Starting phenix.real_space_refine
on Tue Aug  4 21:22:34 2026 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/9ij4_60615/08_2026/9ij4_60615.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/9ij4_60615/08_2026/9ij4_60615.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=2.7
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/cci-nas-00/data/ceres_data/9ij4_60615/08_2026/9ij4_60615.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/9ij4_60615/08_2026/9ij4_60615.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/9ij4_60615/08_2026/9ij4_60615.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/9ij4_60615/08_2026/9ij4_60615.cif"
  }
  resolution = 2.7
  write_initial_geo_file = False
  refinement {
    macro_cycles = 10
  }


Starting job
===============================================================================
-------------------------------------------------------------------------------
Citation:
*********
Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams
PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography.
Acta Cryst. D74:531-544.

Validating inputs
Origin is already at (0, 0, 0), no shifts will be applied
-------------------------------------------------------------------------------
Processing inputs
*****************
Set random seed
  Set to: 0
Set model cs if undefined
Decide on map wrapping
  Map wrapping is set to: False
Normalize map: mean=0, sd=1
  Input map: mean=   0.000 sd=   0.051
Set stop_for_unknowns flag
  Set to: True
Assert model is a single copy model
Assert all atoms have isotropic ADPs
Construct map_model_manager
Extract box with map and model
Check model and map are aligned
Set scattering table
  Set to: electron
  Number of scattering types: 6
    Type Number    sf(0)   Gaussians
     P      51      5.49       5
     Mg      1      5.21       5
     S      42      5.16       5
     C    4357      2.51       5
     N    1237      2.21       5
     O    1441      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 8 residue(s): 0.01s

  Monomer Library directory:
    "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.2rc3-6140/lib/python3.11/site-packages/chem_data/mon_lib"
  Total number of atoms: 7129
  Number of models: 1
  Model: ""
    Number of chains: 4
    Chain: "A"
      Number of atoms: 6047
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 755, 6047
          Classifications: {'peptide': 755}
          Incomplete info: {'truncation_to_alanine': 5}
          Link IDs: {'PTRANS': 37, 'TRANS': 717}
          Chain breaks: 1
          Unresolved non-hydrogen bonds: 16
          Unresolved non-hydrogen angles: 18
          Unresolved non-hydrogen dihedrals: 14
          Unresolved non-hydrogen chiralities: 2
    Chain: "B"
      Number of atoms: 550
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 26, 550
          Classifications: {'RNA': 26}
          Modifications used: {'p5*END': 1, 'rna2p_pyr': 1, 'rna3p': 1, 'rna3p_pur': 12, 'rna3p_pyr': 12}
          Link IDs: {'rna2p': 1, 'rna3p': 24}
          Unresolved non-hydrogen bonds: 1
          Unresolved non-hydrogen angles: 3
    Chain: "C"
      Number of atoms: 531
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 25, 531
          Classifications: {'RNA': 25}
          Modifications used: {'rna2p_pyr': 1, 'rna3p_pur': 12, 'rna3p_pyr': 11}
          Link IDs: {'rna2p': 1, 'rna3p': 23}
          Unresolved chain link angles: 2
          Unresolved non-hydrogen bonds: 2
          Unresolved non-hydrogen angles: 3
          Unresolved non-hydrogen chiralities: 1
    Chain: "A"
      Number of atoms: 1
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 1, 1
          Unusual residues: {' MG': 1}
          Classifications: {'undetermined': 1}
  Time building chain proxies: 1.42, per 1000 atoms: 0.20
  Number of scatterers: 7129
  At special positions: 0
  Unit cell: (76.38, 85.5, 103.74, 90, 90, 90)
  Space group: P 1 (No. 1)
  Number of sites at special positions: 0
  Number of scattering types: 6
    Type Number    sf(0)
     S      42     16.00
     P      51     15.00
     Mg      1     11.99
     O    1441      8.00
     N    1237      7.00
     C    4357      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: 0.55
  Conformation dependent library (CDL) restraints added in 301.6 milliseconds
  

  1502 Ramachandran restraints generated.
    751 Oldfield, 0 Emsley, 751 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  1430

  Finding SS restraints...
    Secondary structure from input PDB file:
      20 helices and 11 sheets defined
      33.2% alpha, 23.4% beta
      23 base pairs and 37 stacking pairs defined.
    Time for finding SS restraints: 1.04
  Creating SS restraints...
    Processing helix  chain 'A' and resid 253 through 262
      removed outlier: 3.834A  pdb=" N   HIS A 262 " --> pdb=" O   MET A 258 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 317 through 331
    Processing helix  chain 'A' and resid 387 through 399
    Processing helix  chain 'A' and resid 402 through 412
      removed outlier: 3.709A  pdb=" N   GLU A 406 " --> pdb=" O   HIS A 402 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 450 through 458
    Processing helix  chain 'A' and resid 502 through 507
      removed outlier: 4.302A  pdb=" N   LYS A 507 " --> pdb=" O   GLU A 503 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 508 through 520
    Processing helix  chain 'A' and resid 522 through 540
    Processing helix  chain 'A' and resid 540 through 550
      removed outlier: 3.964A  pdb=" N   TRP A 550 " --> pdb=" O   GLU A 546 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 612 through 631
      removed outlier: 4.539A  pdb=" N   GLY A 628 " --> pdb=" O   GLU A 624 " (cutoff:3.500A)
      Proline residue:  A 629  - end of helix
    Processing helix  chain 'A' and resid 646 through 661
      removed outlier: 3.512A  pdb=" N   VAL A 660 " --> pdb=" O   SER A 656 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 675 through 688
      removed outlier: 3.601A  pdb=" N   VAL A 688 " --> pdb=" O   LYS A 684 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 707 through 722
    Processing helix  chain 'A' and resid 781 through 802
      removed outlier: 4.354A  pdb=" N   SER A 785 " --> pdb=" O   GLU A 781 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 819 through 826
    Processing helix  chain 'A' and resid 826 through 834
      removed outlier: 3.512A  pdb=" N   GLN A 830 " --> pdb=" O   TYR A 826 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 835 through 838
      removed outlier: 3.581A  pdb=" N   PHE A 838 " --> pdb=" O   PHE A 835 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'A' and resid 835 through 838'
    Processing helix  chain 'A' and resid 914 through 926
    Processing helix  chain 'A' and resid 939 through 955
    Processing helix  chain 'A' and resid 963 through 967
    Processing sheet with id=AA1, first strand: chain 'A' and resid 220 through 225
      removed outlier: 4.312A  pdb=" N   VAL A 885 " --> pdb=" O   CYS A 906 " (cutoff:3.500A)
      removed outlier: 6.566A  pdb=" N   VAL A 847 " --> pdb=" O   VAL A 907 " (cutoff:3.500A)
      removed outlier: 4.417A  pdb=" N   ASN A 909 " --> pdb=" O   MET A 845 " (cutoff:3.500A)
      removed outlier: 7.020A  pdb=" N   MET A 845 " --> pdb=" O   ASN A 909 " (cutoff:3.500A)
      removed outlier: 4.404A  pdb=" N   VAL A 744 " --> pdb=" O   ASP A 813 " (cutoff:3.500A)
      removed outlier: 4.948A  pdb=" N   VAL A 739 " --> pdb=" O   SER A 761 " (cutoff:3.500A)
      removed outlier: 3.755A  pdb=" N   ASP A 743 " --> pdb=" O   GLY A 757 " (cutoff:3.500A)
      removed outlier: 3.589A  pdb=" N   GLY A 757 " --> pdb=" O   ASP A 743 " (cutoff:3.500A)
    Processing sheet with id=AA2, first strand: chain 'A' and resid 335 through 337
    Processing sheet with id=AA3, first strand: chain 'A' and resid 335 through 337
      removed outlier: 4.660A  pdb=" N   LEU A 372 " --> pdb=" O   ILE A 231 " (cutoff:3.500A)
    Processing sheet with id=AA4, first strand: chain 'A' and resid 276 through 279
    Processing sheet with id=AA5, first strand: chain 'A' and resid 287 through 292
      removed outlier: 3.643A  pdb=" N   VAL A 287 " --> pdb=" O   ILE A 304 " (cutoff:3.500A)
    Processing sheet with id=AA6, first strand: chain 'A' and resid 423 through 426
    Processing sheet with id=AA7, first strand: chain 'A' and resid 429 through 431
    Processing sheet with id=AA8, first strand: chain 'A' and resid 439 through 442
    Processing sheet with id=AA9, first strand: chain 'A' and resid 570 through 572
    Processing sheet with id=AB1, first strand: chain 'A' and resid 638 through 641
      removed outlier: 6.088A  pdb=" N   ALA A 605 " --> pdb=" O   VAL A 668 " (cutoff:3.500A)
      removed outlier: 7.710A  pdb=" N   ILE A 670 " --> pdb=" O   ALA A 605 " (cutoff:3.500A)
      removed outlier: 6.839A  pdb=" N   PHE A 607 " --> pdb=" O   ILE A 670 " (cutoff:3.500A)
      removed outlier: 6.387A  pdb=" N   VAL A 667 " --> pdb=" O   GLN A 695 " (cutoff:3.500A)
      removed outlier: 7.838A  pdb=" N   ILE A 697 " --> pdb=" O   VAL A 667 " (cutoff:3.500A)
      removed outlier: 6.346A  pdb=" N   CYS A 669 " --> pdb=" O   ILE A 697 " (cutoff:3.500A)
    Processing sheet with id=AB2, first strand: chain 'A' and resid 860 through 861

