Starting phenix.real_space_refine
on Thu Mar 13 22:02:38 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/8ops_17086/03_2025/8ops_17086.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/8ops_17086/03_2025/8ops_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_17086/03_2025/8ops_17086.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/8ops_17086/03_2025/8ops_17086.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/8ops_17086/03_2025/8ops_17086.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/8ops_17086/03_2025/8ops_17086.cif"
  }
  resolution = 3.82
  write_initial_geo_file = False
  refinement {
    macro_cycles = 10
  }
  qi {
    qm_restraints {
      package {
        program = *test
      }
    }
  }


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): 0.01s

  Monomer Library directory:
    "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5624/modules/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: {'GLU:plan': 2, 'HIS:plan': 1, 'ASN:plan1': 1, 'ARG:plan': 1, 'ASP:plan': 2}
          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: 5.99, per 1000 atoms: 0.65
  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: 2.59
  Conformation dependent library (CDL) restraints added in 501.4 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: 4.30
  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: 3.63

  Time building geometry restraints manager: 3.14 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=" 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
  bond pdb=" CG  PRO B 158 "
       pdb=" CD  PRO B 158 "
    ideal  model  delta    sigma   weight residual
    1.503  1.472  0.031 3.40e-02 8.65e+02 8.11e-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:             3.210
  Set stop_for_unknowns flag:              0.000
  Assert model is a single copy model:     0.000
  Assert all atoms have isotropic ADPs:    0.010
  Construct map_model_manager:             0.140
  Extract box with map and model:          0.320
  Check model and map are aligned:         0.060
  Set scattering table:                    0.080
  Process input model:                     32.050
  Find NCS groups from input model:        0.080
  Set up NCS constraints:                  0.040
  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:2.950
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   38.940
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.5130
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   5230  Z= 0.176
  Angle     :  0.568   9.044   7421  Z= 0.301
  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 (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  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
 TRP   0.035   0.003   TRP A 509 
 HIS   0.013   0.002   HIS A 260 
 PHE   0.021   0.001   PHE A 469 
 TYR   0.009   0.001   TYR A 626 
 ARG   0.006   0.000   ARG A 316 

*********************** 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  : 0.542 
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: 0.3983
  time to fit residues: 43.7694
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  : 0.542 
-------------------------------------------------------------------------------
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 42 optimal weight:    0.4980
   chunk 37 optimal weight:    0.8980
   chunk 21 optimal weight:    0.8980
   chunk 12 optimal weight:    0.8980
   chunk 25 optimal weight:    0.6980
   chunk 20 optimal weight:    2.9990
   chunk 39 optimal weight:    0.9980
   chunk 15 optimal weight:    0.8980
   chunk 23 optimal weight:    0.2980
   chunk 29 optimal weight:    0.0970
   chunk 45 optimal weight:    2.9990
   overall best weight:    0.4978

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

Flipped N/Q/H residues before XYZ refinement:
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 = 0.4690 r_free = 0.4690 target = 0.190737 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 37)----------------|
| r_work = 0.4370 r_free = 0.4370 target = 0.165781 restraints weight = 35683.369|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 42)----------------|
| r_work = 0.4443 r_free = 0.4443 target = 0.171446 restraints weight = 17956.631|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 49)----------------|
| r_work = 0.4488 r_free = 0.4488 target = 0.174895 restraints weight = 10480.986|
|-----------------------------------------------------------------------------|
r_work (final): 0.4475
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.5357
moved from start:          0.1625

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.034   5230  Z= 0.200
  Angle     :  0.555   7.259   7421  Z= 0.296
  Chirality :  0.038   0.211    898
  Planarity :  0.005   0.047    692
  Dihedral  : 22.554 110.712   1544
  Min Nonbonded Distance : 2.121

Molprobity Statistics.
  All-atom Clashscore : 6.49
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  0.23 %
    Favored  : 99.77 %
  Rotamer:
    Outliers :  2.34 %
    Allowed  : 17.66 %
    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 (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.88 (0.38), residues: 437
  helix:  2.45 (0.37), residues: 197
  sheet:  0.63 (0.84), residues: 34
  loop :  0.21 (0.39), residues: 206

