Starting phenix.real_space_refine
on Thu Jul  2 16:20:22 2026 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/8ops_17086/07_2026/8ops_17086.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/8ops_17086/07_2026/8ops_17086.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=3.82
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/cci-nas-00/data/ceres_data/8ops_17086/07_2026/8ops_17086.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/8ops_17086/07_2026/8ops_17086.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/8ops_17086/07_2026/8ops_17086.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/8ops_17086/07_2026/8ops_17086.cif"
  }
  resolution = 3.82
  write_initial_geo_file = False
  refinement {
    macro_cycles = 10
  }


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

Validating inputs
Origin is already at (0, 0, 0), no shifts will be applied
-------------------------------------------------------------------------------
Processing inputs
*****************
Set random seed
  Set to: 0
Set model cs if undefined
Decide on map wrapping
  Map wrapping is set to: False
Normalize map: mean=0, sd=1
  Input map: mean=   0.001 sd=   0.018
Set stop_for_unknowns flag
  Set to: True
Assert model is a single copy model
Assert all atoms have isotropic ADPs
Construct map_model_manager
Extract box with map and model
Check model and map are aligned
Set scattering table
  Set to: electron
  Number of scattering types: 7
    Type Number    sf(0)   Gaussians
     Zn      1      6.06       5
     P      69      5.49       5
     S      19      5.16       5
     C    2905      2.51       5
     N     874      2.21       5
     O    1115      1.98       5
     H    4258      0.53       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 5 residue(s): 0.00s

  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: 9241
  Number of models: 1
  Model: ""
    Number of chains: 4
    Chain: "A"
      Number of atoms: 6459
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 403, 6459
          Classifications: {'peptide': 403}
          Link IDs: {'PTRANS': 22, 'TRANS': 380}
          Chain breaks: 2
          Unresolved non-hydrogen bonds: 52
          Unresolved non-hydrogen angles: 62
          Unresolved non-hydrogen dihedrals: 44
          Unresolved non-hydrogen chiralities: 2
          Planarities with less than four sites: {'ASP:plan': 2, 'GLU:plan': 2, 'ASN:plan1': 1, 'HIS:plan': 1, 'ARG:plan': 1}
          Unresolved non-hydrogen planarities: 27
    Chain: "B"
      Number of atoms: 565
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 42, 565
          Classifications: {'peptide': 42}
          Link IDs: {'PTRANS': 4, 'TRANS': 37}
          Unresolved non-hydrogen bonds: 18
          Unresolved non-hydrogen angles: 19
          Unresolved non-hydrogen dihedrals: 17
          Unresolved non-hydrogen chiralities: 1
    Chain: "C"
      Number of atoms: 2216
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 69, 2216
          Classifications: {'RNA': 69}
          Modifications used: {'rna2p_pur': 7, 'rna2p_pyr': 6, 'rna3p_pur': 31, 'rna3p_pyr': 25}
          Link IDs: {'rna2p': 12, 'rna3p': 56}
    Chain: "B"
      Number of atoms: 1
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 1, 1
          Unusual residues: {' ZN': 1}
          Classifications: {'undetermined': 1}

List of CYS excluded from plausible disulfide bonds:
  (reason: may participate in coordination)
  ATOM   6508  SG  CYS B 139      42.916  39.813  40.495  1.00130.08           S
  ATOM   6553  SG  CYS B 142      46.905  37.913  39.572  1.00133.43           S
  ATOM   6674  SG  CYS B 152      44.444  36.160  40.172  1.00129.36           S

  Time building chain proxies: 1.83, per 1000 atoms: 0.20
  Number of scatterers: 9241
  At special positions: 0
  Unit cell: (79.05, 80.91, 134.85, 90, 90, 90)
  Space group: P 1 (No. 1)
  Number of sites at special positions: 0
  Number of scattering types: 7
    Type Number    sf(0)
     Zn      1     29.99
     S      19     16.00
     P      69     15.00
     O    1115      8.00
     N     874      7.00
     C    2905      6.00
     H    4258      1.00
    sf(0) = scattering factor at diffraction angle 0.

  Number of disulfides: simple=0, symmetry=0

  Automatic linking
    Parameters for automatic linking
      Linking & cutoffs
        Metal                : Auto  - 3.00
        Amino acid           : True  - 1.90
        Carbohydrate         : True  - 1.99
        Ligands              : True  - 1.99
        Small molecules      : False - 1.98
        Amino acid - RNA/DNA : False
      
  Number of custom bonds: simple=0, symmetry=0
  Time building additional restraints: 1.07
  Conformation dependent library (CDL) restraints added in 306.9 milliseconds
  
  Dynamic metal coordination
    Zn2+ tetrahedral coordination
      pdb="  ZN B 301 "
        pdb="ZN    ZN B 301 " - pdb=" SG  CYS B 142 "
        pdb="ZN    ZN B 301 " - pdb=" SG  CYS B 152 "
        pdb="ZN    ZN B 301 " - pdb=" SG  CYS B 139 "


  874 Ramachandran restraints generated.
    437 Oldfield, 0 Emsley, 437 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  852

  Finding SS restraints...
    Secondary structure from input PDB file:
      13 helices and 3 sheets defined
      45.2% alpha, 8.3% beta
      2 base pairs and 25 stacking pairs defined.
    Time for finding SS restraints: 1.93
  Creating SS restraints...
    Processing helix  chain 'A' and resid 210 through 227
    Processing helix  chain 'A' and resid 255 through 265
    Processing helix  chain 'A' and resid 265 through 283
    Processing helix  chain 'A' and resid 288 through 306
    Processing helix  chain 'A' and resid 309 through 329
      removed outlier: 4.247A  pdb=" N   HIS A 329 " --> pdb=" O   ASN A 325 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 340 through 345
    Processing helix  chain 'A' and resid 364 through 379
    Processing helix  chain 'A' and resid 413 through 430
      removed outlier: 3.538A  pdb=" N   CYS A 417 " --> pdb=" O   ASN A 413 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 432 through 447
    Processing helix  chain 'A' and resid 458 through 473
      removed outlier: 3.995A  pdb=" N   PHE A 462 " --> pdb=" O   PRO A 458 " (cutoff:3.500A)
      removed outlier: 3.813A  pdb=" N   ALA A 463 " --> pdb=" O   PRO A 459 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 550 through 564
    Processing helix  chain 'A' and resid 582 through 587
      removed outlier: 3.664A  pdb=" N   LYS A 586 " --> pdb=" O   SER A 582 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 611 through 630
    Processing sheet with id=AA1, first strand: chain 'A' and resid 229 through 231
    Processing sheet with id=AA2, first strand: chain 'A' and resid 335 through 338
      removed outlier: 6.982A  pdb=" N   VAL A 397 " --> pdb=" O   VAL A 385 " (cutoff:3.500A)
      removed outlier: 4.446A  pdb=" N   VAL A 385 " --> pdb=" O   VAL A 397 " (cutoff:3.500A)
    Processing sheet with id=AA3, first strand: chain 'A' and resid 498 through 503
      removed outlier: 7.047A  pdb=" N   ILE A 508 " --> pdb=" O   GLN A 500 " (cutoff:3.500A)
      removed outlier: 5.581A  pdb=" N   ILE A 502 " --> pdb=" O   VAL A 506 " (cutoff:3.500A)
      removed outlier: 7.152A  pdb=" N   VAL A 506 " --> pdb=" O   ILE A 502 " (cutoff:3.500A)

    170 hydrogen bonds defined for protein.
    492 hydrogen bond angles defined for protein.
    Restraints generated for nucleic acids:
      4 hydrogen bonds
      8 hydrogen bond angles
      0 basepair planarities
      2 basepair parallelities
      25 stacking parallelities
  Total time for adding SS restraints: 1.97