    281 hydrogen bonds defined for protein.
    777 hydrogen bond angles defined for protein.
    Restraints generated for nucleic acids:
      56 hydrogen bonds
      112 hydrogen bond angles
      0 basepair planarities
      23 basepair parallelities
      37 stacking parallelities
  Total time for adding SS restraints: 1.51

  Time building geometry restraints manager: 0.69 seconds

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

  Histogram of bond lengths:
        1.16 -     1.29: 1026
        1.29 -     1.42: 2177
        1.42 -     1.55: 4015
        1.55 -     1.68: 107
        1.68 -     1.82: 65
  Bond restraints: 7390
  Sorted by residual:
  bond pdb=" CA  ILE A 318 "
       pdb=" CB  ILE A 318 "
    ideal  model  delta    sigma   weight residual
    1.539  1.506  0.033 5.40e-03 3.43e+04 3.77e+01
  bond pdb=" CA  PRO A 636 "
       pdb=" C   PRO A 636 "
    ideal  model  delta    sigma   weight residual
    1.514  1.536 -0.022 5.50e-03 3.31e+04 1.59e+01
  bond pdb=" CG  ASN A 763 "
       pdb=" OD1 ASN A 763 "
    ideal  model  delta    sigma   weight residual
    1.231  1.156  0.075 1.90e-02 2.77e+03 1.54e+01
  bond pdb=" CB  ILE A 651 "
       pdb=" CG2 ILE A 651 "
    ideal  model  delta    sigma   weight residual
    1.521  1.396  0.125 3.30e-02 9.18e+02 1.44e+01
  bond pdb=" CG  PRO A 863 "
       pdb=" CD  PRO A 863 "
    ideal  model  delta    sigma   weight residual
    1.503  1.377  0.126 3.40e-02 8.65e+02 1.38e+01
  ... (remaining 7385 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     3.12: 10116
        3.12 -     6.25: 110
        6.25 -     9.37: 16
        9.37 -    12.49: 6
       12.49 -    15.61: 5
  Bond angle restraints: 10253
  Sorted by residual:
  angle pdb=" CA  PRO A 468 "
        pdb=" N   PRO A 468 "
        pdb=" CD  PRO A 468 "
      ideal   model   delta    sigma   weight residual
     112.00   97.93   14.07 1.40e+00 5.10e-01 1.01e+02
  angle pdb=" N   PRO A 863 "
        pdb=" CD  PRO A 863 "
        pdb=" CG  PRO A 863 "
      ideal   model   delta    sigma   weight residual
     103.20   89.14   14.06 1.50e+00 4.44e-01 8.78e+01
  angle pdb=" CA  PRO A 863 "
        pdb=" CB  PRO A 863 "
        pdb=" CG  PRO A 863 "
      ideal   model   delta    sigma   weight residual
     104.50   88.89   15.61 1.90e+00 2.77e-01 6.75e+01
  angle pdb=" CA  PRO A 863 "
        pdb=" N   PRO A 863 "
        pdb=" CD  PRO A 863 "
      ideal   model   delta    sigma   weight residual
     112.00  104.20    7.80 1.40e+00 5.10e-01 3.10e+01
  angle pdb=" C1'   C B  24 "
        pdb=" N1    C B  24 "
        pdb=" C2    C B  24 "
      ideal   model   delta    sigma   weight residual
     118.80  124.82   -6.02 1.10e+00 8.26e-01 2.99e+01
  ... (remaining 10248 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    17.90: 3696
       17.90 -    35.80: 525
       35.80 -    53.70: 195
       53.70 -    71.60: 71
       71.60 -    89.50: 24
  Dihedral angle restraints: 4511
    sinusoidal: 2301
      harmonic: 2210
  Sorted by residual:
  dihedral pdb=" CA  ASP A 296 "
           pdb=" C   ASP A 296 "
           pdb=" N   ASP A 297 "
           pdb=" CA  ASP A 297 "
      ideal   model   delta  harmonic     sigma   weight residual
    -180.00 -153.62  -26.38     0      5.00e+00 4.00e-02 2.78e+01
  dihedral pdb=" CA  PRO A 637 "
           pdb=" C   PRO A 637 "
           pdb=" N   ALA A 638 "
           pdb=" CA  ALA A 638 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  158.28   21.72     0      5.00e+00 4.00e-02 1.89e+01
  dihedral pdb=" CA  MET A 442 "
           pdb=" C   MET A 442 "
           pdb=" N   SER A 443 "
           pdb=" CA  SER A 443 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00 -161.38  -18.62     0      5.00e+00 4.00e-02 1.39e+01
  ... (remaining 4508 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.062: 927
       0.062 -    0.124: 212
       0.124 -    0.187: 59
       0.187 -    0.249: 3
       0.249 -    0.311: 1
  Chirality restraints: 1202
  Sorted by residual:
  chirality pdb=" CG  LEU A 490 "
            pdb=" CB  LEU A 490 "
            pdb=" CD1 LEU A 490 "
            pdb=" CD2 LEU A 490 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.59   -2.28   -0.31 2.00e-01 2.50e+01 2.42e+00
  chirality pdb=" CA  MET A 348 "
            pdb=" N   MET A 348 "
            pdb=" C   MET A 348 "
            pdb=" CB  MET A 348 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.30    0.22 2.00e-01 2.50e+01 1.16e+00
  chirality pdb=" CB  ILE A 501 "
            pdb=" CA  ILE A 501 "
            pdb=" CG1 ILE A 501 "
            pdb=" CG2 ILE A 501 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.64    2.44    0.20 2.00e-01 2.50e+01 1.05e+00
  ... (remaining 1199 not shown)

  Planarity restraints: 1113
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   SER A 690 "   -0.074 5.00e-02 4.00e+02   1.13e-01 2.03e+01
        pdb=" N   PRO A 691 "    0.195 5.00e-02 4.00e+02
        pdb=" CA  PRO A 691 "   -0.062 5.00e-02 4.00e+02
        pdb=" CD  PRO A 691 "   -0.060 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   GLN A 467 "   -0.075 5.00e-02 4.00e+02   1.06e-01 1.81e+01
        pdb=" N   PRO A 468 "    0.184 5.00e-02 4.00e+02
        pdb=" CA  PRO A 468 "   -0.047 5.00e-02 4.00e+02
        pdb=" CD  PRO A 468 "   -0.062 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CD  ARG A 652 "    0.312 9.50e-02 1.11e+02   1.41e-01 1.62e+01
        pdb=" NE  ARG A 652 "   -0.007 2.00e-02 2.50e+03
        pdb=" CZ  ARG A 652 "   -0.039 2.00e-02 2.50e+03
        pdb=" NH1 ARG A 652 "    0.009 2.00e-02 2.50e+03
        pdb=" NH2 ARG A 652 "    0.023 2.00e-02 2.50e+03
  ... (remaining 1110 not shown)

  Histogram of nonbonded interaction distances:
        1.73 -     2.36: 13
        2.36 -     3.00: 3326
        3.00 -     3.63: 11213
        3.63 -     4.27: 18181
        4.27 -     4.90: 28276
  Nonbonded interactions: 61009
  Sorted by model distance:
  nonbonded pdb=" OD2 ASP A 813 "
            pdb="MG    MG A1001 "
     model   vdw
     1.731 2.170
  nonbonded pdb=" OD1 ASP A 743 "
            pdb="MG    MG A1001 "
     model   vdw
     2.081 2.170
  nonbonded pdb=" OD1 ASP A 743 "
            pdb=" OD2 ASP A 813 "
     model   vdw
     2.238 3.040
  nonbonded pdb=" O   THR A 649 "
            pdb=" OG1 THR A 653 "
     model   vdw
     2.241 3.040
  nonbonded pdb=" O   SER A 544 "
            pdb=" OG1 THR A 548 "
     model   vdw
     2.290 3.040
  ... (remaining 61004 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:             0.220
  Set stop_for_unknowns flag:              0.000
  Assert model is a single copy model:     0.000
  Assert all atoms have isotropic ADPs:    0.000
  Construct map_model_manager:             0.000
  Extract box with map and model:          0.110
  Check model and map are aligned:         0.020
  Set scattering table:                    0.020
  Process input model:                     8.410
  Find NCS groups from input model:        0.030
  Set up NCS constraints:                  0.020
  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:6.850
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   15.680
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6473
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      :  0.006   0.126   7390  Z= 0.308
  Angle     :  0.957  15.614  10253  Z= 0.618
  Chirality :  0.057   0.311   1202
  Planarity :  0.009   0.141   1113
  Dihedral  : 19.915  89.501   3081
  Min Nonbonded Distance : 1.731