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.014   0.002   TRP A 509 
 HIS   0.006   0.001   HIS A 262 
 PHE   0.012   0.001   PHE A 440 
 TYR   0.014   0.002   TYR A 562 
 ARG   0.005   0.001   ARG A 321 

*********************** 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
  89 residues out of total 404 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 9
    poor density    : 80
  time to evaluate  : 0.646 
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  369 LEU cc_start: 0.7841 (mt) cc_final: 0.7438 (mt)
REVERT: A  378 ASN cc_start: 0.5831 (p0) cc_final: 0.5582 (p0)
REVERT: A  415 ASN cc_start: 0.8101 (m-40) cc_final: 0.7826 (t0)
  outliers start: 9
  outliers final: 5
  residues processed: 85
  average time/residue: 0.4516
  time to fit residues: 46.9323
Evaluate side-chains
  85 residues out of total 404 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 5
    poor density    : 80
  time to evaluate  : 0.607 
-------------------------------------------------------------------------------
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 A residue  380 ASP
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 25 optimal weight:    0.0000
   chunk 21 optimal weight:    0.2980
   chunk 18 optimal weight:    2.9990
   chunk 26 optimal weight:    0.9980
   chunk 2 optimal weight:    0.6980
   chunk 22 optimal weight:    0.5980
   chunk 37 optimal weight:    0.4980
   chunk 23 optimal weight:    0.0980
   chunk 15 optimal weight:    0.0870
   chunk 43 optimal weight:    0.9980
   chunk 14 optimal weight:    0.0980
   overall best weight:    0.1162

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

Flipped N/Q/H residues before XYZ refinement:
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 = 0.4707 r_free = 0.4707 target = 0.191818 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 40)----------------|
| r_work = 0.4396 r_free = 0.4396 target = 0.167287 restraints weight = 36198.565|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 36)----------------|
| r_work = 0.4465 r_free = 0.4465 target = 0.172673 restraints weight = 17926.697|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 40)----------------|
| r_work = 0.4508 r_free = 0.4508 target = 0.176140 restraints weight = 10416.137|
|-----------------------------------------------------------------------------|
r_work (final): 0.4503
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.5314
moved from start:          0.2107

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.020   5230  Z= 0.129
  Angle     :  0.494   6.577   7421  Z= 0.259
  Chirality :  0.036   0.219    898
  Planarity :  0.004   0.044    692
  Dihedral  : 22.425 111.317   1544
  Min Nonbonded Distance : 2.095

Molprobity Statistics.
  All-atom Clashscore : 5.30
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.14 %
    Favored  : 98.86 %
  Rotamer:
    Outliers :  1.30 %
    Allowed  : 17.92 %
    Favored  : 80.78 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.80 (0.39), residues: 437
  helix:  2.54 (0.37), residues: 197
  sheet:  0.09 (0.75), residues: 44
  loop :  0.11 (0.40), residues: 196

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.011   0.001   TRP A 509 
 HIS   0.012   0.002   HIS A 260 
 PHE   0.011   0.001   PHE A 462 
 TYR   0.008   0.001   TYR A 626 
 ARG   0.002   0.000   ARG A 441 

*********************** 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
  87 residues out of total 404 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 5
    poor density    : 82
  time to evaluate  : 0.636 
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: 0.6780 (mmmm) cc_final: 0.6514 (mmmm)
REVERT: A  369 LEU cc_start: 0.7714 (mt) cc_final: 0.7325 (mt)
REVERT: A  415 ASN cc_start: 0.8122 (m-40) cc_final: 0.7835 (t0)
  outliers start: 5
  outliers final: 4
  residues processed: 84
  average time/residue: 0.5304
  time to fit residues: 53.5698
Evaluate side-chains
  81 residues out of total 404 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 4
    poor density    : 77
  time to evaluate  : 1.344 
-------------------------------------------------------------------------------
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 A residue  382 PHE
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 50
   random chunks:
   chunk 28 optimal weight:    2.9990
   chunk 48 optimal weight:    2.9990
   chunk 1 optimal weight:    0.9980
   chunk 3 optimal weight:    0.7980
   chunk 2 optimal weight:    0.9990
   chunk 16 optimal weight:    0.3980
   chunk 32 optimal weight:    0.5980
   chunk 14 optimal weight:    0.9990
   chunk 45 optimal weight:    2.9990
   chunk 12 optimal weight:    1.9990
   chunk 30 optimal weight:    0.9980
   overall best weight:    0.7580