  Time building geometry restraints manager: 1.36 seconds

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

  Histogram of bond lengths:
        0.84 -     1.03: 4244
        1.03 -     1.23: 36
        1.23 -     1.42: 2335
        1.42 -     1.62: 2852
        1.62 -     1.81: 21
  Bond restraints: 9488
  Sorted by residual:
  bond pdb=" CB  PRO A 287 "
       pdb=" CG  PRO A 287 "
    ideal  model  delta    sigma   weight residual
    1.492  1.592 -0.100 5.00e-02 4.00e+02 4.01e+00
  bond pdb=" CA  VAL A 434 "
       pdb=" CB  VAL A 434 "
    ideal  model  delta    sigma   weight residual
    1.539  1.533  0.006 5.40e-03 3.43e+04 1.29e+00
  bond pdb=" CA  ASP B 137 "
       pdb=" CB  ASP B 137 "
    ideal  model  delta    sigma   weight residual
    1.532  1.550 -0.018 1.74e-02 3.30e+03 1.11e+00
  bond pdb=" N9    A C  69 "
       pdb=" C4    A C  69 "
    ideal  model  delta    sigma   weight residual
    1.374  1.380 -0.006 6.00e-03 2.78e+04 9.65e-01
  bond pdb=" CA  TRP A 509 "
       pdb=" CB  TRP A 509 "
    ideal  model  delta    sigma   weight residual
    1.535  1.554 -0.018 1.90e-02 2.77e+03 9.47e-01
  ... (remaining 9483 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     1.81: 16780
        1.81 -     3.62: 363
        3.62 -     5.43: 23
        5.43 -     7.23: 0
        7.23 -     9.04: 1
  Bond angle restraints: 17167
  Sorted by residual:
  angle pdb=" CA  PRO A 287 "
        pdb=" N   PRO A 287 "
        pdb=" CD  PRO A 287 "
      ideal   model   delta    sigma   weight residual
     112.00  106.99    5.01 1.40e+00 5.10e-01 1.28e+01
  angle pdb=" CA  LEU A 371 "
        pdb=" CB  LEU A 371 "
        pdb=" CG  LEU A 371 "
      ideal   model   delta    sigma   weight residual
     116.30  125.34   -9.04 3.50e+00 8.16e-02 6.68e+00
  angle pdb=" CA  PRO B 158 "
        pdb=" N   PRO B 158 "
        pdb=" CD  PRO B 158 "
      ideal   model   delta    sigma   weight residual
     112.00  108.48    3.52 1.40e+00 5.10e-01 6.34e+00
  angle pdb=" C   LEU A 370 "
        pdb=" N   LEU A 371 "
        pdb=" CA  LEU A 371 "
      ideal   model   delta    sigma   weight residual
     120.31  116.53    3.78 1.52e+00 4.33e-01 6.18e+00
  angle pdb=" C2'   A C  69 "
        pdb=" C1'   A C  69 "
        pdb=" N9    A C  69 "
      ideal   model   delta    sigma   weight residual
     112.00  115.54   -3.54 1.50e+00 4.44e-01 5.57e+00
  ... (remaining 17162 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    21.77: 3943
       21.77 -    43.54: 362
       43.54 -    65.32: 206
       65.32 -    87.09: 29
       87.09 -   108.86: 4
  Dihedral angle restraints: 4544
    sinusoidal: 3040
      harmonic: 1504
  Sorted by residual:
  dihedral pdb=" O4'   C C  30 "
           pdb=" C1'   C C  30 "
           pdb=" N1    C C  30 "
           pdb=" C2    C C  30 "
      ideal   model   delta sinusoidal    sigma   weight residual
    -128.00  -61.59  -66.41     1      1.70e+01 3.46e-03 1.99e+01
  dihedral pdb=" O4'   C C  18 "
           pdb=" C1'   C C  18 "
           pdb=" N1    C C  18 "
           pdb=" C2    C C  18 "
      ideal   model   delta sinusoidal    sigma   weight residual
    -128.00  -65.76  -62.24     1      1.70e+01 3.46e-03 1.77e+01
  dihedral pdb=" O4'   U C  36 "
           pdb=" C1'   U C  36 "
           pdb=" N1    U C  36 "
           pdb=" C2    U C  36 "
      ideal   model   delta sinusoidal    sigma   weight residual
    -160.00 -106.72  -53.28     1      1.50e+01 4.44e-03 1.72e+01
  ... (remaining 4541 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.043: 739
       0.043 -    0.085: 113
       0.085 -    0.128: 37
       0.128 -    0.170: 8
       0.170 -    0.213: 1
  Chirality restraints: 898
  Sorted by residual:
  chirality pdb=" C1'   A C  69 "
            pdb=" O4'   A C  69 "
            pdb=" C2'   A C  69 "
            pdb=" N9    A C  69 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.46    2.25    0.21 2.00e-01 2.50e+01 1.13e+00
  chirality pdb=" CB  VAL A 385 "
            pdb=" CA  VAL A 385 "
            pdb=" CG1 VAL A 385 "
            pdb=" CG2 VAL A 385 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.63   -2.79    0.16 2.00e-01 2.50e+01 6.62e-01
  chirality pdb=" CB  VAL A 556 "
            pdb=" CA  VAL A 556 "
            pdb=" CG1 VAL A 556 "
            pdb=" CG2 VAL A 556 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.63   -2.48   -0.15 2.00e-01 2.50e+01 5.65e-01
  ... (remaining 895 not shown)

  Planarity restraints: 1158
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   PRO A 286 "    0.063 5.00e-02 4.00e+02   9.32e-02 1.39e+01
        pdb=" N   PRO A 287 "   -0.161 5.00e-02 4.00e+02
        pdb=" CA  PRO A 287 "    0.047 5.00e-02 4.00e+02
        pdb=" CD  PRO A 287 "    0.051 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CB  TRP A 509 "   -0.014 2.00e-02 2.50e+03   1.04e-02 4.32e+00
        pdb=" CG  TRP A 509 "    0.036 2.00e-02 2.50e+03
        pdb=" CD1 TRP A 509 "   -0.007 2.00e-02 2.50e+03
        pdb=" CD2 TRP A 509 "   -0.000 2.00e-02 2.50e+03
        pdb=" NE1 TRP A 509 "    0.002 2.00e-02 2.50e+03
        pdb=" CE2 TRP A 509 "    0.002 2.00e-02 2.50e+03
        pdb=" CE3 TRP A 509 "   -0.009 2.00e-02 2.50e+03
        pdb=" CZ2 TRP A 509 "   -0.002 2.00e-02 2.50e+03
        pdb=" CZ3 TRP A 509 "    0.004 2.00e-02 2.50e+03
        pdb=" CH2 TRP A 509 "    0.001 2.00e-02 2.50e+03
        pdb=" HD1 TRP A 509 "   -0.006 2.00e-02 2.50e+03
        pdb=" HE1 TRP A 509 "   -0.002 2.00e-02 2.50e+03
        pdb=" HE3 TRP A 509 "   -0.001 2.00e-02 2.50e+03
        pdb=" HZ2 TRP A 509 "   -0.002 2.00e-02 2.50e+03
        pdb=" HZ3 TRP A 509 "   -0.001 2.00e-02 2.50e+03
        pdb=" HH2 TRP A 509 "   -0.001 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   GLN B 157 "    0.035 5.00e-02 4.00e+02   5.16e-02 4.27e+00
        pdb=" N   PRO B 158 "   -0.089 5.00e-02 4.00e+02
        pdb=" CA  PRO B 158 "    0.025 5.00e-02 4.00e+02
        pdb=" CD  PRO B 158 "    0.029 5.00e-02 4.00e+02
  ... (remaining 1155 not shown)

  Histogram of nonbonded interaction distances:
        1.58 -     2.18: 383
        2.18 -     2.79: 17078
        2.79 -     3.39: 25080
        3.39 -     4.00: 32305
        4.00 -     4.60: 48572
  Nonbonded interactions: 123418
  Sorted by model distance:
  nonbonded pdb=" O   MET A 465 "
            pdb=" HH  TYR A 562 "
     model   vdw
     1.577 2.450
  nonbonded pdb=" OE1 GLN A 546 "
            pdb=" H   GLN A 546 "
     model   vdw
     1.665 2.450
  nonbonded pdb=" O   CYS A 447 "
            pdb=" HG  SER A 448 "
     model   vdw
     1.705 2.450
  nonbonded pdb=" OE2 GLU A 318 "
            pdb="HH21 ARG A 321 "
     model   vdw
     1.734 2.450
  nonbonded pdb=" HZ1 LYS A 445 "
            pdb=" OD2 ASP A 450 "
     model   vdw
     1.738 2.450
  ... (remaining 123413 not shown)

  NOTE: a complete listing of the restraints can be obtained by requesting
        output of .geo file.
Find NCS groups from input model
Time spend for trying shortcut: 0.00
========== WARNING! ============

  No NCS relation were found !!!

