02 2.50e+03
        pdb=" O   SER A 352 "   -0.012 2.00e-02 2.50e+03
        pdb=" N   LEU A 353 "   -0.010 2.00e-02 2.50e+03
  ... (remaining 1106 not shown)

  Histogram of nonbonded interaction distances:
        2.16 -     2.70: 176
        2.70 -     3.25: 7018
        3.25 -     3.80: 11225
        3.80 -     4.35: 13444
        4.35 -     4.90: 22891
  Nonbonded interactions: 54754
  Sorted by model distance:
  nonbonded pdb=" OG  SER A 143 "
            pdb=" OD1 ASP A 145 "
     model   vdw
     2.155 3.040
  nonbonded pdb=" OG1 THR A 318 "
            pdb=" OD1 ASP A 851 "
     model   vdw
     2.210 3.040
  nonbonded pdb=" OG1 THR B  69 "
            pdb=" OD2 ASP B  72 "
     model   vdw
     2.250 3.040
  nonbonded pdb=" OE2 GLU A 289 "
            pdb=" NH2 ARG A 859 "
     model   vdw
     2.251 3.120
  nonbonded pdb=" OG  SER A  91 "
            pdb=" OG1 THR A 155 "
     model   vdw
     2.258 3.040
  ... (remaining 54749 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 individual isotropic
Make a string to write initial .geo file
Internal consistency checks
Time:
  Set random seed:                         0.000
  Set model cs if undefined:               0.000
  Decide on map wrapping:                  0.000
  Normalize map: mean=0, sd=1:             1.270
  Set stop_for_unknowns flag:              0.000
  Assert model is a single copy model:     0.000
  Assert all atoms have isotropic ADPs:    0.000
  Construct map_model_manager:             0.010
  Extract box with map and model:          0.090
  Check model and map are aligned:         0.020
  Set scattering table:                    0.020
  Process input model:                     7.670
  Find NCS groups from input model:        0.040
  Set up NCS constraints:                  0.010
  Set refine NCS operators:                0.000
  Adjust number of macro_cycles:           0.000
  Reset NCS operators:                     0.000
  Extract rigid body selections:           0.000
  Check and reset occupancies:             0.000
  Load rotamer database and sin/cos tables:1.490
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   10.620
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7920
moved from start:          0.0000

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.117   6429  Z= 0.204
  Angle     :  0.800  36.727   8759  Z= 0.356
  Chirality :  0.043   0.272   1043
  Planarity :  0.005   0.056   1109
  Dihedral  : 14.219 112.488   2338
  Min Nonbonded Distance : 2.155

Molprobity Statistics.
  All-atom Clashscore : 13.98
  Ramachandran Plot:
    Outliers :  0.12 %
    Allowed  :  2.82 %
    Favored  : 97.06 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  0.15 %
    Favored  : 99.85 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.38 %
    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:  1.56 (0.30), residues: 816
  helix:  1.53 (0.22), residues: 552
  sheet:  0.12 (0.74), residues: 46
  loop :  0.12 (0.46), residues: 218

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARG A 444 
 TYR   0.009   0.001   TYR B  55 
 PHE   0.010   0.001   PHE A 767 
 TRP   0.009   0.001   TRP A 381 
 HIS   0.003   0.001   HIS A 108 

Details of bonding type rmsd
  covalent geometry    : bond        0.00443 ( 6429)
  covalent geometry    : angle       0.80012 ( 8759)
  hydrogen bonds       : bond        0.11293 (  465)
  hydrogen bonds       : angle       5.75511 ( 1356)

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

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

  1632 Ramachandran restraints generated.
    816 Oldfield, 0 Emsley, 816 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1632 Ramachandran restraints generated.
    816 Oldfield, 0 Emsley, 816 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  106 residues out of total 671 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 106
  time to evaluate  : 0.221 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  248 MET cc_start: 0.8085 (tpp) cc_final: 0.7752 (tpt)
REVERT: A  742 GLN cc_start: 0.9294 (tp-100) cc_final: 0.8932 (tp-100)
REVERT: B   28 THR cc_start: 0.7898 (p) cc_final: 0.7581 (p)
REVERT: B   31 LYS cc_start: 0.7177 (ptpp) cc_final: 0.6936 (ptpp)
REVERT: B   68 ARG cc_start: 0.8645 (ptt90) cc_final: 0.8395 (ptt90)
REVERT: B   76 TYR cc_start: 0.8536 (t80) cc_final: 0.8324 (t80)
  outliers start: 0
  outliers final: 0
  residues processed: 106
  average time/residue: 0.0631
  time to fit residues: 9.5548
Evaluate side-chains
  82 residues out of total 671 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 82
  time to evaluate  : 0.237 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 82
   random chunks:
   chunk 49 optimal weight:    0.8980
   chunk 53 optimal weight:    5.9990
   chunk 5 optimal weight:    1.9990
   chunk 33 optimal weight:    0.6980
   chunk 65 optimal weight:    0.7980
   chunk 62 optimal weight:    0.8980
   chunk 51 optimal weight:    1.9990
   chunk 38 optimal weight:    0.7980
   chunk 61 optimal weight:    2.9990
   chunk 45 optimal weight:    1.9990
   chunk 74 optimal weight:    4.9990
   overall best weight:    0.8180

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

Flipped N/Q/H residues before XYZ refinement:
A 108 HIS
B  50 GLN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3392 r_free = 0.3392 target = 0.093469 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 36)----------------|
| r_work = 0.3070 r_free = 0.3070 target = 0.074001 restraints weight = 12504.302|
|-----------------------------------------------------------------------------|
r_work (start): 0.3069 rms_B_bonded: 3.03
r_work: 0.2930 rms_B_bonded: 3.59 restraints_weight: 0.5000
r_work (final): 0.2930
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7957
moved from start:          0.0930

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.034   6429  Z= 0.175
  Angle     :  0.577  10.305   8759  Z= 0.297
  Chirality :  0.042   0.143   1043
  Planarity :  0.005   0.050   1109
  Dihedral  :  7.846  84.367    913
  Min Nonbonded Distance : 2.552

