Starting phenix.real_space_refine
on Tue Feb  3 19:25:12 2026 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/9u4t_63854/02_2026/9u4t_63854.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/9u4t_63854/02_2026/9u4t_63854.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=3.11
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    model {
      file = "/net/cci-nas-00/data/ceres_data/9u4t_63854/02_2026/9u4t_63854.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/9u4t_63854/02_2026/9u4t_63854.cif"
    real_map_files = "/net/cci-nas-00/data/ceres_data/9u4t_63854/02_2026/9u4t_63854.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/9u4t_63854/02_2026/9u4t_63854.map"
  }
  resolution = 3.11
  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=   0.018
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 3 residue(s): 0.01s

  Monomer Library directory:
    "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5952/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
          Planarities with less than four sites: {'4HH:plan-3': 1}
          Unresolved non-hydrogen planarities: 1
  Time building chain proxies: 1.65, per 1000 atoms: 0.26
  Number of scatterers: 6301
  At special positions: 0
  Unit cell: (66, 70.4, 136.4, 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: 0.68
  Conformation dependent library (CDL) restraints added in 241.7 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:
      33 helices and 2 sheets defined
      71.9% alpha, 5.0% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 0.23
  Creating SS restraints...
    Processing helix  chain 'A' and resid 25 through 33
    Processing helix  chain 'A' and resid 33 through 51
    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 120
    Processing helix  chain 'A' and resid 134 through 142
      removed outlier: 4.301A  pdb=" N   SER A 139 " --> pdb=" O   PRO A 135 " (cutoff:3.500A)
      removed outlier: 5.738A  pdb=" N   GLY A 140 " --> pdb=" O   LEU A 136 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 161 through 178
      removed outlier: 3.513A  pdb=" N   VAL A 178 " --> pdb=" O   ILE A 174 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 190 through 226
      removed outlier: 4.654A  pdb=" N   ARG A 207 " --> pdb=" O   ASP A 203 " (cutoff:3.500A)
      removed outlier: 4.675A  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 328
      removed outlier: 5.637A  pdb=" N   HIS A 310 " --> pdb=" O   HIS A 306 " (cutoff:3.500A)
      removed outlier: 5.172A  pdb=" N   VAL A 311 " --> pdb=" O   SER A 307 " (cutoff:3.500A)
      removed outlier: 3.885A  pdb=" N   LEU A 326 " --> pdb=" O   ALA A 322 " (cutoff:3.500A)
      removed outlier: 3.688A  pdb=" N   HIS A 327 " --> pdb=" O   THR A 323 " (cutoff:3.500A)
      removed outlier: 3.815A  pdb=" N   PHE A 328 " --> pdb=" O   LEU A 324 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 331 through 366
      removed outlier: 3.813A  pdb=" N   ILE A 339 " --> pdb=" O   GLN A 335 " (cutoff:3.500A)
      Proline residue:  A 340  - end of helix
      removed outlier: 4.152A  pdb=" N   ALA A 357 " --> pdb=" O   LEU A 353 " (cutoff:3.500A)
      removed outlier: 3.642A  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
    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 476
    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: 3.773A  pdb=" N   ASP A 738 " --> pdb=" O   ILE A 734 " (cutoff:3.500A)
      removed outlier: 3.882A  pdb=" N   ALA A 739 " --> pdb=" O   LYS A 735 " (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: 4.001A  pdb=" N   LEU A 838 " --> pdb=" O   HIS A 834 " (cutoff:3.500A)
      removed outlier: 4.019A  pdb=" N   ALA A 839 " --> pdb=" O   TRP A 835 " (cutoff:3.500A)
      removed outlier: 3.798A  pdb=" N   ALA A 850 " --> pdb=" O   LEU A 846 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 867 through 896
      removed outlier: 5.311A  pdb=" N   SER A 881 " --> pdb=" O   GLY A 877 " (cutoff:3.500A)
      removed outlier: 5.211A  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 926 through 936
    Processing helix  chain 'A' and resid 937 through 941
      removed outlier: 3.790A  pdb=" N   TRP A 940 " --> pdb=" O   LYS A 937 " (cutoff:3.500A)
      removed outlier: 3.593A  pdb=" N   TRP A 941 " --> pdb=" O   TRP A 938 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'A' and resid 937 through 941'
    Processing helix  chain 'B' and resid 4 through 20
      removed outlier: 3.637A  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 40 through 56
    Processing helix  chain 'B' and resid 60 through 65
      removed outlier: 3.737A  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: 4.212A  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
      removed outlier: 3.581A  pdb=" N   VAL A 718 " --> pdb=" O   ILE A 452 " (cutoff:3.500A)
      removed outlier: 3.781A  pdb=" N   ILE A 452 " --> pdb=" O   VAL A 718 " (cutoff:3.500A)

    464 hydrogen bonds defined for protein.
    1365 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: 1.17