Molprobity Statistics.
  All-atom Clashscore : 8.91
  Ramachandran Plot:
    Outliers :  0.13 %
    Allowed  :  6.52 %
    Favored  : 93.34 %
  Rotamer:
    Outliers :  0.88 %
    Allowed  : 28.42 %
    Favored  : 70.69 %
  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: -1.89 (0.29), residues: 751
  helix: -0.70 (0.31), residues: 225
  sheet: -0.79 (0.40), residues: 171
  loop : -1.81 (0.30), residues: 355

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.035   0.001   ARG A 652 
 TYR   0.034   0.003   TYR A 904 
 PHE   0.028   0.003   PHE A 835 
 TRP   0.011   0.002   TRP A 586 
 HIS   0.006   0.001   HIS A 865 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00630 /  0.31 ( 7390)
  covalent geometry    : angle       0.95741 /  0.62 (10253)
  hydrogen bonds       : bond        0.12709 /  8.17 (  331)
  hydrogen bonds       : angle       7.10267 /  4.87 (  889)

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

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

  1502 Ramachandran restraints generated.
    751 Oldfield, 0 Emsley, 751 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1502 Ramachandran restraints generated.
    751 Oldfield, 0 Emsley, 751 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  94 residues out of total 684 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 6
    poor density    : 88
  time to evaluate  : 0.233 
Fit side-chains
  outliers start: 6
  outliers final: 3
  residues processed: 93
  average time/residue: 0.3423
  time to fit residues: 34.2778
Evaluate side-chains
  81 residues out of total 684 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 3
    poor density    : 78
  time to evaluate  : 0.219 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  369 ASP
Chi-restraints excluded: chain A residue  435 THR
Chi-restraints excluded: chain A residue  774 VAL
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 79
   random chunks:
   chunk 49 optimal weight:    0.7980
   chunk 53 optimal weight:    9.9990
   chunk 5 optimal weight:    4.9990
   chunk 33 optimal weight:    6.9990
   chunk 65 optimal weight:    3.9990
   chunk 62 optimal weight:    0.9990
   chunk 51 optimal weight:    0.4980
   chunk 38 optimal weight:    7.9990
   chunk 61 optimal weight:    1.9990
   chunk 45 optimal weight:    0.9980
   chunk 74 optimal weight:    4.9990
   overall best weight:    1.0584

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
A 222 GLN
** A 467 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 946 HIS

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4444 r_free = 0.4444 target = 0.211305 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 61)----------------|
| r_work = 0.4095 r_free = 0.4095 target = 0.174008 restraints weight = 7784.013|
|-----------------------------------------------------------------------------|
r_work (start): 0.4173 rms_B_bonded: 2.06
r_work: 0.4078 rms_B_bonded: 2.62 restraints_weight: 0.5000
r_work: 0.3968 rms_B_bonded: 4.38 restraints_weight: 0.2500
r_work (final): 0.3968
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6667
moved from start:          0.0798

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.071   7390  Z= 0.136
  Angle     :  0.584   7.798  10253  Z= 0.305
  Chirality :  0.042   0.162   1202
  Planarity :  0.006   0.086   1113
  Dihedral  : 17.426 121.813   1585
  Min Nonbonded Distance : 1.982

Molprobity Statistics.
  All-atom Clashscore : 10.29
  Ramachandran Plot:
    Outliers :  0.13 %
    Allowed  :  6.39 %
    Favored  : 93.48 %
  Rotamer:
    Outliers :  3.68 %
    Allowed  : 27.25 %
    Favored  : 69.07 %
  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: -1.29 (0.30), residues: 751
  helix:  0.25 (0.33), residues: 228
  sheet: -0.83 (0.39), residues: 177
  loop : -1.59 (0.32), residues: 346

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG A 536 
 TYR   0.028   0.002   TYR A 904 
 PHE   0.013   0.001   PHE A 835 
 TRP   0.009   0.001   TRP A 586 
 HIS   0.003   0.001   HIS A 242 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00306 /  0.14 ( 7390)
  covalent geometry    : angle       0.58355 /  0.31 (10253)
  hydrogen bonds       : bond        0.04586 /  3.08 (  331)
  hydrogen bonds       : angle       5.58011 /  3.82 (  889)

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

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

  1502 Ramachandran restraints generated.
    751 Oldfield, 0 Emsley, 751 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1502 Ramachandran restraints generated.
    751 Oldfield, 0 Emsley, 751 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  110 residues out of total 684 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 25
    poor density    : 85
  time to evaluate  : 0.238 
Fit side-chains
   revert: symmetry clash
REVERT: A  294 LYS cc_start: 0.5073 (OUTLIER) cc_final: 0.4799 (ptpp)
REVERT: A  531 GLU cc_start: 0.6484 (OUTLIER) cc_final: 0.6212 (mm-30)
REVERT: A  624 GLU cc_start: 0.6828 (mt-10) cc_final: 0.6099 (pt0)
  outliers start: 25
  outliers final: 10
  residues processed: 105
  average time/residue: 0.3605
  time to fit residues: 40.6574
Evaluate side-chains
  93 residues out of total 684 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 81
  time to evaluate  : 0.161 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  224 LEU
Chi-restraints excluded: chain A residue  266 THR
Chi-restraints excluded: chain A residue  294 LYS
Chi-restraints excluded: chain A residue  302 ILE
Chi-restraints excluded: chain A residue  304 ILE
Chi-restraints excluded: chain A residue  435 THR
Chi-restraints excluded: chain A residue  531 GLU
Chi-restraints excluded: chain A residue  590 VAL
Chi-restraints excluded: chain A residue  734 LEU
Chi-restraints excluded: chain A residue  742 MET
Chi-restraints excluded: chain A residue  755 VAL
Chi-restraints excluded: chain A residue  774 VAL
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 79
   random chunks:
   chunk 60 optimal weight:    5.9990
   chunk 8 optimal weight:    4.9990
   chunk 30 optimal weight:    4.9990
   chunk 9 optimal weight:    5.9990
   chunk 26 optimal weight:    1.9990
   chunk 76 optimal weight:    9.9990
   chunk 25 optimal weight:    8.9990
   chunk 45 optimal weight:    4.9990
   chunk 47 optimal weight:    1.9990
   chunk 0 optimal weight:   30.0000
   chunk 38 optimal weight:    0.9980
   overall best weight:    2.9988

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
A 954 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4351 r_free = 0.4351 target = 0.202881 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 53)----------------|
| r_work = 0.3943 r_free = 0.3943 target = 0.162168 restraints weight = 7468.992|
|-----------------------------------------------------------------------------|
r_work (start): 0.3989 rms_B_bonded: 1.93
r_work: 0.3869 rms_B_bonded: 2.60 restraints_weight: 0.5000
r_work: 0.3738 rms_B_bonded: 4.27 restraints_weight: 0.2500
r_work (final): 0.3738
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6929
moved from start:          0.1569

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.051   7390  Z= 0.237
  Angle     :  0.684   9.736  10253  Z= 0.351
  Chirality :  0.047   0.170   1202
  Planarity :  0.006   0.074   1113
  Dihedral  : 17.043  79.691   1583
  Min Nonbonded Distance : 1.974

Molprobity Statistics.
  All-atom Clashscore : 11.59
  Ramachandran Plot:
    Outliers :  0.13 %
    Allowed  :  5.99 %
    Favored  : 93.87 %
  Rotamer:
    Outliers :  6.63 %
    Allowed  : 24.01 %
    Favored  : 69.37 %
  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: -1.42 (0.30), residues: 751
  helix:  0.12 (0.34), residues: 235
  sheet: -1.02 (0.39), residues: 177
  loop : -1.60 (0.32), residues: 339

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.009   0.001   ARG A 652 
 TYR   0.019   0.003   TYR A 454 
 PHE   0.020   0.002   PHE A 835 
 TRP   0.011   0.002   TRP A 769 
 HIS   0.008   0.001   HIS A 242 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00532 /  0.24 ( 7390)
  covalent geometry    : angle       0.68398 /  0.35 (10253)
  hydrogen bonds       : bond        0.05104 /  3.52 (  331)
  hydrogen bonds       : angle       5.55661 /  3.81 (  889)