Molprobity Statistics.
  All-atom Clashscore : 12.80
  Ramachandran Plot:
    Outliers :  0.12 %
    Allowed  :  2.57 %
    Favored  : 97.30 %
  Rotamer:
    Outliers :  1.19 %
    Allowed  :  8.79 %
    Favored  : 90.01 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.38 %
    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:  1.55 (0.30), residues: 816
  helix:  1.51 (0.22), residues: 557
  sheet:  0.09 (0.74), residues: 46
  loop :  0.15 (0.46), residues: 213

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.000   ARG B  68 
 TYR   0.014   0.001   TYR B  55 
 PHE   0.012   0.001   PHE A 251 
 TRP   0.010   0.001   TRP A 825 
 HIS   0.003   0.001   HIS A 827 

Details of bonding type rmsd
  covalent geometry    : bond        0.00397 ( 6429)
  covalent geometry    : angle       0.57732 ( 8759)
  hydrogen bonds       : bond        0.04448 (  465)
  hydrogen bonds       : angle       5.08388 ( 1356)

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

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

  1632 Ramachandran restraints generated.
    816 Oldfield, 0 Emsley, 816 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1632 Ramachandran restraints generated.
    816 Oldfield, 0 Emsley, 816 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  102 residues out of total 671 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 8
    poor density    : 94
  time to evaluate  : 0.235 
Fit side-chains
   revert: symmetry clash
REVERT: A   94 MET cc_start: 0.8899 (mmp) cc_final: 0.8512 (mmp)
REVERT: A  248 MET cc_start: 0.8131 (tpp) cc_final: 0.7863 (tpt)
REVERT: A  702 ASP cc_start: 0.8699 (t0) cc_final: 0.7838 (t0)
REVERT: A  705 ARG cc_start: 0.9248 (ttp-110) cc_final: 0.8462 (ttp-110)
REVERT: A  742 GLN cc_start: 0.9418 (tp-100) cc_final: 0.9108 (tp-100)
REVERT: B   31 LYS cc_start: 0.7768 (ptpp) cc_final: 0.7550 (ptpp)
REVERT: B   55 TYR cc_start: 0.8678 (m-80) cc_final: 0.8320 (m-80)
REVERT: B   68 ARG cc_start: 0.9000 (ptt90) cc_final: 0.8424 (ptm-80)
REVERT: B   76 TYR cc_start: 0.8561 (t80) cc_final: 0.8229 (t80)
  outliers start: 8
  outliers final: 8
  residues processed: 99
  average time/residue: 0.0634
  time to fit residues: 8.7497
Evaluate side-chains
  91 residues out of total 671 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 8
    poor density    : 83
  time to evaluate  : 0.238 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  232 ILE
Chi-restraints excluded: chain A residue  235 LEU
Chi-restraints excluded: chain A residue  795 ILE
Chi-restraints excluded: chain A residue  817 SER
Chi-restraints excluded: chain A residue  828 ILE
Chi-restraints excluded: chain A residue  838 LEU
Chi-restraints excluded: chain B residue   45 VAL
Chi-restraints excluded: chain B residue   77 ILE
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 82
   random chunks:
   chunk 67 optimal weight:    0.6980
   chunk 80 optimal weight:    0.4980
   chunk 12 optimal weight:    1.9990
   chunk 73 optimal weight:    0.8980
   chunk 69 optimal weight:    0.5980
   chunk 4 optimal weight:    0.8980
   chunk 27 optimal weight:    0.4980
   chunk 75 optimal weight:    0.0770
   chunk 74 optimal weight:    0.8980
   chunk 52 optimal weight:    0.9980
   chunk 35 optimal weight:    2.9990
   overall best weight:    0.4738

-------------------------------------------------------------------------------
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 = 0.3406 r_free = 0.3406 target = 0.094442 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 38)----------------|
| r_work = 0.3091 r_free = 0.3091 target = 0.075163 restraints weight = 12397.336|
|-----------------------------------------------------------------------------|
r_work (start): 0.3084 rms_B_bonded: 3.03
r_work: 0.2947 rms_B_bonded: 3.60 restraints_weight: 0.5000
r_work (final): 0.2947
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7971
moved from start:          0.1154

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.030   6429  Z= 0.138
  Angle     :  0.539   6.738   8759  Z= 0.278
  Chirality :  0.041   0.144   1043
  Planarity :  0.005   0.051   1109
  Dihedral  :  7.500  80.587    913
  Min Nonbonded Distance : 2.588

Molprobity Statistics.
  All-atom Clashscore : 12.25
  Ramachandran Plot:
    Outliers :  0.12 %
    Allowed  :  2.57 %
    Favored  : 97.30 %
  Rotamer:
    Outliers :  1.19 %
    Allowed  : 12.52 %
    Favored  : 86.29 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.38 %
    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:  1.63 (0.30), residues: 816
  helix:  1.57 (0.22), residues: 559
  sheet:  0.19 (0.74), residues: 46
  loop :  0.14 (0.47), residues: 211

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG B  68 
 TYR   0.014   0.001   TYR B  55 
 PHE   0.012   0.001   PHE A 890 
 TRP   0.009   0.001   TRP A 825 
 HIS   0.003   0.001   HIS A 827 

Details of bonding type rmsd
  covalent geometry    : bond        0.00304 ( 6429)
  covalent geometry    : angle       0.53867 ( 8759)
  hydrogen bonds       : bond        0.04128 (  465)
  hydrogen bonds       : angle       4.89158 ( 1356)