  Time building geometry restraints manager: 0.87 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: 1597
        1.44 -     1.56: 3732
        1.56 -     1.69: 2
        1.69 -     1.82: 59
  Bond restraints: 6429
  Sorted by residual:
  bond pdb=" CQ  4HH B  41 "
       pdb=" NR  4HH B  41 "
    ideal  model  delta    sigma   weight residual
    1.374  1.449 -0.075 2.00e-02 2.50e+03 1.42e+01
  bond pdb=" CQ  4HH B  41 "
       pdb=" OR  4HH B  41 "
    ideal  model  delta    sigma   weight residual
    1.256  1.184  0.072 2.00e-02 2.50e+03 1.29e+01
  bond pdb=" CL3 4HH B  41 "
       pdb=" NN  4HH B  41 "
    ideal  model  delta    sigma   weight residual
    1.386  1.453 -0.067 2.00e-02 2.50e+03 1.13e+01
  bond pdb=" OG  4HH B  41 "
       pdb=" P   4HH B  41 "
    ideal  model  delta    sigma   weight residual
    1.624  1.558  0.066 2.00e-02 2.50e+03 1.10e+01
  bond pdb=" CL3 4HH B  41 "
       pdb=" ON  4HH B  41 "
    ideal  model  delta    sigma   weight residual
    1.250  1.185  0.065 2.00e-02 2.50e+03 1.07e+01
  ... (remaining 6424 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     5.69: 8745
        5.69 -    11.39: 9
       11.39 -    17.08: 2
       17.08 -    22.78: 1
       22.78 -    28.47: 2
  Bond angle restraints: 8759
  Sorted by residual:
  angle pdb=" OG  4HH B  41 "
        pdb=" P   4HH B  41 "
        pdb=" O3P 4HH B  41 "
      ideal   model   delta    sigma   weight residual
      96.91  125.38  -28.47 3.00e+00 1.11e-01 9.01e+01
  angle pdb=" OG  4HH B  41 "
        pdb=" P   4HH B  41 "
        pdb=" O2P 4HH B  41 "
      ideal   model   delta    sigma   weight residual
     113.19   87.98   25.21 3.00e+00 1.11e-01 7.06e+01
  angle pdb=" O1P 4HH B  41 "
        pdb=" P   4HH B  41 "
        pdb=" O2P 4HH B  41 "
      ideal   model   delta    sigma   weight residual
     122.75  104.26   18.49 3.00e+00 1.11e-01 3.80e+01
  angle pdb=" CB  MET B  44 "
        pdb=" CG  MET B  44 "
        pdb=" SD  MET B  44 "
      ideal   model   delta    sigma   weight residual
     112.70  127.54  -14.84 3.00e+00 1.11e-01 2.45e+01
  angle pdb=" N   GLU A 746 "
        pdb=" CA  GLU A 746 "
        pdb=" CB  GLU A 746 "
      ideal   model   delta    sigma   weight residual
     110.40  116.62   -6.22 1.63e+00 3.76e-01 1.46e+01
  ... (remaining 8754 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    24.96: 3645
       24.96 -    49.91: 172
       49.91 -    74.87: 17
       74.87 -    99.83: 4
       99.83 -   124.79: 2
  Dihedral angle restraints: 3840
    sinusoidal: 1470
      harmonic: 2370
  Sorted by residual:
  dihedral pdb=" CA  PHE B  33 "
           pdb=" C   PHE B  33 "
           pdb=" N   VAL B  34 "
           pdb=" CA  VAL B  34 "
      ideal   model   delta  harmonic     sigma   weight residual
    -180.00 -158.10  -21.90     0      5.00e+00 4.00e-02 1.92e+01
  dihedral pdb=" CA  SER B  43 "
           pdb=" C   SER B  43 "
           pdb=" N   MET B  44 "
           pdb=" CA  MET B  44 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  158.17   21.83     0      5.00e+00 4.00e-02 1.91e+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
     173.45  -61.76 -124.79     1      3.00e+01 1.11e-03 1.68e+01
  ... (remaining 3837 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.051: 817
       0.051 -    0.102: 189
       0.102 -    0.154: 34
       0.154 -    0.205: 2
       0.205 -    0.256: 1
  Chirality restraints: 1043
  Sorted by residual:
  chirality pdb=" CG  LEU A 313 "
            pdb=" CB  LEU A 313 "
            pdb=" CD1 LEU A 313 "
            pdb=" CD2 LEU A 313 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.59   -2.33   -0.26 2.00e-01 2.50e+01 1.64e+00
  chirality pdb=" CB  ILE A 824 "
            pdb=" CA  ILE A 824 "
            pdb=" CG1 ILE A 824 "
            pdb=" CG2 ILE A 824 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.64    2.48    0.17 2.00e-01 2.50e+01 6.87e-01
  chirality pdb=" CB  ILE A 758 "
            pdb=" CA  ILE A 758 "
            pdb=" CG1 ILE A 758 "
            pdb=" CG2 ILE A 758 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.64    2.80   -0.16 2.00e-01 2.50e+01 6.16e-01
  ... (remaining 1040 not shown)

  Planarity restraints: 1109
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  SER A 352 "   -0.009 2.00e-02 2.50e+03   1.80e-02 3.24e+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
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  ILE A 824 "    0.009 2.00e-02 2.50e+03   1.72e-02 2.94e+00
        pdb=" C   ILE A 824 "   -0.030 2.00e-02 2.50e+03
        pdb=" O   ILE A 824 "    0.011 2.00e-02 2.50e+03
        pdb=" N   TRP A 825 "    0.010 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CB  ASP A 278 "    0.007 2.00e-02 2.50e+03   1.39e-02 1.94e+00
        pdb=" CG  ASP A 278 "   -0.024 2.00e-02 2.50e+03
        pdb=" OD1 ASP A 278 "    0.009 2.00e-02 2.50e+03
        pdb=" OD2 ASP A 278 "    0.009 2.00e-02 2.50e+03
  ... (remaining 1106 not shown)

  Histogram of nonbonded interaction distances:
        2.20 -     2.74: 747
        2.74 -     3.28: 7040
        3.28 -     3.82: 11566
        3.82 -     4.36: 12749
        4.36 -     4.90: 22562
  Nonbonded interactions: 54664
  Sorted by model distance:
  nonbonded pdb=" O   PHE B  33 "
            pdb=" N   ASP B  36 "
     model   vdw
     2.202 3.120
  nonbonded pdb=" O   PRO A 122 "
            pdb=" NH2 ARG A 156 "
     model   vdw
     2.249 3.120
  nonbonded pdb=" OG  SER A  91 "
            pdb=" OG1 THR A 155 "
     model   vdw
     2.262 3.040
  nonbonded pdb=" OH  TYR A 422 "
            pdb=" O   GLU A 832 "
     model   vdw
     2.265 3.040
  nonbonded pdb=" OG1 THR A 318 "
            pdb=" OD1 ASP A 851 "
     model   vdw
     2.283 3.040
  ... (remaining 54659 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:             1.010
  Set stop_for_unknowns flag:              0.000
  Assert model is a single copy model:     0.000
  Assert all atoms have isotropic ADPs:    0.000
  Construct map_model_manager:             0.000
  Extract box with map and model:          0.080
  Check model and map are aligned:         0.010
  Set scattering table:                    0.020
  Process input model:                     8.220
  Find NCS groups from input model:        0.030
  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:1.270
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   10.640
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7911
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   0.075   6429  Z= 0.205
  Angle     :  0.822  28.472   8759  Z= 0.370
  Chirality :  0.044   0.256   1043
  Planarity :  0.004   0.044   1109
  Dihedral  : 14.469 124.787   2314
  Min Nonbonded Distance : 2.202

Molprobity Statistics.
  All-atom Clashscore : 16.26
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.43 %
    Favored  : 96.57 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  0.00 %
    Favored  : 100.00 %
  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:  1.58 (0.30), residues: 816
  helix:  1.44 (0.21), residues: 552
  sheet:  0.40 (0.85), residues: 41
  loop :  0.40 (0.48), residues: 223

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.011   0.000   ARG B  68 
 TYR   0.012   0.001   TYR A 759 
 PHE   0.011   0.001   PHE B  33 
 TRP   0.017   0.001   TRP A 835 
 HIS   0.002   0.001   HIS A 108 

Details of bonding type rmsd
  covalent geometry    : bond        0.00462 ( 6429)
  covalent geometry    : angle       0.82174 ( 8759)
  hydrogen bonds       : bond        0.10596 (  464)
  hydrogen bonds       : angle       5.94434 ( 1365)