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

Flipped N/Q/H residues before XYZ refinement:
** A 268 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
A 291 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4611 r_free = 0.4611 target = 0.183037 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.4276 r_free = 0.4276 target = 0.157840 restraints weight = 35406.301|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 35)----------------|
| r_work = 0.4350 r_free = 0.4350 target = 0.163251 restraints weight = 17998.834|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 42)----------------|
| r_work = 0.4396 r_free = 0.4396 target = 0.166773 restraints weight = 10615.821|
|-----------------------------------------------------------------------------|
r_work (final): 0.4387
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.5678
moved from start:          0.3389

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.052   5230  Z= 0.264
  Angle     :  0.613   7.730   7421  Z= 0.326
  Chirality :  0.040   0.200    898
  Planarity :  0.005   0.049    692
  Dihedral  : 22.563 111.094   1544
  Min Nonbonded Distance : 2.249

Molprobity Statistics.
  All-atom Clashscore : 11.47
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  0.92 %
    Favored  : 99.08 %
  Rotamer:
    Outliers :  2.86 %
    Allowed  : 17.92 %
    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 (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.99 (0.37), residues: 437
  helix:  1.54 (0.36), residues: 190
  sheet: -0.12 (0.83), residues: 37
  loop :  0.07 (0.39), residues: 210

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.011   0.003   TRP A 555 
 HIS   0.015   0.002   HIS A 260 
 PHE   0.011   0.002   PHE B 163 
 TYR   0.016   0.002   TYR A 562 
 ARG   0.006   0.001   ARG A 623 

*********************** 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
  88 residues out of total 404 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 77
  time to evaluate  : 1.272 
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  312 ASN cc_start: 0.8460 (m110) cc_final: 0.8193 (m110)
REVERT: A  369 LEU cc_start: 0.7976 (mt) cc_final: 0.7603 (mt)
REVERT: A  415 ASN cc_start: 0.8093 (m-40) cc_final: 0.7886 (t0)
  outliers start: 11
  outliers final: 8
  residues processed: 83
  average time/residue: 0.6470
  time to fit residues: 66.6039
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  : 0.689 
-------------------------------------------------------------------------------
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
Chi-restraints excluded: chain A residue  382 PHE
Chi-restraints excluded: chain B residue  169 HIS
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 50
   random chunks:
   chunk 42 optimal weight:    0.0040
   chunk 4 optimal weight:    5.9990
   chunk 24 optimal weight:    0.0070
   chunk 30 optimal weight:    1.9990
   chunk 33 optimal weight:    1.9990
   chunk 21 optimal weight:    0.9990
   chunk 8 optimal weight:    0.2980
   chunk 15 optimal weight:    0.9980
   chunk 48 optimal weight:    1.9990
   chunk 27 optimal weight:    0.6980
   chunk 14 optimal weight:    0.2980
   overall best weight:    0.2610

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

Flipped N/Q/H residues before XYZ refinement:
A 354 ASN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4640 r_free = 0.4640 target = 0.185397 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 43)----------------|
| r_work = 0.4311 r_free = 0.4311 target = 0.160343 restraints weight = 35587.394|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 40)----------------|
| r_work = 0.4383 r_free = 0.4383 target = 0.165780 restraints weight = 18082.304|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 29)----------------|
| r_work = 0.4429 r_free = 0.4429 target = 0.169347 restraints weight = 10668.871|
|-----------------------------------------------------------------------------|
r_work (final): 0.4420
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.5608
moved from start:          0.3532

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.031   5230  Z= 0.140
  Angle     :  0.502   5.688   7421  Z= 0.266
  Chirality :  0.036   0.228    898
  Planarity :  0.004   0.044    692
  Dihedral  : 22.480 111.486   1544
  Min Nonbonded Distance : 2.403

Molprobity Statistics.
  All-atom Clashscore : 6.49
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  0.46 %
    Favored  : 99.54 %
  Rotamer:
    Outliers :  2.34 %
    Allowed  : 18.44 %
    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 (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.38 (0.39), residues: 437
  helix:  2.13 (0.38), residues: 191
  sheet: -0.26 (0.77), residues: 43
  loop :  0.08 (0.41), residues: 203

