Starting phenix.real_space_refine
on Thu Jul  2 13:52:03 2026 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/8zty_60476/07_2026/8zty_60476.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/8zty_60476/07_2026/8zty_60476.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=2.85
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/cci-nas-00/data/ceres_data/8zty_60476/07_2026/8zty_60476.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/8zty_60476/07_2026/8zty_60476.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/8zty_60476/07_2026/8zty_60476.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/8zty_60476/07_2026/8zty_60476.cif"
  }
  resolution = 2.85
  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=   0.021
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      56      5.49       5
     S      27      5.16       5
     C    5470      2.51       5
     N    1529      2.21       5
     O    1841      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 23 residue(s): 0.01s

  Monomer Library directory:
    "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/chem_data/mon_lib"
  Total number of atoms: 8923
  Number of models: 1
  Model: ""
    Number of chains: 2
    Chain: "A"
      Number of atoms: 7712
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 928, 7712
          Classifications: {'peptide': 928}
          Link IDs: {'PTRANS': 21, 'TRANS': 906}
          Chain breaks: 13
    Chain: "B"
      Number of atoms: 1211
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 57, 1211
          Classifications: {'RNA': 57}
          Modifications used: {'5*END': 1, 'rna2p_pur': 8, 'rna2p_pyr': 9, 'rna3p_pur': 22, 'rna3p_pyr': 18}
          Link IDs: {'rna2p': 17, 'rna3p': 39}
          Chain breaks: 1
  Time building chain proxies: 1.78, per 1000 atoms: 0.20
  Number of scatterers: 8923
  At special positions: 0
  Unit cell: (78.1, 91.3, 115.5, 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      27     16.00
     P      56     15.00
     O    1841      8.00
     N    1529      7.00
     C    5470      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: 0.79
  Conformation dependent library (CDL) restraints added in 258.0 milliseconds
  

  1800 Ramachandran restraints generated.
    900 Oldfield, 0 Emsley, 900 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  1814

  Finding SS restraints...
    Secondary structure from input PDB file:
      43 helices and 5 sheets defined
      70.3% alpha, 3.0% beta
      8 base pairs and 19 stacking pairs defined.
    Time for finding SS restraints: 1.08
  Creating SS restraints...
    Processing helix  chain 'A' and resid 68 through 75
    Processing helix  chain 'A' and resid 75 through 88
    Processing helix  chain 'A' and resid 93 through 105
    Processing helix  chain 'A' and resid 153 through 164
    Processing helix  chain 'A' and resid 180 through 203
    Processing helix  chain 'A' and resid 211 through 226
    Processing helix  chain 'A' and resid 232 through 241
    Processing helix  chain 'A' and resid 241 through 256
    Processing helix  chain 'A' and resid 263 through 283
      removed outlier: 4.979A  pdb=" N   GLU A 280 " --> pdb=" O   ARG A 276 " (cutoff:3.500A)
      removed outlier: 6.130A  pdb=" N   GLU A 281 " --> pdb=" O   GLN A 277 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 285 through 303
    Processing helix  chain 'A' and resid 314 through 318
    Processing helix  chain 'A' and resid 319 through 348
    Processing helix  chain 'A' and resid 355 through 387
    Processing helix  chain 'A' and resid 409 through 422
    Processing helix  chain 'A' and resid 429 through 450
      Proline residue:  A 443  - end of helix
      removed outlier: 3.907A  pdb=" N   HIS A 450 " --> pdb=" O   ASN A 446 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 455 through 462
      removed outlier: 4.560A  pdb=" N   ASN A 462 " --> pdb=" O   LYS A 458 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 489 through 513
      removed outlier: 3.885A  pdb=" N   ASP A 493 " --> pdb=" O   THR A 489 " (cutoff:3.500A)
      Proline residue:  A 503  - end of helix
    Processing helix  chain 'A' and resid 520 through 526
      removed outlier: 3.787A  pdb=" N   GLN A 526 " --> pdb=" O   ASP A 522 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 547 through 560
    Processing helix  chain 'A' and resid 582 through 599
    Processing helix  chain 'A' and resid 599 through 607
      removed outlier: 4.321A  pdb=" N   GLN A 603 " --> pdb=" O   VAL A 599 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 608 through 623
      removed outlier: 4.363A  pdb=" N   ASN A 622 " --> pdb=" O   ILE A 618 " (cutoff:3.500A)
      removed outlier: 4.481A  pdb=" N   LYS A 623 " --> pdb=" O   LEU A 619 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 643 through 658
    Processing helix  chain 'A' and resid 670 through 690
    Processing helix  chain 'A' and resid 692 through 697
      removed outlier: 3.676A  pdb=" N   ILE A 695 " --> pdb=" O   LEU A 692 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 721 through 730
    Processing helix  chain 'A' and resid 732 through 750
    Processing helix  chain 'A' and resid 752 through 774
      removed outlier: 4.313A  pdb=" N   GLU A 774 " --> pdb=" O   LEU A 770 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 786 through 796
      removed outlier: 3.694A  pdb=" N   LEU A 796 " --> pdb=" O   LYS A 792 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 819 through 828
    Processing helix  chain 'A' and resid 830 through 839
    Processing helix  chain 'A' and resid 841 through 845
      removed outlier: 3.955A  pdb=" N   TYR A 844 " --> pdb=" O   SER A 841 " (cutoff:3.500A)
      removed outlier: 4.254A  pdb=" N   LYS A 845 " --> pdb=" O   ASP A 842 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'A' and resid 841 through 845'
    Processing helix  chain 'A' and resid 847 through 857
      removed outlier: 3.797A  pdb=" N   LEU A 854 " --> pdb=" O   ASP A 850 " (cutoff:3.500A)
      removed outlier: 4.040A  pdb=" N   HIS A 855 " --> pdb=" O   ILE A 851 " (cutoff:3.500A)
      removed outlier: 4.504A  pdb=" N   TYR A 857 " --> pdb=" O   LYS A 853 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 858 through 876
    Processing helix  chain 'A' and resid 877 through 881
    Processing helix  chain 'A' and resid 882 through 907
    Processing helix  chain 'A' and resid 908 through 946
      removed outlier: 3.503A  pdb=" N   ARG A 912 " --> pdb=" O   LEU A 908 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 1010 through 1020
    Processing helix  chain 'A' and resid 1022 through 1027
      removed outlier: 3.770A  pdb=" N   ASN A1026 " --> pdb=" O   PHE A1022 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 1032 through 1044
    Processing helix  chain 'A' and resid 1047 through 1065
      removed outlier: 3.539A  pdb=" N   ALA A1053 " --> pdb=" O   LYS A1049 " (cutoff:3.500A)
      removed outlier: 3.741A  pdb=" N   SER A1055 " --> pdb=" O   LYS A1051 " (cutoff:3.500A)
      removed outlier: 4.024A  pdb=" N   LEU A1058 " --> pdb=" O   VAL A1054 " (cutoff:3.500A)
      removed outlier: 3.837A  pdb=" N   LYS A1059 " --> pdb=" O   SER A1055 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 1073 through 1077
    Processing helix  chain 'A' and resid 1106 through 1118
    Processing sheet with id=AA1, first strand: chain 'A' and resid 40 through 42
      removed outlier: 3.928A  pdb=" N   VAL A  40 " --> pdb=" O   VAL A  47 " (cutoff:3.500A)
    Processing sheet with id=AA2, first strand: chain 'A' and resid 135 through 136
    Processing sheet with id=AA3, first strand: chain 'A' and resid 464 through 466
    Processing sheet with id=AA4, first strand: chain 'A' and resid 1067 through 1071
      removed outlier: 4.264A  pdb=" N   THR A1070 " --> pdb=" O   LYS A1085 " (cutoff:3.500A)
      removed outlier: 4.867A  pdb=" N   LYS A1085 " --> pdb=" O   THR A1070 " (cutoff:3.500A)
    Processing sheet with id=AA5, first strand: chain 'A' and resid 1090 through 1092

    471 hydrogen bonds defined for protein.
    1380 hydrogen bond angles defined for protein.
    Restraints generated for nucleic acids:
      22 hydrogen bonds
      44 hydrogen bond angles
      0 basepair planarities
      8 basepair parallelities
      19 stacking parallelities
  Total time for adding SS restraints: 1.51

  Time building geometry restraints manager: 1.03 seconds

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

  Histogram of bond lengths:
        1.22 -     1.34: 2551
        1.34 -     1.46: 1734
        1.46 -     1.57: 4761
        1.57 -     1.69: 112
        1.69 -     1.81: 46
  Bond restraints: 9204
  Sorted by residual:
  bond pdb=" CB  PRO A 602 "
       pdb=" CG  PRO A 602 "
    ideal  model  delta    sigma   weight residual
    1.492  1.619 -0.127 5.00e-02 4.00e+02 6.41e+00
  bond pdb=" N9    A B  36 "
       pdb=" C4    A B  36 "
    ideal  model  delta    sigma   weight residual
    1.374  1.385 -0.011 6.00e-03 2.78e+04 3.50e+00
  bond pdb=" CB  GLN A 804 "
       pdb=" CG  GLN A 804 "
    ideal  model  delta    sigma   weight residual
    1.520  1.569 -0.049 3.00e-02 1.11e+03 2.65e+00
  bond pdb=" CB  ASP A  43 "
       pdb=" CG  ASP A  43 "
    ideal  model  delta    sigma   weight residual
    1.516  1.553 -0.037 2.50e-02 1.60e+03 2.22e+00
  bond pdb=" CB  GLU A 351 "
       pdb=" CG  GLU A 351 "
    ideal  model  delta    sigma   weight residual
    1.520  1.561 -0.041 3.00e-02 1.11e+03 1.91e+00
  ... (remaining 9199 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     2.27: 12432
        2.27 -     4.54: 158
        4.54 -     6.82: 40
        6.82 -     9.09: 9
        9.09 -    11.36: 3
  Bond angle restraints: 12642
  Sorted by residual:
  angle pdb=" CA  PRO A 602 "
        pdb=" N   PRO A 602 "
        pdb=" CD  PRO A 602 "
      ideal   model   delta    sigma   weight residual
     112.00  100.64   11.36 1.40e+00 5.10e-01 6.59e+01
  angle pdb=" CA  GLN A 804 "
        pdb=" CB  GLN A 804 "
        pdb=" CG  GLN A 804 "
      ideal   model   delta    sigma   weight residual
     114.10  121.52   -7.42 2.00e+00 2.50e-01 1.38e+01
  angle pdb=" CB  GLN A 804 "
        pdb=" CG  GLN A 804 "
        pdb=" CD  GLN A 804 "
      ideal   model   delta    sigma   weight residual
     112.60  118.86   -6.26 1.70e+00 3.46e-01 1.36e+01
  angle pdb=" CA  GLU A 365 "
        pdb=" CB  GLU A 365 "
        pdb=" CG  GLU A 365 "
      ideal   model   delta    sigma   weight residual
     114.10  121.28   -7.18 2.00e+00 2.50e-01 1.29e+01
  angle pdb=" CA  GLU A 351 "
        pdb=" CB  GLU A 351 "
        pdb=" CG  GLU A 351 "
      ideal   model   delta    sigma   weight residual
     114.10  120.85   -6.75 2.00e+00 2.50e-01 1.14e+01
  ... (remaining 12637 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    35.98: 5260
       35.98 -    71.95: 396
       71.95 -   107.93: 31
      107.93 -   143.90: 1
      143.90 -   179.88: 2
  Dihedral angle restraints: 5690
    sinusoidal: 2921
      harmonic: 2769
  Sorted by residual:
  dihedral pdb=" O4'   C B  38 "
           pdb=" C1'   C B  38 "
           pdb=" N1    C B  38 "
           pdb=" C2    C B  38 "
      ideal   model   delta sinusoidal    sigma   weight residual
     232.00   52.12  179.88     1      1.70e+01 3.46e-03 6.64e+01
  dihedral pdb=" O4'   U B   1 "
           pdb=" C1'   U B   1 "
           pdb=" N1    U B   1 "
           pdb=" C2    U B   1 "
      ideal   model   delta sinusoidal    sigma   weight residual
    -160.00  -50.48 -109.52     1      1.50e+01 4.44e-03 5.69e+01
  dihedral pdb=" CA  ASP A 232 "
           pdb=" C   ASP A 232 "
           pdb=" N   ILE A 233 "
           pdb=" CA  ILE A 233 "
      ideal   model   delta  harmonic     sigma   weight residual
    -180.00 -152.49  -27.51     0      5.00e+00 4.00e-02 3.03e+01
  ... (remaining 5687 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.049: 1175
       0.049 -    0.098: 222
       0.098 -    0.147: 40
       0.147 -    0.196: 1
       0.196 -    0.245: 1
  Chirality restraints: 1439
  Sorted by residual:
  chirality pdb=" CG  LEU A 601 "
            pdb=" CB  LEU A 601 "
            pdb=" CD1 LEU A 601 "
            pdb=" CD2 LEU A 601 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.59   -2.83    0.24 2.00e-01 2.50e+01 1.50e+00
  chirality pdb=" CG  LEU A 154 "
            pdb=" CB  LEU A 154 "
            pdb=" CD1 LEU A 154 "
            pdb=" CD2 LEU A 154 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.59   -2.43   -0.16 2.00e-01 2.50e+01 6.47e-01
  chirality pdb=" CA  GLU A 322 "
            pdb=" N   GLU A 322 "
            pdb=" C   GLU A 322 "
            pdb=" CB  GLU A 322 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.37    0.14 2.00e-01 2.50e+01 5.06e-01
  ... (remaining 1436 not shown)