*********************** 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
  136 residues out of total 671 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 136
  time to evaluate  : 0.204 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   66 MET cc_start: 0.9175 (tmm) cc_final: 0.8244 (tpp)
REVERT: A   94 MET cc_start: 0.8408 (mmp) cc_final: 0.7987 (mmp)
REVERT: A  402 LEU cc_start: 0.8755 (tp) cc_final: 0.8503 (tp)
REVERT: A  460 ASN cc_start: 0.9195 (t0) cc_final: 0.8924 (t0)
REVERT: A  746 GLU cc_start: 0.8349 (pm20) cc_final: 0.7945 (pm20)
REVERT: B   18 GLU cc_start: 0.8318 (tm-30) cc_final: 0.8014 (tm-30)
REVERT: B   26 GLU cc_start: 0.7951 (tp30) cc_final: 0.7640 (tp30)
REVERT: B   34 VAL cc_start: 0.8502 (p) cc_final: 0.8148 (p)
REVERT: B   72 ASP cc_start: 0.8859 (m-30) cc_final: 0.8481 (m-30)
  outliers start: 0
  outliers final: 0
  residues processed: 136
  average time/residue: 0.0668
  time to fit residues: 12.9588
Evaluate side-chains
  107 residues out of total 671 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 107
  time to evaluate  : 0.241 
-------------------------------------------------------------------------------
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:    5.9990
   chunk 53 optimal weight:    0.8980
   chunk 5 optimal weight:    0.7980
   chunk 33 optimal weight:    0.8980
   chunk 65 optimal weight:    0.7980
   chunk 62 optimal weight:    0.9980
   chunk 51 optimal weight:   10.0000
   chunk 38 optimal weight:    0.5980
   chunk 61 optimal weight:    0.6980
   chunk 45 optimal weight:    1.9990
   chunk 74 optimal weight:    2.9990
   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 165 ASN
A 199 HIS
A 266 ASN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3416 r_free = 0.3416 target = 0.098230 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 33)----------------|
| r_work = 0.3106 r_free = 0.3106 target = 0.079279 restraints weight = 12737.645|
|-----------------------------------------------------------------------------|
r_work (start): 0.3097 rms_B_bonded: 3.14
r_work: 0.2957 rms_B_bonded: 3.74 restraints_weight: 0.5000
r_work (final): 0.2957
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7971
moved from start:          0.1082

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.049   6429  Z= 0.170
  Angle     :  0.588  10.269   8759  Z= 0.302
  Chirality :  0.043   0.184   1043
  Planarity :  0.004   0.035   1109
  Dihedral  :  7.042 116.923    889
  Min Nonbonded Distance : 2.516

Molprobity Statistics.
  All-atom Clashscore : 13.67
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.31 %
    Favored  : 96.69 %
  Rotamer:
    Outliers :  1.19 %
    Allowed  : 10.58 %
    Favored  : 88.23 %
  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:  1.57 (0.30), residues: 816
  helix:  1.43 (0.21), residues: 560
  sheet:  0.49 (0.82), residues: 41
  loop :  0.34 (0.49), residues: 215

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG B  68 
 TYR   0.011   0.001   TYR A 759 
 PHE   0.029   0.002   PHE A 818 
 TRP   0.012   0.001   TRP A 835 
 HIS   0.002   0.001   HIS A 255 

Details of bonding type rmsd
  covalent geometry    : bond        0.00393 ( 6429)
  covalent geometry    : angle       0.58755 ( 8759)
  hydrogen bonds       : bond        0.04230 (  464)
  hydrogen bonds       : angle       5.07564 ( 1365)

*********************** 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
  121 residues out of total 671 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 8
    poor density    : 113
  time to evaluate  : 0.241 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   94 MET cc_start: 0.8680 (mmt) cc_final: 0.8237 (mmt)
REVERT: A  214 PHE cc_start: 0.7110 (m-10) cc_final: 0.6867 (m-10)
REVERT: A  402 LEU cc_start: 0.8820 (tp) cc_final: 0.8598 (tt)
REVERT: A  460 ASN cc_start: 0.9310 (t0) cc_final: 0.8866 (t0)
REVERT: B   72 ASP cc_start: 0.9044 (m-30) cc_final: 0.8672 (m-30)
  outliers start: 8
  outliers final: 7
  residues processed: 114
  average time/residue: 0.0638
  time to fit residues: 10.3753
Evaluate side-chains
  105 residues out of total 671 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 7
    poor density    : 98
  time to evaluate  : 0.245 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   38 ILE
Chi-restraints excluded: chain A residue  313 LEU
Chi-restraints excluded: chain A residue  331 MET
Chi-restraints excluded: chain A residue  405 VAL
Chi-restraints excluded: chain A residue  410 LEU
Chi-restraints excluded: chain A residue  718 VAL
Chi-restraints excluded: chain A residue  828 ILE
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 82
   random chunks:
   chunk 67 optimal weight:    1.9990
   chunk 80 optimal weight:    0.8980
   chunk 12 optimal weight:    1.9990
   chunk 73 optimal weight:    0.0970
   chunk 69 optimal weight:    0.6980
   chunk 4 optimal weight:    0.9990
   chunk 27 optimal weight:    1.9990
   chunk 75 optimal weight:    0.9990
   chunk 74 optimal weight:    0.9990
   chunk 52 optimal weight:    0.9990
   chunk 35 optimal weight:    4.9990
   overall best weight:    0.7382

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

Flipped N/Q/H residues before XYZ refinement:
A 142 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3417 r_free = 0.3417 target = 0.096063 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 33)----------------|
| r_work = 0.3114 r_free = 0.3114 target = 0.077427 restraints weight = 12713.501|
|-----------------------------------------------------------------------------|
r_work (start): 0.3109 rms_B_bonded: 3.02
r_work: 0.2967 rms_B_bonded: 3.65 restraints_weight: 0.5000
r_work (final): 0.2967
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8091
moved from start:          0.1353

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.067   6429  Z= 0.166
  Angle     :  0.590  13.034   8759  Z= 0.299
  Chirality :  0.043   0.174   1043
  Planarity :  0.004   0.037   1109
  Dihedral  :  6.602 113.358    889
  Min Nonbonded Distance : 2.547

Molprobity Statistics.
  All-atom Clashscore : 13.51
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.55 %
    Favored  : 96.45 %
  Rotamer:
    Outliers :  2.68 %
    Allowed  : 12.07 %
    Favored  : 85.25 %
  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:  1.69 (0.30), residues: 816
  helix:  1.48 (0.21), residues: 554
  sheet:  0.60 (0.81), residues: 41
  loop :  0.53 (0.49), residues: 221

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG B  68 
 TYR   0.009   0.001   TYR A 759 
 PHE   0.017   0.001   PHE A 818 
 TRP   0.010   0.001   TRP A 835 
 HIS   0.002   0.001   HIS A 827 

Details of bonding type rmsd
  covalent geometry    : bond        0.00383 ( 6429)
  covalent geometry    : angle       0.59014 ( 8759)
  hydrogen bonds       : bond        0.04115 (  464)
  hydrogen bonds       : angle       4.92852 ( 1365)