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.008   0.001   TRP A 555 
 HIS   0.009   0.001   HIS A 260 
 PHE   0.016   0.001   PHE A 462 
 TYR   0.008   0.001   TYR A 626 
 ARG   0.003   0.000   ARG A 226 

*********************** 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
  82 residues out of total 404 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 9
    poor density    : 73
  time to evaluate  : 0.697 
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  312 ASN cc_start: 0.8509 (m110) cc_final: 0.8242 (m110)
REVERT: A  369 LEU cc_start: 0.7885 (mt) cc_final: 0.7515 (mt)
REVERT: A  374 GLU cc_start: 0.7653 (tm-30) cc_final: 0.7372 (tm-30)
  outliers start: 9
  outliers final: 6
  residues processed: 77
  average time/residue: 0.4857
  time to fit residues: 45.7022
Evaluate side-chains
  79 residues out of total 404 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 6
    poor density    : 73
  time to evaluate  : 0.570 
-------------------------------------------------------------------------------
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  382 PHE
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 50
   random chunks:
   chunk 12 optimal weight:    0.9990
   chunk 9 optimal weight:    1.9990
   chunk 29 optimal weight:    2.9990
   chunk 31 optimal weight:    0.9980
   chunk 2 optimal weight:    1.9990
   chunk 37 optimal weight:    0.4980
   chunk 1 optimal weight:    0.3980
   chunk 43 optimal weight:    1.9990
   chunk 20 optimal weight:    2.9990
   chunk 27 optimal weight:    0.8980
   chunk 0 optimal weight:    4.9990
   overall best weight:    0.7582

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

Flipped N/Q/H residues before XYZ refinement:
A 262 HIS
** A 268 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 471 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 = 0.4565 r_free = 0.4565 target = 0.178220 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 38)----------------|
| r_work = 0.4217 r_free = 0.4217 target = 0.152661 restraints weight = 34918.820|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 26)----------------|
| r_work = 0.4293 r_free = 0.4293 target = 0.158108 restraints weight = 17950.906|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 44)----------------|
| r_work = 0.4341 r_free = 0.4341 target = 0.161719 restraints weight = 10703.515|
|-----------------------------------------------------------------------------|
r_work (final): 0.4334
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.5871
moved from start:          0.4608

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.047   5230  Z= 0.278
  Angle     :  0.597   6.402   7421  Z= 0.321
  Chirality :  0.040   0.213    898
  Planarity :  0.005   0.049    692
  Dihedral  : 22.648 111.352   1542
  Min Nonbonded Distance : 2.331

Molprobity Statistics.
  All-atom Clashscore : 13.10
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.97 %
    Favored  : 97.03 %
  Rotamer:
    Outliers :  1.82 %
    Allowed  : 20.00 %
    Favored  : 78.18 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.79 (0.38), residues: 437
  helix:  1.49 (0.37), residues: 190
  sheet: -0.32 (0.83), residues: 38
  loop : -0.13 (0.40), residues: 209

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.010   0.003   TRP A 555 
 HIS   0.006   0.001   HIS A 268 
 PHE   0.020   0.002   PHE B 163 
 TYR   0.019   0.003   TYR A 626 
 ARG   0.006   0.001   ARG A 583 

*********************** 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
  82 residues out of total 404 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 7
    poor density    : 75
  time to evaluate  : 0.677 
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  312 ASN cc_start: 0.8503 (m110) cc_final: 0.8258 (m110)
REVERT: A  369 LEU cc_start: 0.8035 (mt) cc_final: 0.7824 (mt)
  outliers start: 7
  outliers final: 7
  residues processed: 80
  average time/residue: 0.6254
  time to fit residues: 59.3448
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  : 0.576 
-------------------------------------------------------------------------------
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 B residue  142 CYS
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 50
   random chunks:
   chunk 22 optimal weight:    0.9980
   chunk 13 optimal weight:    1.9990
   chunk 1 optimal weight:    0.9980
   chunk 17 optimal weight:    0.9990
   chunk 25 optimal weight:    0.1980
   chunk 19 optimal weight:    0.9990
   chunk 15 optimal weight:    0.5980
   chunk 47 optimal weight:    2.9990
   chunk 5 optimal weight:    0.4980
   chunk 29 optimal weight:    0.5980
   chunk 31 optimal weight:    0.6980
   overall best weight:    0.5180