  Planarity restraints: 1389
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   LEU A 601 "   -0.085 5.00e-02 4.00e+02   1.22e-01 2.36e+01
        pdb=" N   PRO A 602 "    0.210 5.00e-02 4.00e+02
        pdb=" CA  PRO A 602 "   -0.060 5.00e-02 4.00e+02
        pdb=" CD  PRO A 602 "   -0.065 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  ASP A  43 "   -0.013 2.00e-02 2.50e+03   2.59e-02 6.70e+00
        pdb=" C   ASP A  43 "    0.045 2.00e-02 2.50e+03
        pdb=" O   ASP A  43 "   -0.017 2.00e-02 2.50e+03
        pdb=" N   ARG A  44 "   -0.015 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CB  PHE A 585 "    0.004 2.00e-02 2.50e+03   1.54e-02 4.16e+00
        pdb=" CG  PHE A 585 "   -0.031 2.00e-02 2.50e+03
        pdb=" CD1 PHE A 585 "    0.014 2.00e-02 2.50e+03
        pdb=" CD2 PHE A 585 "    0.022 2.00e-02 2.50e+03
        pdb=" CE1 PHE A 585 "   -0.000 2.00e-02 2.50e+03
        pdb=" CE2 PHE A 585 "   -0.008 2.00e-02 2.50e+03
        pdb=" CZ  PHE A 585 "   -0.001 2.00e-02 2.50e+03
  ... (remaining 1386 not shown)

  Histogram of nonbonded interaction distances:
        2.16 -     2.71: 379
        2.71 -     3.26: 9091
        3.26 -     3.80: 15957
        3.80 -     4.35: 18941
        4.35 -     4.90: 30299
  Nonbonded interactions: 74667
  Sorted by model distance:
  nonbonded pdb=" OE2 GLU A 672 "
            pdb=" O2'   A B  29 "
     model   vdw
     2.161 3.040
  nonbonded pdb=" O   THR A 815 "
            pdb=" OG1 THR A 815 "
     model   vdw
     2.178 3.040
  nonbonded pdb=" NZ  LYS A 363 "
            pdb=" OP2   A B  26 "
     model   vdw
     2.216 3.120
  nonbonded pdb=" O2'   U B  46 "
            pdb=" O5'   C B  47 "
     model   vdw
     2.237 3.040
  nonbonded pdb=" OG  SER A 145 "
            pdb=" OE1 GLU A 147 "
     model   vdw
     2.253 3.040
  ... (remaining 74662 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:             1.210
  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:          0.140
  Check model and map are aligned:         0.030
  Set scattering table:                    0.030
  Process input model:                     9.750
  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:6.420
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   17.640
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6857
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      :  0.003   0.127   9204  Z= 0.145
  Angle     :  0.687  11.361  12642  Z= 0.384
  Chirality :  0.038   0.245   1439
  Planarity :  0.005   0.122   1389
  Dihedral  : 21.973 179.881   3876
  Min Nonbonded Distance : 2.161

Molprobity Statistics.
  All-atom Clashscore : 14.98
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.22 %
    Favored  : 95.78 %
  Rotamer:
    Outliers :  5.14 %
    Allowed  : 42.40 %
    Favored  : 52.46 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  1.26 (0.29), residues: 900
  helix:  1.98 (0.21), residues: 590
  sheet: -4.70 (0.67), residues: 10
  loop : -1.36 (0.36), residues: 300

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.009   0.001   ARG A 149 
 TYR   0.031   0.001   TYR A 844 
 PHE   0.031   0.002   PHE A 585 
 TRP   0.027   0.002   TRP A 435 
 HIS   0.011   0.001   HIS A 915 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00317 /  0.14 ( 9204)
  covalent geometry    : angle       0.68747 /  0.38 (12642)
  hydrogen bonds       : bond        0.05385 /  3.80 (  493)
  hydrogen bonds       : angle       4.02875 /  2.86 ( 1424)

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

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

  1800 Ramachandran restraints generated.
    900 Oldfield, 0 Emsley, 900 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1800 Ramachandran restraints generated.
    900 Oldfield, 0 Emsley, 900 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  225 residues out of total 875 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 45
    poor density    : 180
  time to evaluate  : 0.304 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   60 TYR cc_start: 0.7507 (m-80) cc_final: 0.7279 (m-80)
REVERT: A  150 ILE cc_start: 0.7667 (tp) cc_final: 0.7319 (tt)
REVERT: A  156 GLN cc_start: 0.7734 (mm-40) cc_final: 0.7456 (tp-100)
REVERT: A  219 ARG cc_start: 0.7212 (ttm-80) cc_final: 0.6878 (ttp-170)
REVERT: A  368 PHE cc_start: 0.7517 (t80) cc_final: 0.7291 (t80)
REVERT: A  432 LEU cc_start: 0.7464 (tt) cc_final: 0.7188 (tt)
REVERT: A  511 GLU cc_start: 0.6984 (tm-30) cc_final: 0.6640 (tm-30)
REVERT: A  648 MET cc_start: 0.6833 (ttm) cc_final: 0.6584 (tpp)
REVERT: A  686 PHE cc_start: 0.6761 (t80) cc_final: 0.6463 (t80)
REVERT: A  730 LEU cc_start: 0.7755 (mp) cc_final: 0.7493 (mt)
REVERT: A  735 GLN cc_start: 0.6812 (OUTLIER) cc_final: 0.6564 (mt0)
REVERT: A  797 TYR cc_start: 0.6986 (m-80) cc_final: 0.6751 (m-80)
REVERT: A 1016 ARG cc_start: 0.6632 (ttm-80) cc_final: 0.6312 (mtt90)
REVERT: A 1047 ASP cc_start: 0.6340 (p0) cc_final: 0.6048 (p0)
  outliers start: 45
  outliers final: 37
  residues processed: 221
  average time/residue: 0.4426
  time to fit residues: 105.3322
Evaluate side-chains
  213 residues out of total 875 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 38
    poor density    : 175
  time to evaluate  : 0.237 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   42 VAL
Chi-restraints excluded: chain A residue  101 HIS
Chi-restraints excluded: chain A residue  145 SER
Chi-restraints excluded: chain A residue  246 THR
Chi-restraints excluded: chain A residue  286 SER
Chi-restraints excluded: chain A residue  299 LEU
Chi-restraints excluded: chain A residue  354 VAL
Chi-restraints excluded: chain A residue  360 GLN
Chi-restraints excluded: chain A residue  362 ILE
Chi-restraints excluded: chain A residue  410 HIS
Chi-restraints excluded: chain A residue  425 ILE
Chi-restraints excluded: chain A residue  460 PHE
Chi-restraints excluded: chain A residue  502 VAL
Chi-restraints excluded: chain A residue  536 SER
Chi-restraints excluded: chain A residue  551 VAL
Chi-restraints excluded: chain A residue  608 ASN
Chi-restraints excluded: chain A residue  615 VAL
Chi-restraints excluded: chain A residue  621 LEU
Chi-restraints excluded: chain A residue  632 PHE
Chi-restraints excluded: chain A residue  658 TYR
Chi-restraints excluded: chain A residue  719 ASP
Chi-restraints excluded: chain A residue  729 LYS
Chi-restraints excluded: chain A residue  735 GLN
Chi-restraints excluded: chain A residue  747 SER
Chi-restraints excluded: chain A residue  748 CYS
Chi-restraints excluded: chain A residue  760 THR
Chi-restraints excluded: chain A residue  764 GLU
Chi-restraints excluded: chain A residue  782 GLU
Chi-restraints excluded: chain A residue  815 THR
Chi-restraints excluded: chain A residue  849 LYS
Chi-restraints excluded: chain A residue  886 THR
Chi-restraints excluded: chain A residue  919 ILE
Chi-restraints excluded: chain A residue  939 SER
Chi-restraints excluded: chain A residue 1020 SER
Chi-restraints excluded: chain A residue 1069 VAL
Chi-restraints excluded: chain A residue 1070 THR
Chi-restraints excluded: chain A residue 1094 LEU
Chi-restraints excluded: chain A residue 1105 VAL
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 97
   random chunks:
   chunk 49 optimal weight:    0.5980
   chunk 53 optimal weight:    1.9990
   chunk 5 optimal weight:    2.9990
   chunk 33 optimal weight:    0.8980
   chunk 65 optimal weight:    2.9990
   chunk 62 optimal weight:    0.0170
   chunk 51 optimal weight:    0.9990
   chunk 38 optimal weight:    1.9990
   chunk 61 optimal weight:    0.6980
   chunk 45 optimal weight:    0.8980
   chunk 74 optimal weight:    0.6980
   overall best weight:    0.5818

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
A  67 ASN
A 298 HIS
A 355 ASN
** A 890 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
A1023 ASN

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4348 r_free = 0.4348 target = 0.183017 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 40)----------------|
| r_work = 0.4213 r_free = 0.4213 target = 0.170029 restraints weight = 12724.827|
|-----------------------------------------------------------------------------|
r_work (start): 0.4205 rms_B_bonded: 1.92
r_work: 0.4108 rms_B_bonded: 2.75 restraints_weight: 0.5000
r_work (final): 0.4108
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6894
moved from start:          0.0958

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.064   9204  Z= 0.169
  Angle     :  0.603   8.240  12642  Z= 0.314
  Chirality :  0.040   0.144   1439
  Planarity :  0.004   0.048   1389
  Dihedral  : 19.672 178.738   1922
  Min Nonbonded Distance : 2.485