*********************** 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
  131 residues out of total 671 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 18
    poor density    : 113
  time to evaluate  : 0.246 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   94 MET cc_start: 0.8767 (mmt) cc_final: 0.8303 (mmt)
REVERT: A  402 LEU cc_start: 0.8893 (tp) cc_final: 0.8673 (tt)
REVERT: A  460 ASN cc_start: 0.9294 (t0) cc_final: 0.8951 (t0)
REVERT: A  935 MET cc_start: 0.8606 (mtp) cc_final: 0.8315 (mtt)
REVERT: B   72 ASP cc_start: 0.9082 (m-30) cc_final: 0.8655 (m-30)
  outliers start: 18
  outliers final: 8
  residues processed: 118
  average time/residue: 0.0558
  time to fit residues: 9.4275
Evaluate side-chains
  110 residues out of total 671 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 8
    poor density    : 102
  time to evaluate  : 0.288 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  313 LEU
Chi-restraints excluded: chain A residue  331 MET
Chi-restraints excluded: chain A residue  405 VAL
Chi-restraints excluded: chain A residue  718 VAL
Chi-restraints excluded: chain A residue  813 SER
Chi-restraints excluded: chain A residue  824 ILE
Chi-restraints excluded: chain A residue  828 ILE
Chi-restraints excluded: chain B residue   39 ILE
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 82
   random chunks:
   chunk 78 optimal weight:    0.6980
   chunk 17 optimal weight:    0.7980
   chunk 62 optimal weight:    0.7980
   chunk 31 optimal weight:    0.9990
   chunk 3 optimal weight:    1.9990
   chunk 42 optimal weight:    0.5980
   chunk 9 optimal weight:    0.5980
   chunk 80 optimal weight:    0.2980
   chunk 61 optimal weight:    0.9980
   chunk 51 optimal weight:    1.9990
   chunk 23 optimal weight:    2.9990
   overall best weight:    0.5980

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

Flipped N/Q/H residues before XYZ refinement:
B  78 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3427 r_free = 0.3427 target = 0.096948 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 35)----------------|
| r_work = 0.3134 r_free = 0.3134 target = 0.078658 restraints weight = 12673.748|
|-----------------------------------------------------------------------------|
r_work (start): 0.3127 rms_B_bonded: 3.00
r_work: 0.2983 rms_B_bonded: 3.64 restraints_weight: 0.5000
r_work (final): 0.2983
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8078
moved from start:          0.1547

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.065   6429  Z= 0.152
  Angle     :  0.591  14.417   8759  Z= 0.298
  Chirality :  0.043   0.186   1043
  Planarity :  0.004   0.037   1109
  Dihedral  :  6.233 109.405    889
  Min Nonbonded Distance : 2.522

Molprobity Statistics.
  All-atom Clashscore : 12.65
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.68 %
    Favored  : 96.32 %
  Rotamer:
    Outliers :  2.09 %
    Allowed  : 15.05 %
    Favored  : 82.86 %
  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:  1.73 (0.30), residues: 816
  helix:  1.49 (0.21), residues: 555
  sheet:  0.68 (0.83), residues: 41
  loop :  0.60 (0.49), residues: 220

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG B  68 
 TYR   0.008   0.001   TYR A 759 
 PHE   0.011   0.001   PHE A 818 
 TRP   0.009   0.001   TRP A 835 
 HIS   0.002   0.001   HIS A 827 

Details of bonding type rmsd
  covalent geometry    : bond        0.00346 ( 6429)
  covalent geometry    : angle       0.59096 ( 8759)
  hydrogen bonds       : bond        0.04015 (  464)
  hydrogen bonds       : angle       4.86940 ( 1365)

*********************** 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
  133 residues out of total 671 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 119
  time to evaluate  : 0.239 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  169 GLU cc_start: 0.8965 (mm-30) cc_final: 0.8269 (tp30)
REVERT: A  402 LEU cc_start: 0.8900 (tp) cc_final: 0.8675 (tt)
REVERT: A  460 ASN cc_start: 0.9370 (t0) cc_final: 0.9053 (t0)
REVERT: A  729 MET cc_start: 0.8491 (ptt) cc_final: 0.8236 (ptt)
REVERT: A  732 GLU cc_start: 0.9221 (mp0) cc_final: 0.8999 (mp0)
REVERT: B   72 ASP cc_start: 0.9043 (m-30) cc_final: 0.8638 (m-30)
  outliers start: 14
  outliers final: 9
  residues processed: 125
  average time/residue: 0.0568
  time to fit residues: 10.4528
Evaluate side-chains
  116 residues out of total 671 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 9
    poor density    : 107
  time to evaluate  : 0.150 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  313 LEU
Chi-restraints excluded: chain A residue  331 MET
Chi-restraints excluded: chain A residue  405 VAL
Chi-restraints excluded: chain A residue  410 LEU
Chi-restraints excluded: chain A residue  718 VAL
Chi-restraints excluded: chain A residue  813 SER
Chi-restraints excluded: chain A residue  828 ILE
Chi-restraints excluded: chain A residue  904 VAL
Chi-restraints excluded: chain B residue   81 GLU
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 82
   random chunks:
   chunk 61 optimal weight:    0.5980
   chunk 29 optimal weight:    0.7980
   chunk 78 optimal weight:    0.9980
   chunk 80 optimal weight:    1.9990
   chunk 27 optimal weight:    1.9990
   chunk 10 optimal weight:    2.9990
   chunk 38 optimal weight:    0.8980
   chunk 34 optimal weight:    0.7980
   chunk 5 optimal weight:    0.9980
   chunk 43 optimal weight:    2.9990
   chunk 11 optimal weight:    2.9990
   overall best weight:    0.8180

-------------------------------------------------------------------------------
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 = 0.3411 r_free = 0.3411 target = 0.097479 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 32)----------------|
| r_work = 0.3107 r_free = 0.3107 target = 0.079036 restraints weight = 12920.143|
|-----------------------------------------------------------------------------|
r_work (start): 0.3086 rms_B_bonded: 3.08
r_work: 0.2949 rms_B_bonded: 3.70 restraints_weight: 0.5000
r_work (final): 0.2949
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7937
moved from start:          0.1685

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.065   6429  Z= 0.171
  Angle     :  0.616  14.249   8759  Z= 0.309
  Chirality :  0.044   0.194   1043
  Planarity :  0.004   0.038   1109
  Dihedral  :  5.997 105.971    889
  Min Nonbonded Distance : 2.478

Molprobity Statistics.
  All-atom Clashscore : 12.65
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.55 %
    Favored  : 96.45 %
  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:  1.76 (0.30), residues: 816
  helix:  1.54 (0.21), residues: 549
  sheet:  0.78 (0.83), residues: 40
  loop :  0.52 (0.47), residues: 227