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

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

  1632 Ramachandran restraints generated.
    816 Oldfield, 0 Emsley, 816 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1632 Ramachandran restraints generated.
    816 Oldfield, 0 Emsley, 816 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  107 residues out of total 671 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 8
    poor density    : 99
  time to evaluate  : 0.232 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   94 MET cc_start: 0.8996 (mmp) cc_final: 0.8587 (mmp)
REVERT: A  742 GLN cc_start: 0.9417 (tp-100) cc_final: 0.9103 (tp-100)
REVERT: B   31 LYS cc_start: 0.7714 (ptpp) cc_final: 0.7480 (ptpp)
REVERT: B   55 TYR cc_start: 0.8796 (m-80) cc_final: 0.8508 (m-10)
REVERT: B   68 ARG cc_start: 0.9015 (ptt90) cc_final: 0.8461 (ptm-80)
REVERT: B   76 TYR cc_start: 0.8497 (t80) cc_final: 0.8235 (t80)
  outliers start: 8
  outliers final: 7
  residues processed: 102
  average time/residue: 0.0630
  time to fit residues: 9.1339
Evaluate side-chains
  98 residues out of total 671 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 7
    poor density    : 91
  time to evaluate  : 0.245 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  232 ILE
Chi-restraints excluded: chain A residue  235 LEU
Chi-restraints excluded: chain A residue  817 SER
Chi-restraints excluded: chain A residue  828 ILE
Chi-restraints excluded: chain A residue  838 LEU
Chi-restraints excluded: chain B residue   45 VAL
Chi-restraints excluded: chain B residue   77 ILE
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 82
   random chunks:
   chunk 78 optimal weight:    3.9990
   chunk 17 optimal weight:    2.9990
   chunk 62 optimal weight:    0.8980
   chunk 31 optimal weight:    4.9990
   chunk 3 optimal weight:    1.9990
   chunk 42 optimal weight:    0.5980
   chunk 9 optimal weight:    0.8980
   chunk 80 optimal weight:    3.9990
   chunk 61 optimal weight:    0.6980
   chunk 51 optimal weight:    5.9990
   chunk 23 optimal weight:    0.6980
   overall best weight:    0.7580

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

Flipped N/Q/H residues before XYZ refinement:
A 198 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3401 r_free = 0.3401 target = 0.093970 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 32)----------------|
| r_work = 0.3083 r_free = 0.3083 target = 0.074734 restraints weight = 12431.295|
|-----------------------------------------------------------------------------|
r_work (start): 0.3050 rms_B_bonded: 2.97
r_work: 0.2914 rms_B_bonded: 3.55 restraints_weight: 0.5000
r_work (final): 0.2914
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7981
moved from start:          0.1337

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.032   6429  Z= 0.160
  Angle     :  0.550   8.055   8759  Z= 0.281
  Chirality :  0.041   0.153   1043
  Planarity :  0.005   0.050   1109
  Dihedral  :  7.278  77.999    913
  Min Nonbonded Distance : 2.590

Molprobity Statistics.
  All-atom Clashscore : 12.33
  Ramachandran Plot:
    Outliers :  0.12 %
    Allowed  :  2.82 %
    Favored  : 97.06 %
  Rotamer:
    Outliers :  2.38 %
    Allowed  : 14.61 %
    Favored  : 83.01 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.38 %
    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 (0.30), residues: 816
  helix:  1.63 (0.22), residues: 558
  sheet:  0.24 (0.76), residues: 46
  loop :  0.14 (0.47), residues: 212

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG A  62 
 TYR   0.009   0.001   TYR B  55 
 PHE   0.009   0.001   PHE A 767 
 TRP   0.009   0.001   TRP A 825 
 HIS   0.003   0.001   HIS A 827 

Details of bonding type rmsd
  covalent geometry    : bond        0.00363 ( 6429)
  covalent geometry    : angle       0.54960 ( 8759)
  hydrogen bonds       : bond        0.04119 (  465)
  hydrogen bonds       : angle       4.84747 ( 1356)

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

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

  1632 Ramachandran restraints generated.
    816 Oldfield, 0 Emsley, 816 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1632 Ramachandran restraints generated.
    816 Oldfield, 0 Emsley, 816 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  114 residues out of total 671 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 98
  time to evaluate  : 0.235 
Fit side-chains
   revert: symmetry clash
REVERT: A   94 MET cc_start: 0.9032 (mmp) cc_final: 0.8440 (mmp)
REVERT: A  702 ASP cc_start: 0.8853 (t70) cc_final: 0.8652 (t0)
REVERT: A  705 ARG cc_start: 0.9343 (ttp-110) cc_final: 0.8970 (ttp-110)
REVERT: A  742 GLN cc_start: 0.9417 (tp-100) cc_final: 0.9110 (tp-100)
REVERT: A  935 MET cc_start: 0.8852 (mtp) cc_final: 0.8587 (mtt)
REVERT: B   55 TYR cc_start: 0.8913 (m-80) cc_final: 0.8648 (m-80)
REVERT: B   67 LEU cc_start: 0.8157 (mt) cc_final: 0.7839 (tp)
REVERT: B   76 TYR cc_start: 0.8526 (t80) cc_final: 0.8248 (t80)
  outliers start: 16
  outliers final: 10
  residues processed: 108
  average time/residue: 0.0656
  time to fit residues: 10.0092
Evaluate side-chains
  98 residues out of total 671 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 88
  time to evaluate  : 0.236 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  232 ILE
Chi-restraints excluded: chain A residue  235 LEU
Chi-restraints excluded: chain A residue  807 VAL
Chi-restraints excluded: chain A residue  817 SER
Chi-restraints excluded: chain A residue  828 ILE
Chi-restraints excluded: chain A residue  838 LEU
Chi-restraints excluded: chain A residue  904 VAL
Chi-restraints excluded: chain B residue    9 ILE
Chi-restraints excluded: chain B residue   45 VAL
Chi-restraints excluded: chain B residue   77 ILE
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 82
   random chunks:
   chunk 61 optimal weight:    2.9990
   chunk 29 optimal weight:    0.6980
   chunk 78 optimal weight:    0.9980
   chunk 80 optimal weight:    2.9990
   chunk 27 optimal weight:    1.9990
   chunk 10 optimal weight:    3.9990
   chunk 38 optimal weight:    2.9990
   chunk 34 optimal weight:    2.9990
   chunk 5 optimal weight:    0.8980
   chunk 43 optimal weight:    0.9990
   chunk 11 optimal weight:    0.0870
   overall best weight:    0.7360