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

Flipped N/Q/H residues before XYZ refinement:
A 471 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4583 r_free = 0.4583 target = 0.180113 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 53)----------------|
| r_work = 0.4239 r_free = 0.4239 target = 0.154660 restraints weight = 34932.625|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 35)----------------|
| r_work = 0.4314 r_free = 0.4314 target = 0.160191 restraints weight = 17940.104|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 47)----------------|
| r_work = 0.4361 r_free = 0.4361 target = 0.163766 restraints weight = 10609.652|
|-----------------------------------------------------------------------------|
r_work (final): 0.4357
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.5832
moved from start:          0.4886

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.025   5230  Z= 0.166
  Angle     :  0.512   6.080   7421  Z= 0.272
  Chirality :  0.036   0.235    898
  Planarity :  0.004   0.044    692
  Dihedral  : 22.559 111.730   1542
  Min Nonbonded Distance : 2.407

Molprobity Statistics.
  All-atom Clashscore : 8.01
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.83 %
    Favored  : 98.17 %
  Rotamer:
    Outliers :  1.30 %
    Allowed  : 21.04 %
    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 (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.99 (0.40), residues: 437
  helix:  1.96 (0.38), residues: 190
  sheet: -0.89 (0.69), residues: 47
  loop : -0.18 (0.42), residues: 200

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.010   0.002   TRP A 555 
 HIS   0.004   0.001   HIS A 262 
 PHE   0.019   0.001   PHE A 462 
 TYR   0.010   0.002   TYR A 626 
 ARG   0.003   0.000   ARG A 226 

*********************** 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
  78 residues out of total 404 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 5
    poor density    : 73
  time to evaluate  : 0.536 
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  369 LEU cc_start: 0.8009 (mt) cc_final: 0.7801 (mt)
  outliers start: 5
  outliers final: 4
  residues processed: 74
  average time/residue: 0.5423
  time to fit residues: 47.3901
Evaluate side-chains
  74 residues out of total 404 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 4
    poor density    : 70
  time to evaluate  : 0.556 
-------------------------------------------------------------------------------
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  380 ASP
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 50
   random chunks:
   chunk 3 optimal weight:    2.9990
   chunk 45 optimal weight:    2.9990
   chunk 47 optimal weight:    2.9990
   chunk 34 optimal weight:    0.7980
   chunk 35 optimal weight:    0.6980
   chunk 29 optimal weight:    0.9980
   chunk 16 optimal weight:    0.9990
   chunk 42 optimal weight:    0.0370
   chunk 28 optimal weight:    2.9990
   chunk 5 optimal weight:    1.9990
   chunk 18 optimal weight:    2.9990
   overall best weight:    0.7060

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

Flipped N/Q/H residues before XYZ refinement:
** 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 = 0.4534 r_free = 0.4534 target = 0.175604 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 41)----------------|
| r_work = 0.4178 r_free = 0.4178 target = 0.149930 restraints weight = 34816.278|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 34)----------------|
| r_work = 0.4256 r_free = 0.4256 target = 0.155601 restraints weight = 17587.539|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 35)----------------|
| r_work = 0.4305 r_free = 0.4305 target = 0.159254 restraints weight = 10291.439|
|-----------------------------------------------------------------------------|
r_work (final): 0.4300
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.5968
moved from start:          0.5595

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.047   5230  Z= 0.244
  Angle     :  0.561   6.445   7421  Z= 0.301
  Chirality :  0.038   0.226    898
  Planarity :  0.005   0.045    692
  Dihedral  : 22.634 111.190   1539
  Min Nonbonded Distance : 2.381

Molprobity Statistics.
  All-atom Clashscore : 12.67
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.20 %
    Favored  : 96.80 %
  Rotamer:
    Outliers :  2.08 %
    Allowed  : 21.30 %
    Favored  : 76.62 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.66 (0.39), residues: 437
  helix:  1.69 (0.37), residues: 190
  sheet: -1.15 (0.66), residues: 47
  loop : -0.32 (0.42), residues: 200