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

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

  1502 Ramachandran restraints generated.
    751 Oldfield, 0 Emsley, 751 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1502 Ramachandran restraints generated.
    751 Oldfield, 0 Emsley, 751 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  140 residues out of total 684 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 45
    poor density    : 95
  time to evaluate  : 0.153 
Fit side-chains
   revert: symmetry clash
REVERT: A  294 LYS cc_start: 0.5190 (OUTLIER) cc_final: 0.4875 (ptpp)
REVERT: A  329 MET cc_start: 0.8152 (OUTLIER) cc_final: 0.6783 (mpp)
REVERT: A  333 ASP cc_start: 0.7681 (m-30) cc_final: 0.6771 (t0)
REVERT: A  369 ASP cc_start: 0.6695 (t0) cc_final: 0.6437 (t0)
REVERT: A  498 MET cc_start: 0.7086 (mtt) cc_final: 0.6828 (mtt)
REVERT: A  530 LEU cc_start: 0.6214 (OUTLIER) cc_final: 0.5982 (mp)
REVERT: A  531 GLU cc_start: 0.6891 (OUTLIER) cc_final: 0.6625 (mm-30)
REVERT: A  555 HIS cc_start: 0.7298 (t-90) cc_final: 0.7044 (t-90)
REVERT: A  651 ILE cc_start: 0.7392 (mt) cc_final: 0.7151 (mt)
REVERT: A  794 LEU cc_start: 0.6281 (OUTLIER) cc_final: 0.5578 (mm)
  outliers start: 45
  outliers final: 17
  residues processed: 128
  average time/residue: 0.3691
  time to fit residues: 50.7004
Evaluate side-chains
  111 residues out of total 684 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 22
    poor density    : 89
  time to evaluate  : 0.249 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  224 LEU
Chi-restraints excluded: chain A residue  244 THR
Chi-restraints excluded: chain A residue  266 THR
Chi-restraints excluded: chain A residue  294 LYS
Chi-restraints excluded: chain A residue  302 ILE
Chi-restraints excluded: chain A residue  304 ILE
Chi-restraints excluded: chain A residue  328 VAL
Chi-restraints excluded: chain A residue  329 MET
Chi-restraints excluded: chain A residue  435 THR
Chi-restraints excluded: chain A residue  530 LEU
Chi-restraints excluded: chain A residue  531 GLU
Chi-restraints excluded: chain A residue  590 VAL
Chi-restraints excluded: chain A residue  634 ILE
Chi-restraints excluded: chain A residue  730 VAL
Chi-restraints excluded: chain A residue  742 MET
Chi-restraints excluded: chain A residue  755 VAL
Chi-restraints excluded: chain A residue  774 VAL
Chi-restraints excluded: chain A residue  782 ILE
Chi-restraints excluded: chain A residue  794 LEU
Chi-restraints excluded: chain A residue  860 LEU
Chi-restraints excluded: chain A residue  874 VAL
Chi-restraints excluded: chain A residue  894 VAL
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 79
   random chunks:
   chunk 10 optimal weight:    0.7980
   chunk 56 optimal weight:    0.9990
   chunk 73 optimal weight:    0.9980
   chunk 26 optimal weight:   10.0000
   chunk 54 optimal weight:    2.9990
   chunk 51 optimal weight:    0.8980
   chunk 48 optimal weight:    8.9990
   chunk 16 optimal weight:    1.9990
   chunk 76 optimal weight:   10.0000
   chunk 66 optimal weight:    0.8980
   chunk 78 optimal weight:   10.0000
   overall best weight:    0.9182

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
A 954 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4396 r_free = 0.4396 target = 0.208173 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 59)----------------|
| r_work = 0.4009 r_free = 0.4009 target = 0.168530 restraints weight = 7528.920|
|-----------------------------------------------------------------------------|
r_work (start): 0.3991 rms_B_bonded: 1.93
r_work: 0.3873 rms_B_bonded: 2.66 restraints_weight: 0.5000
r_work: 0.3743 rms_B_bonded: 4.39 restraints_weight: 0.2500
r_work (final): 0.3743
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6854
moved from start:          0.1529

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.034   7390  Z= 0.126
  Angle     :  0.561   9.108  10253  Z= 0.289
  Chirality :  0.042   0.136   1202
  Planarity :  0.005   0.062   1113
  Dihedral  : 17.162  83.897   1583
  Min Nonbonded Distance : 2.090

Molprobity Statistics.
  All-atom Clashscore : 11.88
  Ramachandran Plot:
    Outliers :  0.13 %
    Allowed  :  5.59 %
    Favored  : 94.27 %
  Rotamer:
    Outliers :  3.98 %
    Allowed  : 27.10 %
    Favored  : 68.92 %
  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: -1.07 (0.31), residues: 751
  helix:  0.61 (0.35), residues: 233
  sheet: -0.99 (0.39), residues: 176
  loop : -1.45 (0.33), residues: 342

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARG A 652 
 TYR   0.010   0.001   TYR A 342 
 PHE   0.016   0.002   PHE A 835 
 TRP   0.007   0.001   TRP A 604 
 HIS   0.003   0.001   HIS A 865 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00275 /  0.13 ( 7390)
  covalent geometry    : angle       0.56100 /  0.29 (10253)
  hydrogen bonds       : bond        0.03935 /  2.73 (  331)
  hydrogen bonds       : angle       5.32586 /  3.65 (  889)

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

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

  1502 Ramachandran restraints generated.
    751 Oldfield, 0 Emsley, 751 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1502 Ramachandran restraints generated.
    751 Oldfield, 0 Emsley, 751 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  118 residues out of total 684 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 27
    poor density    : 91
  time to evaluate  : 0.158 
Fit side-chains
   revert: symmetry clash
REVERT: A  294 LYS cc_start: 0.5149 (OUTLIER) cc_final: 0.4841 (ptpp)
REVERT: A  333 ASP cc_start: 0.7568 (m-30) cc_final: 0.6717 (t0)
REVERT: A  369 ASP cc_start: 0.6546 (t0) cc_final: 0.6321 (t0)
REVERT: A  436 PRO cc_start: 0.6122 (Cg_exo) cc_final: 0.5844 (Cg_endo)
REVERT: A  498 MET cc_start: 0.7037 (mtt) cc_final: 0.6790 (mtt)
REVERT: A  624 GLU cc_start: 0.6771 (mt-10) cc_final: 0.6040 (pt0)
REVERT: A  763 ASN cc_start: 0.7247 (p0) cc_final: 0.6485 (p0)
REVERT: A  794 LEU cc_start: 0.6253 (OUTLIER) cc_final: 0.5616 (mm)
  outliers start: 27
  outliers final: 13
  residues processed: 111
  average time/residue: 0.3329
  time to fit residues: 39.8794
Evaluate side-chains
  102 residues out of total 684 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 15
    poor density    : 87
  time to evaluate  : 0.242 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  224 LEU
Chi-restraints excluded: chain A residue  294 LYS
Chi-restraints excluded: chain A residue  302 ILE
Chi-restraints excluded: chain A residue  435 THR
Chi-restraints excluded: chain A residue  517 GLN
Chi-restraints excluded: chain A residue  634 ILE
Chi-restraints excluded: chain A residue  730 VAL
Chi-restraints excluded: chain A residue  734 LEU
Chi-restraints excluded: chain A residue  738 MET
Chi-restraints excluded: chain A residue  742 MET
Chi-restraints excluded: chain A residue  794 LEU
Chi-restraints excluded: chain A residue  860 LEU
Chi-restraints excluded: chain A residue  874 VAL
Chi-restraints excluded: chain A residue  918 MET
Chi-restraints excluded: chain A residue  935 THR
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 79
   random chunks:
   chunk 71 optimal weight:    1.9990
   chunk 22 optimal weight:    9.9990
   chunk 35 optimal weight:    0.1980
   chunk 5 optimal weight:    0.4980
   chunk 4 optimal weight:    0.0470
   chunk 2 optimal weight:    9.9990
   chunk 59 optimal weight:    1.9990
   chunk 73 optimal weight:    4.9990
   chunk 43 optimal weight:    7.9990
   chunk 63 optimal weight:    0.9980
   chunk 66 optimal weight:    6.9990
   overall best weight:    0.7480

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

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4405 r_free = 0.4405 target = 0.209483 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 49)----------------|
| r_work = 0.4022 r_free = 0.4022 target = 0.169993 restraints weight = 7479.995|
|-----------------------------------------------------------------------------|
r_work (start): 0.4004 rms_B_bonded: 1.93
r_work: 0.3888 rms_B_bonded: 2.66 restraints_weight: 0.5000
r_work: 0.3757 rms_B_bonded: 4.40 restraints_weight: 0.2500
r_work (final): 0.3757
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6836
moved from start:          0.1534