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

Flipped N/Q/H residues before XYZ refinement:
A 198 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3399 r_free = 0.3399 target = 0.093844 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 34)----------------|
| r_work = 0.3077 r_free = 0.3077 target = 0.074424 restraints weight = 12726.246|
|-----------------------------------------------------------------------------|
r_work (start): 0.3045 rms_B_bonded: 2.99
r_work: 0.2908 rms_B_bonded: 3.57 restraints_weight: 0.5000
r_work (final): 0.2908
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7985
moved from start:          0.1443

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.034   6429  Z= 0.158
  Angle     :  0.559   7.570   8759  Z= 0.282
  Chirality :  0.041   0.158   1043
  Planarity :  0.005   0.052   1109
  Dihedral  :  7.197  76.258    913
  Min Nonbonded Distance : 2.501

Molprobity Statistics.
  All-atom Clashscore : 12.73
  Ramachandran Plot:
    Outliers :  0.12 %
    Allowed  :  2.94 %
    Favored  : 96.94 %
  Rotamer:
    Outliers :  2.83 %
    Allowed  : 15.65 %
    Favored  : 81.52 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.38 %
    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:  1.71 (0.30), residues: 816
  helix:  1.63 (0.22), residues: 558
  sheet:  0.26 (0.77), residues: 46
  loop :  0.15 (0.47), residues: 212

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.007   0.000   ARG B  68 
 TYR   0.009   0.001   TYR B  55 
 PHE   0.009   0.001   PHE A 440 
 TRP   0.009   0.001   TRP A 825 
 HIS   0.003   0.001   HIS A 827 

Details of bonding type rmsd
  covalent geometry    : bond        0.00361 ( 6429)
  covalent geometry    : angle       0.55855 ( 8759)
  hydrogen bonds       : bond        0.04076 (  465)
  hydrogen bonds       : angle       4.81827 ( 1356)

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

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

  1632 Ramachandran restraints generated.
    816 Oldfield, 0 Emsley, 816 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1632 Ramachandran restraints generated.
    816 Oldfield, 0 Emsley, 816 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  114 residues out of total 671 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 19
    poor density    : 95
  time to evaluate  : 0.230 
Fit side-chains
   revert: symmetry clash
REVERT: A   94 MET cc_start: 0.8991 (mmp) cc_final: 0.8539 (mmp)
REVERT: A  448 GLU cc_start: 0.7789 (mm-30) cc_final: 0.7472 (mm-30)
REVERT: A  476 GLN cc_start: 0.9382 (mm-40) cc_final: 0.9151 (mm-40)
REVERT: A  702 ASP cc_start: 0.8846 (t70) cc_final: 0.7440 (t0)
REVERT: A  705 ARG cc_start: 0.9344 (ttp-110) cc_final: 0.8617 (mtm-85)
REVERT: A  742 GLN cc_start: 0.9424 (tp-100) cc_final: 0.9112 (tp-100)
REVERT: A  935 MET cc_start: 0.8863 (mtp) cc_final: 0.8602 (mtt)
REVERT: B   55 TYR cc_start: 0.8980 (m-80) cc_final: 0.8625 (m-80)
REVERT: B   68 ARG cc_start: 0.9007 (ptt90) cc_final: 0.8374 (ptm-80)
REVERT: B   76 TYR cc_start: 0.8544 (t80) cc_final: 0.8302 (t80)
  outliers start: 19
  outliers final: 12
  residues processed: 106
  average time/residue: 0.0626
  time to fit residues: 9.3332
Evaluate side-chains
  101 residues out of total 671 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 89
  time to evaluate  : 0.170 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  232 ILE
Chi-restraints excluded: chain A residue  235 LEU
Chi-restraints excluded: chain A residue  389 VAL
Chi-restraints excluded: chain A residue  795 ILE
Chi-restraints excluded: chain A residue  807 VAL
Chi-restraints excluded: chain A residue  817 SER
Chi-restraints excluded: chain A residue  828 ILE
Chi-restraints excluded: chain A residue  838 LEU
Chi-restraints excluded: chain A residue  904 VAL
Chi-restraints excluded: chain B residue    9 ILE
Chi-restraints excluded: chain B residue   45 VAL
Chi-restraints excluded: chain B residue   77 ILE
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 82
   random chunks:
   chunk 33 optimal weight:    2.9990
   chunk 38 optimal weight:    2.9990
   chunk 22 optimal weight:    0.6980
   chunk 67 optimal weight:    0.2980
   chunk 76 optimal weight:    2.9990
   chunk 58 optimal weight:    0.9990
   chunk 68 optimal weight:    0.0870
   chunk 46 optimal weight:    2.9990
   chunk 27 optimal weight:    1.9990
   chunk 54 optimal weight:    0.8980
   chunk 43 optimal weight:    0.8980
   overall best weight:    0.5758

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

Flipped N/Q/H residues before XYZ refinement:
A 152 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3406 r_free = 0.3406 target = 0.094623 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 35)----------------|
| r_work = 0.3080 r_free = 0.3080 target = 0.075065 restraints weight = 12654.433|
|-----------------------------------------------------------------------------|
r_work (start): 0.3056 rms_B_bonded: 3.04
r_work: 0.2920 rms_B_bonded: 3.59 restraints_weight: 0.5000
r_work (final): 0.2920
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7944
moved from start:          0.1568

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.029   6429  Z= 0.143
  Angle     :  0.544   6.985   8759  Z= 0.277
  Chirality :  0.041   0.159   1043
  Planarity :  0.004   0.051   1109
  Dihedral  :  7.072  74.350    913
  Min Nonbonded Distance : 2.557

Molprobity Statistics.
  All-atom Clashscore : 12.25
  Ramachandran Plot:
    Outliers :  0.12 %
    Allowed  :  2.94 %
    Favored  : 96.94 %
  Rotamer:
    Outliers :  2.68 %
    Allowed  : 16.99 %
    Favored  : 80.33 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.38 %
    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:  1.77 (0.30), residues: 816
  helix:  1.68 (0.22), residues: 558
  sheet:  0.30 (0.77), residues: 46
  loop :  0.18 (0.47), residues: 212