Molprobity Statistics.
  All-atom Clashscore : 12.03
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.78 %
    Favored  : 96.22 %
  Rotamer:
    Outliers :  9.37 %
    Allowed  : 34.86 %
    Favored  : 55.77 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  0.98 (0.28), residues: 900
  helix:  1.75 (0.21), residues: 599
  sheet: -5.06 (0.63), residues: 10
  loop : -1.53 (0.36), residues: 291

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.006   0.001   ARG A 149 
 TYR   0.015   0.001   TYR A 136 
 PHE   0.027   0.002   PHE A 491 
 TRP   0.014   0.002   TRP A 435 
 HIS   0.006   0.001   HIS A 915 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00383 /  0.17 ( 9204)
  covalent geometry    : angle       0.60310 /  0.31 (12642)
  hydrogen bonds       : bond        0.03756 /  2.55 (  493)
  hydrogen bonds       : angle       3.90361 /  2.80 ( 1424)

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

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

  1800 Ramachandran restraints generated.
    900 Oldfield, 0 Emsley, 900 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1800 Ramachandran restraints generated.
    900 Oldfield, 0 Emsley, 900 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  268 residues out of total 875 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 82
    poor density    : 186
  time to evaluate  : 0.301 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   36 ARG cc_start: 0.7527 (mmm160) cc_final: 0.7170 (ttm-80)
REVERT: A  164 LYS cc_start: 0.7121 (mppt) cc_final: 0.6847 (mttp)
REVERT: A  185 TRP cc_start: 0.7119 (OUTLIER) cc_final: 0.6771 (t-100)
REVERT: A  239 LYS cc_start: 0.7548 (tttm) cc_final: 0.7274 (tttm)
REVERT: A  282 LEU cc_start: 0.7668 (tt) cc_final: 0.7322 (tt)
REVERT: A  435 TRP cc_start: 0.6279 (OUTLIER) cc_final: 0.5725 (m-10)
REVERT: A  710 GLU cc_start: 0.7224 (mp0) cc_final: 0.6955 (mp0)
REVERT: A  797 TYR cc_start: 0.6980 (m-80) cc_final: 0.6618 (m-80)
REVERT: A 1032 SER cc_start: 0.1952 (OUTLIER) cc_final: 0.1594 (m)
REVERT: A 1043 VAL cc_start: 0.2711 (OUTLIER) cc_final: 0.1637 (m)
  outliers start: 82
  outliers final: 39
  residues processed: 253
  average time/residue: 0.4468
  time to fit residues: 121.4805
Evaluate side-chains
  226 residues out of total 875 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 43
    poor density    : 183
  time to evaluate  : 0.303 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   42 VAL
Chi-restraints excluded: chain A residue   49 ILE
Chi-restraints excluded: chain A residue   70 GLN
Chi-restraints excluded: chain A residue  101 HIS
Chi-restraints excluded: chain A residue  185 TRP
Chi-restraints excluded: chain A residue  272 GLN
Chi-restraints excluded: chain A residue  299 LEU
Chi-restraints excluded: chain A residue  354 VAL
Chi-restraints excluded: chain A residue  360 GLN
Chi-restraints excluded: chain A residue  392 LYS
Chi-restraints excluded: chain A residue  408 ILE
Chi-restraints excluded: chain A residue  410 HIS
Chi-restraints excluded: chain A residue  435 TRP
Chi-restraints excluded: chain A residue  460 PHE
Chi-restraints excluded: chain A residue  502 VAL
Chi-restraints excluded: chain A residue  536 SER
Chi-restraints excluded: chain A residue  551 VAL
Chi-restraints excluded: chain A residue  608 ASN
Chi-restraints excluded: chain A residue  615 VAL
Chi-restraints excluded: chain A residue  632 PHE
Chi-restraints excluded: chain A residue  658 TYR
Chi-restraints excluded: chain A residue  709 ILE
Chi-restraints excluded: chain A residue  722 ILE
Chi-restraints excluded: chain A residue  747 SER
Chi-restraints excluded: chain A residue  748 CYS
Chi-restraints excluded: chain A residue  760 THR
Chi-restraints excluded: chain A residue  771 LEU
Chi-restraints excluded: chain A residue  794 MET
Chi-restraints excluded: chain A residue  803 LEU
Chi-restraints excluded: chain A residue  832 THR
Chi-restraints excluded: chain A residue  849 LYS
Chi-restraints excluded: chain A residue  874 ILE
Chi-restraints excluded: chain A residue  886 THR
Chi-restraints excluded: chain A residue  917 LEU
Chi-restraints excluded: chain A residue  919 ILE
Chi-restraints excluded: chain A residue  929 MET
Chi-restraints excluded: chain A residue 1012 LEU
Chi-restraints excluded: chain A residue 1032 SER
Chi-restraints excluded: chain A residue 1043 VAL
Chi-restraints excluded: chain A residue 1057 SER
Chi-restraints excluded: chain A residue 1069 VAL
Chi-restraints excluded: chain A residue 1094 LEU
Chi-restraints excluded: chain A residue 1105 VAL
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 97
   random chunks:
   chunk 95 optimal weight:    4.9990
   chunk 46 optimal weight:    0.8980
   chunk 74 optimal weight:    0.0670
   chunk 69 optimal weight:    0.5980
   chunk 23 optimal weight:    1.9990
   chunk 11 optimal weight:    0.8980
   chunk 15 optimal weight:    1.9990
   chunk 16 optimal weight:    1.9990
   chunk 51 optimal weight:    0.9990
   chunk 34 optimal weight:    0.9990
   chunk 10 optimal weight:    5.9990
   overall best weight:    0.6920

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
A 127 ASN
A 355 ASN
** A 890 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4324 r_free = 0.4324 target = 0.180736 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 44)----------------|
| r_work = 0.4185 r_free = 0.4185 target = 0.167695 restraints weight = 12663.912|
|-----------------------------------------------------------------------------|
r_work (start): 0.4179 rms_B_bonded: 1.92
r_work: 0.4084 rms_B_bonded: 2.74 restraints_weight: 0.5000
r_work (final): 0.4084
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6935
moved from start:          0.1371

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.037   9204  Z= 0.184
  Angle     :  0.598   8.240  12642  Z= 0.313
  Chirality :  0.041   0.173   1439
  Planarity :  0.004   0.041   1389
  Dihedral  : 19.475 179.139   1894
  Min Nonbonded Distance : 2.463

Molprobity Statistics.
  All-atom Clashscore : 12.38
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.11 %
    Favored  : 95.89 %
  Rotamer:
    Outliers :  9.03 %
    Allowed  : 34.97 %
    Favored  : 56.00 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  0.85 (0.28), residues: 900
  helix:  1.63 (0.21), residues: 599
  sheet: -4.97 (0.73), residues: 10
  loop : -1.52 (0.35), residues: 291

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.001   ARG A1041 
 TYR   0.015   0.001   TYR A 589 
 PHE   0.019   0.002   PHE A 491 
 TRP   0.013   0.002   TRP A 435 
 HIS   0.004   0.001   HIS A 298 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00411 /  0.18 ( 9204)
  covalent geometry    : angle       0.59846 /  0.31 (12642)
  hydrogen bonds       : bond        0.03801 /  2.57 (  493)
  hydrogen bonds       : angle       3.92584 /  2.85 ( 1424)

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

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

  1800 Ramachandran restraints generated.
    900 Oldfield, 0 Emsley, 900 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1800 Ramachandran restraints generated.
    900 Oldfield, 0 Emsley, 900 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  271 residues out of total 875 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 79
    poor density    : 192
  time to evaluate  : 0.308 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  149 ARG cc_start: 0.7041 (ttt-90) cc_final: 0.6807 (ttt-90)
REVERT: A  281 GLU cc_start: 0.6519 (tm-30) cc_final: 0.6255 (tm-30)
REVERT: A  710 GLU cc_start: 0.7476 (mp0) cc_final: 0.7189 (mp0)
REVERT: A  797 TYR cc_start: 0.7053 (m-80) cc_final: 0.6325 (m-80)
REVERT: A  919 ILE cc_start: 0.6257 (OUTLIER) cc_final: 0.5721 (mp)
REVERT: A 1032 SER cc_start: 0.1998 (OUTLIER) cc_final: 0.1549 (m)
  outliers start: 79
  outliers final: 44
  residues processed: 252
  average time/residue: 0.4437
  time to fit residues: 120.7128
Evaluate side-chains
  226 residues out of total 875 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 46
    poor density    : 180
  time to evaluate  : 0.308 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   49 ILE
Chi-restraints excluded: chain A residue   70 GLN
Chi-restraints excluded: chain A residue   88 ILE
Chi-restraints excluded: chain A residue  101 HIS
Chi-restraints excluded: chain A residue  145 SER
Chi-restraints excluded: chain A residue  217 MET
Chi-restraints excluded: chain A residue  272 GLN
Chi-restraints excluded: chain A residue  299 LEU
Chi-restraints excluded: chain A residue  354 VAL
Chi-restraints excluded: chain A residue  360 GLN
Chi-restraints excluded: chain A residue  362 ILE
Chi-restraints excluded: chain A residue  392 LYS
Chi-restraints excluded: chain A residue  408 ILE
Chi-restraints excluded: chain A residue  410 HIS
Chi-restraints excluded: chain A residue  435 TRP
Chi-restraints excluded: chain A residue  444 ILE
Chi-restraints excluded: chain A residue  460 PHE
Chi-restraints excluded: chain A residue  487 LYS
Chi-restraints excluded: chain A residue  502 VAL
Chi-restraints excluded: chain A residue  536 SER
Chi-restraints excluded: chain A residue  551 VAL
Chi-restraints excluded: chain A residue  573 ASN
Chi-restraints excluded: chain A residue  608 ASN
Chi-restraints excluded: chain A residue  615 VAL
Chi-restraints excluded: chain A residue  621 LEU
Chi-restraints excluded: chain A residue  632 PHE
Chi-restraints excluded: chain A residue  651 ILE
Chi-restraints excluded: chain A residue  658 TYR
Chi-restraints excluded: chain A residue  709 ILE
Chi-restraints excluded: chain A residue  748 CYS
Chi-restraints excluded: chain A residue  760 THR
Chi-restraints excluded: chain A residue  770 LEU
Chi-restraints excluded: chain A residue  771 LEU
Chi-restraints excluded: chain A residue  794 MET
Chi-restraints excluded: chain A residue  803 LEU
Chi-restraints excluded: chain A residue  832 THR
Chi-restraints excluded: chain A residue  849 LYS
Chi-restraints excluded: chain A residue  874 ILE
Chi-restraints excluded: chain A residue  917 LEU
Chi-restraints excluded: chain A residue  919 ILE
Chi-restraints excluded: chain A residue 1012 LEU
Chi-restraints excluded: chain A residue 1032 SER
Chi-restraints excluded: chain A residue 1057 SER
Chi-restraints excluded: chain A residue 1069 VAL
Chi-restraints excluded: chain A residue 1094 LEU
Chi-restraints excluded: chain A residue 1105 VAL
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 97
   random chunks:
   chunk 7 optimal weight:    0.0170
   chunk 15 optimal weight:    1.9990
   chunk 73 optimal weight:    1.9990
   chunk 3 optimal weight:    0.9990
   chunk 44 optimal weight:    2.9990
   chunk 19 optimal weight:    1.9990
   chunk 46 optimal weight:    0.7980
   chunk 68 optimal weight:    0.0970
   chunk 93 optimal weight:    3.9990
   chunk 70 optimal weight:    1.9990
   chunk 37 optimal weight:    0.0000
   overall best weight:    0.3822