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.035   7390  Z= 0.119
  Angle     :  0.549   8.737  10253  Z= 0.282
  Chirality :  0.041   0.143   1202
  Planarity :  0.005   0.052   1113
  Dihedral  : 17.114  83.829   1582
  Min Nonbonded Distance : 2.146

Molprobity Statistics.
  All-atom Clashscore : 11.66
  Ramachandran Plot:
    Outliers :  0.13 %
    Allowed  :  5.59 %
    Favored  : 94.27 %
  Rotamer:
    Outliers :  3.98 %
    Allowed  : 27.69 %
    Favored  : 68.34 %
  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: -0.89 (0.31), residues: 751
  helix:  0.79 (0.35), residues: 234
  sheet: -0.98 (0.38), residues: 176
  loop : -1.31 (0.33), residues: 341

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.000   ARG A 652 
 TYR   0.011   0.001   TYR A 342 
 PHE   0.015   0.001   PHE A 835 
 TRP   0.006   0.001   TRP A 604 
 HIS   0.002   0.001   HIS A 865 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00266 /  0.12 ( 7390)
  covalent geometry    : angle       0.54946 /  0.28 (10253)
  hydrogen bonds       : bond        0.03715 /  2.55 (  331)
  hydrogen bonds       : angle       5.16646 /  3.53 (  889)

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

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

  1502 Ramachandran restraints generated.
    751 Oldfield, 0 Emsley, 751 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1502 Ramachandran restraints generated.
    751 Oldfield, 0 Emsley, 751 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  118 residues out of total 684 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 27
    poor density    : 91
  time to evaluate  : 0.237 
Fit side-chains
   revert: symmetry clash
REVERT: A  294 LYS cc_start: 0.5124 (OUTLIER) cc_final: 0.4838 (ptpp)
REVERT: A  333 ASP cc_start: 0.7623 (m-30) cc_final: 0.6784 (t0)
REVERT: A  369 ASP cc_start: 0.6512 (t0) cc_final: 0.6293 (t0)
REVERT: A  436 PRO cc_start: 0.6094 (Cg_exo) cc_final: 0.5836 (Cg_endo)
REVERT: A  498 MET cc_start: 0.7044 (mtt) cc_final: 0.6745 (mtt)
REVERT: A  515 LEU cc_start: 0.6729 (tp) cc_final: 0.6352 (tp)
REVERT: A  624 GLU cc_start: 0.6774 (mt-10) cc_final: 0.6037 (pt0)
REVERT: A  763 ASN cc_start: 0.7179 (p0) cc_final: 0.6445 (p0)
REVERT: A  794 LEU cc_start: 0.6398 (OUTLIER) cc_final: 0.5796 (mm)
  outliers start: 27
  outliers final: 17
  residues processed: 112
  average time/residue: 0.3256
  time to fit residues: 39.3890
Evaluate side-chains
  106 residues out of total 684 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 19
    poor density    : 87
  time to evaluate  : 0.168 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  224 LEU
Chi-restraints excluded: chain A residue  244 THR
Chi-restraints excluded: chain A residue  266 THR
Chi-restraints excluded: chain A residue  294 LYS
Chi-restraints excluded: chain A residue  302 ILE
Chi-restraints excluded: chain A residue  304 ILE
Chi-restraints excluded: chain A residue  435 THR
Chi-restraints excluded: chain A residue  461 THR
Chi-restraints excluded: chain A residue  517 GLN
Chi-restraints excluded: chain A residue  530 LEU
Chi-restraints excluded: chain A residue  730 VAL
Chi-restraints excluded: chain A residue  734 LEU
Chi-restraints excluded: chain A residue  738 MET
Chi-restraints excluded: chain A residue  742 MET
Chi-restraints excluded: chain A residue  774 VAL
Chi-restraints excluded: chain A residue  794 LEU
Chi-restraints excluded: chain A residue  860 LEU
Chi-restraints excluded: chain A residue  874 VAL
Chi-restraints excluded: chain A residue  894 VAL
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 79
   random chunks:
   chunk 45 optimal weight:    5.9990
   chunk 3 optimal weight:    3.9990
   chunk 50 optimal weight:    0.9980
   chunk 57 optimal weight:    9.9990
   chunk 7 optimal weight:    3.9990
   chunk 27 optimal weight:    4.9990
   chunk 17 optimal weight:    5.9990
   chunk 58 optimal weight:    4.9990
   chunk 70 optimal weight:    2.9990
   chunk 46 optimal weight:    4.9990
   chunk 25 optimal weight:    7.9990
   overall best weight:    3.3988

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
A 322 ASN
** A 353 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
A 954 GLN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4338 r_free = 0.4338 target = 0.201393 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 50)----------------|
| r_work = 0.3925 r_free = 0.3925 target = 0.160606 restraints weight = 7476.269|
|-----------------------------------------------------------------------------|
r_work (start): 0.3902 rms_B_bonded: 1.94
r_work: 0.3789 rms_B_bonded: 2.56 restraints_weight: 0.5000
r_work: 0.3663 rms_B_bonded: 4.19 restraints_weight: 0.2500
r_work (final): 0.3663
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6921
moved from start:          0.1946

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.006   0.051   7390  Z= 0.263
  Angle     :  0.693   9.631  10253  Z= 0.355
  Chirality :  0.048   0.169   1202
  Planarity :  0.006   0.064   1113
  Dihedral  : 17.004  82.361   1582
  Min Nonbonded Distance : 2.134

Molprobity Statistics.
  All-atom Clashscore : 13.26
  Ramachandran Plot:
    Outliers :  0.13 %
    Allowed  :  6.52 %
    Favored  : 93.34 %
  Rotamer:
    Outliers :  5.45 %
    Allowed  : 26.51 %
    Favored  : 68.04 %
  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: -1.23 (0.31), residues: 751
  helix:  0.40 (0.35), residues: 236
  sheet: -1.11 (0.39), residues: 177
  loop : -1.46 (0.33), residues: 338

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.001   ARG A 646 
 TYR   0.018   0.003   TYR A 342 
 PHE   0.022   0.002   PHE A 835 
 TRP   0.011   0.002   TRP A 769 
 HIS   0.008   0.001   HIS A 526 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00599 /  0.26 ( 7390)
  covalent geometry    : angle       0.69288 /  0.36 (10253)
  hydrogen bonds       : bond        0.04962 /  3.38 (  331)
  hydrogen bonds       : angle       5.46225 /  3.72 (  889)

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

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

  1502 Ramachandran restraints generated.
    751 Oldfield, 0 Emsley, 751 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1502 Ramachandran restraints generated.
    751 Oldfield, 0 Emsley, 751 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  129 residues out of total 684 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 37
    poor density    : 92
  time to evaluate  : 0.197 
Fit side-chains
REVERT: A  258 MET cc_start: 0.7145 (mmm) cc_final: 0.6709 (mtt)
REVERT: A  294 LYS cc_start: 0.5234 (OUTLIER) cc_final: 0.4919 (ptpp)
REVERT: A  329 MET cc_start: 0.8171 (OUTLIER) cc_final: 0.6588 (mpp)
REVERT: A  333 ASP cc_start: 0.7729 (m-30) cc_final: 0.6821 (t0)
REVERT: A  369 ASP cc_start: 0.6676 (t0) cc_final: 0.6462 (t0)
REVERT: A  436 PRO cc_start: 0.6112 (Cg_exo) cc_final: 0.5832 (Cg_endo)
REVERT: A  498 MET cc_start: 0.7276 (mtt) cc_final: 0.6901 (mtt)
REVERT: A  531 GLU cc_start: 0.6712 (OUTLIER) cc_final: 0.6439 (mm-30)
REVERT: A  555 HIS cc_start: 0.7235 (t-90) cc_final: 0.6995 (t-90)
REVERT: A  562 GLU cc_start: 0.7446 (OUTLIER) cc_final: 0.6992 (mt-10)
REVERT: A  794 LEU cc_start: 0.6279 (OUTLIER) cc_final: 0.5525 (mm)
REVERT: A  918 MET cc_start: 0.6133 (OUTLIER) cc_final: 0.5692 (ttp)
  outliers start: 37
  outliers final: 22
  residues processed: 119
  average time/residue: 0.3457
  time to fit residues: 44.1749
Evaluate side-chains
  113 residues out of total 684 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 28
    poor density    : 85
  time to evaluate  : 0.153 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  224 LEU
Chi-restraints excluded: chain A residue  244 THR
Chi-restraints excluded: chain A residue  266 THR
Chi-restraints excluded: chain A residue  294 LYS
Chi-restraints excluded: chain A residue  302 ILE
Chi-restraints excluded: chain A residue  329 MET
Chi-restraints excluded: chain A residue  435 THR
Chi-restraints excluded: chain A residue  461 THR
Chi-restraints excluded: chain A residue  517 GLN
Chi-restraints excluded: chain A residue  531 GLU
Chi-restraints excluded: chain A residue  538 SER
Chi-restraints excluded: chain A residue  562 GLU
Chi-restraints excluded: chain A residue  590 VAL
Chi-restraints excluded: chain A residue  597 LEU
Chi-restraints excluded: chain A residue  634 ILE
Chi-restraints excluded: chain A residue  730 VAL
Chi-restraints excluded: chain A residue  734 LEU
Chi-restraints excluded: chain A residue  738 MET
Chi-restraints excluded: chain A residue  742 MET
Chi-restraints excluded: chain A residue  755 VAL
Chi-restraints excluded: chain A residue  774 VAL
Chi-restraints excluded: chain A residue  782 ILE
Chi-restraints excluded: chain A residue  794 LEU
Chi-restraints excluded: chain A residue  860 LEU
Chi-restraints excluded: chain A residue  874 VAL
Chi-restraints excluded: chain A residue  894 VAL
Chi-restraints excluded: chain A residue  918 MET
Chi-restraints excluded: chain A residue  964 LEU
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 79
   random chunks:
   chunk 44 optimal weight:    4.9990
   chunk 8 optimal weight:    6.9990
   chunk 63 optimal weight:    0.5980
   chunk 33 optimal weight:    4.9990
   chunk 47 optimal weight:    0.9980
   chunk 6 optimal weight:    5.9990
   chunk 71 optimal weight:    1.9990
   chunk 23 optimal weight:    5.9990
   chunk 0 optimal weight:   30.0000
   chunk 41 optimal weight:    9.9990
   chunk 64 optimal weight:    0.8980
   overall best weight:    1.8984