================================

Found NCS groups:
  found none.
Set up NCS constraints
  No NCS constraints will be used in refinement.
Set refine NCS operators
Adjust number of macro_cycles
  Number of macro_cycles: 10
Reset NCS operators
Extract rigid body selections
Check and reset occupancies
  Occupancies: min=1.00 max=1.00 mean=1.00
Load rotamer database and sin/cos tables
Set ADP refinement strategy
  ADPs will be refined as group one per residue
Make a string to write initial .geo file
Internal consistency checks
Time:
  Set random seed:                         0.000
  Set model cs if undefined:               0.000
  Decide on map wrapping:                  0.000
  Normalize map: mean=0, sd=1:             2.890
  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:             0.060
  Extract box with map and model:          0.120
  Check model and map are aligned:         0.020
  Set scattering table:                    0.020
  Process input model:                     14.840
  Find NCS groups from input model:        0.020
  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:1.190
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   19.180
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.5006
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   0.100   5233  Z= 0.130
  Angle     :  0.568   9.044   7421  Z= 0.345
  Chirality :  0.038   0.213    898
  Planarity :  0.006   0.093    692
  Dihedral  : 21.448 108.861   2407
  Min Nonbonded Distance : 1.982

Molprobity Statistics.
  All-atom Clashscore : 6.28
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  0.69 %
    Favored  : 99.31 %
  Rotamer:
    Outliers :  0.78 %
    Allowed  : 18.70 %
    Favored  : 80.52 %
  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:  1.99 (0.39), residues: 437
  helix:  2.78 (0.37), residues: 190
  sheet:  0.03 (0.77), residues: 38
  loop :  0.26 (0.39), residues: 209

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.006   0.000   ARG A 316 
 TYR   0.009   0.001   TYR A 626 
 PHE   0.021   0.001   PHE A 469 
 TRP   0.035   0.003   TRP A 509 
 HIS   0.013   0.002   HIS A 260 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00275 /  0.13 ( 5230)
  covalent geometry    : angle       0.56839 /  0.34 ( 7421)
  hydrogen bonds       : bond        0.12563 /  8.10 (  174)
  hydrogen bonds       : angle       5.82545 /  4.16 (  500)
  metal coordination   : bond        0.00681 /  0.36 (    3)

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

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

  874 Ramachandran restraints generated.
    437 Oldfield, 0 Emsley, 437 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  874 Ramachandran restraints generated.
    437 Oldfield, 0 Emsley, 437 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Residue THR  241 is missing expected H atoms. Skipping.
Residue LYS  261 is missing expected H atoms. Skipping.
Residue LYS  270 is missing expected H atoms. Skipping.
Residue LYS  349 is missing expected H atoms. Skipping.
Residue MET  363 is missing expected H atoms. Skipping.
Residue LYS  493 is missing expected H atoms. Skipping.
Residue VAL  506 is missing expected H atoms. Skipping.
Residue LYS  150 is missing expected H atoms. Skipping.
Residue LEU  154 is missing expected H atoms. Skipping.
Residue LYS  159 is missing expected H atoms. Skipping.
Residue MET  170 is missing expected H atoms. Skipping.
Evaluate side-chains
  89 residues out of total 404 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 3
    poor density    : 86
  time to evaluate  : 0.227 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  275 LYS cc_start: 0.6727 (mmmm) cc_final: 0.6418 (mmmm)
REVERT: A  415 ASN cc_start: 0.8104 (m-40) cc_final: 0.7789 (t0)
  outliers start: 3
  outliers final: 2
  residues processed: 89
  average time/residue: 0.1750
  time to fit residues: 19.5805
Evaluate side-chains
  78 residues out of total 404 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 2
    poor density    : 76
  time to evaluate  : 0.208 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  338 LEU
Chi-restraints excluded: chain A residue  373 GLN
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 50
   random chunks:
   chunk 24 optimal weight:    0.0870
   chunk 48 optimal weight:    3.9990
   chunk 26 optimal weight:    0.9980
   chunk 2 optimal weight:    0.7980
   chunk 16 optimal weight:    0.9990
   chunk 32 optimal weight:    0.4980
   chunk 31 optimal weight:    0.9980
   chunk 25 optimal weight:    0.0980
   chunk 19 optimal weight:    2.9990
   chunk 30 optimal weight:    0.6980
   chunk 22 optimal weight:    0.9990
   overall best weight:    0.4358

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
A 329 HIS
** A 373 GLN ** 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 = 0.4705 r_free = 0.4705 target = 0.192260 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 41)----------------|
| r_work = 0.4392 r_free = 0.4392 target = 0.167642 restraints weight = 35678.378|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 42)----------------|
| r_work = 0.4463 r_free = 0.4463 target = 0.173225 restraints weight = 17721.254|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 41)----------------|
| r_work = 0.4507 r_free = 0.4507 target = 0.176661 restraints weight = 10295.452|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 36)----------------|
| r_work = 0.4536 r_free = 0.4536 target = 0.178918 restraints weight = 6767.784|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 52)----------------|
| r_work = 0.4555 r_free = 0.4555 target = 0.180441 restraints weight = 4909.899|
|-----------------------------------------------------------------------------|
r_work (final): 0.4547
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.5092
moved from start:          0.1349

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.046   5233  Z= 0.139
  Angle     :  0.531   7.609   7421  Z= 0.293
  Chirality :  0.038   0.203    898
  Planarity :  0.005   0.061    692
  Dihedral  : 22.587 110.317   1544
  Min Nonbonded Distance : 2.104

Molprobity Statistics.
  All-atom Clashscore : 6.82
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.14 %
    Favored  : 98.86 %
  Rotamer:
    Outliers :  1.56 %
    Allowed  : 17.40 %
    Favored  : 81.04 %
  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:  1.63 (0.39), residues: 437
  helix:  2.37 (0.37), residues: 197
  sheet:  0.10 (0.77), residues: 44
  loop :  0.03 (0.40), residues: 196

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.006   0.001   ARG A 345 
 TYR   0.015   0.002   TYR A 562 
 PHE   0.010   0.001   PHE A 469 
 TRP   0.021   0.002   TRP A 509 
 HIS   0.005   0.001   HIS A 262 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00298 /  0.14 ( 5230)
  covalent geometry    : angle       0.53076 /  0.29 ( 7421)
  hydrogen bonds       : bond        0.04802 /  3.08 (  174)
  hydrogen bonds       : angle       5.14013 /  3.66 (  500)
  metal coordination   : bond        0.00193 /  0.10 (    3)