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG B  68 
 TYR   0.006   0.001   TYR A 759 
 PHE   0.009   0.001   PHE B  33 
 TRP   0.009   0.001   TRP A  41 
 HIS   0.002   0.001   HIS A 827 

Details of bonding type rmsd
  covalent geometry    : bond        0.00395 ( 6429)
  covalent geometry    : angle       0.61563 ( 8759)
  hydrogen bonds       : bond        0.04113 (  464)
  hydrogen bonds       : angle       4.81032 ( 1365)

*********************** 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
  132 residues out of total 671 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 18
    poor density    : 114
  time to evaluate  : 0.168 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  169 GLU cc_start: 0.8917 (mm-30) cc_final: 0.8234 (tp30)
REVERT: A  402 LEU cc_start: 0.8758 (tp) cc_final: 0.8516 (tt)
REVERT: A  460 ASN cc_start: 0.9420 (t0) cc_final: 0.9206 (t0)
REVERT: A  732 GLU cc_start: 0.9283 (mp0) cc_final: 0.9029 (mp0)
REVERT: A  742 GLN cc_start: 0.8990 (pp30) cc_final: 0.8643 (tm-30)
REVERT: A  746 GLU cc_start: 0.8750 (pp20) cc_final: 0.8309 (pp20)
REVERT: A  935 MET cc_start: 0.8510 (mtp) cc_final: 0.8185 (mtt)
REVERT: B   33 PHE cc_start: 0.7138 (OUTLIER) cc_final: 0.6627 (t80)
REVERT: B   72 ASP cc_start: 0.9051 (m-30) cc_final: 0.8645 (m-30)
  outliers start: 18
  outliers final: 11
  residues processed: 121
  average time/residue: 0.0550
  time to fit residues: 9.7476
Evaluate side-chains
  120 residues out of total 671 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 108
  time to evaluate  : 0.282 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  313 LEU
Chi-restraints excluded: chain A residue  331 MET
Chi-restraints excluded: chain A residue  405 VAL
Chi-restraints excluded: chain A residue  410 LEU
Chi-restraints excluded: chain A residue  718 VAL
Chi-restraints excluded: chain A residue  813 SER
Chi-restraints excluded: chain A residue  824 ILE
Chi-restraints excluded: chain A residue  828 ILE
Chi-restraints excluded: chain A residue  904 VAL
Chi-restraints excluded: chain B residue   16 ILE
Chi-restraints excluded: chain B residue   33 PHE
Chi-restraints excluded: chain B residue   39 ILE
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 82
   random chunks:
   chunk 33 optimal weight:    0.7980
   chunk 38 optimal weight:    0.9980
   chunk 22 optimal weight:    0.6980
   chunk 67 optimal weight:    2.9990
   chunk 76 optimal weight:    4.9990
   chunk 58 optimal weight:    1.9990
   chunk 68 optimal weight:    0.6980
   chunk 46 optimal weight:    6.9990
   chunk 27 optimal weight:    0.7980
   chunk 54 optimal weight:    3.9990
   chunk 43 optimal weight:    0.9980
   overall best weight:    0.7980

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

Flipped N/Q/H residues before XYZ refinement:
B  78 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3404 r_free = 0.3404 target = 0.097702 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 33)----------------|
| r_work = 0.3094 r_free = 0.3094 target = 0.079092 restraints weight = 12888.619|
|-----------------------------------------------------------------------------|
r_work (start): 0.3089 rms_B_bonded: 3.09
r_work: 0.2949 rms_B_bonded: 3.72 restraints_weight: 0.5000
r_work (final): 0.2949
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7987
moved from start:          0.1789

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.071   6429  Z= 0.169
  Angle     :  0.621  14.283   8759  Z= 0.309
  Chirality :  0.044   0.231   1043
  Planarity :  0.004   0.038   1109
  Dihedral  :  5.838 103.037    889
  Min Nonbonded Distance : 2.502

Molprobity Statistics.
  All-atom Clashscore : 13.28
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.43 %
    Favored  : 96.57 %
  Rotamer:
    Outliers :  2.98 %
    Allowed  : 18.03 %
    Favored  : 78.99 %
  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:  1.81 (0.30), residues: 816
  helix:  1.59 (0.21), residues: 548
  sheet:  0.79 (0.85), residues: 40
  loop :  0.52 (0.47), residues: 228

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG B  68 
 TYR   0.006   0.001   TYR A 759 
 PHE   0.015   0.001   PHE B  33 
 TRP   0.009   0.001   TRP A  41 
 HIS   0.002   0.001   HIS A 827 

Details of bonding type rmsd
  covalent geometry    : bond        0.00392 ( 6429)
  covalent geometry    : angle       0.62097 ( 8759)
  hydrogen bonds       : bond        0.04082 (  464)
  hydrogen bonds       : angle       4.82069 ( 1365)

*********************** 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
  132 residues out of total 671 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 20
    poor density    : 112
  time to evaluate  : 0.212 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  169 GLU cc_start: 0.8928 (mm-30) cc_final: 0.8243 (tp30)
REVERT: A  460 ASN cc_start: 0.9430 (t0) cc_final: 0.9229 (t0)
REVERT: A  729 MET cc_start: 0.8493 (ptt) cc_final: 0.7710 (ptt)
REVERT: A  732 GLU cc_start: 0.9337 (mp0) cc_final: 0.9056 (mp0)
REVERT: A  742 GLN cc_start: 0.9004 (pp30) cc_final: 0.8686 (tm-30)
REVERT: A  746 GLU cc_start: 0.8634 (pp20) cc_final: 0.8233 (pp20)
REVERT: B   33 PHE cc_start: 0.7362 (OUTLIER) cc_final: 0.6806 (t80)
REVERT: B   72 ASP cc_start: 0.9046 (m-30) cc_final: 0.8631 (m-30)
  outliers start: 20
  outliers final: 15
  residues processed: 122
  average time/residue: 0.0579
  time to fit residues: 10.1065
Evaluate side-chains
  123 residues out of total 671 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 107
  time to evaluate  : 0.218 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  313 LEU
Chi-restraints excluded: chain A residue  331 MET
Chi-restraints excluded: chain A residue  405 VAL
Chi-restraints excluded: chain A residue  410 LEU
Chi-restraints excluded: chain A residue  718 VAL
Chi-restraints excluded: chain A residue  813 SER
Chi-restraints excluded: chain A residue  824 ILE
Chi-restraints excluded: chain A residue  828 ILE
Chi-restraints excluded: chain A residue  836 MET
Chi-restraints excluded: chain A residue  873 ILE
Chi-restraints excluded: chain A residue  904 VAL
Chi-restraints excluded: chain A residue  905 ILE
Chi-restraints excluded: chain B residue   16 ILE
Chi-restraints excluded: chain B residue   33 PHE
Chi-restraints excluded: chain B residue   39 ILE
Chi-restraints excluded: chain B residue   81 GLU
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 82
   random chunks:
   chunk 71 optimal weight:    0.6980
   chunk 30 optimal weight:    3.9990
   chunk 31 optimal weight:    0.7980
   chunk 41 optimal weight:    0.8980
   chunk 67 optimal weight:    2.9990
   chunk 64 optimal weight:    0.9980
   chunk 52 optimal weight:    4.9990
   chunk 24 optimal weight:    0.9990
   chunk 50 optimal weight:    0.2980
   chunk 72 optimal weight:    0.0980
   chunk 47 optimal weight:    0.9980
   overall best weight:    0.5580