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
** A 353 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
A 954 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4358 r_free = 0.4358 target = 0.203826 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 54)----------------|
| r_work = 0.3954 r_free = 0.3954 target = 0.163459 restraints weight = 7485.659|
|-----------------------------------------------------------------------------|
r_work (start): 0.3927 rms_B_bonded: 1.94
r_work: 0.3814 rms_B_bonded: 2.59 restraints_weight: 0.5000
r_work: 0.3688 rms_B_bonded: 4.25 restraints_weight: 0.2500
r_work (final): 0.3688
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6872
moved from start:          0.1918

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.035   7390  Z= 0.173
  Angle     :  0.611   9.582  10253  Z= 0.313
  Chirality :  0.044   0.162   1202
  Planarity :  0.005   0.082   1113
  Dihedral  : 17.096  84.169   1582
  Min Nonbonded Distance : 2.189

Molprobity Statistics.
  All-atom Clashscore : 13.11
  Ramachandran Plot:
    Outliers :  0.13 %
    Allowed  :  6.52 %
    Favored  : 93.34 %
  Rotamer:
    Outliers :  4.86 %
    Allowed  : 28.13 %
    Favored  : 67.01 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -1.04 (0.31), residues: 751
  helix:  0.65 (0.36), residues: 229
  sheet: -1.08 (0.38), residues: 177
  loop : -1.33 (0.33), residues: 345

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.006   0.000   ARG A 937 
 TYR   0.030   0.002   TYR A 904 
 PHE   0.017   0.002   PHE A 835 
 TRP   0.008   0.001   TRP A 769 
 HIS   0.008   0.001   HIS A 526 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00390 /  0.17 ( 7390)
  covalent geometry    : angle       0.61099 /  0.31 (10253)
  hydrogen bonds       : bond        0.04142 /  2.85 (  331)
  hydrogen bonds       : angle       5.37174 /  3.68 (  889)

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

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

  1502 Ramachandran restraints generated.
    751 Oldfield, 0 Emsley, 751 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1502 Ramachandran restraints generated.
    751 Oldfield, 0 Emsley, 751 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  122 residues out of total 684 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 33
    poor density    : 89
  time to evaluate  : 0.181 
Fit side-chains
   revert: symmetry clash
REVERT: A  258 MET cc_start: 0.6877 (OUTLIER) cc_final: 0.6546 (mtt)
REVERT: A  294 LYS cc_start: 0.5207 (OUTLIER) cc_final: 0.4893 (ptpp)
REVERT: A  329 MET cc_start: 0.8130 (OUTLIER) cc_final: 0.6222 (mpp)
REVERT: A  333 ASP cc_start: 0.7689 (m-30) cc_final: 0.6778 (t0)
REVERT: A  369 ASP cc_start: 0.6591 (t0) cc_final: 0.6389 (t0)
REVERT: A  436 PRO cc_start: 0.6087 (Cg_exo) cc_final: 0.5821 (Cg_endo)
REVERT: A  498 MET cc_start: 0.7489 (mtt) cc_final: 0.7161 (mtt)
REVERT: A  562 GLU cc_start: 0.7405 (OUTLIER) cc_final: 0.6954 (mt-10)
REVERT: A  647 ILE cc_start: 0.7106 (mt) cc_final: 0.6825 (mt)
REVERT: A  794 LEU cc_start: 0.6326 (OUTLIER) cc_final: 0.5664 (mm)
REVERT: A  918 MET cc_start: 0.6324 (OUTLIER) cc_final: 0.5860 (ttp)
  outliers start: 33
  outliers final: 21
  residues processed: 111
  average time/residue: 0.3285
  time to fit residues: 39.3220
Evaluate side-chains
  114 residues out of total 684 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 27
    poor density    : 87
  time to evaluate  : 0.143 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  224 LEU
Chi-restraints excluded: chain A residue  244 THR
Chi-restraints excluded: chain A residue  258 MET
Chi-restraints excluded: chain A residue  266 THR
Chi-restraints excluded: chain A residue  294 LYS
Chi-restraints excluded: chain A residue  302 ILE
Chi-restraints excluded: chain A residue  329 MET
Chi-restraints excluded: chain A residue  435 THR
Chi-restraints excluded: chain A residue  461 THR
Chi-restraints excluded: chain A residue  499 THR
Chi-restraints excluded: chain A residue  517 GLN
Chi-restraints excluded: chain A residue  538 SER
Chi-restraints excluded: chain A residue  562 GLU
Chi-restraints excluded: chain A residue  580 THR
Chi-restraints excluded: chain A residue  634 ILE
Chi-restraints excluded: chain A residue  730 VAL
Chi-restraints excluded: chain A residue  734 LEU
Chi-restraints excluded: chain A residue  738 MET
Chi-restraints excluded: chain A residue  742 MET
Chi-restraints excluded: chain A residue  765 THR
Chi-restraints excluded: chain A residue  774 VAL
Chi-restraints excluded: chain A residue  794 LEU
Chi-restraints excluded: chain A residue  860 LEU
Chi-restraints excluded: chain A residue  874 VAL
Chi-restraints excluded: chain A residue  894 VAL
Chi-restraints excluded: chain A residue  918 MET
Chi-restraints excluded: chain A residue  964 LEU
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 79
   random chunks:
   chunk 66 optimal weight:    2.9990
   chunk 70 optimal weight:    0.9980
   chunk 68 optimal weight:    0.8980
   chunk 31 optimal weight:    0.9980
   chunk 8 optimal weight:    6.9990
   chunk 17 optimal weight:    5.9990
   chunk 30 optimal weight:    2.9990
   chunk 36 optimal weight:    8.9990
   chunk 6 optimal weight:    7.9990
   chunk 12 optimal weight:    0.7980
   chunk 19 optimal weight:    9.9990
   overall best weight:    1.3382

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
** A 353 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
A 954 GLN
A 963 GLN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4369 r_free = 0.4369 target = 0.204948 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 51)----------------|
| r_work = 0.3975 r_free = 0.3975 target = 0.165141 restraints weight = 7512.597|
|-----------------------------------------------------------------------------|
r_work (start): 0.3957 rms_B_bonded: 1.93
r_work: 0.3844 rms_B_bonded: 2.59 restraints_weight: 0.5000
r_work: 0.3718 rms_B_bonded: 4.25 restraints_weight: 0.2500
r_work (final): 0.3718
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6842
moved from start:          0.1926

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.030   7390  Z= 0.146
  Angle     :  0.589  10.456  10253  Z= 0.301
  Chirality :  0.043   0.175   1202
  Planarity :  0.005   0.074   1113
  Dihedral  : 17.105  84.436   1582
  Min Nonbonded Distance : 2.247

Molprobity Statistics.
  All-atom Clashscore : 12.32
  Ramachandran Plot:
    Outliers :  0.13 %
    Allowed  :  6.26 %
    Favored  : 93.61 %
  Rotamer:
    Outliers :  5.01 %
    Allowed  : 28.57 %
    Favored  : 66.42 %
  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: -0.91 (0.31), residues: 751
  helix:  0.77 (0.36), residues: 229
  sheet: -1.09 (0.38), residues: 177
  loop : -1.22 (0.33), residues: 345