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

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

  874 Ramachandran restraints generated.
    437 Oldfield, 0 Emsley, 437 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  874 Ramachandran restraints generated.
    437 Oldfield, 0 Emsley, 437 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Residue THR  241 is missing expected H atoms. Skipping.
Residue LYS  261 is missing expected H atoms. Skipping.
Residue LYS  270 is missing expected H atoms. Skipping.
Residue LYS  349 is missing expected H atoms. Skipping.
Residue MET  363 is missing expected H atoms. Skipping.
Residue LYS  493 is missing expected H atoms. Skipping.
Residue VAL  506 is missing expected H atoms. Skipping.
Residue LYS  150 is missing expected H atoms. Skipping.
Residue LEU  154 is missing expected H atoms. Skipping.
Residue LYS  159 is missing expected H atoms. Skipping.
Residue MET  170 is missing expected H atoms. Skipping.
Evaluate side-chains
  86 residues out of total 404 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 6
    poor density    : 80
  time to evaluate  : 0.268 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  369 LEU cc_start: 0.7811 (mt) cc_final: 0.7401 (mt)
REVERT: A  378 ASN cc_start: 0.5901 (p0) cc_final: 0.5604 (p0)
REVERT: A  415 ASN cc_start: 0.8091 (m-40) cc_final: 0.7803 (t0)
  outliers start: 6
  outliers final: 4
  residues processed: 84
  average time/residue: 0.1990
  time to fit residues: 20.4689
Evaluate side-chains
  82 residues out of total 404 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 4
    poor density    : 78
  time to evaluate  : 0.222 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  325 ASN
Chi-restraints excluded: chain A residue  338 LEU
Chi-restraints excluded: chain A residue  373 GLN
Chi-restraints excluded: chain B residue  164 CYS
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 50
   random chunks:
   chunk 49 optimal weight:    5.9990
   chunk 20 optimal weight:    1.9990
   chunk 30 optimal weight:    0.0980
   chunk 40 optimal weight:    0.8980
   chunk 45 optimal weight:    3.9990
   chunk 36 optimal weight:    0.8980
   chunk 48 optimal weight:    3.9990
   chunk 18 optimal weight:    0.4980
   chunk 33 optimal weight:    1.9990
   chunk 4 optimal weight:    0.0030
   chunk 3 optimal weight:    0.7980
   overall best weight:    0.4590

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
A 262 HIS
A 329 HIS
** A 373 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 = 0.4680 r_free = 0.4680 target = 0.189596 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 34)----------------|
| r_work = 0.4355 r_free = 0.4355 target = 0.164708 restraints weight = 35527.473|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 34)----------------|
| r_work = 0.4428 r_free = 0.4428 target = 0.170221 restraints weight = 17598.684|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 26)----------------|
| r_work = 0.4472 r_free = 0.4472 target = 0.173665 restraints weight = 10256.715|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 46)----------------|
| r_work = 0.4503 r_free = 0.4503 target = 0.175957 restraints weight = 6765.409|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 35)----------------|
| r_work = 0.4523 r_free = 0.4523 target = 0.177523 restraints weight = 4879.698|
|-----------------------------------------------------------------------------|
r_work (final): 0.4514
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.5207
moved from start:          0.2037

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.042   5233  Z= 0.128
  Angle     :  0.508   7.111   7421  Z= 0.277
  Chirality :  0.037   0.219    898
  Planarity :  0.004   0.038    692
  Dihedral  : 22.544 111.080   1544
  Min Nonbonded Distance : 2.084

Molprobity Statistics.
  All-atom Clashscore : 5.85
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  0.92 %
    Favored  : 99.08 %
  Rotamer:
    Outliers :  2.08 %
    Allowed  : 17.92 %
    Favored  : 80.00 %
  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:  1.43 (0.39), residues: 437
  helix:  2.19 (0.37), residues: 197
  sheet:  0.07 (0.75), residues: 44
  loop : -0.07 (0.40), residues: 196

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG A 337 
 TYR   0.009   0.001   TYR A 562 
 PHE   0.012   0.001   PHE A 462 
 TRP   0.012   0.002   TRP A 509 
 HIS   0.012   0.002   HIS A 260 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00269 /  0.13 ( 5230)
  covalent geometry    : angle       0.50761 /  0.28 ( 7421)
  hydrogen bonds       : bond        0.04619 /  2.97 (  174)
  hydrogen bonds       : angle       4.84592 /  3.47 (  500)
  metal coordination   : bond        0.00223 /  0.11 (    3)

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

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

  874 Ramachandran restraints generated.
    437 Oldfield, 0 Emsley, 437 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  874 Ramachandran restraints generated.
    437 Oldfield, 0 Emsley, 437 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Residue THR  241 is missing expected H atoms. Skipping.
Residue LYS  261 is missing expected H atoms. Skipping.
Residue LYS  270 is missing expected H atoms. Skipping.
Residue LYS  349 is missing expected H atoms. Skipping.
Residue MET  363 is missing expected H atoms. Skipping.
Residue LYS  493 is missing expected H atoms. Skipping.
Residue VAL  506 is missing expected H atoms. Skipping.
Residue LYS  150 is missing expected H atoms. Skipping.
Residue LEU  154 is missing expected H atoms. Skipping.
Residue LYS  159 is missing expected H atoms. Skipping.
Residue MET  170 is missing expected H atoms. Skipping.
Evaluate side-chains
  89 residues out of total 404 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 8
    poor density    : 81
  time to evaluate  : 0.224 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  275 LYS cc_start: 0.6785 (mmmm) cc_final: 0.6502 (mmmm)
REVERT: A  308 LEU cc_start: 0.6555 (tt) cc_final: 0.6043 (tt)
REVERT: A  369 LEU cc_start: 0.7766 (mt) cc_final: 0.7379 (mt)
REVERT: A  415 ASN cc_start: 0.8128 (m-40) cc_final: 0.7849 (t0)
  outliers start: 8
  outliers final: 6
  residues processed: 85
  average time/residue: 0.2139
  time to fit residues: 22.0442
Evaluate side-chains
  87 residues out of total 404 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 6
    poor density    : 81
  time to evaluate  : 0.200 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  299 ILE
Chi-restraints excluded: chain A residue  325 ASN
Chi-restraints excluded: chain A residue  338 LEU
Chi-restraints excluded: chain A residue  367 ASP
Chi-restraints excluded: chain A residue  373 GLN
Chi-restraints excluded: chain A residue  380 ASP
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 50
   random chunks:
   chunk 3 optimal weight:    0.0670
   chunk 1 optimal weight:    0.9980
   chunk 19 optimal weight:    1.9990
   chunk 35 optimal weight:    0.9980
   chunk 8 optimal weight:    0.9980
   chunk 5 optimal weight:    0.6980
   chunk 27 optimal weight:    0.9990
   chunk 41 optimal weight:    1.9990
   chunk 26 optimal weight:    0.4980
   chunk 21 optimal weight:    0.5980
   chunk 25 optimal weight:    0.4980
   overall best weight:    0.4718

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
A 262 HIS
A 329 HIS
A 553 GLN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4670 r_free = 0.4670 target = 0.188241 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 37)----------------|
| r_work = 0.4341 r_free = 0.4341 target = 0.163213 restraints weight = 36450.941|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 35)----------------|
| r_work = 0.4417 r_free = 0.4417 target = 0.168751 restraints weight = 18494.860|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 50)----------------|
| r_work = 0.4461 r_free = 0.4461 target = 0.172316 restraints weight = 10868.691|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 36)----------------|
| r_work = 0.4490 r_free = 0.4490 target = 0.174524 restraints weight = 7138.952|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 51)----------------|
| r_work = 0.4511 r_free = 0.4511 target = 0.176119 restraints weight = 5196.146|
|-----------------------------------------------------------------------------|
r_work (final): 0.4508
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.5280
moved from start:          0.2631

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.064   5233  Z= 0.139
  Angle     :  0.504   6.488   7421  Z= 0.281
  Chirality :  0.038   0.247    898
  Planarity :  0.005   0.045    692
  Dihedral  : 22.492 111.438   1544
  Min Nonbonded Distance : 2.129

Molprobity Statistics.
  All-atom Clashscore : 6.93
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.14 %
    Favored  : 98.86 %
  Rotamer:
    Outliers :  2.08 %
    Allowed  : 17.92 %
    Favored  : 80.00 %
  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:  1.10 (0.38), residues: 437
  helix:  1.81 (0.36), residues: 191
  sheet:  0.04 (0.74), residues: 44
  loop : -0.09 (0.39), residues: 202