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
A 127 ASN
A 454 HIS
A1023 ASN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4336 r_free = 0.4336 target = 0.181714 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 36)----------------|
| r_work = 0.4199 r_free = 0.4199 target = 0.168722 restraints weight = 12900.835|
|-----------------------------------------------------------------------------|
r_work (start): 0.4192 rms_B_bonded: 1.95
r_work: 0.4094 rms_B_bonded: 2.78 restraints_weight: 0.5000
r_work (final): 0.4094
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6914
moved from start:          0.1422

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.031   9204  Z= 0.141
  Angle     :  0.586   9.943  12642  Z= 0.304
  Chirality :  0.039   0.182   1439
  Planarity :  0.004   0.036   1389
  Dihedral  : 19.408 179.339   1891
  Min Nonbonded Distance : 2.518

Molprobity Statistics.
  All-atom Clashscore : 12.72
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.00 %
    Favored  : 96.00 %
  Rotamer:
    Outliers :  7.89 %
    Allowed  : 36.11 %
    Favored  : 56.00 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  0.90 (0.28), residues: 900
  helix:  1.68 (0.21), residues: 597
  sheet: -4.91 (0.81), residues: 10
  loop : -1.52 (0.35), residues: 293

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG A 205 
 TYR   0.012   0.001   TYR A 647 
 PHE   0.014   0.002   PHE A 585 
 TRP   0.016   0.002   TRP A 435 
 HIS   0.005   0.001   HIS A 915 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00316 /  0.14 ( 9204)
  covalent geometry    : angle       0.58555 /  0.30 (12642)
  hydrogen bonds       : bond        0.03624 /  2.45 (  493)
  hydrogen bonds       : angle       3.89535 /  2.82 ( 1424)

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

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

  1800 Ramachandran restraints generated.
    900 Oldfield, 0 Emsley, 900 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1800 Ramachandran restraints generated.
    900 Oldfield, 0 Emsley, 900 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  257 residues out of total 875 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 69
    poor density    : 188
  time to evaluate  : 0.209 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  149 ARG cc_start: 0.7013 (ttt-90) cc_final: 0.6750 (ttt-90)
REVERT: A  185 TRP cc_start: 0.7339 (OUTLIER) cc_final: 0.6998 (t-100)
REVERT: A  281 GLU cc_start: 0.6312 (tm-30) cc_final: 0.5995 (tm-30)
REVERT: A  445 ARG cc_start: 0.6896 (tmm-80) cc_final: 0.6632 (tmm-80)
REVERT: A  578 LYS cc_start: 0.6968 (OUTLIER) cc_final: 0.6636 (ttmt)
REVERT: A  588 GLN cc_start: 0.8214 (OUTLIER) cc_final: 0.7852 (tt0)
REVERT: A  615 VAL cc_start: 0.6252 (OUTLIER) cc_final: 0.5978 (p)
REVERT: A  710 GLU cc_start: 0.7364 (mp0) cc_final: 0.7053 (mp0)
REVERT: A  786 ASP cc_start: 0.6765 (p0) cc_final: 0.6543 (p0)
REVERT: A  797 TYR cc_start: 0.7047 (m-80) cc_final: 0.6573 (m-80)
REVERT: A  919 ILE cc_start: 0.6205 (OUTLIER) cc_final: 0.5550 (mp)
REVERT: A 1047 ASP cc_start: 0.6344 (p0) cc_final: 0.5844 (p0)
  outliers start: 69
  outliers final: 45
  residues processed: 233
  average time/residue: 0.4452
  time to fit residues: 111.7656
Evaluate side-chains
  231 residues out of total 875 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 50
    poor density    : 181
  time to evaluate  : 0.286 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   49 ILE
Chi-restraints excluded: chain A residue   70 GLN
Chi-restraints excluded: chain A residue  101 HIS
Chi-restraints excluded: chain A residue  185 TRP
Chi-restraints excluded: chain A residue  195 LYS
Chi-restraints excluded: chain A residue  215 GLN
Chi-restraints excluded: chain A residue  272 GLN
Chi-restraints excluded: chain A residue  299 LEU
Chi-restraints excluded: chain A residue  354 VAL
Chi-restraints excluded: chain A residue  360 GLN
Chi-restraints excluded: chain A residue  362 ILE
Chi-restraints excluded: chain A residue  392 LYS
Chi-restraints excluded: chain A residue  408 ILE
Chi-restraints excluded: chain A residue  410 HIS
Chi-restraints excluded: chain A residue  435 TRP
Chi-restraints excluded: chain A residue  444 ILE
Chi-restraints excluded: chain A residue  454 HIS
Chi-restraints excluded: chain A residue  460 PHE
Chi-restraints excluded: chain A residue  505 LEU
Chi-restraints excluded: chain A residue  536 SER
Chi-restraints excluded: chain A residue  551 VAL
Chi-restraints excluded: chain A residue  573 ASN
Chi-restraints excluded: chain A residue  578 LYS
Chi-restraints excluded: chain A residue  588 GLN
Chi-restraints excluded: chain A residue  608 ASN
Chi-restraints excluded: chain A residue  615 VAL
Chi-restraints excluded: chain A residue  621 LEU
Chi-restraints excluded: chain A residue  632 PHE
Chi-restraints excluded: chain A residue  651 ILE
Chi-restraints excluded: chain A residue  658 TYR
Chi-restraints excluded: chain A residue  709 ILE
Chi-restraints excluded: chain A residue  760 THR
Chi-restraints excluded: chain A residue  770 LEU
Chi-restraints excluded: chain A residue  771 LEU
Chi-restraints excluded: chain A residue  782 GLU
Chi-restraints excluded: chain A residue  794 MET
Chi-restraints excluded: chain A residue  832 THR
Chi-restraints excluded: chain A residue  849 LYS
Chi-restraints excluded: chain A residue  874 ILE
Chi-restraints excluded: chain A residue  917 LEU
Chi-restraints excluded: chain A residue  919 ILE
Chi-restraints excluded: chain A residue  924 ARG
Chi-restraints excluded: chain A residue  929 MET
Chi-restraints excluded: chain A residue 1012 LEU
Chi-restraints excluded: chain A residue 1057 SER
Chi-restraints excluded: chain A residue 1069 VAL
Chi-restraints excluded: chain A residue 1070 THR
Chi-restraints excluded: chain A residue 1094 LEU
Chi-restraints excluded: chain A residue 1102 SER
Chi-restraints excluded: chain A residue 1105 VAL
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 97
   random chunks:
   chunk 2 optimal weight:    2.9990
   chunk 51 optimal weight:    0.9990
   chunk 71 optimal weight:    0.8980
   chunk 85 optimal weight:    1.9990
   chunk 83 optimal weight:    1.9990
   chunk 20 optimal weight:    0.9980
   chunk 74 optimal weight:    0.0270
   chunk 67 optimal weight:    1.9990
   chunk 22 optimal weight:    0.5980
   chunk 88 optimal weight:    2.9990
   chunk 73 optimal weight:    0.9990
   overall best weight:    0.7040

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
A  54 ASN
A 127 ASN
A 156 GLN
A 355 ASN
A 890 GLN

Total number of N/Q/H flips: 5

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4319 r_free = 0.4319 target = 0.179932 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 49)----------------|
| r_work = 0.4182 r_free = 0.4182 target = 0.166985 restraints weight = 12633.800|
|-----------------------------------------------------------------------------|
r_work (start): 0.4172 rms_B_bonded: 1.93
r_work: 0.4072 rms_B_bonded: 2.77 restraints_weight: 0.5000
r_work (final): 0.4072
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6951
moved from start:          0.1657

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.038   9204  Z= 0.185
  Angle     :  0.607   8.836  12642  Z= 0.317
  Chirality :  0.041   0.149   1439
  Planarity :  0.004   0.040   1389
  Dihedral  : 19.428 179.422   1889
  Min Nonbonded Distance : 2.274

Molprobity Statistics.
  All-atom Clashscore : 13.24
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.33 %
    Favored  : 95.67 %
  Rotamer:
    Outliers :  8.46 %
    Allowed  : 36.69 %
    Favored  : 54.86 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  0.66 (0.28), residues: 900
  helix:  1.46 (0.21), residues: 603
  sheet: -4.97 (0.78), residues: 10
  loop : -1.59 (0.35), residues: 287

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARG A 820 
 TYR   0.015   0.001   TYR A 589 
 PHE   0.017   0.002   PHE A 585 
 TRP   0.015   0.002   TRP A 435 
 HIS   0.005   0.001   HIS A 454 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00416 /  0.18 ( 9204)
  covalent geometry    : angle       0.60696 /  0.32 (12642)
  hydrogen bonds       : bond        0.03748 /  2.53 (  493)
  hydrogen bonds       : angle       3.95399 /  2.87 ( 1424)