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.006   0.000   ARG A 652 
 TYR   0.024   0.002   TYR A 904 
 PHE   0.017   0.002   PHE A 835 
 TRP   0.007   0.001   TRP A 604 
 HIS   0.008   0.001   HIS A 526 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00330 /  0.15 ( 7390)
  covalent geometry    : angle       0.58950 /  0.30 (10253)
  hydrogen bonds       : bond        0.03888 /  2.67 (  331)
  hydrogen bonds       : angle       5.28236 /  3.61 (  889)

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

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

  1502 Ramachandran restraints generated.
    751 Oldfield, 0 Emsley, 751 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1502 Ramachandran restraints generated.
    751 Oldfield, 0 Emsley, 751 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  126 residues out of total 684 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 34
    poor density    : 92
  time to evaluate  : 0.308 
Fit side-chains
   revert: symmetry clash
REVERT: A  294 LYS cc_start: 0.5291 (OUTLIER) cc_final: 0.4987 (ptpp)
REVERT: A  333 ASP cc_start: 0.7700 (m-30) cc_final: 0.6780 (t0)
REVERT: A  369 ASP cc_start: 0.6549 (t0) cc_final: 0.6347 (t0)
REVERT: A  436 PRO cc_start: 0.6131 (Cg_exo) cc_final: 0.5891 (Cg_endo)
REVERT: A  498 MET cc_start: 0.7470 (mtt) cc_final: 0.7153 (mtt)
REVERT: A  562 GLU cc_start: 0.7385 (OUTLIER) cc_final: 0.6940 (mt-10)
REVERT: A  647 ILE cc_start: 0.7153 (mt) cc_final: 0.6867 (mt)
REVERT: A  782 ILE cc_start: 0.5612 (OUTLIER) cc_final: 0.5234 (mp)
REVERT: A  794 LEU cc_start: 0.6294 (OUTLIER) cc_final: 0.5642 (mm)
REVERT: A  918 MET cc_start: 0.6257 (OUTLIER) cc_final: 0.5791 (ttp)
  outliers start: 34
  outliers final: 21
  residues processed: 114
  average time/residue: 0.3720
  time to fit residues: 45.9619
Evaluate side-chains
  115 residues out of total 684 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 26
    poor density    : 89
  time to evaluate  : 0.245 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  224 LEU
Chi-restraints excluded: chain A residue  244 THR
Chi-restraints excluded: chain A residue  266 THR
Chi-restraints excluded: chain A residue  294 LYS
Chi-restraints excluded: chain A residue  302 ILE
Chi-restraints excluded: chain A residue  435 THR
Chi-restraints excluded: chain A residue  461 THR
Chi-restraints excluded: chain A residue  495 LEU
Chi-restraints excluded: chain A residue  517 GLN
Chi-restraints excluded: chain A residue  538 SER
Chi-restraints excluded: chain A residue  562 GLU
Chi-restraints excluded: chain A residue  580 THR
Chi-restraints excluded: chain A residue  590 VAL
Chi-restraints excluded: chain A residue  634 ILE
Chi-restraints excluded: chain A residue  730 VAL
Chi-restraints excluded: chain A residue  734 LEU
Chi-restraints excluded: chain A residue  738 MET
Chi-restraints excluded: chain A residue  742 MET
Chi-restraints excluded: chain A residue  774 VAL
Chi-restraints excluded: chain A residue  782 ILE
Chi-restraints excluded: chain A residue  794 LEU
Chi-restraints excluded: chain A residue  860 LEU
Chi-restraints excluded: chain A residue  874 VAL
Chi-restraints excluded: chain A residue  894 VAL
Chi-restraints excluded: chain A residue  918 MET
Chi-restraints excluded: chain A residue  964 LEU
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 79
   random chunks:
   chunk 52 optimal weight:    5.9990
   chunk 11 optimal weight:    2.9990
   chunk 46 optimal weight:    2.9990
   chunk 14 optimal weight:    0.9980
   chunk 4 optimal weight:    0.9990
   chunk 31 optimal weight:    0.8980
   chunk 71 optimal weight:    4.9990
   chunk 49 optimal weight:    0.9980
   chunk 3 optimal weight:    2.9990
   chunk 8 optimal weight:    8.9990
   chunk 68 optimal weight:    5.9990
   overall best weight:    1.3784

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
A 322 ASN
** A 353 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
A 954 GLN
A 963 GLN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4371 r_free = 0.4371 target = 0.205194 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 56)----------------|
| r_work = 0.3977 r_free = 0.3977 target = 0.165483 restraints weight = 7440.056|
|-----------------------------------------------------------------------------|
r_work (start): 0.3959 rms_B_bonded: 1.92
r_work: 0.3848 rms_B_bonded: 2.58 restraints_weight: 0.5000
r_work: 0.3722 rms_B_bonded: 4.23 restraints_weight: 0.2500
r_work (final): 0.3722
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6840
moved from start:          0.1949

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.031   7390  Z= 0.146
  Angle     :  0.590  10.715  10253  Z= 0.301
  Chirality :  0.043   0.170   1202
  Planarity :  0.005   0.069   1113
  Dihedral  : 17.103  84.032   1582
  Min Nonbonded Distance : 2.281

Molprobity Statistics.
  All-atom Clashscore : 12.39
  Ramachandran Plot:
    Outliers :  0.13 %
    Allowed  :  5.99 %
    Favored  : 93.87 %
  Rotamer:
    Outliers :  5.15 %
    Allowed  : 28.42 %
    Favored  : 66.42 %
  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: -0.89 (0.31), residues: 751
  helix:  0.79 (0.35), residues: 231
  sheet: -1.05 (0.39), residues: 176
  loop : -1.24 (0.33), residues: 344

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.000   ARG A 937 
 TYR   0.018   0.002   TYR A 904 
 PHE   0.017   0.002   PHE A 835 
 TRP   0.006   0.001   TRP A 884 
 HIS   0.007   0.001   HIS A 526 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00329 /  0.15 ( 7390)
  covalent geometry    : angle       0.59029 /  0.30 (10253)
  hydrogen bonds       : bond        0.03854 /  2.65 (  331)
  hydrogen bonds       : angle       5.24350 /  3.59 (  889)

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

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

  1502 Ramachandran restraints generated.
    751 Oldfield, 0 Emsley, 751 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1502 Ramachandran restraints generated.
    751 Oldfield, 0 Emsley, 751 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  126 residues out of total 684 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 35
    poor density    : 91
  time to evaluate  : 0.184 
Fit side-chains
   revert: symmetry clash
REVERT: A  294 LYS cc_start: 0.5263 (OUTLIER) cc_final: 0.4973 (ptpp)
REVERT: A  333 ASP cc_start: 0.7698 (m-30) cc_final: 0.6772 (t0)
REVERT: A  436 PRO cc_start: 0.6106 (Cg_exo) cc_final: 0.5873 (Cg_endo)
REVERT: A  498 MET cc_start: 0.7505 (mtt) cc_final: 0.7244 (mtt)
REVERT: A  647 ILE cc_start: 0.7162 (mt) cc_final: 0.6877 (mt)
REVERT: A  782 ILE cc_start: 0.5688 (OUTLIER) cc_final: 0.5306 (mp)
REVERT: A  794 LEU cc_start: 0.6187 (OUTLIER) cc_final: 0.5552 (mm)
REVERT: A  918 MET cc_start: 0.6173 (OUTLIER) cc_final: 0.5692 (ttp)
  outliers start: 35
  outliers final: 21
  residues processed: 115
  average time/residue: 0.3737
  time to fit residues: 46.3578
Evaluate side-chains
  114 residues out of total 684 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 25
    poor density    : 89
  time to evaluate  : 0.208 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  224 LEU
Chi-restraints excluded: chain A residue  244 THR
Chi-restraints excluded: chain A residue  266 THR
Chi-restraints excluded: chain A residue  294 LYS
Chi-restraints excluded: chain A residue  302 ILE
Chi-restraints excluded: chain A residue  435 THR
Chi-restraints excluded: chain A residue  461 THR
Chi-restraints excluded: chain A residue  517 GLN
Chi-restraints excluded: chain A residue  538 SER
Chi-restraints excluded: chain A residue  580 THR
Chi-restraints excluded: chain A residue  590 VAL
Chi-restraints excluded: chain A residue  634 ILE
Chi-restraints excluded: chain A residue  730 VAL
Chi-restraints excluded: chain A residue  734 LEU
Chi-restraints excluded: chain A residue  738 MET
Chi-restraints excluded: chain A residue  742 MET
Chi-restraints excluded: chain A residue  755 VAL
Chi-restraints excluded: chain A residue  774 VAL
Chi-restraints excluded: chain A residue  782 ILE
Chi-restraints excluded: chain A residue  794 LEU
Chi-restraints excluded: chain A residue  860 LEU
Chi-restraints excluded: chain A residue  874 VAL
Chi-restraints excluded: chain A residue  894 VAL
Chi-restraints excluded: chain A residue  918 MET
Chi-restraints excluded: chain A residue  964 LEU
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 79
   random chunks:
   chunk 43 optimal weight:    7.9990
   chunk 25 optimal weight:    8.9990
   chunk 21 optimal weight:    4.9990
   chunk 65 optimal weight:    3.9990
   chunk 48 optimal weight:    7.9990
   chunk 7 optimal weight:    9.9990
   chunk 51 optimal weight:    0.2980
   chunk 57 optimal weight:    9.9990
   chunk 69 optimal weight:    5.9990
   chunk 71 optimal weight:    0.0980
   chunk 47 optimal weight:    0.6980
   overall best weight:    2.0184