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.000   ARG B  68 
 TYR   0.010   0.001   TYR B  55 
 PHE   0.010   0.001   PHE A 767 
 TRP   0.008   0.001   TRP A 825 
 HIS   0.003   0.001   HIS A 827 

Details of bonding type rmsd
  covalent geometry    : bond        0.00322 ( 6429)
  covalent geometry    : angle       0.54448 ( 8759)
  hydrogen bonds       : bond        0.03951 (  465)
  hydrogen bonds       : angle       4.76171 ( 1356)

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

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

  1632 Ramachandran restraints generated.
    816 Oldfield, 0 Emsley, 816 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1632 Ramachandran restraints generated.
    816 Oldfield, 0 Emsley, 816 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  117 residues out of total 671 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 18
    poor density    : 99
  time to evaluate  : 0.183 
Fit side-chains
   revert: symmetry clash
REVERT: A   94 MET cc_start: 0.8943 (mmt) cc_final: 0.8436 (mmp)
REVERT: A  445 MET cc_start: 0.9105 (tpp) cc_final: 0.8496 (tpp)
REVERT: A  476 GLN cc_start: 0.9358 (mm-40) cc_final: 0.9146 (mm-40)
REVERT: A  702 ASP cc_start: 0.8849 (t70) cc_final: 0.7451 (t0)
REVERT: A  705 ARG cc_start: 0.9347 (ttp-110) cc_final: 0.8583 (mtm-85)
REVERT: A  742 GLN cc_start: 0.9424 (tp-100) cc_final: 0.9116 (tp-100)
REVERT: B   55 TYR cc_start: 0.9010 (m-80) cc_final: 0.8671 (m-80)
REVERT: B   68 ARG cc_start: 0.8976 (ptt90) cc_final: 0.8571 (ptm-80)
REVERT: B   72 ASP cc_start: 0.8786 (m-30) cc_final: 0.8317 (t0)
REVERT: B   76 TYR cc_start: 0.8482 (t80) cc_final: 0.8266 (t80)
  outliers start: 18
  outliers final: 12
  residues processed: 111
  average time/residue: 0.0647
  time to fit residues: 10.2843
Evaluate side-chains
  106 residues out of total 671 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 94
  time to evaluate  : 0.228 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  232 ILE
Chi-restraints excluded: chain A residue  235 LEU
Chi-restraints excluded: chain A residue  389 VAL
Chi-restraints excluded: chain A residue  807 VAL
Chi-restraints excluded: chain A residue  817 SER
Chi-restraints excluded: chain A residue  828 ILE
Chi-restraints excluded: chain A residue  838 LEU
Chi-restraints excluded: chain A residue  904 VAL
Chi-restraints excluded: chain B residue    9 ILE
Chi-restraints excluded: chain B residue   39 ILE
Chi-restraints excluded: chain B residue   45 VAL
Chi-restraints excluded: chain B residue   77 ILE
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 82
   random chunks:
   chunk 71 optimal weight:    1.9990
   chunk 30 optimal weight:    0.5980
   chunk 31 optimal weight:    0.6980
   chunk 41 optimal weight:    0.5980
   chunk 67 optimal weight:    0.3980
   chunk 64 optimal weight:    0.8980
   chunk 52 optimal weight:    0.5980
   chunk 24 optimal weight:    0.6980
   chunk 50 optimal weight:    0.3980
   chunk 72 optimal weight:    0.9980
   chunk 47 optimal weight:    0.0570
   overall best weight:    0.4098

-------------------------------------------------------------------------------
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 = 0.3417 r_free = 0.3417 target = 0.094983 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 34)----------------|
| r_work = 0.3105 r_free = 0.3105 target = 0.075853 restraints weight = 12573.632|
|-----------------------------------------------------------------------------|
r_work (start): 0.3087 rms_B_bonded: 2.99
r_work: 0.2951 rms_B_bonded: 3.58 restraints_weight: 0.5000
r_work (final): 0.2951
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7944
moved from start:          0.1681

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.035   6429  Z= 0.131
  Angle     :  0.555   8.025   8759  Z= 0.284
  Chirality :  0.041   0.162   1043
  Planarity :  0.004   0.053   1109
  Dihedral  :  7.027  73.252    913
  Min Nonbonded Distance : 2.543

Molprobity Statistics.
  All-atom Clashscore : 12.02
  Ramachandran Plot:
    Outliers :  0.12 %
    Allowed  :  2.94 %
    Favored  : 96.94 %
  Rotamer:
    Outliers :  2.68 %
    Allowed  : 17.29 %
    Favored  : 80.03 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.38 %
    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:  1.83 (0.30), residues: 816
  helix:  1.73 (0.22), residues: 558
  sheet:  0.34 (0.77), residues: 46
  loop :  0.18 (0.47), residues: 212

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARG B  68 
 TYR   0.010   0.001   TYR B  55 
 PHE   0.016   0.001   PHE A 818 
 TRP   0.007   0.001   TRP A 825 
 HIS   0.002   0.001   HIS A 827 

Details of bonding type rmsd
  covalent geometry    : bond        0.00290 ( 6429)
  covalent geometry    : angle       0.55522 ( 8759)
  hydrogen bonds       : bond        0.03902 (  465)
  hydrogen bonds       : angle       4.73409 ( 1356)