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

Flipped N/Q/H residues before XYZ refinement:
B  78 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3410 r_free = 0.3410 target = 0.097981 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 45)----------------|
| r_work = 0.3110 r_free = 0.3110 target = 0.079648 restraints weight = 12902.928|
|-----------------------------------------------------------------------------|
r_work (start): 0.3104 rms_B_bonded: 3.06
r_work: 0.2969 rms_B_bonded: 3.69 restraints_weight: 0.5000
r_work (final): 0.2969
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7878
moved from start:          0.1895

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.064   6429  Z= 0.154
  Angle     :  0.635  14.281   8759  Z= 0.312
  Chirality :  0.045   0.353   1043
  Planarity :  0.004   0.038   1109
  Dihedral  :  5.715 100.502    889
  Min Nonbonded Distance : 2.473

Molprobity Statistics.
  All-atom Clashscore : 13.51
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.55 %
    Favored  : 96.45 %
  Rotamer:
    Outliers :  3.58 %
    Allowed  : 19.52 %
    Favored  : 76.90 %
  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:  1.76 (0.30), residues: 816
  helix:  1.54 (0.21), residues: 548
  sheet:  0.78 (0.85), residues: 40
  loop :  0.53 (0.47), residues: 228

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG B  68 
 TYR   0.006   0.001   TYR A 759 
 PHE   0.016   0.001   PHE B  33 
 TRP   0.008   0.001   TRP A  41 
 HIS   0.002   0.000   HIS A 827 

Details of bonding type rmsd
  covalent geometry    : bond        0.00355 ( 6429)
  covalent geometry    : angle       0.63477 ( 8759)
  hydrogen bonds       : bond        0.04039 (  464)
  hydrogen bonds       : angle       4.85183 ( 1365)

*********************** 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
  142 residues out of total 671 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 24
    poor density    : 118
  time to evaluate  : 0.223 
Fit side-chains
   revert: symmetry clash
REVERT: A   50 THR cc_start: 0.9003 (OUTLIER) cc_final: 0.8681 (p)
REVERT: A   66 MET cc_start: 0.9425 (tmm) cc_final: 0.8467 (tpp)
REVERT: A  169 GLU cc_start: 0.8909 (mm-30) cc_final: 0.8215 (tp30)
REVERT: A  729 MET cc_start: 0.8614 (ptt) cc_final: 0.7965 (ptt)
REVERT: A  742 GLN cc_start: 0.9041 (pp30) cc_final: 0.8753 (tm-30)
REVERT: A  746 GLU cc_start: 0.8656 (pp20) cc_final: 0.8227 (pp20)
REVERT: B   33 PHE cc_start: 0.7364 (OUTLIER) cc_final: 0.6752 (t80)
REVERT: B   72 ASP cc_start: 0.9039 (m-30) cc_final: 0.8616 (m-30)
  outliers start: 24
  outliers final: 18
  residues processed: 129
  average time/residue: 0.0606
  time to fit residues: 11.2608
Evaluate side-chains
  129 residues out of total 671 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 20
    poor density    : 109
  time to evaluate  : 0.265 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   50 THR
Chi-restraints excluded: chain A residue  313 LEU
Chi-restraints excluded: chain A residue  331 MET
Chi-restraints excluded: chain A residue  355 MET
Chi-restraints excluded: chain A residue  398 THR
Chi-restraints excluded: chain A residue  405 VAL
Chi-restraints excluded: chain A residue  410 LEU
Chi-restraints excluded: chain A residue  718 VAL
Chi-restraints excluded: chain A residue  813 SER
Chi-restraints excluded: chain A residue  824 ILE
Chi-restraints excluded: chain A residue  828 ILE
Chi-restraints excluded: chain A residue  836 MET
Chi-restraints excluded: chain A residue  873 ILE
Chi-restraints excluded: chain A residue  904 VAL
Chi-restraints excluded: chain A residue  905 ILE
Chi-restraints excluded: chain B residue   16 ILE
Chi-restraints excluded: chain B residue   33 PHE
Chi-restraints excluded: chain B residue   37 LEU
Chi-restraints excluded: chain B residue   39 ILE
Chi-restraints excluded: chain B residue   81 GLU
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 82
   random chunks:
   chunk 56 optimal weight:    0.8980
   chunk 71 optimal weight:    0.5980
   chunk 30 optimal weight:    2.9990
   chunk 66 optimal weight:    2.9990
   chunk 40 optimal weight:    0.6980
   chunk 61 optimal weight:    1.9990
   chunk 68 optimal weight:    0.3980
   chunk 31 optimal weight:    1.9990
   chunk 10 optimal weight:    0.0030
   chunk 15 optimal weight:    0.9980
   chunk 67 optimal weight:    0.9980
   overall best weight:    0.5190

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

Flipped N/Q/H residues before XYZ refinement:
B  78 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3419 r_free = 0.3419 target = 0.098605 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 38)----------------|
| r_work = 0.3120 r_free = 0.3120 target = 0.080314 restraints weight = 12870.798|
|-----------------------------------------------------------------------------|
r_work (start): 0.3115 rms_B_bonded: 3.08
r_work: 0.2981 rms_B_bonded: 3.71 restraints_weight: 0.5000
r_work (final): 0.2981
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7872
moved from start:          0.2025

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.061   6429  Z= 0.152
  Angle     :  0.661  13.037   8759  Z= 0.326
  Chirality :  0.045   0.349   1043
  Planarity :  0.004   0.042   1109
  Dihedral  :  5.639  97.969    889
  Min Nonbonded Distance : 2.479

Molprobity Statistics.
  All-atom Clashscore : 13.67
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.43 %
    Favored  : 96.57 %
  Rotamer:
    Outliers :  2.98 %
    Allowed  : 20.42 %
    Favored  : 76.60 %
  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:  1.72 (0.30), residues: 816
  helix:  1.50 (0.21), residues: 549
  sheet:  0.79 (0.85), residues: 40
  loop :  0.54 (0.47), residues: 227

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG B  68 
 TYR   0.006   0.001   TYR A 759 
 PHE   0.016   0.001   PHE B  33 
 TRP   0.008   0.001   TRP A  41 
 HIS   0.002   0.000   HIS A 827 