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

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

  1800 Ramachandran restraints generated.
    900 Oldfield, 0 Emsley, 900 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1800 Ramachandran restraints generated.
    900 Oldfield, 0 Emsley, 900 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  269 residues out of total 875 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 74
    poor density    : 195
  time to evaluate  : 0.370 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  149 ARG cc_start: 0.7108 (ttt-90) cc_final: 0.6833 (ttt-90)
REVERT: A  154 LEU cc_start: 0.6164 (OUTLIER) cc_final: 0.5903 (tm)
REVERT: A  185 TRP cc_start: 0.7346 (OUTLIER) cc_final: 0.6925 (t-100)
REVERT: A  272 GLN cc_start: 0.6753 (OUTLIER) cc_final: 0.6071 (mp-120)
REVERT: A  281 GLU cc_start: 0.6538 (tm-30) cc_final: 0.6306 (pp20)
REVERT: A  445 ARG cc_start: 0.6970 (tmm-80) cc_final: 0.6703 (tmm-80)
REVERT: A  573 ASN cc_start: 0.5681 (OUTLIER) cc_final: 0.5200 (p0)
REVERT: A  588 GLN cc_start: 0.8237 (OUTLIER) cc_final: 0.7812 (tt0)
REVERT: A  599 VAL cc_start: 0.7302 (t) cc_final: 0.7008 (t)
REVERT: A  685 SER cc_start: 0.6974 (OUTLIER) cc_final: 0.6688 (p)
REVERT: A  710 GLU cc_start: 0.7375 (mp0) cc_final: 0.7084 (mp0)
REVERT: A  786 ASP cc_start: 0.6817 (p0) cc_final: 0.6538 (p0)
REVERT: A  797 TYR cc_start: 0.7040 (m-80) cc_final: 0.6624 (m-80)
REVERT: A  919 ILE cc_start: 0.6415 (OUTLIER) cc_final: 0.5736 (mp)
REVERT: A 1024 TYR cc_start: 0.6565 (t80) cc_final: 0.6343 (t80)
REVERT: A 1032 SER cc_start: 0.1948 (OUTLIER) cc_final: 0.1321 (m)
REVERT: A 1047 ASP cc_start: 0.6476 (p0) cc_final: 0.5992 (p0)
  outliers start: 74
  outliers final: 45
  residues processed: 247
  average time/residue: 0.4181
  time to fit residues: 111.2685
Evaluate side-chains
  241 residues out of total 875 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 53
    poor density    : 188
  time to evaluate  : 0.257 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   40 VAL
Chi-restraints excluded: chain A residue   49 ILE
Chi-restraints excluded: chain A residue   70 GLN
Chi-restraints excluded: chain A residue  101 HIS
Chi-restraints excluded: chain A residue  154 LEU
Chi-restraints excluded: chain A residue  185 TRP
Chi-restraints excluded: chain A residue  195 LYS
Chi-restraints excluded: chain A residue  215 GLN
Chi-restraints excluded: chain A residue  217 MET
Chi-restraints excluded: chain A residue  272 GLN
Chi-restraints excluded: chain A residue  299 LEU
Chi-restraints excluded: chain A residue  354 VAL
Chi-restraints excluded: chain A residue  360 GLN
Chi-restraints excluded: chain A residue  362 ILE
Chi-restraints excluded: chain A residue  392 LYS
Chi-restraints excluded: chain A residue  408 ILE
Chi-restraints excluded: chain A residue  410 HIS
Chi-restraints excluded: chain A residue  425 ILE
Chi-restraints excluded: chain A residue  435 TRP
Chi-restraints excluded: chain A residue  451 LEU
Chi-restraints excluded: chain A residue  454 HIS
Chi-restraints excluded: chain A residue  460 PHE
Chi-restraints excluded: chain A residue  505 LEU
Chi-restraints excluded: chain A residue  536 SER
Chi-restraints excluded: chain A residue  551 VAL
Chi-restraints excluded: chain A residue  573 ASN
Chi-restraints excluded: chain A residue  588 GLN
Chi-restraints excluded: chain A residue  608 ASN
Chi-restraints excluded: chain A residue  621 LEU
Chi-restraints excluded: chain A residue  632 PHE
Chi-restraints excluded: chain A residue  651 ILE
Chi-restraints excluded: chain A residue  658 TYR
Chi-restraints excluded: chain A residue  685 SER
Chi-restraints excluded: chain A residue  692 LEU
Chi-restraints excluded: chain A residue  709 ILE
Chi-restraints excluded: chain A residue  760 THR
Chi-restraints excluded: chain A residue  764 GLU
Chi-restraints excluded: chain A residue  771 LEU
Chi-restraints excluded: chain A residue  782 GLU
Chi-restraints excluded: chain A residue  794 MET
Chi-restraints excluded: chain A residue  832 THR
Chi-restraints excluded: chain A residue  849 LYS
Chi-restraints excluded: chain A residue  874 ILE
Chi-restraints excluded: chain A residue  917 LEU
Chi-restraints excluded: chain A residue  919 ILE
Chi-restraints excluded: chain A residue  929 MET
Chi-restraints excluded: chain A residue 1012 LEU
Chi-restraints excluded: chain A residue 1032 SER
Chi-restraints excluded: chain A residue 1057 SER
Chi-restraints excluded: chain A residue 1069 VAL
Chi-restraints excluded: chain A residue 1094 LEU
Chi-restraints excluded: chain A residue 1102 SER
Chi-restraints excluded: chain A residue 1105 VAL
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 97
   random chunks:
   chunk 83 optimal weight:    1.9990
   chunk 25 optimal weight:    0.5980
   chunk 57 optimal weight:    0.9990
   chunk 44 optimal weight:    1.9990
   chunk 18 optimal weight:    0.9980
   chunk 95 optimal weight:    4.9990
   chunk 46 optimal weight:    0.6980
   chunk 56 optimal weight:    0.5980
   chunk 45 optimal weight:    0.4980
   chunk 61 optimal weight:    0.6980
   chunk 19 optimal weight:    0.6980
   overall best weight:    0.6180

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
A 127 ASN
A 654 GLN
A1023 ASN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4318 r_free = 0.4318 target = 0.179981 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 43)----------------|
| r_work = 0.4180 r_free = 0.4180 target = 0.166846 restraints weight = 12665.962|
|-----------------------------------------------------------------------------|
r_work (start): 0.4171 rms_B_bonded: 1.94
r_work: 0.4071 rms_B_bonded: 2.76 restraints_weight: 0.5000
r_work (final): 0.4071
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6953
moved from start:          0.1741

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.037   9204  Z= 0.173
  Angle     :  0.602   8.491  12642  Z= 0.314
  Chirality :  0.041   0.213   1439
  Planarity :  0.004   0.038   1389
  Dihedral  : 19.428 179.622   1888
  Min Nonbonded Distance : 2.523

Molprobity Statistics.
  All-atom Clashscore : 12.78
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.44 %
    Favored  : 95.56 %
  Rotamer:
    Outliers :  8.46 %
    Allowed  : 36.34 %
    Favored  : 55.20 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  0.60 (0.28), residues: 900
  helix:  1.42 (0.21), residues: 601
  sheet: -5.08 (0.74), residues: 10
  loop : -1.61 (0.35), residues: 289

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.006   0.000   ARG A 820 
 TYR   0.015   0.001   TYR A 647 
 PHE   0.020   0.002   PHE A 585 
 TRP   0.017   0.002   TRP A 435 
 HIS   0.005   0.001   HIS A 454 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00391 /  0.17 ( 9204)
  covalent geometry    : angle       0.60176 /  0.31 (12642)
  hydrogen bonds       : bond        0.03757 /  2.54 (  493)
  hydrogen bonds       : angle       3.99498 /  2.90 ( 1424)

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

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

  1800 Ramachandran restraints generated.
    900 Oldfield, 0 Emsley, 900 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1800 Ramachandran restraints generated.
    900 Oldfield, 0 Emsley, 900 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  263 residues out of total 875 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 74
    poor density    : 189
  time to evaluate  : 0.186 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  149 ARG cc_start: 0.7127 (ttt-90) cc_final: 0.6819 (ttt-90)
REVERT: A  154 LEU cc_start: 0.6228 (OUTLIER) cc_final: 0.5943 (tm)
REVERT: A  156 GLN cc_start: 0.7881 (mm-40) cc_final: 0.7580 (tp-100)
REVERT: A  185 TRP cc_start: 0.7342 (OUTLIER) cc_final: 0.6906 (t-100)
REVERT: A  272 GLN cc_start: 0.6781 (OUTLIER) cc_final: 0.6079 (mp-120)
REVERT: A  281 GLU cc_start: 0.6520 (tm-30) cc_final: 0.6100 (pp20)
REVERT: A  288 LEU cc_start: 0.7264 (OUTLIER) cc_final: 0.6810 (mt)
REVERT: A  445 ARG cc_start: 0.6983 (tmm-80) cc_final: 0.6741 (tmm-80)
REVERT: A  588 GLN cc_start: 0.8238 (OUTLIER) cc_final: 0.7827 (tt0)
REVERT: A  685 SER cc_start: 0.6975 (OUTLIER) cc_final: 0.6684 (p)
REVERT: A  710 GLU cc_start: 0.7526 (mp0) cc_final: 0.7220 (mp0)
REVERT: A  757 SER cc_start: 0.7785 (t) cc_final: 0.7508 (t)
REVERT: A  786 ASP cc_start: 0.6967 (p0) cc_final: 0.6712 (p0)
REVERT: A  797 TYR cc_start: 0.6995 (m-80) cc_final: 0.6546 (m-80)
REVERT: A  895 ASP cc_start: 0.6982 (m-30) cc_final: 0.6707 (m-30)
REVERT: A  919 ILE cc_start: 0.6321 (OUTLIER) cc_final: 0.5567 (mp)
REVERT: A 1032 SER cc_start: 0.1672 (OUTLIER) cc_final: 0.1052 (m)
REVERT: A 1047 ASP cc_start: 0.6521 (p0) cc_final: 0.6053 (m-30)
  outliers start: 74
  outliers final: 45
  residues processed: 239
  average time/residue: 0.3888
  time to fit residues: 100.4242
Evaluate side-chains
  240 residues out of total 875 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 53
    poor density    : 187
  time to evaluate  : 0.294 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   40 VAL
Chi-restraints excluded: chain A residue   49 ILE
Chi-restraints excluded: chain A residue   70 GLN
Chi-restraints excluded: chain A residue  101 HIS
Chi-restraints excluded: chain A residue  154 LEU
Chi-restraints excluded: chain A residue  185 TRP
Chi-restraints excluded: chain A residue  195 LYS
Chi-restraints excluded: chain A residue  217 MET
Chi-restraints excluded: chain A residue  272 GLN
Chi-restraints excluded: chain A residue  288 LEU
Chi-restraints excluded: chain A residue  299 LEU
Chi-restraints excluded: chain A residue  354 VAL
Chi-restraints excluded: chain A residue  360 GLN
Chi-restraints excluded: chain A residue  362 ILE
Chi-restraints excluded: chain A residue  392 LYS
Chi-restraints excluded: chain A residue  408 ILE
Chi-restraints excluded: chain A residue  410 HIS
Chi-restraints excluded: chain A residue  435 TRP
Chi-restraints excluded: chain A residue  454 HIS
Chi-restraints excluded: chain A residue  465 PHE
Chi-restraints excluded: chain A residue  505 LEU
Chi-restraints excluded: chain A residue  536 SER
Chi-restraints excluded: chain A residue  551 VAL
Chi-restraints excluded: chain A residue  588 GLN
Chi-restraints excluded: chain A residue  608 ASN
Chi-restraints excluded: chain A residue  621 LEU
Chi-restraints excluded: chain A residue  632 PHE
Chi-restraints excluded: chain A residue  651 ILE
Chi-restraints excluded: chain A residue  658 TYR
Chi-restraints excluded: chain A residue  685 SER
Chi-restraints excluded: chain A residue  709 ILE
Chi-restraints excluded: chain A residue  747 SER
Chi-restraints excluded: chain A residue  756 ILE
Chi-restraints excluded: chain A residue  760 THR
Chi-restraints excluded: chain A residue  764 GLU
Chi-restraints excluded: chain A residue  771 LEU
Chi-restraints excluded: chain A residue  782 GLU
Chi-restraints excluded: chain A residue  794 MET
Chi-restraints excluded: chain A residue  832 THR
Chi-restraints excluded: chain A residue  845 LYS
Chi-restraints excluded: chain A residue  849 LYS
Chi-restraints excluded: chain A residue  874 ILE
Chi-restraints excluded: chain A residue  886 THR
Chi-restraints excluded: chain A residue  908 LEU
Chi-restraints excluded: chain A residue  917 LEU
Chi-restraints excluded: chain A residue  919 ILE
Chi-restraints excluded: chain A residue  929 MET
Chi-restraints excluded: chain A residue 1012 LEU
Chi-restraints excluded: chain A residue 1032 SER
Chi-restraints excluded: chain A residue 1057 SER
Chi-restraints excluded: chain A residue 1069 VAL
Chi-restraints excluded: chain A residue 1094 LEU
Chi-restraints excluded: chain A residue 1105 VAL
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 97
   random chunks:
   chunk 64 optimal weight:    0.5980
   chunk 58 optimal weight:    0.6980
   chunk 17 optimal weight:    1.9990
   chunk 43 optimal weight:    0.7980
   chunk 50 optimal weight:    0.4980
   chunk 44 optimal weight:    0.0970
   chunk 24 optimal weight:    0.9990
   chunk 93 optimal weight:    3.9990
   chunk 19 optimal weight:    0.9990
   chunk 66 optimal weight:    0.0970
   chunk 20 optimal weight:    0.6980
   overall best weight:    0.3976

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
A 127 ASN
A 454 HIS
A 654 GLN
A 684 ASN
A 890 GLN