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

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

  1632 Ramachandran restraints generated.
    816 Oldfield, 0 Emsley, 816 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1632 Ramachandran restraints generated.
    816 Oldfield, 0 Emsley, 816 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  113 residues out of total 671 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 18
    poor density    : 95
  time to evaluate  : 0.225 
Fit side-chains
   revert: symmetry clash
REVERT: A   94 MET cc_start: 0.8930 (mmt) cc_final: 0.8494 (mmp)
REVERT: A  476 GLN cc_start: 0.9342 (mm-40) cc_final: 0.9135 (mm-40)
REVERT: A  742 GLN cc_start: 0.9425 (tp-100) cc_final: 0.9117 (tp-100)
REVERT: A  935 MET cc_start: 0.8768 (mtp) cc_final: 0.8492 (mtt)
REVERT: B   55 TYR cc_start: 0.9019 (m-80) cc_final: 0.8730 (m-80)
REVERT: B   68 ARG cc_start: 0.8963 (ptt90) cc_final: 0.8405 (ptm-80)
REVERT: B   72 ASP cc_start: 0.8792 (m-30) cc_final: 0.8056 (m-30)
REVERT: B   76 TYR cc_start: 0.8468 (t80) cc_final: 0.8259 (t80)
  outliers start: 18
  outliers final: 14
  residues processed: 107
  average time/residue: 0.0590
  time to fit residues: 9.2221
Evaluate side-chains
  104 residues out of total 671 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 90
  time to evaluate  : 0.228 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   51 VAL
Chi-restraints excluded: chain A residue  232 ILE
Chi-restraints excluded: chain A residue  235 LEU
Chi-restraints excluded: chain A residue  389 VAL
Chi-restraints excluded: chain A residue  795 ILE
Chi-restraints excluded: chain A residue  807 VAL
Chi-restraints excluded: chain A residue  828 ILE
Chi-restraints excluded: chain A residue  838 LEU
Chi-restraints excluded: chain A residue  904 VAL
Chi-restraints excluded: chain B residue    9 ILE
Chi-restraints excluded: chain B residue   39 ILE
Chi-restraints excluded: chain B residue   42 LEU
Chi-restraints excluded: chain B residue   45 VAL
Chi-restraints excluded: chain B residue   77 ILE
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 82
   random chunks:
   chunk 56 optimal weight:    3.9990
   chunk 71 optimal weight:    0.5980
   chunk 30 optimal weight:    0.8980
   chunk 66 optimal weight:    1.9990
   chunk 40 optimal weight:    0.7980
   chunk 61 optimal weight:    0.9980
   chunk 68 optimal weight:    0.7980
   chunk 31 optimal weight:    0.6980
   chunk 10 optimal weight:    6.9990
   chunk 15 optimal weight:    1.9990
   chunk 67 optimal weight:    0.7980
   overall best weight:    0.7380

-------------------------------------------------------------------------------
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 = 0.3399 r_free = 0.3399 target = 0.093695 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 31)----------------|
| r_work = 0.3081 r_free = 0.3081 target = 0.074535 restraints weight = 12585.694|
|-----------------------------------------------------------------------------|
r_work (start): 0.3050 rms_B_bonded: 2.97
r_work: 0.2914 rms_B_bonded: 3.54 restraints_weight: 0.5000
r_work (final): 0.2914
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7981
moved from start:          0.1698

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.033   6429  Z= 0.157
  Angle     :  0.558   7.648   8759  Z= 0.286
  Chirality :  0.041   0.173   1043
  Planarity :  0.004   0.053   1109
  Dihedral  :  6.961  71.747    913
  Min Nonbonded Distance : 2.530

Molprobity Statistics.
  All-atom Clashscore : 12.18
  Ramachandran Plot:
    Outliers :  0.12 %
    Allowed  :  2.94 %
    Favored  : 96.94 %
  Rotamer:
    Outliers :  2.38 %
    Allowed  : 17.88 %
    Favored  : 79.73 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.38 %
    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:  1.82 (0.30), residues: 816
  helix:  1.72 (0.22), residues: 558
  sheet:  0.35 (0.77), residues: 46
  loop :  0.18 (0.47), residues: 212

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG B  68 
 TYR   0.009   0.001   TYR B  55 
 PHE   0.014   0.001   PHE A 818 
 TRP   0.010   0.001   TRP A 825 
 HIS   0.003   0.001   HIS A 827 

Details of bonding type rmsd
  covalent geometry    : bond        0.00360 ( 6429)
  covalent geometry    : angle       0.55818 ( 8759)
  hydrogen bonds       : bond        0.03980 (  465)
  hydrogen bonds       : angle       4.74719 ( 1356)

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

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

  1632 Ramachandran restraints generated.
    816 Oldfield, 0 Emsley, 816 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1632 Ramachandran restraints generated.
    816 Oldfield, 0 Emsley, 816 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  108 residues out of total 671 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 92
  time to evaluate  : 0.223 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   94 MET cc_start: 0.8892 (mmt) cc_final: 0.8549 (mmt)
REVERT: A  476 GLN cc_start: 0.9343 (mm-40) cc_final: 0.9140 (mm-40)
REVERT: A  702 ASP cc_start: 0.8936 (t0) cc_final: 0.8437 (t0)
REVERT: A  705 ARG cc_start: 0.9380 (ttp-110) cc_final: 0.8802 (ttp-110)
REVERT: A  742 GLN cc_start: 0.9420 (tp-100) cc_final: 0.9137 (tp-100)
REVERT: A  935 MET cc_start: 0.8777 (mtp) cc_final: 0.8524 (mtt)
REVERT: B   54 LYS cc_start: 0.9192 (tttp) cc_final: 0.8590 (ttpp)
REVERT: B   68 ARG cc_start: 0.8974 (ptt90) cc_final: 0.8493 (ptm-80)
REVERT: B   72 ASP cc_start: 0.8789 (m-30) cc_final: 0.8358 (t0)
REVERT: B   76 TYR cc_start: 0.8603 (t80) cc_final: 0.8268 (t80)
  outliers start: 16
  outliers final: 14
  residues processed: 103
  average time/residue: 0.0626
  time to fit residues: 9.2115
Evaluate side-chains
  100 residues out of total 671 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 86
  time to evaluate  : 0.230 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   51 VAL
Chi-restraints excluded: chain A residue  232 ILE
Chi-restraints excluded: chain A residue  235 LEU
Chi-restraints excluded: chain A residue  389 VAL
Chi-restraints excluded: chain A residue  795 ILE
Chi-restraints excluded: chain A residue  807 VAL
Chi-restraints excluded: chain A residue  817 SER
Chi-restraints excluded: chain A residue  828 ILE
Chi-restraints excluded: chain A residue  838 LEU
Chi-restraints excluded: chain A residue  904 VAL
Chi-restraints excluded: chain B residue    9 ILE
Chi-restraints excluded: chain B residue   42 LEU
Chi-restraints excluded: chain B residue   45 VAL
Chi-restraints excluded: chain B residue   77 ILE
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 82
   random chunks:
   chunk 79 optimal weight:    0.8980
   chunk 35 optimal weight:    0.0070
   chunk 42 optimal weight:    4.9990
   chunk 50 optimal weight:    0.6980
   chunk 27 optimal weight:    0.7980
   chunk 24 optimal weight:    0.9990
   chunk 55 optimal weight:    1.9990
   chunk 73 optimal weight:    0.9980
   chunk 41 optimal weight:    0.9980
   chunk 34 optimal weight:    0.9980
   chunk 32 optimal weight:    0.9980
   overall best weight:    0.6798