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.010   0.001   ARG A 226 
 TYR   0.012   0.001   TYR A 562 
 PHE   0.012   0.001   PHE A 462 
 TRP   0.008   0.001   TRP A 509 
 HIS   0.014   0.002   HIS A 260 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00296 /  0.14 ( 5230)
  covalent geometry    : angle       0.50388 /  0.28 ( 7421)
  hydrogen bonds       : bond        0.04379 /  2.89 (  174)
  hydrogen bonds       : angle       4.78196 /  3.39 (  500)
  metal coordination   : bond        0.00144 /  0.07 (    3)

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

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

  874 Ramachandran restraints generated.
    437 Oldfield, 0 Emsley, 437 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  874 Ramachandran restraints generated.
    437 Oldfield, 0 Emsley, 437 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Residue THR  241 is missing expected H atoms. Skipping.
Residue LYS  261 is missing expected H atoms. Skipping.
Residue LYS  270 is missing expected H atoms. Skipping.
Residue LYS  349 is missing expected H atoms. Skipping.
Residue MET  363 is missing expected H atoms. Skipping.
Residue LYS  493 is missing expected H atoms. Skipping.
Residue VAL  506 is missing expected H atoms. Skipping.
Residue LYS  150 is missing expected H atoms. Skipping.
Residue LEU  154 is missing expected H atoms. Skipping.
Residue LYS  159 is missing expected H atoms. Skipping.
Residue MET  170 is missing expected H atoms. Skipping.
Evaluate side-chains
  87 residues out of total 404 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 8
    poor density    : 79
  time to evaluate  : 0.233 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  275 LYS cc_start: 0.6748 (mmmm) cc_final: 0.6503 (mmmm)
REVERT: A  369 LEU cc_start: 0.7726 (mt) cc_final: 0.7344 (mt)
REVERT: A  415 ASN cc_start: 0.8123 (m-40) cc_final: 0.7839 (t0)
  outliers start: 8
  outliers final: 6
  residues processed: 83
  average time/residue: 0.2200
  time to fit residues: 22.0574
Evaluate side-chains
  86 residues out of total 404 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 6
    poor density    : 80
  time to evaluate  : 0.189 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  325 ASN
Chi-restraints excluded: chain A residue  338 LEU
Chi-restraints excluded: chain A residue  367 ASP
Chi-restraints excluded: chain A residue  373 GLN
Chi-restraints excluded: chain A residue  380 ASP
Chi-restraints excluded: chain A residue  382 PHE
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 50
   random chunks:
   chunk 41 optimal weight:    1.9990
   chunk 8 optimal weight:    0.7980
   chunk 29 optimal weight:    1.9990
   chunk 45 optimal weight:    3.9990
   chunk 39 optimal weight:    0.9980
   chunk 5 optimal weight:    2.9990
   chunk 4 optimal weight:    0.9980
   chunk 30 optimal weight:    0.5980
   chunk 23 optimal weight:    0.7980
   chunk 16 optimal weight:    0.3980
   chunk 25 optimal weight:    0.6980
   overall best weight:    0.6580

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
** A 268 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 = 0.4621 r_free = 0.4621 target = 0.183666 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 42)----------------|
| r_work = 0.4285 r_free = 0.4285 target = 0.158414 restraints weight = 35476.790|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 41)----------------|
| r_work = 0.4360 r_free = 0.4360 target = 0.163910 restraints weight = 17918.914|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 41)----------------|
| r_work = 0.4406 r_free = 0.4406 target = 0.167476 restraints weight = 10546.095|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 42)----------------|
| r_work = 0.4435 r_free = 0.4435 target = 0.169706 restraints weight = 6941.047|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 38)----------------|
| r_work = 0.4454 r_free = 0.4454 target = 0.171168 restraints weight = 5052.537|
|-----------------------------------------------------------------------------|
r_work (final): 0.4450
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.5467
moved from start:          0.3411

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.062   5233  Z= 0.160
  Angle     :  0.525   6.550   7421  Z= 0.292
  Chirality :  0.038   0.220    898
  Planarity :  0.005   0.045    692
  Dihedral  : 22.543 111.701   1544
  Min Nonbonded Distance : 2.199

Molprobity Statistics.
  All-atom Clashscore : 7.25
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.60 %
    Favored  : 98.40 %
  Rotamer:
    Outliers :  2.34 %
    Allowed  : 17.40 %
    Favored  : 80.26 %
  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 (0.38), residues: 437
  helix:  1.48 (0.36), residues: 190
  sheet: -0.26 (0.74), residues: 44
  loop :  0.05 (0.40), residues: 203

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG A 226 
 TYR   0.017   0.002   TYR B 140 
 PHE   0.027   0.002   PHE A 327 
 TRP   0.006   0.002   TRP A 555 
 HIS   0.013   0.002   HIS A 260 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00340 /  0.16 ( 5230)
  covalent geometry    : angle       0.52549 /  0.29 ( 7421)
  hydrogen bonds       : bond        0.04730 /  3.06 (  174)
  hydrogen bonds       : angle       4.86487 /  3.49 (  500)
  metal coordination   : bond        0.00507 /  0.25 (    3)

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

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

  874 Ramachandran restraints generated.
    437 Oldfield, 0 Emsley, 437 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  874 Ramachandran restraints generated.
    437 Oldfield, 0 Emsley, 437 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Residue THR  241 is missing expected H atoms. Skipping.
Residue LYS  261 is missing expected H atoms. Skipping.
Residue LYS  270 is missing expected H atoms. Skipping.
Residue LYS  349 is missing expected H atoms. Skipping.
Residue MET  363 is missing expected H atoms. Skipping.
Residue LYS  493 is missing expected H atoms. Skipping.
Residue VAL  506 is missing expected H atoms. Skipping.
Residue LYS  150 is missing expected H atoms. Skipping.
Residue LEU  154 is missing expected H atoms. Skipping.
Residue LYS  159 is missing expected H atoms. Skipping.
Residue MET  170 is missing expected H atoms. Skipping.
Evaluate side-chains
  87 residues out of total 404 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 9
    poor density    : 78
  time to evaluate  : 0.223 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  312 ASN cc_start: 0.8483 (m110) cc_final: 0.8166 (m110)
REVERT: A  327 PHE cc_start: 0.7317 (m-80) cc_final: 0.6943 (m-80)
REVERT: A  369 LEU cc_start: 0.7821 (mt) cc_final: 0.7459 (mt)
REVERT: A  374 GLU cc_start: 0.7818 (tm-30) cc_final: 0.7490 (tm-30)
REVERT: A  415 ASN cc_start: 0.7939 (m-40) cc_final: 0.7711 (t0)
  outliers start: 9
  outliers final: 7
  residues processed: 83
  average time/residue: 0.2259
  time to fit residues: 22.4660
Evaluate side-chains
  80 residues out of total 404 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 7
    poor density    : 73
  time to evaluate  : 0.226 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  308 LEU
Chi-restraints excluded: chain A residue  325 ASN
Chi-restraints excluded: chain A residue  338 LEU
Chi-restraints excluded: chain A residue  367 ASP
Chi-restraints excluded: chain A residue  373 GLN
Chi-restraints excluded: chain A residue  380 ASP
Chi-restraints excluded: chain A residue  382 PHE
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 50
   random chunks:
   chunk 39 optimal weight:    0.7980
   chunk 16 optimal weight:    0.9980
   chunk 32 optimal weight:    0.0970
   chunk 4 optimal weight:    5.9990
   chunk 29 optimal weight:    0.0040
   chunk 34 optimal weight:    0.0980
   chunk 11 optimal weight:    0.6980
   chunk 43 optimal weight:    0.4980
   chunk 42 optimal weight:    0.0870
   chunk 19 optimal weight:    1.9990
   chunk 44 optimal weight:    4.9990
   overall best weight:    0.1568

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
A 354 ASN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4644 r_free = 0.4644 target = 0.185703 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 33)----------------|
| r_work = 0.4315 r_free = 0.4315 target = 0.160789 restraints weight = 35827.547|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 33)----------------|
| r_work = 0.4389 r_free = 0.4389 target = 0.166241 restraints weight = 18207.401|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 44)----------------|
| r_work = 0.4435 r_free = 0.4435 target = 0.169811 restraints weight = 10763.578|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 38)----------------|
| r_work = 0.4465 r_free = 0.4465 target = 0.172057 restraints weight = 7096.890|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 44)----------------|
| r_work = 0.4484 r_free = 0.4484 target = 0.173532 restraints weight = 5163.672|
|-----------------------------------------------------------------------------|
r_work (final): 0.4479
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.5405
moved from start:          0.3487