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.010   0.002   TRP A 555 
 HIS   0.009   0.001   HIS A 262 
 PHE   0.015   0.002   PHE A 462 
 TYR   0.017   0.002   TYR A 626 
 ARG   0.003   0.000   ARG A 583 

*********************** 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
  79 residues out of total 404 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 8
    poor density    : 71
  time to evaluate  : 0.590 
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  591 LYS cc_start: 0.7572 (tptp) cc_final: 0.7352 (tptp)
  outliers start: 8
  outliers final: 7
  residues processed: 76
  average time/residue: 0.5262
  time to fit residues: 47.6457
Evaluate side-chains
  76 residues out of total 404 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 7
    poor density    : 69
  time to evaluate  : 0.772 
-------------------------------------------------------------------------------
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  407 CYS
Chi-restraints excluded: chain B residue  142 CYS
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 50
   random chunks:
   chunk 44 optimal weight:    2.9990
   chunk 10 optimal weight:    0.9990
   chunk 6 optimal weight:    0.9980
   chunk 3 optimal weight:    0.8980
   chunk 46 optimal weight:    2.9990
   chunk 23 optimal weight:    0.0970
   chunk 38 optimal weight:    0.9990
   chunk 35 optimal weight:    0.0470
   chunk 28 optimal weight:    0.8980
   chunk 12 optimal weight:    0.9980
   chunk 37 optimal weight:    0.0980
   overall best weight:    0.4076

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4561 r_free = 0.4561 target = 0.178086 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 54)----------------|
| r_work = 0.4208 r_free = 0.4208 target = 0.152372 restraints weight = 35149.510|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 33)----------------|
| r_work = 0.4285 r_free = 0.4285 target = 0.158019 restraints weight = 17984.601|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 45)----------------|
| r_work = 0.4334 r_free = 0.4334 target = 0.161663 restraints weight = 10613.953|
|-----------------------------------------------------------------------------|
r_work (final): 0.4330
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.5920
moved from start:          0.5727

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.042   5230  Z= 0.162
  Angle     :  0.511   6.317   7421  Z= 0.272
  Chirality :  0.036   0.242    898
  Planarity :  0.006   0.093    692
  Dihedral  : 22.533 111.240   1539
  Min Nonbonded Distance : 2.388

Molprobity Statistics.
  All-atom Clashscore : 8.55
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.52 %
    Favored  : 97.48 %
  Rotamer:
    Outliers :  1.04 %
    Allowed  : 23.90 %
    Favored  : 75.06 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.92 (0.40), residues: 437
  helix:  2.00 (0.38), residues: 190
  sheet: -1.24 (0.64), residues: 46
  loop : -0.24 (0.43), residues: 201

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.012   0.002   TRP A 555 
 HIS   0.007   0.001   HIS A 262 
 PHE   0.022   0.002   PHE A 327 
 TYR   0.014   0.002   TYR A 626 
 ARG   0.010   0.001   ARG A 441 

*********************** 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
  75 residues out of total 404 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 4
    poor density    : 71
  time to evaluate  : 1.059 
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  219 GLN cc_start: 0.6294 (tm-30) cc_final: 0.5438 (tt0)
REVERT: A  591 LYS cc_start: 0.7538 (tptp) cc_final: 0.7318 (tptp)
  outliers start: 4
  outliers final: 4
  residues processed: 71
  average time/residue: 0.5896
  time to fit residues: 48.9048
Evaluate side-chains
  74 residues out of total 404 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 4
    poor density    : 70
  time to evaluate  : 0.567 
-------------------------------------------------------------------------------
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  380 ASP
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 50
   random chunks:
   chunk 34 optimal weight:    0.9980
   chunk 15 optimal weight:    0.0370
   chunk 2 optimal weight:    0.9990
   chunk 32 optimal weight:    0.0770
   chunk 17 optimal weight:    0.6980
   chunk 30 optimal weight:    1.9990
   chunk 19 optimal weight:    0.9980
   chunk 25 optimal weight:    0.3980
   chunk 44 optimal weight:    2.9990
   chunk 42 optimal weight:    0.9980
   chunk 41 optimal weight:    3.9990
   overall best weight:    0.4416