Total number of N/Q/H flips: 5

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4327 r_free = 0.4327 target = 0.180740 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.4191 r_free = 0.4191 target = 0.167779 restraints weight = 12738.669|
|-----------------------------------------------------------------------------|
r_work (start): 0.4183 rms_B_bonded: 1.93
r_work: 0.4085 rms_B_bonded: 2.76 restraints_weight: 0.5000
r_work (final): 0.4085
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6933
moved from start:          0.1747

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.035   9204  Z= 0.145
  Angle     :  0.598   9.381  12642  Z= 0.311
  Chirality :  0.040   0.181   1439
  Planarity :  0.004   0.061   1389
  Dihedral  : 19.367 179.571   1886
  Min Nonbonded Distance : 2.504

Molprobity Statistics.
  All-atom Clashscore : 13.53
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.44 %
    Favored  : 95.56 %
  Rotamer:
    Outliers :  7.89 %
    Allowed  : 37.37 %
    Favored  : 54.74 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  0.71 (0.28), residues: 900
  helix:  1.51 (0.21), residues: 602
  sheet: -5.04 (0.76), residues: 10
  loop : -1.59 (0.35), residues: 288

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.006   0.001   ARG A 820 
 TYR   0.019   0.001   TYR A 647 
 PHE   0.023   0.002   PHE A 585 
 TRP   0.017   0.001   TRP A 435 
 HIS   0.005   0.001   HIS A 915 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00327 /  0.15 ( 9204)
  covalent geometry    : angle       0.59822 /  0.31 (12642)
  hydrogen bonds       : bond        0.03702 /  2.50 (  493)
  hydrogen bonds       : angle       3.96191 /  2.88 ( 1424)

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

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

  1800 Ramachandran restraints generated.
    900 Oldfield, 0 Emsley, 900 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1800 Ramachandran restraints generated.
    900 Oldfield, 0 Emsley, 900 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  262 residues out of total 875 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 69
    poor density    : 193
  time to evaluate  : 0.329 
Fit side-chains
   revert: symmetry clash
REVERT: A  149 ARG cc_start: 0.7111 (ttt-90) cc_final: 0.6789 (ttt-90)
REVERT: A  154 LEU cc_start: 0.6232 (OUTLIER) cc_final: 0.5925 (tm)
REVERT: A  156 GLN cc_start: 0.7882 (mm-40) cc_final: 0.7576 (tp-100)
REVERT: A  272 GLN cc_start: 0.6787 (OUTLIER) cc_final: 0.6139 (mp-120)
REVERT: A  281 GLU cc_start: 0.6454 (tm-30) cc_final: 0.6090 (pp20)
REVERT: A  288 LEU cc_start: 0.7264 (OUTLIER) cc_final: 0.6578 (mt)
REVERT: A  435 TRP cc_start: 0.6270 (OUTLIER) cc_final: 0.6069 (t60)
REVERT: A  445 ARG cc_start: 0.6949 (tmm-80) cc_final: 0.6728 (tmm-80)
REVERT: A  588 GLN cc_start: 0.8216 (OUTLIER) cc_final: 0.7829 (tt0)
REVERT: A  685 SER cc_start: 0.6977 (OUTLIER) cc_final: 0.6669 (p)
REVERT: A  710 GLU cc_start: 0.7328 (mp0) cc_final: 0.7030 (mp0)
REVERT: A  786 ASP cc_start: 0.6846 (p0) cc_final: 0.6616 (p0)
REVERT: A  797 TYR cc_start: 0.6962 (m-80) cc_final: 0.6491 (m-80)
REVERT: A  919 ILE cc_start: 0.6233 (OUTLIER) cc_final: 0.5400 (mp)
REVERT: A 1047 ASP cc_start: 0.6452 (p0) cc_final: 0.6012 (p0)
  outliers start: 69
  outliers final: 45
  residues processed: 239
  average time/residue: 0.3932
  time to fit residues: 101.5975
Evaluate side-chains
  240 residues out of total 875 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 52
    poor density    : 188
  time to evaluate  : 0.203 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   40 VAL
Chi-restraints excluded: chain A residue   49 ILE
Chi-restraints excluded: chain A residue   70 GLN
Chi-restraints excluded: chain A residue   88 ILE
Chi-restraints excluded: chain A residue  101 HIS
Chi-restraints excluded: chain A residue  154 LEU
Chi-restraints excluded: chain A residue  195 LYS
Chi-restraints excluded: chain A residue  224 ILE
Chi-restraints excluded: chain A residue  272 GLN
Chi-restraints excluded: chain A residue  288 LEU
Chi-restraints excluded: chain A residue  299 LEU
Chi-restraints excluded: chain A residue  354 VAL
Chi-restraints excluded: chain A residue  360 GLN
Chi-restraints excluded: chain A residue  362 ILE
Chi-restraints excluded: chain A residue  392 LYS
Chi-restraints excluded: chain A residue  408 ILE
Chi-restraints excluded: chain A residue  410 HIS
Chi-restraints excluded: chain A residue  435 TRP
Chi-restraints excluded: chain A residue  451 LEU
Chi-restraints excluded: chain A residue  454 HIS
Chi-restraints excluded: chain A residue  465 PHE
Chi-restraints excluded: chain A residue  505 LEU
Chi-restraints excluded: chain A residue  536 SER
Chi-restraints excluded: chain A residue  551 VAL
Chi-restraints excluded: chain A residue  588 GLN
Chi-restraints excluded: chain A residue  608 ASN
Chi-restraints excluded: chain A residue  621 LEU
Chi-restraints excluded: chain A residue  632 PHE
Chi-restraints excluded: chain A residue  651 ILE
Chi-restraints excluded: chain A residue  685 SER
Chi-restraints excluded: chain A residue  709 ILE
Chi-restraints excluded: chain A residue  747 SER
Chi-restraints excluded: chain A residue  760 THR
Chi-restraints excluded: chain A residue  764 GLU
Chi-restraints excluded: chain A residue  770 LEU
Chi-restraints excluded: chain A residue  771 LEU
Chi-restraints excluded: chain A residue  782 GLU
Chi-restraints excluded: chain A residue  794 MET
Chi-restraints excluded: chain A residue  812 ASP
Chi-restraints excluded: chain A residue  832 THR
Chi-restraints excluded: chain A residue  845 LYS
Chi-restraints excluded: chain A residue  849 LYS
Chi-restraints excluded: chain A residue  874 ILE
Chi-restraints excluded: chain A residue  908 LEU
Chi-restraints excluded: chain A residue  917 LEU
Chi-restraints excluded: chain A residue  919 ILE
Chi-restraints excluded: chain A residue  929 MET
Chi-restraints excluded: chain A residue 1057 SER
Chi-restraints excluded: chain A residue 1069 VAL
Chi-restraints excluded: chain A residue 1070 THR
Chi-restraints excluded: chain A residue 1094 LEU
Chi-restraints excluded: chain A residue 1105 VAL
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 97
   random chunks:
   chunk 91 optimal weight:    2.9990
   chunk 21 optimal weight:    0.9990
   chunk 84 optimal weight:    0.5980
   chunk 11 optimal weight:    0.0870
   chunk 80 optimal weight:    0.9990
   chunk 85 optimal weight:    0.5980
   chunk 2 optimal weight:    0.9980
   chunk 71 optimal weight:    0.9990
   chunk 61 optimal weight:    0.6980
   chunk 89 optimal weight:    0.8980
   chunk 56 optimal weight:    1.9990
   overall best weight:    0.5758

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
A 127 ASN
A 654 GLN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4319 r_free = 0.4319 target = 0.179966 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 40)----------------|
| r_work = 0.4182 r_free = 0.4182 target = 0.166898 restraints weight = 12792.347|
|-----------------------------------------------------------------------------|
r_work (start): 0.4172 rms_B_bonded: 1.96
r_work: 0.4073 rms_B_bonded: 2.78 restraints_weight: 0.5000
r_work (final): 0.4073
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6949
moved from start:          0.1823

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.036   9204  Z= 0.173
  Angle     :  0.637  10.096  12642  Z= 0.328
  Chirality :  0.041   0.154   1439
  Planarity :  0.004   0.054   1389
  Dihedral  : 19.335 179.559   1884
  Min Nonbonded Distance : 2.430

Molprobity Statistics.
  All-atom Clashscore : 13.88
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.44 %
    Favored  : 95.56 %
  Rotamer:
    Outliers :  7.77 %
    Allowed  : 37.94 %
    Favored  : 54.29 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  0.60 (0.28), residues: 900
  helix:  1.43 (0.21), residues: 602
  sheet: -4.89 (0.77), residues: 10
  loop : -1.64 (0.35), residues: 288

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.007   0.001   ARG A 820 
 TYR   0.015   0.001   TYR A 647 
 PHE   0.025   0.002   PHE A 585 
 TRP   0.017   0.002   TRP A 435 
 HIS   0.006   0.001   HIS A 915 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00389 /  0.17 ( 9204)
  covalent geometry    : angle       0.63684 /  0.33 (12642)
  hydrogen bonds       : bond        0.03792 /  2.56 (  493)
  hydrogen bonds       : angle       4.01650 /  2.91 ( 1424)