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
A 322 ASN
** A 353 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4353 r_free = 0.4353 target = 0.203360 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 38)----------------|
| r_work = 0.3951 r_free = 0.3951 target = 0.163194 restraints weight = 7495.730|
|-----------------------------------------------------------------------------|
r_work (start): 0.3931 rms_B_bonded: 1.92
r_work: 0.3820 rms_B_bonded: 2.58 restraints_weight: 0.5000
r_work: 0.3694 rms_B_bonded: 4.22 restraints_weight: 0.2500
r_work (final): 0.3694
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6874
moved from start:          0.2040

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.035   7390  Z= 0.181
  Angle     :  0.635  11.070  10253  Z= 0.323
  Chirality :  0.045   0.177   1202
  Planarity :  0.005   0.078   1113
  Dihedral  : 17.087  83.613   1582
  Min Nonbonded Distance : 2.430

Molprobity Statistics.
  All-atom Clashscore : 12.68
  Ramachandran Plot:
    Outliers :  0.13 %
    Allowed  :  6.66 %
    Favored  : 93.21 %
  Rotamer:
    Outliers :  4.86 %
    Allowed  : 29.16 %
    Favored  : 65.98 %
  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 (0.31), residues: 751
  helix:  0.72 (0.36), residues: 231
  sheet: -1.05 (0.39), residues: 175
  loop : -1.32 (0.33), residues: 345

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.006   0.000   ARG A 646 
 TYR   0.018   0.002   TYR A 904 
 PHE   0.017   0.002   PHE A 835 
 TRP   0.007   0.002   TRP A 586 
 HIS   0.007   0.001   HIS A 526 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00413 /  0.18 ( 7390)
  covalent geometry    : angle       0.63548 /  0.32 (10253)
  hydrogen bonds       : bond        0.04122 /  2.82 (  331)
  hydrogen bonds       : angle       5.33356 /  3.65 (  889)

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

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

  1502 Ramachandran restraints generated.
    751 Oldfield, 0 Emsley, 751 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1502 Ramachandran restraints generated.
    751 Oldfield, 0 Emsley, 751 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  122 residues out of total 684 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 33
    poor density    : 89
  time to evaluate  : 0.244 
Fit side-chains
   revert: symmetry clash
REVERT: A  294 LYS cc_start: 0.5227 (OUTLIER) cc_final: 0.4927 (ptpp)
REVERT: A  333 ASP cc_start: 0.7797 (m-30) cc_final: 0.6914 (t0)
REVERT: A  436 PRO cc_start: 0.6185 (Cg_exo) cc_final: 0.5944 (Cg_endo)
REVERT: A  498 MET cc_start: 0.7520 (mtt) cc_final: 0.7246 (mtt)
REVERT: A  562 GLU cc_start: 0.7418 (OUTLIER) cc_final: 0.6986 (mt-10)
REVERT: A  647 ILE cc_start: 0.7193 (mt) cc_final: 0.6911 (mt)
REVERT: A  719 MET cc_start: 0.7144 (OUTLIER) cc_final: 0.5499 (mmt)
REVERT: A  782 ILE cc_start: 0.5776 (OUTLIER) cc_final: 0.5355 (mp)
REVERT: A  794 LEU cc_start: 0.6259 (OUTLIER) cc_final: 0.5580 (mm)
REVERT: A  918 MET cc_start: 0.6312 (OUTLIER) cc_final: 0.5869 (ttp)
  outliers start: 33
  outliers final: 24
  residues processed: 111
  average time/residue: 0.3696
  time to fit residues: 44.4255
Evaluate side-chains
  116 residues out of total 684 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 30
    poor density    : 86
  time to evaluate  : 0.211 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  224 LEU
Chi-restraints excluded: chain A residue  244 THR
Chi-restraints excluded: chain A residue  266 THR
Chi-restraints excluded: chain A residue  294 LYS
Chi-restraints excluded: chain A residue  302 ILE
Chi-restraints excluded: chain A residue  435 THR
Chi-restraints excluded: chain A residue  461 THR
Chi-restraints excluded: chain A residue  499 THR
Chi-restraints excluded: chain A residue  517 GLN
Chi-restraints excluded: chain A residue  538 SER
Chi-restraints excluded: chain A residue  562 GLU
Chi-restraints excluded: chain A residue  580 THR
Chi-restraints excluded: chain A residue  590 VAL
Chi-restraints excluded: chain A residue  634 ILE
Chi-restraints excluded: chain A residue  719 MET
Chi-restraints excluded: chain A residue  730 VAL
Chi-restraints excluded: chain A residue  734 LEU
Chi-restraints excluded: chain A residue  738 MET
Chi-restraints excluded: chain A residue  742 MET
Chi-restraints excluded: chain A residue  755 VAL
Chi-restraints excluded: chain A residue  774 VAL
Chi-restraints excluded: chain A residue  777 MET
Chi-restraints excluded: chain A residue  782 ILE
Chi-restraints excluded: chain A residue  794 LEU
Chi-restraints excluded: chain A residue  860 LEU
Chi-restraints excluded: chain A residue  874 VAL
Chi-restraints excluded: chain A residue  894 VAL
Chi-restraints excluded: chain A residue  918 MET
Chi-restraints excluded: chain A residue  928 MET
Chi-restraints excluded: chain A residue  964 LEU
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 79
   random chunks:
   chunk 2 optimal weight:    7.9990
   chunk 36 optimal weight:    6.9990
   chunk 15 optimal weight:    3.9990
   chunk 20 optimal weight:    1.9990
   chunk 13 optimal weight:    6.9990
   chunk 59 optimal weight:    0.8980
   chunk 33 optimal weight:    0.9990
   chunk 41 optimal weight:    8.9990
   chunk 29 optimal weight:    1.9990
   chunk 12 optimal weight:    0.9990
   chunk 43 optimal weight:    0.9980
   overall best weight:    1.1786

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
** A 353 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4373 r_free = 0.4373 target = 0.205655 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 47)----------------|
| r_work = 0.3981 r_free = 0.3981 target = 0.166052 restraints weight = 7481.018|
|-----------------------------------------------------------------------------|
r_work (start): 0.3963 rms_B_bonded: 1.92
r_work: 0.3852 rms_B_bonded: 2.57 restraints_weight: 0.5000
r_work: 0.3726 rms_B_bonded: 4.22 restraints_weight: 0.2500
r_work (final): 0.3726
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6830
moved from start:          0.2001

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.033   7390  Z= 0.140
  Angle     :  0.608  12.867  10253  Z= 0.307
  Chirality :  0.043   0.179   1202
  Planarity :  0.005   0.073   1113
  Dihedral  : 17.127  84.538   1582
  Min Nonbonded Distance : 2.417

Molprobity Statistics.
  All-atom Clashscore : 12.68
  Ramachandran Plot:
    Outliers :  0.13 %
    Allowed  :  5.86 %
    Favored  : 94.01 %
  Rotamer:
    Outliers :  4.86 %
    Allowed  : 29.46 %
    Favored  : 65.68 %
  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 (0.31), residues: 751
  helix:  0.78 (0.35), residues: 232
  sheet: -1.05 (0.38), residues: 175
  loop : -1.25 (0.33), residues: 344

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.000   ARG A 646 
 TYR   0.016   0.002   TYR A 904 
 PHE   0.016   0.002   PHE A 835 
 TRP   0.007   0.001   TRP A 604 
 HIS   0.007   0.001   HIS A 526 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00315 /  0.14 ( 7390)
  covalent geometry    : angle       0.60787 /  0.31 (10253)
  hydrogen bonds       : bond        0.03782 /  2.61 (  331)
  hydrogen bonds       : angle       5.23675 /  3.59 (  889)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 2225.23 seconds
wall clock time: 38 minutes 40.41 seconds (2320.41 seconds total)