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4554 r_free = 0.4554 target = 0.177302 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 46)----------------|
| r_work = 0.4206 r_free = 0.4206 target = 0.151981 restraints weight = 35187.326|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 44)----------------|
| r_work = 0.4281 r_free = 0.4281 target = 0.157450 restraints weight = 17992.057|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 54)----------------|
| r_work = 0.4330 r_free = 0.4330 target = 0.160966 restraints weight = 10667.595|
|-----------------------------------------------------------------------------|
r_work (final): 0.4327
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.5938
moved from start:          0.5958

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.035   5230  Z= 0.184
  Angle     :  0.526   6.500   7421  Z= 0.282
  Chirality :  0.036   0.241    898
  Planarity :  0.008   0.146    692
  Dihedral  : 22.507 111.103   1539
  Min Nonbonded Distance : 2.276

Molprobity Statistics.
  All-atom Clashscore : 9.63
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.75 %
    Favored  : 97.25 %
  Rotamer:
    Outliers :  1.56 %
    Allowed  : 23.90 %
    Favored  : 74.55 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.83 (0.40), residues: 437
  helix:  1.89 (0.38), residues: 190
  sheet: -1.25 (0.65), residues: 46
  loop : -0.25 (0.43), residues: 201

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.011   0.002   TRP A 555 
 HIS   0.007   0.001   HIS A 262 
 PHE   0.020   0.002   PHE A 327 
 TYR   0.020   0.002   TYR A 562 
 ARG   0.009   0.001   ARG A 441 

********************** 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
  80 residues out of total 404 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 6
    poor density    : 74
  time to evaluate  : 0.932 
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: 6
  outliers final: 5
  residues processed: 76
  average time/residue: 0.5576
  time to fit residues: 50.0088
Evaluate side-chains
  74 residues out of total 404 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 5
    poor density    : 69
  time to evaluate  : 0.646 
-------------------------------------------------------------------------------
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  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 46 optimal weight:    2.9990
   chunk 19 optimal weight:    0.3980
   chunk 29 optimal weight:    0.9980
   chunk 47 optimal weight:    2.9990
   chunk 14 optimal weight:    0.5980
   chunk 32 optimal weight:    0.8980
   chunk 4 optimal weight:    2.9990
   chunk 12 optimal weight:    0.2980
   chunk 6 optimal weight:    1.9990
   chunk 39 optimal weight:    0.9990
   chunk 7 optimal weight:    0.6980
   overall best weight:    0.5780

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4538 r_free = 0.4538 target = 0.176086 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 35)----------------|
| r_work = 0.4185 r_free = 0.4185 target = 0.150423 restraints weight = 33656.682|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 32)----------------|
| r_work = 0.4263 r_free = 0.4263 target = 0.156012 restraints weight = 17170.088|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 54)----------------|
| r_work = 0.4315 r_free = 0.4315 target = 0.159642 restraints weight = 10123.529|
|-----------------------------------------------------------------------------|
r_work (final): 0.4313
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.5980
moved from start:          0.6287

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.039   5230  Z= 0.202
  Angle     :  0.534   6.384   7421  Z= 0.286
  Chirality :  0.037   0.243    898
  Planarity :  0.007   0.093    692
  Dihedral  : 22.551 110.914   1539
  Min Nonbonded Distance : 2.414

Molprobity Statistics.
  All-atom Clashscore : 10.61
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.97 %
    Favored  : 97.03 %
  Rotamer:
    Outliers :  1.30 %
    Allowed  : 24.42 %
    Favored  : 74.29 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.75 (0.40), residues: 437
  helix:  1.83 (0.38), residues: 190
  sheet: -1.36 (0.66), residues: 46
  loop : -0.29 (0.44), residues: 201

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.008   0.002   TRP A 555 
 HIS   0.007   0.001   HIS A 262 
 PHE   0.016   0.002   PHE A 327 
 TYR   0.018   0.002   TYR A 562 
 ARG   0.030   0.001   ARG A 623 
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 4983.48 seconds
wall clock time: 87 minutes 53.74 seconds (5273.74 seconds total)