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

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

  1800 Ramachandran restraints generated.
    900 Oldfield, 0 Emsley, 900 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1800 Ramachandran restraints generated.
    900 Oldfield, 0 Emsley, 900 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  261 residues out of total 875 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 68
    poor density    : 193
  time to evaluate  : 0.384 
Fit side-chains
   revert: symmetry clash
REVERT: A  149 ARG cc_start: 0.7124 (ttt-90) cc_final: 0.6798 (ttt-90)
REVERT: A  154 LEU cc_start: 0.6266 (OUTLIER) cc_final: 0.5953 (tm)
REVERT: A  156 GLN cc_start: 0.7871 (mm-40) cc_final: 0.7577 (tp-100)
REVERT: A  185 TRP cc_start: 0.7356 (OUTLIER) cc_final: 0.6981 (t-100)
REVERT: A  272 GLN cc_start: 0.6793 (OUTLIER) cc_final: 0.6162 (mp-120)
REVERT: A  281 GLU cc_start: 0.6589 (tm-30) cc_final: 0.6255 (pp20)
REVERT: A  288 LEU cc_start: 0.7107 (OUTLIER) cc_final: 0.6830 (mt)
REVERT: A  322 GLU cc_start: 0.6999 (OUTLIER) cc_final: 0.6430 (pm20)
REVERT: A  435 TRP cc_start: 0.6345 (OUTLIER) cc_final: 0.6140 (t60)
REVERT: A  445 ARG cc_start: 0.6969 (tmm-80) cc_final: 0.6739 (tmm-80)
REVERT: A  578 LYS cc_start: 0.7039 (OUTLIER) cc_final: 0.6683 (ttmt)
REVERT: A  588 GLN cc_start: 0.8197 (OUTLIER) cc_final: 0.7813 (tt0)
REVERT: A  685 SER cc_start: 0.7030 (OUTLIER) cc_final: 0.6715 (p)
REVERT: A  710 GLU cc_start: 0.7360 (mp0) cc_final: 0.7060 (mp0)
REVERT: A  786 ASP cc_start: 0.6854 (p0) cc_final: 0.6635 (p0)
REVERT: A  797 TYR cc_start: 0.6954 (m-80) cc_final: 0.6479 (m-80)
REVERT: A  804 GLN cc_start: 0.7807 (pp30) cc_final: 0.7475 (pp30)
REVERT: A  919 ILE cc_start: 0.6202 (OUTLIER) cc_final: 0.5403 (mp)
REVERT: A 1047 ASP cc_start: 0.6562 (p0) cc_final: 0.6168 (p0)
  outliers start: 68
  outliers final: 45
  residues processed: 241
  average time/residue: 0.4184
  time to fit residues: 108.7411
Evaluate side-chains
  244 residues out of total 875 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 55
    poor density    : 189
  time to evaluate  : 0.254 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   40 VAL
Chi-restraints excluded: chain A residue   49 ILE
Chi-restraints excluded: chain A residue   70 GLN
Chi-restraints excluded: chain A residue   88 ILE
Chi-restraints excluded: chain A residue  101 HIS
Chi-restraints excluded: chain A residue  154 LEU
Chi-restraints excluded: chain A residue  185 TRP
Chi-restraints excluded: chain A residue  195 LYS
Chi-restraints excluded: chain A residue  224 ILE
Chi-restraints excluded: chain A residue  272 GLN
Chi-restraints excluded: chain A residue  288 LEU
Chi-restraints excluded: chain A residue  299 LEU
Chi-restraints excluded: chain A residue  322 GLU
Chi-restraints excluded: chain A residue  354 VAL
Chi-restraints excluded: chain A residue  360 GLN
Chi-restraints excluded: chain A residue  362 ILE
Chi-restraints excluded: chain A residue  392 LYS
Chi-restraints excluded: chain A residue  408 ILE
Chi-restraints excluded: chain A residue  410 HIS
Chi-restraints excluded: chain A residue  435 TRP
Chi-restraints excluded: chain A residue  451 LEU
Chi-restraints excluded: chain A residue  454 HIS
Chi-restraints excluded: chain A residue  536 SER
Chi-restraints excluded: chain A residue  551 VAL
Chi-restraints excluded: chain A residue  578 LYS
Chi-restraints excluded: chain A residue  588 GLN
Chi-restraints excluded: chain A residue  608 ASN
Chi-restraints excluded: chain A residue  621 LEU
Chi-restraints excluded: chain A residue  632 PHE
Chi-restraints excluded: chain A residue  651 ILE
Chi-restraints excluded: chain A residue  685 SER
Chi-restraints excluded: chain A residue  709 ILE
Chi-restraints excluded: chain A residue  747 SER
Chi-restraints excluded: chain A residue  756 ILE
Chi-restraints excluded: chain A residue  760 THR
Chi-restraints excluded: chain A residue  764 GLU
Chi-restraints excluded: chain A residue  770 LEU
Chi-restraints excluded: chain A residue  771 LEU
Chi-restraints excluded: chain A residue  782 GLU
Chi-restraints excluded: chain A residue  794 MET
Chi-restraints excluded: chain A residue  812 ASP
Chi-restraints excluded: chain A residue  832 THR
Chi-restraints excluded: chain A residue  845 LYS
Chi-restraints excluded: chain A residue  849 LYS
Chi-restraints excluded: chain A residue  874 ILE
Chi-restraints excluded: chain A residue  886 THR
Chi-restraints excluded: chain A residue  908 LEU
Chi-restraints excluded: chain A residue  917 LEU
Chi-restraints excluded: chain A residue  919 ILE
Chi-restraints excluded: chain A residue  929 MET
Chi-restraints excluded: chain A residue 1057 SER
Chi-restraints excluded: chain A residue 1069 VAL
Chi-restraints excluded: chain A residue 1070 THR
Chi-restraints excluded: chain A residue 1094 LEU
Chi-restraints excluded: chain A residue 1105 VAL
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 97
   random chunks:
   chunk 88 optimal weight:    0.9980
   chunk 65 optimal weight:    0.5980
   chunk 33 optimal weight:    0.3980
   chunk 18 optimal weight:    2.9990
   chunk 13 optimal weight:    0.5980
   chunk 43 optimal weight:    0.0270
   chunk 35 optimal weight:    0.6980
   chunk 62 optimal weight:    0.9990
   chunk 0 optimal weight:    2.9990
   chunk 53 optimal weight:    0.7980
   chunk 78 optimal weight:    0.7980
   overall best weight:    0.4638

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
A 127 ASN
A 654 GLN
A 890 GLN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4323 r_free = 0.4323 target = 0.180253 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 44)----------------|
| r_work = 0.4188 r_free = 0.4188 target = 0.167392 restraints weight = 12664.388|
|-----------------------------------------------------------------------------|
r_work (start): 0.4180 rms_B_bonded: 1.92
r_work: 0.4083 rms_B_bonded: 2.73 restraints_weight: 0.5000
r_work: 0.3944 rms_B_bonded: 4.96 restraints_weight: 0.2500
r_work (final): 0.3944
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7081
moved from start:          0.1848

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.066   9204  Z= 0.159
  Angle     :  0.637   9.417  12642  Z= 0.327
  Chirality :  0.041   0.231   1439
  Planarity :  0.004   0.051   1389
  Dihedral  : 19.306 179.609   1884
  Min Nonbonded Distance : 2.422

Molprobity Statistics.
  All-atom Clashscore : 13.82
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.22 %
    Favored  : 95.78 %
  Rotamer:
    Outliers :  7.31 %
    Allowed  : 38.29 %
    Favored  : 54.40 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.11 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  0.61 (0.28), residues: 900
  helix:  1.43 (0.21), residues: 603
  sheet: -4.78 (0.78), residues: 10
  loop : -1.64 (0.35), residues: 287

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.008   0.001   ARG A 820 
 TYR   0.019   0.001   TYR A 647 
 PHE   0.026   0.002   PHE A 585 
 TRP   0.018   0.002   TRP A 435 
 HIS   0.006   0.001   HIS A 915 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00362 /  0.16 ( 9204)
  covalent geometry    : angle       0.63700 /  0.33 (12642)
  hydrogen bonds       : bond        0.03784 /  2.56 (  493)
  hydrogen bonds       : angle       4.05007 /  2.94 ( 1424)

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

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

  1800 Ramachandran restraints generated.
    900 Oldfield, 0 Emsley, 900 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1800 Ramachandran restraints generated.
    900 Oldfield, 0 Emsley, 900 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  256 residues out of total 875 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 64
    poor density    : 192
  time to evaluate  : 0.243 
Fit side-chains
   revert: symmetry clash
REVERT: A   57 LYS cc_start: 0.8008 (mptt) cc_final: 0.7620 (mptt)
REVERT: A   69 GLU cc_start: 0.7311 (mp0) cc_final: 0.7073 (mp0)
REVERT: A   79 PHE cc_start: 0.8107 (m-10) cc_final: 0.7847 (m-10)
REVERT: A  149 ARG cc_start: 0.7313 (ttt-90) cc_final: 0.6954 (ttt-90)
REVERT: A  154 LEU cc_start: 0.6346 (OUTLIER) cc_final: 0.6034 (tm)
REVERT: A  156 GLN cc_start: 0.7943 (mm-40) cc_final: 0.7588 (tp-100)
REVERT: A  185 TRP cc_start: 0.7263 (OUTLIER) cc_final: 0.6891 (t-100)
REVERT: A  272 GLN cc_start: 0.6893 (OUTLIER) cc_final: 0.6293 (mp-120)
REVERT: A  281 GLU cc_start: 0.6791 (tm-30) cc_final: 0.6410 (pp20)
REVERT: A  288 LEU cc_start: 0.7224 (OUTLIER) cc_final: 0.6944 (mt)
REVERT: A  322 GLU cc_start: 0.7046 (OUTLIER) cc_final: 0.6481 (pm20)
REVERT: A  445 ARG cc_start: 0.7105 (tmm-80) cc_final: 0.6880 (tmm-80)
REVERT: A  578 LYS cc_start: 0.6938 (OUTLIER) cc_final: 0.6621 (ttmt)
REVERT: A  588 GLN cc_start: 0.8265 (OUTLIER) cc_final: 0.7909 (tt0)
REVERT: A  685 SER cc_start: 0.7191 (OUTLIER) cc_final: 0.6859 (p)
REVERT: A  710 GLU cc_start: 0.7672 (mp0) cc_final: 0.7361 (mp0)
REVERT: A  786 ASP cc_start: 0.7011 (p0) cc_final: 0.6776 (p0)
REVERT: A  793 ASN cc_start: 0.7750 (t0) cc_final: 0.7499 (t0)
REVERT: A  797 TYR cc_start: 0.7211 (m-80) cc_final: 0.6758 (m-80)
REVERT: A  804 GLN cc_start: 0.7997 (pp30) cc_final: 0.7650 (pp30)
REVERT: A  919 ILE cc_start: 0.6266 (OUTLIER) cc_final: 0.5418 (mp)
REVERT: A 1032 SER cc_start: 0.1923 (OUTLIER) cc_final: 0.1496 (m)
REVERT: A 1047 ASP cc_start: 0.6626 (p0) cc_final: 0.6214 (p0)
  outliers start: 64
  outliers final: 46
  residues processed: 236
  average time/residue: 0.4155
  time to fit residues: 105.8264
Evaluate side-chains
  246 residues out of total 875 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 56
    poor density    : 190
  time to evaluate  : 0.233 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   40 VAL
Chi-restraints excluded: chain A residue   49 ILE
Chi-restraints excluded: chain A residue   70 GLN
Chi-restraints excluded: chain A residue  101 HIS
Chi-restraints excluded: chain A residue  154 LEU
Chi-restraints excluded: chain A residue  185 TRP
Chi-restraints excluded: chain A residue  195 LYS
Chi-restraints excluded: chain A residue  224 ILE
Chi-restraints excluded: chain A residue  272 GLN
Chi-restraints excluded: chain A residue  288 LEU
Chi-restraints excluded: chain A residue  299 LEU
Chi-restraints excluded: chain A residue  322 GLU
Chi-restraints excluded: chain A residue  354 VAL
Chi-restraints excluded: chain A residue  360 GLN
Chi-restraints excluded: chain A residue  362 ILE
Chi-restraints excluded: chain A residue  392 LYS
Chi-restraints excluded: chain A residue  408 ILE
Chi-restraints excluded: chain A residue  410 HIS
Chi-restraints excluded: chain A residue  451 LEU
Chi-restraints excluded: chain A residue  454 HIS
Chi-restraints excluded: chain A residue  465 PHE
Chi-restraints excluded: chain A residue  505 LEU
Chi-restraints excluded: chain A residue  536 SER
Chi-restraints excluded: chain A residue  551 VAL
Chi-restraints excluded: chain A residue  578 LYS
Chi-restraints excluded: chain A residue  588 GLN
Chi-restraints excluded: chain A residue  608 ASN
Chi-restraints excluded: chain A residue  621 LEU
Chi-restraints excluded: chain A residue  632 PHE
Chi-restraints excluded: chain A residue  651 ILE
Chi-restraints excluded: chain A residue  685 SER
Chi-restraints excluded: chain A residue  709 ILE
Chi-restraints excluded: chain A residue  747 SER
Chi-restraints excluded: chain A residue  760 THR
Chi-restraints excluded: chain A residue  764 GLU
Chi-restraints excluded: chain A residue  770 LEU
Chi-restraints excluded: chain A residue  771 LEU
Chi-restraints excluded: chain A residue  782 GLU
Chi-restraints excluded: chain A residue  794 MET
Chi-restraints excluded: chain A residue  812 ASP
Chi-restraints excluded: chain A residue  832 THR
Chi-restraints excluded: chain A residue  845 LYS
Chi-restraints excluded: chain A residue  849 LYS
Chi-restraints excluded: chain A residue  874 ILE
Chi-restraints excluded: chain A residue  886 THR
Chi-restraints excluded: chain A residue  893 ILE
Chi-restraints excluded: chain A residue  908 LEU
Chi-restraints excluded: chain A residue  917 LEU
Chi-restraints excluded: chain A residue  919 ILE
Chi-restraints excluded: chain A residue  929 MET
Chi-restraints excluded: chain A residue 1032 SER
Chi-restraints excluded: chain A residue 1057 SER
Chi-restraints excluded: chain A residue 1069 VAL
Chi-restraints excluded: chain A residue 1070 THR
Chi-restraints excluded: chain A residue 1094 LEU
Chi-restraints excluded: chain A residue 1105 VAL
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 97
   random chunks:
   chunk 19 optimal weight:    1.9990
   chunk 53 optimal weight:    0.9980
   chunk 10 optimal weight:    1.9990
   chunk 40 optimal weight:    0.6980
   chunk 29 optimal weight:    0.7980
   chunk 32 optimal weight:    2.9990
   chunk 42 optimal weight:    1.9990
   chunk 16 optimal weight:    2.9990
   chunk 58 optimal weight:    0.9990
   chunk 48 optimal weight:    0.5980
   chunk 25 optimal weight:    1.9990
   overall best weight:    0.8182