Details of bonding type rmsd
  covalent geometry    : bond        0.00349 ( 6429)
  covalent geometry    : angle       0.66115 ( 8759)
  hydrogen bonds       : bond        0.03955 (  464)
  hydrogen bonds       : angle       4.87673 ( 1365)

*********************** 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
  133 residues out of total 671 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 20
    poor density    : 113
  time to evaluate  : 0.238 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   50 THR cc_start: 0.8990 (t) cc_final: 0.8594 (p)
REVERT: A   66 MET cc_start: 0.9431 (tmm) cc_final: 0.8485 (tpp)
REVERT: A  169 GLU cc_start: 0.8913 (mm-30) cc_final: 0.8227 (tp30)
REVERT: A  742 GLN cc_start: 0.9028 (pp30) cc_final: 0.8746 (tm-30)
REVERT: A  746 GLU cc_start: 0.8654 (pp20) cc_final: 0.8208 (pp20)
REVERT: B   33 PHE cc_start: 0.7337 (OUTLIER) cc_final: 0.6827 (t80)
REVERT: B   68 ARG cc_start: 0.9229 (ptp-110) cc_final: 0.8298 (ptm-80)
REVERT: B   72 ASP cc_start: 0.9020 (m-30) cc_final: 0.8508 (m-30)
  outliers start: 20
  outliers final: 15
  residues processed: 123
  average time/residue: 0.0550
  time to fit residues: 9.7529
Evaluate side-chains
  125 residues out of total 671 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 109
  time to evaluate  : 0.158 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  313 LEU
Chi-restraints excluded: chain A residue  331 MET
Chi-restraints excluded: chain A residue  405 VAL
Chi-restraints excluded: chain A residue  410 LEU
Chi-restraints excluded: chain A residue  718 VAL
Chi-restraints excluded: chain A residue  813 SER
Chi-restraints excluded: chain A residue  824 ILE
Chi-restraints excluded: chain A residue  828 ILE
Chi-restraints excluded: chain A residue  836 MET
Chi-restraints excluded: chain A residue  873 ILE
Chi-restraints excluded: chain A residue  904 VAL
Chi-restraints excluded: chain A residue  905 ILE
Chi-restraints excluded: chain B residue   16 ILE
Chi-restraints excluded: chain B residue   33 PHE
Chi-restraints excluded: chain B residue   39 ILE
Chi-restraints excluded: chain B residue   81 GLU
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 82
   random chunks:
   chunk 79 optimal weight:    0.6980
   chunk 35 optimal weight:    0.0970
   chunk 42 optimal weight:    0.9990
   chunk 50 optimal weight:    0.7980
   chunk 27 optimal weight:    0.8980
   chunk 24 optimal weight:    0.7980
   chunk 55 optimal weight:    0.6980
   chunk 73 optimal weight:    2.9990
   chunk 41 optimal weight:    0.7980
   chunk 34 optimal weight:    0.8980
   chunk 32 optimal weight:    0.7980
   overall best weight:    0.6178

-------------------------------------------------------------------------------
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 = 0.3416 r_free = 0.3416 target = 0.098591 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 32)----------------|
| r_work = 0.3118 r_free = 0.3118 target = 0.080269 restraints weight = 12912.114|
|-----------------------------------------------------------------------------|
r_work (start): 0.3113 rms_B_bonded: 3.10
r_work: 0.2977 rms_B_bonded: 3.71 restraints_weight: 0.5000
r_work (final): 0.2977
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7876
moved from start:          0.2070

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.048   6429  Z= 0.156
  Angle     :  0.655  13.674   8759  Z= 0.322
  Chirality :  0.045   0.347   1043
  Planarity :  0.004   0.046   1109
  Dihedral  :  5.559  95.503    889
  Min Nonbonded Distance : 2.459

Molprobity Statistics.
  All-atom Clashscore : 13.67
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.68 %
    Favored  : 96.32 %
  Rotamer:
    Outliers :  3.13 %
    Allowed  : 20.57 %
    Favored  : 76.30 %
  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:  1.69 (0.30), residues: 816
  helix:  1.48 (0.21), residues: 555
  sheet:  1.17 (0.91), residues: 34
  loop :  0.41 (0.47), residues: 227

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG B  68 
 TYR   0.005   0.001   TYR A 759 
 PHE   0.018   0.001   PHE B  33 
 TRP   0.008   0.001   TRP A  41 
 HIS   0.002   0.001   HIS A 827 

Details of bonding type rmsd
  covalent geometry    : bond        0.00361 ( 6429)
  covalent geometry    : angle       0.65493 ( 8759)
  hydrogen bonds       : bond        0.03975 (  464)
  hydrogen bonds       : angle       4.87789 ( 1365)

*********************** 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
  129 residues out of total 671 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 21
    poor density    : 108
  time to evaluate  : 0.237 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   61 MET cc_start: 0.8961 (ptm) cc_final: 0.8549 (ppp)
REVERT: A   66 MET cc_start: 0.9472 (tmm) cc_final: 0.8584 (tpp)
REVERT: A  169 GLU cc_start: 0.8910 (mm-30) cc_final: 0.8221 (tp30)
REVERT: A  742 GLN cc_start: 0.9027 (pp30) cc_final: 0.8771 (tm-30)
REVERT: A  746 GLU cc_start: 0.8660 (pp20) cc_final: 0.8216 (pp20)
REVERT: B   33 PHE cc_start: 0.6839 (OUTLIER) cc_final: 0.6582 (t80)
REVERT: B   68 ARG cc_start: 0.9203 (ptp-110) cc_final: 0.8236 (ptm-80)
REVERT: B   72 ASP cc_start: 0.8997 (m-30) cc_final: 0.8486 (m-30)
REVERT: B   79 LYS cc_start: 0.9282 (mttp) cc_final: 0.9038 (mtmm)
  outliers start: 21
  outliers final: 14
  residues processed: 119
  average time/residue: 0.0510
  time to fit residues: 8.8697
Evaluate side-chains
  122 residues out of total 671 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 15
    poor density    : 107
  time to evaluate  : 0.291 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  313 LEU
Chi-restraints excluded: chain A residue  331 MET
Chi-restraints excluded: chain A residue  405 VAL
Chi-restraints excluded: chain A residue  718 VAL
Chi-restraints excluded: chain A residue  813 SER
Chi-restraints excluded: chain A residue  824 ILE
Chi-restraints excluded: chain A residue  828 ILE
Chi-restraints excluded: chain A residue  836 MET
Chi-restraints excluded: chain A residue  873 ILE
Chi-restraints excluded: chain A residue  904 VAL
Chi-restraints excluded: chain A residue  905 ILE
Chi-restraints excluded: chain B residue   16 ILE
Chi-restraints excluded: chain B residue   33 PHE
Chi-restraints excluded: chain B residue   39 ILE
Chi-restraints excluded: chain B residue   81 GLU
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 82
   random chunks:
   chunk 11 optimal weight:    1.9990
   chunk 13 optimal weight:    3.9990
   chunk 38 optimal weight:    4.9990
   chunk 9 optimal weight:    0.5980
   chunk 60 optimal weight:    0.6980
   chunk 36 optimal weight:    0.9990
   chunk 67 optimal weight:    0.6980
   chunk 48 optimal weight:    0.6980
   chunk 80 optimal weight:    2.9990
   chunk 79 optimal weight:    0.9990
   chunk 26 optimal weight:    0.8980
   overall best weight:    0.7180