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.033   5233  Z= 0.101
  Angle     :  0.476   6.288   7421  Z= 0.263
  Chirality :  0.036   0.227    898
  Planarity :  0.005   0.041    692
  Dihedral  : 22.485 111.645   1544
  Min Nonbonded Distance : 2.399

Molprobity Statistics.
  All-atom Clashscore : 5.63
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.37 %
    Favored  : 98.63 %
  Rotamer:
    Outliers :  2.08 %
    Allowed  : 18.70 %
    Favored  : 79.22 %
  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:  1.27 (0.38), residues: 437
  helix:  1.86 (0.36), residues: 191
  sheet:  0.13 (0.86), residues: 37
  loop :  0.10 (0.40), residues: 209

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG A 623 
 TYR   0.011   0.001   TYR A 626 
 PHE   0.014   0.001   PHE A 462 
 TRP   0.007   0.001   TRP A 555 
 HIS   0.007   0.001   HIS A 262 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00212 /  0.10 ( 5230)
  covalent geometry    : angle       0.47606 /  0.26 ( 7421)
  hydrogen bonds       : bond        0.04170 /  2.70 (  174)
  hydrogen bonds       : angle       4.56324 /  3.27 (  500)
  metal coordination   : bond        0.00581 /  0.29 (    3)

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

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

  874 Ramachandran restraints generated.
    437 Oldfield, 0 Emsley, 437 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  874 Ramachandran restraints generated.
    437 Oldfield, 0 Emsley, 437 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Residue THR  241 is missing expected H atoms. Skipping.
Residue LYS  261 is missing expected H atoms. Skipping.
Residue LYS  270 is missing expected H atoms. Skipping.
Residue LYS  349 is missing expected H atoms. Skipping.
Residue MET  363 is missing expected H atoms. Skipping.
Residue LYS  493 is missing expected H atoms. Skipping.
Residue VAL  506 is missing expected H atoms. Skipping.
Residue LYS  150 is missing expected H atoms. Skipping.
Residue LEU  154 is missing expected H atoms. Skipping.
Residue LYS  159 is missing expected H atoms. Skipping.
Residue MET  170 is missing expected H atoms. Skipping.
Evaluate side-chains
  84 residues out of total 404 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 8
    poor density    : 76
  time to evaluate  : 0.157 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  245 THR cc_start: 0.6364 (OUTLIER) cc_final: 0.5956 (m)
REVERT: A  316 ARG cc_start: 0.8220 (ttm170) cc_final: 0.7986 (ttm170)
REVERT: A  327 PHE cc_start: 0.7239 (m-80) cc_final: 0.6910 (m-80)
REVERT: A  369 LEU cc_start: 0.7705 (mt) cc_final: 0.7337 (mt)
REVERT: A  374 GLU cc_start: 0.7637 (tm-30) cc_final: 0.7406 (tm-30)
REVERT: A  415 ASN cc_start: 0.7900 (m-40) cc_final: 0.7678 (t0)
  outliers start: 8
  outliers final: 6
  residues processed: 79
  average time/residue: 0.2177
  time to fit residues: 20.7702
Evaluate side-chains
  82 residues out of total 404 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 7
    poor density    : 75
  time to evaluate  : 0.295 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  245 THR
Chi-restraints excluded: chain A residue  308 LEU
Chi-restraints excluded: chain A residue  325 ASN
Chi-restraints excluded: chain A residue  367 ASP
Chi-restraints excluded: chain A residue  373 GLN
Chi-restraints excluded: chain A residue  380 ASP
Chi-restraints excluded: chain A residue  382 PHE
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 50
   random chunks:
   chunk 28 optimal weight:    1.9990
   chunk 34 optimal weight:    0.8980
   chunk 38 optimal weight:    0.9990
   chunk 6 optimal weight:    0.9990
   chunk 35 optimal weight:    0.8980
   chunk 29 optimal weight:    0.5980
   chunk 46 optimal weight:    4.9990
   chunk 30 optimal weight:    0.9980
   chunk 23 optimal weight:    0.0870
   chunk 49 optimal weight:    4.9990
   chunk 19 optimal weight:    1.9990
   overall best weight:    0.6958

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
** A 268 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
A 471 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4586 r_free = 0.4586 target = 0.180482 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 37)----------------|
| r_work = 0.4240 r_free = 0.4240 target = 0.154879 restraints weight = 35811.050|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 33)----------------|
| r_work = 0.4315 r_free = 0.4315 target = 0.160360 restraints weight = 18383.829|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 44)----------------|
| r_work = 0.4364 r_free = 0.4364 target = 0.163996 restraints weight = 10909.391|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 42)----------------|
| r_work = 0.4395 r_free = 0.4395 target = 0.166268 restraints weight = 7236.858|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 30)----------------|
| r_work = 0.4410 r_free = 0.4410 target = 0.167519 restraints weight = 5275.041|
|-----------------------------------------------------------------------------|
r_work (final): 0.4405
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.5614
moved from start:          0.4224

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.044   5233  Z= 0.170
  Angle     :  0.552   6.632   7421  Z= 0.305
  Chirality :  0.039   0.220    898
  Planarity :  0.005   0.048    692
  Dihedral  : 22.579 111.558   1542
  Min Nonbonded Distance : 2.340

Molprobity Statistics.
  All-atom Clashscore : 10.61
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.06 %
    Favored  : 97.94 %
  Rotamer:
    Outliers :  2.08 %
    Allowed  : 18.70 %
    Favored  : 79.22 %
  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 (0.38), residues: 437
  helix:  1.58 (0.36), residues: 190
  sheet: -0.61 (0.73), residues: 48
  loop : -0.02 (0.42), residues: 199

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.007   0.001   ARG A 583 
 TYR   0.019   0.002   TYR A 626 
 PHE   0.018   0.002   PHE A 327 
 TRP   0.009   0.002   TRP A 443 
 HIS   0.010   0.002   HIS A 260 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00356 /  0.17 ( 5230)
  covalent geometry    : angle       0.55240 /  0.31 ( 7421)
  hydrogen bonds       : bond        0.04893 /  3.18 (  174)
  hydrogen bonds       : angle       4.71337 /  3.37 (  500)
  metal coordination   : bond        0.00909 /  0.44 (    3)

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

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

  874 Ramachandran restraints generated.
    437 Oldfield, 0 Emsley, 437 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  874 Ramachandran restraints generated.
    437 Oldfield, 0 Emsley, 437 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Residue THR  241 is missing expected H atoms. Skipping.
Residue LYS  261 is missing expected H atoms. Skipping.
Residue LYS  270 is missing expected H atoms. Skipping.
Residue LYS  349 is missing expected H atoms. Skipping.
Residue MET  363 is missing expected H atoms. Skipping.
Residue LYS  493 is missing expected H atoms. Skipping.
Residue VAL  506 is missing expected H atoms. Skipping.
Residue LYS  150 is missing expected H atoms. Skipping.
Residue LEU  154 is missing expected H atoms. Skipping.
Residue LYS  159 is missing expected H atoms. Skipping.
Residue MET  170 is missing expected H atoms. Skipping.
Evaluate side-chains
  82 residues out of total 404 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 8
    poor density    : 74
  time to evaluate  : 0.213 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  316 ARG cc_start: 0.8196 (ttm170) cc_final: 0.7934 (ttm170)
REVERT: A  369 LEU cc_start: 0.7955 (mt) cc_final: 0.7622 (mt)
  outliers start: 8
  outliers final: 5
  residues processed: 79
  average time/residue: 0.2372
  time to fit residues: 22.3855
Evaluate side-chains
  78 residues out of total 404 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 5
    poor density    : 73
  time to evaluate  : 0.209 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  308 LEU
Chi-restraints excluded: chain A residue  325 ASN
Chi-restraints excluded: chain A residue  367 ASP
Chi-restraints excluded: chain A residue  373 GLN
Chi-restraints excluded: chain A residue  380 ASP
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 50
   random chunks:
   chunk 0 optimal weight:    5.9990
   chunk 5 optimal weight:    2.9990
   chunk 35 optimal weight:    0.5980
   chunk 45 optimal weight:    3.9990
   chunk 17 optimal weight:    0.9990
   chunk 22 optimal weight:    0.9980
   chunk 23 optimal weight:    0.7980
   chunk 9 optimal weight:    0.9980
   chunk 31 optimal weight:    0.4980
   chunk 39 optimal weight:    0.9980
   chunk 14 optimal weight:    0.5980
   overall best weight:    0.6980