-------------------------------------------------------------------------------
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 = 0.3403 r_free = 0.3403 target = 0.093941 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 33)----------------|
| r_work = 0.3083 r_free = 0.3083 target = 0.074700 restraints weight = 12662.202|
|-----------------------------------------------------------------------------|
r_work (start): 0.3052 rms_B_bonded: 3.00
r_work: 0.2913 rms_B_bonded: 3.59 restraints_weight: 0.5000
r_work (final): 0.2913
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7988
moved from start:          0.1757

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.035   6429  Z= 0.153
  Angle     :  0.565   9.252   8759  Z= 0.288
  Chirality :  0.042   0.170   1043
  Planarity :  0.004   0.052   1109
  Dihedral  :  6.960  71.041    913
  Min Nonbonded Distance : 2.523

Molprobity Statistics.
  All-atom Clashscore : 12.88
  Ramachandran Plot:
    Outliers :  0.12 %
    Allowed  :  2.82 %
    Favored  : 97.06 %
  Rotamer:
    Outliers :  2.09 %
    Allowed  : 18.18 %
    Favored  : 79.73 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.38 %
    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:  1.78 (0.30), residues: 816
  helix:  1.66 (0.22), residues: 559
  sheet:  0.54 (0.77), residues: 45
  loop :  0.21 (0.48), residues: 212

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG B  68 
 TYR   0.010   0.001   TYR B  55 
 PHE   0.013   0.001   PHE A 818 
 TRP   0.009   0.001   TRP A 825 
 HIS   0.003   0.001   HIS A 827 

Details of bonding type rmsd
  covalent geometry    : bond        0.00350 ( 6429)
  covalent geometry    : angle       0.56543 ( 8759)
  hydrogen bonds       : bond        0.03983 (  465)
  hydrogen bonds       : angle       4.75109 ( 1356)

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

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

  1632 Ramachandran restraints generated.
    816 Oldfield, 0 Emsley, 816 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1632 Ramachandran restraints generated.
    816 Oldfield, 0 Emsley, 816 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  103 residues out of total 671 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 89
  time to evaluate  : 0.242 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  476 GLN cc_start: 0.9348 (mm-40) cc_final: 0.9144 (mm-40)
REVERT: A  702 ASP cc_start: 0.8922 (t0) cc_final: 0.8424 (t0)
REVERT: A  705 ARG cc_start: 0.9403 (ttp-110) cc_final: 0.8838 (ttp-110)
REVERT: A  742 GLN cc_start: 0.9427 (tp-100) cc_final: 0.9146 (tp-100)
REVERT: A  777 ASP cc_start: 0.7290 (t70) cc_final: 0.6992 (t70)
REVERT: A  935 MET cc_start: 0.8800 (mtp) cc_final: 0.8542 (mtt)
REVERT: B   54 LYS cc_start: 0.9193 (tttp) cc_final: 0.8585 (ttpp)
REVERT: B   72 ASP cc_start: 0.8789 (m-30) cc_final: 0.8398 (t0)
REVERT: B   76 TYR cc_start: 0.8527 (t80) cc_final: 0.8274 (t80)
  outliers start: 14
  outliers final: 12
  residues processed: 99
  average time/residue: 0.0644
  time to fit residues: 9.0530
Evaluate side-chains
  99 residues out of total 671 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 87
  time to evaluate  : 0.237 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   51 VAL
Chi-restraints excluded: chain A residue  235 LEU
Chi-restraints excluded: chain A residue  389 VAL
Chi-restraints excluded: chain A residue  795 ILE
Chi-restraints excluded: chain A residue  807 VAL
Chi-restraints excluded: chain A residue  817 SER
Chi-restraints excluded: chain A residue  828 ILE
Chi-restraints excluded: chain A residue  838 LEU
Chi-restraints excluded: chain A residue  904 VAL
Chi-restraints excluded: chain B residue   42 LEU
Chi-restraints excluded: chain B residue   45 VAL
Chi-restraints excluded: chain B residue   77 ILE
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 82
   random chunks:
   chunk 11 optimal weight:    3.9990
   chunk 13 optimal weight:    0.8980
   chunk 38 optimal weight:    0.7980
   chunk 9 optimal weight:    0.4980
   chunk 60 optimal weight:    0.9980
   chunk 36 optimal weight:    0.9990
   chunk 67 optimal weight:    0.5980
   chunk 48 optimal weight:    0.5980
   chunk 80 optimal weight:    0.5980
   chunk 79 optimal weight:    0.8980
   chunk 26 optimal weight:    1.9990
   overall best weight:    0.6180

-------------------------------------------------------------------------------
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 = 0.3405 r_free = 0.3405 target = 0.094129 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 32)----------------|
| r_work = 0.3087 r_free = 0.3087 target = 0.074973 restraints weight = 12558.593|
|-----------------------------------------------------------------------------|
r_work (start): 0.3060 rms_B_bonded: 3.00
r_work: 0.2922 rms_B_bonded: 3.58 restraints_weight: 0.5000
r_work (final): 0.2922
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7987
moved from start:          0.1791