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
A 127 ASN
** A 274 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
A 454 HIS
A 654 GLN
A1023 ASN

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4300 r_free = 0.4300 target = 0.178040 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 42)----------------|
| r_work = 0.4161 r_free = 0.4161 target = 0.165047 restraints weight = 12657.488|
|-----------------------------------------------------------------------------|
r_work (start): 0.4152 rms_B_bonded: 1.92
r_work: 0.4053 rms_B_bonded: 2.73 restraints_weight: 0.5000
r_work: 0.3910 rms_B_bonded: 4.96 restraints_weight: 0.2500
r_work (final): 0.3910
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7133
moved from start:          0.2067

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.058   9204  Z= 0.218
  Angle     :  0.693   9.565  12642  Z= 0.356
  Chirality :  0.044   0.236   1439
  Planarity :  0.004   0.055   1389
  Dihedral  : 19.383 179.725   1884
  Min Nonbonded Distance : 2.398

Molprobity Statistics.
  All-atom Clashscore : 14.57
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.56 %
    Favored  : 95.44 %
  Rotamer:
    Outliers :  7.54 %
    Allowed  : 38.74 %
    Favored  : 53.71 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.11 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  0.34 (0.28), residues: 900
  helix:  1.20 (0.21), residues: 602
  sheet: -4.85 (0.74), residues: 10
  loop : -1.68 (0.34), residues: 288

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.007   0.001   ARG A 820 
 TYR   0.019   0.002   TYR A 647 
 PHE   0.046   0.003   PHE A 600 
 TRP   0.022   0.002   TRP A 435 
 HIS   0.005   0.001   HIS A 915 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00496 /  0.22 ( 9204)
  covalent geometry    : angle       0.69343 /  0.36 (12642)
  hydrogen bonds       : bond        0.04072 /  2.75 (  493)
  hydrogen bonds       : angle       4.20057 /  3.03 ( 1424)

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

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

  1800 Ramachandran restraints generated.
    900 Oldfield, 0 Emsley, 900 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1800 Ramachandran restraints generated.
    900 Oldfield, 0 Emsley, 900 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  253 residues out of total 875 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 66
    poor density    : 187
  time to evaluate  : 0.292 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   57 LYS cc_start: 0.8103 (mptt) cc_final: 0.7723 (mptt)
REVERT: A   69 GLU cc_start: 0.7283 (mp0) cc_final: 0.7041 (mp0)
REVERT: A   79 PHE cc_start: 0.8150 (m-10) cc_final: 0.7896 (m-10)
REVERT: A  149 ARG cc_start: 0.7389 (ttt-90) cc_final: 0.7009 (ttt-90)
REVERT: A  154 LEU cc_start: 0.6493 (OUTLIER) cc_final: 0.6169 (tm)
REVERT: A  156 GLN cc_start: 0.7904 (mm-40) cc_final: 0.7584 (tp-100)
REVERT: A  272 GLN cc_start: 0.7099 (OUTLIER) cc_final: 0.6469 (mp10)
REVERT: A  281 GLU cc_start: 0.6837 (tm-30) cc_final: 0.6446 (pp20)
REVERT: A  288 LEU cc_start: 0.7246 (OUTLIER) cc_final: 0.6868 (mt)
REVERT: A  322 GLU cc_start: 0.7122 (OUTLIER) cc_final: 0.6574 (pm20)
REVERT: A  365 GLU cc_start: 0.7699 (tm-30) cc_final: 0.7350 (tm-30)
REVERT: A  445 ARG cc_start: 0.7097 (tmm-80) cc_final: 0.6852 (tmm-80)
REVERT: A  578 LYS cc_start: 0.7281 (OUTLIER) cc_final: 0.6949 (ttmt)
REVERT: A  588 GLN cc_start: 0.8286 (OUTLIER) cc_final: 0.7925 (tt0)
REVERT: A  685 SER cc_start: 0.7291 (OUTLIER) cc_final: 0.6938 (p)
REVERT: A  710 GLU cc_start: 0.7729 (mp0) cc_final: 0.7398 (mp0)
REVERT: A  786 ASP cc_start: 0.7142 (p0) cc_final: 0.6852 (p0)
REVERT: A  793 ASN cc_start: 0.7805 (t0) cc_final: 0.7578 (t0)
REVERT: A  797 TYR cc_start: 0.7245 (m-80) cc_final: 0.6753 (m-80)
REVERT: A  804 GLN cc_start: 0.8107 (pp30) cc_final: 0.7773 (pp30)
REVERT: A  919 ILE cc_start: 0.6411 (OUTLIER) cc_final: 0.5671 (mp)
REVERT: A 1032 SER cc_start: 0.1479 (OUTLIER) cc_final: 0.1005 (m)
REVERT: A 1047 ASP cc_start: 0.6743 (p0) cc_final: 0.6326 (p0)
  outliers start: 66
  outliers final: 42
  residues processed: 234
  average time/residue: 0.4564
  time to fit residues: 115.0110
Evaluate side-chains
  235 residues out of total 875 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 51
    poor density    : 184
  time to evaluate  : 0.293 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   40 VAL
Chi-restraints excluded: chain A residue   49 ILE
Chi-restraints excluded: chain A residue   70 GLN
Chi-restraints excluded: chain A residue  101 HIS
Chi-restraints excluded: chain A residue  154 LEU
Chi-restraints excluded: chain A residue  195 LYS
Chi-restraints excluded: chain A residue  215 GLN
Chi-restraints excluded: chain A residue  272 GLN
Chi-restraints excluded: chain A residue  288 LEU
Chi-restraints excluded: chain A residue  299 LEU
Chi-restraints excluded: chain A residue  322 GLU
Chi-restraints excluded: chain A residue  354 VAL
Chi-restraints excluded: chain A residue  360 GLN
Chi-restraints excluded: chain A residue  362 ILE
Chi-restraints excluded: chain A residue  392 LYS
Chi-restraints excluded: chain A residue  408 ILE
Chi-restraints excluded: chain A residue  410 HIS
Chi-restraints excluded: chain A residue  451 LEU
Chi-restraints excluded: chain A residue  454 HIS
Chi-restraints excluded: chain A residue  465 PHE
Chi-restraints excluded: chain A residue  505 LEU
Chi-restraints excluded: chain A residue  536 SER
Chi-restraints excluded: chain A residue  551 VAL
Chi-restraints excluded: chain A residue  578 LYS
Chi-restraints excluded: chain A residue  588 GLN
Chi-restraints excluded: chain A residue  608 ASN
Chi-restraints excluded: chain A residue  621 LEU
Chi-restraints excluded: chain A residue  632 PHE
Chi-restraints excluded: chain A residue  651 ILE
Chi-restraints excluded: chain A residue  685 SER
Chi-restraints excluded: chain A residue  709 ILE
Chi-restraints excluded: chain A residue  756 ILE
Chi-restraints excluded: chain A residue  760 THR
Chi-restraints excluded: chain A residue  764 GLU
Chi-restraints excluded: chain A residue  771 LEU
Chi-restraints excluded: chain A residue  782 GLU
Chi-restraints excluded: chain A residue  794 MET
Chi-restraints excluded: chain A residue  832 THR
Chi-restraints excluded: chain A residue  849 LYS
Chi-restraints excluded: chain A residue  886 THR
Chi-restraints excluded: chain A residue  908 LEU
Chi-restraints excluded: chain A residue  917 LEU
Chi-restraints excluded: chain A residue  919 ILE
Chi-restraints excluded: chain A residue  929 MET
Chi-restraints excluded: chain A residue 1032 SER
Chi-restraints excluded: chain A residue 1046 TYR
Chi-restraints excluded: chain A residue 1057 SER
Chi-restraints excluded: chain A residue 1069 VAL
Chi-restraints excluded: chain A residue 1094 LEU
Chi-restraints excluded: chain A residue 1102 SER
Chi-restraints excluded: chain A residue 1105 VAL
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 97
   random chunks:
   chunk 82 optimal weight:    2.9990
   chunk 58 optimal weight:    0.3980
   chunk 31 optimal weight:    0.8980
   chunk 16 optimal weight:    1.9990
   chunk 22 optimal weight:    0.5980
   chunk 87 optimal weight:    0.7980
   chunk 91 optimal weight:    0.9990
   chunk 37 optimal weight:    0.5980
   chunk 3 optimal weight:    2.9990
   chunk 43 optimal weight:    0.0670
   chunk 42 optimal weight:    0.0980
   overall best weight:    0.3518

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
A 127 ASN
** A 274 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
A 654 GLN
A 735 GLN
A1023 ASN

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4320 r_free = 0.4320 target = 0.180118 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 43)----------------|
| r_work = 0.4188 r_free = 0.4188 target = 0.167438 restraints weight = 12473.783|
|-----------------------------------------------------------------------------|
r_work (start): 0.4179 rms_B_bonded: 1.89
r_work: 0.4083 rms_B_bonded: 2.69 restraints_weight: 0.5000
r_work: 0.3942 rms_B_bonded: 4.91 restraints_weight: 0.2500
r_work (final): 0.3942
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7083
moved from start:          0.1967

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.042   9204  Z= 0.153
  Angle     :  0.667  10.665  12642  Z= 0.340
  Chirality :  0.041   0.275   1439
  Planarity :  0.004   0.055   1389
  Dihedral  : 19.317 179.609   1884
  Min Nonbonded Distance : 2.358

Molprobity Statistics.
  All-atom Clashscore : 15.15
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.33 %
    Favored  : 95.67 %
  Rotamer:
    Outliers :  6.40 %
    Allowed  : 39.66 %
    Favored  : 53.94 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.11 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  0.48 (0.28), residues: 900
  helix:  1.30 (0.21), residues: 603
  sheet: -4.79 (0.76), residues: 10
  loop : -1.63 (0.35), residues: 287

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.008   0.001   ARG A 820 
 TYR   0.023   0.002   TYR A 647 
 PHE   0.037   0.002   PHE A 600 
 TRP   0.036   0.002   TRP A 435 
 HIS   0.006   0.001   HIS A 915 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00346 /  0.15 ( 9204)
  covalent geometry    : angle       0.66666 /  0.34 (12642)
  hydrogen bonds       : bond        0.03853 /  2.61 (  493)
  hydrogen bonds       : angle       4.13998 /  2.98 ( 1424)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 2780.02 seconds
wall clock time: 48 minutes 19.04 seconds (2899.04 seconds total)