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
** A 268 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 = 0.4590 r_free = 0.4590 target = 0.180542 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.4247 r_free = 0.4247 target = 0.155316 restraints weight = 35556.822|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 32)----------------|
| r_work = 0.4323 r_free = 0.4323 target = 0.160763 restraints weight = 18171.607|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 51)----------------|
| r_work = 0.4372 r_free = 0.4372 target = 0.164361 restraints weight = 10804.894|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 39)----------------|
| r_work = 0.4402 r_free = 0.4402 target = 0.166610 restraints weight = 7140.258|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 27)----------------|
| r_work = 0.4421 r_free = 0.4421 target = 0.168038 restraints weight = 5207.556|
|-----------------------------------------------------------------------------|
r_work (final): 0.4409
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.5622
moved from start:          0.4517

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.030   5233  Z= 0.138
  Angle     :  0.504   6.549   7421  Z= 0.280
  Chirality :  0.037   0.233    898
  Planarity :  0.005   0.043    692
  Dihedral  : 22.605 111.842   1542
  Min Nonbonded Distance : 2.379

Molprobity Statistics.
  All-atom Clashscore : 8.23
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.52 %
    Favored  : 97.48 %
  Rotamer:
    Outliers :  2.08 %
    Allowed  : 19.22 %
    Favored  : 78.70 %
  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:  0.82 (0.39), residues: 437
  helix:  1.66 (0.36), residues: 190
  sheet: -0.60 (0.74), residues: 47
  loop : -0.18 (0.42), residues: 200

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG A 226 
 TYR   0.014   0.002   TYR A 626 
 PHE   0.016   0.001   PHE A 462 
 TRP   0.008   0.002   TRP A 555 
 HIS   0.010   0.001   HIS A 262 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00292 /  0.14 ( 5230)
  covalent geometry    : angle       0.50404 /  0.28 ( 7421)
  hydrogen bonds       : bond        0.04445 /  2.90 (  174)
  hydrogen bonds       : angle       4.67163 /  3.33 (  500)
  metal coordination   : bond        0.01402 /  0.70 (    3)

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

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

  874 Ramachandran restraints generated.
    437 Oldfield, 0 Emsley, 437 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  874 Ramachandran restraints generated.
    437 Oldfield, 0 Emsley, 437 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Residue THR  241 is missing expected H atoms. Skipping.
Residue LYS  261 is missing expected H atoms. Skipping.
Residue LYS  270 is missing expected H atoms. Skipping.
Residue LYS  349 is missing expected H atoms. Skipping.
Residue MET  363 is missing expected H atoms. Skipping.
Residue LYS  493 is missing expected H atoms. Skipping.
Residue VAL  506 is missing expected H atoms. Skipping.
Residue LYS  150 is missing expected H atoms. Skipping.
Residue LEU  154 is missing expected H atoms. Skipping.
Residue LYS  159 is missing expected H atoms. Skipping.
Residue MET  170 is missing expected H atoms. Skipping.
Evaluate side-chains
  81 residues out of total 404 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 8
    poor density    : 73
  time to evaluate  : 0.215 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  316 ARG cc_start: 0.8212 (ttm170) cc_final: 0.7938 (ttm170)
REVERT: A  369 LEU cc_start: 0.7968 (mt) cc_final: 0.7634 (mt)
  outliers start: 8
  outliers final: 6
  residues processed: 76
  average time/residue: 0.2519
  time to fit residues: 22.6699
Evaluate side-chains
  78 residues out of total 404 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 6
    poor density    : 72
  time to evaluate  : 0.243 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  308 LEU
Chi-restraints excluded: chain A residue  325 ASN
Chi-restraints excluded: chain A residue  367 ASP
Chi-restraints excluded: chain A residue  373 GLN
Chi-restraints excluded: chain A residue  380 ASP
Chi-restraints excluded: chain A residue  407 CYS
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 50
   random chunks:
   chunk 46 optimal weight:    4.9990
   chunk 37 optimal weight:    0.5980
   chunk 27 optimal weight:    0.9980
   chunk 15 optimal weight:    0.7980
   chunk 35 optimal weight:    0.9980
   chunk 39 optimal weight:    0.9980
   chunk 4 optimal weight:    2.9990
   chunk 36 optimal weight:    0.8980
   chunk 2 optimal weight:    0.5980
   chunk 0 optimal weight:    5.9990
   chunk 44 optimal weight:    6.9990
   overall best weight:    0.7780

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
** A 268 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 = 0.4539 r_free = 0.4539 target = 0.176727 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.4198 r_free = 0.4198 target = 0.151512 restraints weight = 34350.031|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 39)----------------|
| r_work = 0.4275 r_free = 0.4275 target = 0.157095 restraints weight = 17233.052|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 38)----------------|
| r_work = 0.4323 r_free = 0.4323 target = 0.160663 restraints weight = 10060.478|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 45)----------------|
| r_work = 0.4353 r_free = 0.4353 target = 0.162905 restraints weight = 6581.056|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 43)----------------|
| r_work = 0.4374 r_free = 0.4374 target = 0.164437 restraints weight = 4764.923|
|-----------------------------------------------------------------------------|
r_work (final): 0.4367
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.5729
moved from start:          0.5120

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.044   5233  Z= 0.180
  Angle     :  0.550   7.233   7421  Z= 0.305
  Chirality :  0.039   0.227    898
  Planarity :  0.005   0.045    692
  Dihedral  : 22.655 112.018   1542
  Min Nonbonded Distance : 2.378

Molprobity Statistics.
  All-atom Clashscore : 11.80
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.20 %
    Favored  : 96.80 %
  Rotamer:
    Outliers :  2.08 %
    Allowed  : 20.26 %
    Favored  : 77.66 %
  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:  0.59 (0.39), residues: 437
  helix:  1.57 (0.36), residues: 190
  sheet: -0.83 (0.73), residues: 47
  loop : -0.39 (0.43), residues: 200

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.001   ARG A 226 
 TYR   0.016   0.002   TYR A 626 
 PHE   0.018   0.002   PHE A 327 
 TRP   0.009   0.002   TRP A 443 
 HIS   0.010   0.001   HIS A 262 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00379 /  0.18 ( 5230)
  covalent geometry    : angle       0.55050 /  0.30 ( 7421)
  hydrogen bonds       : bond        0.04804 /  3.14 (  174)
  hydrogen bonds       : angle       4.80805 /  3.41 (  500)
  metal coordination   : bond        0.01014 /  0.53 (    3)