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.041   6429  Z= 0.150
  Angle     :  0.581   8.635   8759  Z= 0.293
  Chirality :  0.042   0.172   1043
  Planarity :  0.004   0.052   1109
  Dihedral  :  6.942  70.691    913
  Min Nonbonded Distance : 2.517

Molprobity Statistics.
  All-atom Clashscore : 12.88
  Ramachandran Plot:
    Outliers :  0.12 %
    Allowed  :  2.94 %
    Favored  : 96.94 %
  Rotamer:
    Outliers :  1.94 %
    Allowed  : 18.63 %
    Favored  : 79.43 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.38 %
    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:  1.78 (0.30), residues: 816
  helix:  1.66 (0.22), residues: 558
  sheet:  0.46 (0.77), residues: 46
  loop :  0.24 (0.48), residues: 212

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG A  62 
 TYR   0.009   0.001   TYR B  55 
 PHE   0.012   0.001   PHE A 818 
 TRP   0.009   0.001   TRP A 825 
 HIS   0.003   0.001   HIS A 827 

Details of bonding type rmsd
  covalent geometry    : bond        0.00343 ( 6429)
  covalent geometry    : angle       0.58058 ( 8759)
  hydrogen bonds       : bond        0.03962 (  465)
  hydrogen bonds       : angle       4.75387 ( 1356)

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

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

  1632 Ramachandran restraints generated.
    816 Oldfield, 0 Emsley, 816 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1632 Ramachandran restraints generated.
    816 Oldfield, 0 Emsley, 816 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  102 residues out of total 671 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 89
  time to evaluate  : 0.222 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  476 GLN cc_start: 0.9346 (mm-40) cc_final: 0.9144 (mm-40)
REVERT: A  702 ASP cc_start: 0.8916 (t0) cc_final: 0.8415 (t0)
REVERT: A  705 ARG cc_start: 0.9404 (ttp-110) cc_final: 0.8838 (ttp-110)
REVERT: A  742 GLN cc_start: 0.9425 (tp-100) cc_final: 0.9145 (tp-100)
REVERT: A  935 MET cc_start: 0.8803 (mtp) cc_final: 0.8545 (mtt)
REVERT: B   44 MET cc_start: 0.8679 (tpp) cc_final: 0.8416 (tpp)
REVERT: B   54 LYS cc_start: 0.9200 (tttp) cc_final: 0.8559 (ttpp)
REVERT: B   72 ASP cc_start: 0.8707 (m-30) cc_final: 0.8379 (t0)
REVERT: B   76 TYR cc_start: 0.8553 (t80) cc_final: 0.8301 (t80)
  outliers start: 13
  outliers final: 13
  residues processed: 98
  average time/residue: 0.0619
  time to fit residues: 8.6207
Evaluate side-chains
  99 residues out of total 671 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 86
  time to evaluate  : 0.231 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   51 VAL
Chi-restraints excluded: chain A residue  235 LEU
Chi-restraints excluded: chain A residue  389 VAL
Chi-restraints excluded: chain A residue  795 ILE
Chi-restraints excluded: chain A residue  807 VAL
Chi-restraints excluded: chain A residue  817 SER
Chi-restraints excluded: chain A residue  828 ILE
Chi-restraints excluded: chain A residue  838 LEU
Chi-restraints excluded: chain A residue  846 LEU
Chi-restraints excluded: chain A residue  904 VAL
Chi-restraints excluded: chain B residue   42 LEU
Chi-restraints excluded: chain B residue   45 VAL
Chi-restraints excluded: chain B residue   77 ILE
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 82
   random chunks:
   chunk 40 optimal weight:    2.9990
   chunk 7 optimal weight:    1.9990
   chunk 59 optimal weight:    0.6980
   chunk 70 optimal weight:    0.9980
   chunk 43 optimal weight:    3.9990
   chunk 77 optimal weight:    0.7980
   chunk 80 optimal weight:    0.9990
   chunk 50 optimal weight:    0.9980
   chunk 6 optimal weight:    0.9980
   chunk 44 optimal weight:    1.9990
   chunk 12 optimal weight:    0.7980
   overall best weight:    0.8580

-------------------------------------------------------------------------------
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 = 0.3381 r_free = 0.3381 target = 0.092688 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 31)----------------|
| r_work = 0.3062 r_free = 0.3062 target = 0.073641 restraints weight = 12600.779|
|-----------------------------------------------------------------------------|
r_work (start): 0.3027 rms_B_bonded: 2.96
r_work: 0.2891 rms_B_bonded: 3.52 restraints_weight: 0.5000
r_work (final): 0.2891
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7992
moved from start:          0.1840

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.043   6429  Z= 0.173
  Angle     :  0.587   9.150   8759  Z= 0.297
  Chirality :  0.042   0.175   1043
  Planarity :  0.005   0.052   1109
  Dihedral  :  6.949  70.085    913
  Min Nonbonded Distance : 2.516

Molprobity Statistics.
  All-atom Clashscore : 13.04
  Ramachandran Plot:
    Outliers :  0.12 %
    Allowed  :  3.06 %
    Favored  : 96.81 %
  Rotamer:
    Outliers :  2.53 %
    Allowed  : 18.18 %
    Favored  : 79.28 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.38 %
    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:  1.75 (0.30), residues: 816
  helix:  1.61 (0.22), residues: 559
  sheet:  0.55 (0.78), residues: 45
  loop :  0.27 (0.48), residues: 212

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.006   0.000   ARG B  68 
 TYR   0.009   0.001   TYR B  55 
 PHE   0.011   0.001   PHE A 818 
 TRP   0.010   0.001   TRP A 825 
 HIS   0.003   0.001   HIS A 827 

Details of bonding type rmsd
  covalent geometry    : bond        0.00401 ( 6429)
  covalent geometry    : angle       0.58739 ( 8759)
  hydrogen bonds       : bond        0.04046 (  465)
  hydrogen bonds       : angle       4.77687 ( 1356)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 1310.46 seconds
wall clock time: 23 minutes 19.60 seconds (1399.60 seconds total)