-------------------------------------------------------------------------------
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 = 0.3408 r_free = 0.3408 target = 0.097976 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 34)----------------|
| r_work = 0.3109 r_free = 0.3109 target = 0.079646 restraints weight = 12836.336|
|-----------------------------------------------------------------------------|
r_work (start): 0.3106 rms_B_bonded: 3.09
r_work: 0.2969 rms_B_bonded: 3.71 restraints_weight: 0.5000
r_work (final): 0.2969
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7879
moved from start:          0.2111

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.047   6429  Z= 0.165
  Angle     :  0.658  13.785   8759  Z= 0.327
  Chirality :  0.045   0.353   1043
  Planarity :  0.004   0.045   1109
  Dihedral  :  5.517  93.615    889
  Min Nonbonded Distance : 2.464

Molprobity Statistics.
  All-atom Clashscore : 13.83
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.68 %
    Favored  : 96.32 %
  Rotamer:
    Outliers :  2.53 %
    Allowed  : 20.86 %
    Favored  : 76.60 %
  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:  1.69 (0.30), residues: 816
  helix:  1.49 (0.21), residues: 555
  sheet:  1.19 (0.91), residues: 34
  loop :  0.39 (0.46), residues: 227

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG B  68 
 TYR   0.005   0.001   TYR A 759 
 PHE   0.019   0.001   PHE B  33 
 TRP   0.008   0.001   TRP A  41 
 HIS   0.002   0.001   HIS A 827 

Details of bonding type rmsd
  covalent geometry    : bond        0.00384 ( 6429)
  covalent geometry    : angle       0.65769 ( 8759)
  hydrogen bonds       : bond        0.04019 (  464)
  hydrogen bonds       : angle       4.88608 ( 1365)

********************** 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
  125 residues out of total 671 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 17
    poor density    : 108
  time to evaluate  : 0.185 
Fit side-chains
   revert: symmetry clash
REVERT: A   66 MET cc_start: 0.9452 (tmm) cc_final: 0.8504 (tpp)
REVERT: A  169 GLU cc_start: 0.8908 (mm-30) cc_final: 0.8221 (tp30)
REVERT: A  345 MET cc_start: 0.8734 (mmm) cc_final: 0.8515 (mmm)
REVERT: A  742 GLN cc_start: 0.9012 (pp30) cc_final: 0.8756 (tm-30)
REVERT: A  746 GLU cc_start: 0.8668 (pp20) cc_final: 0.8223 (pp20)
REVERT: B   33 PHE cc_start: 0.6402 (OUTLIER) cc_final: 0.6069 (t80)
REVERT: B   68 ARG cc_start: 0.9244 (ptp-110) cc_final: 0.8222 (ptm-80)
REVERT: B   72 ASP cc_start: 0.8970 (m-30) cc_final: 0.8432 (m-30)
REVERT: B   80 LEU cc_start: 0.8997 (tp) cc_final: 0.8796 (tt)
  outliers start: 17
  outliers final: 13
  residues processed: 117
  average time/residue: 0.0525
  time to fit residues: 8.9395
Evaluate side-chains
  120 residues out of total 671 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 106
  time to evaluate  : 0.212 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  313 LEU
Chi-restraints excluded: chain A residue  331 MET
Chi-restraints excluded: chain A residue  405 VAL
Chi-restraints excluded: chain A residue  718 VAL
Chi-restraints excluded: chain A residue  813 SER
Chi-restraints excluded: chain A residue  824 ILE
Chi-restraints excluded: chain A residue  828 ILE
Chi-restraints excluded: chain A residue  836 MET
Chi-restraints excluded: chain A residue  873 ILE
Chi-restraints excluded: chain A residue  904 VAL
Chi-restraints excluded: chain A residue  905 ILE
Chi-restraints excluded: chain B residue   16 ILE
Chi-restraints excluded: chain B residue   33 PHE
Chi-restraints excluded: chain B residue   39 ILE
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 82
   random chunks:
   chunk 40 optimal weight:    0.8980
   chunk 7 optimal weight:    1.9990
   chunk 59 optimal weight:    0.9980
   chunk 70 optimal weight:    0.7980
   chunk 43 optimal weight:    4.9990
   chunk 77 optimal weight:    1.9990
   chunk 80 optimal weight:    0.9990
   chunk 50 optimal weight:    2.9990
   chunk 6 optimal weight:    0.7980
   chunk 44 optimal weight:    0.9990
   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 = 0.3390 r_free = 0.3390 target = 0.096824 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 32)----------------|
| r_work = 0.3088 r_free = 0.3088 target = 0.078422 restraints weight = 12914.638|
|-----------------------------------------------------------------------------|
r_work (start): 0.3084 rms_B_bonded: 3.09
r_work: 0.2947 rms_B_bonded: 3.69 restraints_weight: 0.5000
r_work (final): 0.2947
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7891
moved from start:          0.2129

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.050   6429  Z= 0.178
  Angle     :  0.664  12.490   8759  Z= 0.330
  Chirality :  0.046   0.362   1043
  Planarity :  0.004   0.045   1109
  Dihedral  :  5.504  91.685    889
  Min Nonbonded Distance : 2.466

Molprobity Statistics.
  All-atom Clashscore : 14.06
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.68 %
    Favored  : 96.32 %
  Rotamer:
    Outliers :  2.38 %
    Allowed  : 20.86 %
    Favored  : 76.75 %
  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:  1.68 (0.30), residues: 816
  helix:  1.55 (0.21), residues: 550
  sheet:  1.13 (0.90), residues: 34
  loop :  0.23 (0.46), residues: 232

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG B  68 
 TYR   0.011   0.001   TYR B  55 
 PHE   0.019   0.001   PHE B  33 
 TRP   0.009   0.001   TRP A  41 
 HIS   0.002   0.001   HIS A 827 

Details of bonding type rmsd
  covalent geometry    : bond        0.00417 ( 6429)
  covalent geometry    : angle       0.66395 ( 8759)
  hydrogen bonds       : bond        0.04051 (  464)
  hydrogen bonds       : angle       4.89733 ( 1365)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 1312.19 seconds
wall clock time: 23 minutes 15.42 seconds (1395.42 seconds total)