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

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

  874 Ramachandran restraints generated.
    437 Oldfield, 0 Emsley, 437 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  874 Ramachandran restraints generated.
    437 Oldfield, 0 Emsley, 437 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Residue THR  241 is missing expected H atoms. Skipping.
Residue LYS  261 is missing expected H atoms. Skipping.
Residue LYS  270 is missing expected H atoms. Skipping.
Residue LYS  349 is missing expected H atoms. Skipping.
Residue MET  363 is missing expected H atoms. Skipping.
Residue LYS  493 is missing expected H atoms. Skipping.
Residue VAL  506 is missing expected H atoms. Skipping.
Residue LYS  150 is missing expected H atoms. Skipping.
Residue LEU  154 is missing expected H atoms. Skipping.
Residue LYS  159 is missing expected H atoms. Skipping.
Residue MET  170 is missing expected H atoms. Skipping.
Evaluate side-chains
  84 residues out of total 404 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 8
    poor density    : 76
  time to evaluate  : 0.220 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
  outliers start: 8
  outliers final: 7
  residues processed: 80
  average time/residue: 0.2376
  time to fit residues: 22.6756
Evaluate side-chains
  79 residues out of total 404 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 7
    poor density    : 72
  time to evaluate  : 0.218 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  308 LEU
Chi-restraints excluded: chain A residue  325 ASN
Chi-restraints excluded: chain A residue  338 LEU
Chi-restraints excluded: chain A residue  367 ASP
Chi-restraints excluded: chain A residue  373 GLN
Chi-restraints excluded: chain A residue  380 ASP
Chi-restraints excluded: chain A residue  407 CYS
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 50
   random chunks:
   chunk 19 optimal weight:    1.9990
   chunk 9 optimal weight:    0.9980
   chunk 34 optimal weight:    0.1980
   chunk 6 optimal weight:    0.9990
   chunk 16 optimal weight:    0.4980
   chunk 8 optimal weight:    0.0980
   chunk 15 optimal weight:    0.1980
   chunk 36 optimal weight:    0.9990
   chunk 40 optimal weight:    0.4980
   chunk 41 optimal weight:    0.9990
   chunk 7 optimal weight:    0.0980
   overall best weight:    0.2180

-------------------------------------------------------------------------------
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 = 0.4587 r_free = 0.4587 target = 0.180146 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 37)----------------|
| r_work = 0.4250 r_free = 0.4250 target = 0.155056 restraints weight = 34777.076|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 35)----------------|
| r_work = 0.4327 r_free = 0.4327 target = 0.160617 restraints weight = 17813.231|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 44)----------------|
| r_work = 0.4373 r_free = 0.4373 target = 0.164181 restraints weight = 10531.896|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 43)----------------|
| r_work = 0.4403 r_free = 0.4403 target = 0.166398 restraints weight = 6939.627|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 29)----------------|
| r_work = 0.4423 r_free = 0.4423 target = 0.167938 restraints weight = 5060.387|
|-----------------------------------------------------------------------------|
r_work (final): 0.4416
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.5657
moved from start:          0.5115

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.033   5233  Z= 0.106
  Angle     :  0.496   6.556   7421  Z= 0.273
  Chirality :  0.037   0.245    898
  Planarity :  0.006   0.084    692
  Dihedral  : 22.574 111.724   1542
  Min Nonbonded Distance : 2.401

Molprobity Statistics.
  All-atom Clashscore : 7.79
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.97 %
    Favored  : 97.03 %
  Rotamer:
    Outliers :  1.30 %
    Allowed  : 21.56 %
    Favored  : 77.14 %
  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 (0.39), residues: 437
  helix:  1.85 (0.36), residues: 190
  sheet: -0.90 (0.71), residues: 47
  loop : -0.17 (0.44), residues: 200

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.010   0.001   ARG A 441 
 TYR   0.016   0.002   TYR A 626 
 PHE   0.018   0.001   PHE A 462 
 TRP   0.011   0.001   TRP A 555 
 HIS   0.009   0.001   HIS A 262 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00232 /  0.11 ( 5230)
  covalent geometry    : angle       0.49571 /  0.27 ( 7421)
  hydrogen bonds       : bond        0.04244 /  2.77 (  174)
  hydrogen bonds       : angle       4.51617 /  3.23 (  500)
  metal coordination   : bond        0.00253 /  0.12 (    3)

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

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

  874 Ramachandran restraints generated.
    437 Oldfield, 0 Emsley, 437 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  874 Ramachandran restraints generated.
    437 Oldfield, 0 Emsley, 437 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Residue THR  241 is missing expected H atoms. Skipping.
Residue LYS  261 is missing expected H atoms. Skipping.
Residue LYS  270 is missing expected H atoms. Skipping.
Residue LYS  349 is missing expected H atoms. Skipping.
Residue MET  363 is missing expected H atoms. Skipping.
Residue LYS  493 is missing expected H atoms. Skipping.
Residue VAL  506 is missing expected H atoms. Skipping.
Residue LYS  150 is missing expected H atoms. Skipping.
Residue LEU  154 is missing expected H atoms. Skipping.
Residue LYS  159 is missing expected H atoms. Skipping.
Residue MET  170 is missing expected H atoms. Skipping.
Evaluate side-chains
  75 residues out of total 404 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 5
    poor density    : 70
  time to evaluate  : 0.217 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  316 ARG cc_start: 0.8223 (ttm170) cc_final: 0.7919 (ttm170)
  outliers start: 5
  outliers final: 5
  residues processed: 72
  average time/residue: 0.2374
  time to fit residues: 20.3627
Evaluate side-chains
  75 residues out of total 404 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 5
    poor density    : 70
  time to evaluate  : 0.213 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  308 LEU
Chi-restraints excluded: chain A residue  325 ASN
Chi-restraints excluded: chain A residue  338 LEU
Chi-restraints excluded: chain A residue  367 ASP
Chi-restraints excluded: chain A residue  380 ASP
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 50
   random chunks:
   chunk 19 optimal weight:    0.5980
   chunk 48 optimal weight:    3.9990
   chunk 36 optimal weight:    0.0980
   chunk 39 optimal weight:    1.9990
   chunk 14 optimal weight:    0.9980
   chunk 6 optimal weight:    0.9980
   chunk 25 optimal weight:    0.6980
   chunk 7 optimal weight:    0.7980
   chunk 28 optimal weight:    1.9990
   chunk 11 optimal weight:    0.5980
   chunk 47 optimal weight:    3.9990
   overall best weight:    0.5580

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
** A 268 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 = 0.4555 r_free = 0.4555 target = 0.177757 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 38)----------------|
| r_work = 0.4215 r_free = 0.4215 target = 0.152581 restraints weight = 33737.465|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 32)----------------|
| r_work = 0.4290 r_free = 0.4290 target = 0.158092 restraints weight = 16956.907|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 31)----------------|
| r_work = 0.4338 r_free = 0.4338 target = 0.161639 restraints weight = 9960.786|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 43)----------------|
| r_work = 0.4368 r_free = 0.4368 target = 0.163873 restraints weight = 6556.179|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 39)----------------|
| r_work = 0.4387 r_free = 0.4387 target = 0.165390 restraints weight = 4758.820|
|-----------------------------------------------------------------------------|
r_work (final): 0.4387
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.5720
moved from start:          0.5399

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.035   5233  Z= 0.145
  Angle     :  0.507   6.653   7421  Z= 0.280
  Chirality :  0.037   0.239    898
  Planarity :  0.006   0.081    692
  Dihedral  : 22.556 111.508   1539
  Min Nonbonded Distance : 2.406

Molprobity Statistics.
  All-atom Clashscore : 10.07
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.75 %
    Favored  : 97.25 %
  Rotamer:
    Outliers :  1.30 %
    Allowed  : 21.56 %
    Favored  : 77.14 %
  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:  0.81 (0.39), residues: 437
  helix:  1.80 (0.36), residues: 190
  sheet: -0.96 (0.70), residues: 47
  loop : -0.25 (0.44), residues: 200

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.009   0.001   ARG A 441 
 TYR   0.016   0.002   TYR A 626 
 PHE   0.015   0.002   PHE A 327 
 TRP   0.009   0.002   TRP A 555 
 HIS   0.010   0.001   HIS A 262 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00307 /  0.15 ( 5230)
  covalent geometry    : angle       0.50715 /  0.28 ( 7421)
  hydrogen bonds       : bond        0.04412 /  2.90 (  174)
  hydrogen bonds       : angle       4.57650 /  3.27 (  500)
  metal coordination   : bond        0.00554 /  0.27 (    3)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 2441.59 seconds
wall clock time: 42 minutes 17.69 seconds (2537.69 seconds total)