Starting phenix.real_space_refine
on Tue Aug  4 14:23:45 2026 by dcliebschner
===============================================================================

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

  Found model, restraint, /net/cci-nas-00/data/ceres_data/8b6z_15893/08_2026/8b6z_15893.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/8b6z_15893/08_2026/8b6z_15893.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=2.9
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    model {
      file = "/net/cci-nas-00/data/ceres_data/8b6z_15893/08_2026/8b6z_15893.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/8b6z_15893/08_2026/8b6z_15893.cif"
    real_map_files = "/net/cci-nas-00/data/ceres_data/8b6z_15893/08_2026/8b6z_15893.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/8b6z_15893/08_2026/8b6z_15893.map"
    restraint_files = "/net/cci-nas-00/data/ceres_data/8b6z_15893/08_2026/8b6z_15893.cif"
    default_restraint = "/net/cci-nas-00/data/ceres_data/8b6z_15893/08_2026/8b6z_15893.cif"
  }
  resolution = 2.9
  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=   0.007
Set stop_for_unknowns flag
  Set to: True
Assert model is a single copy model
Assert all atoms have isotropic ADPs
Construct map_model_manager
Extract box with map and model
Check model and map are aligned
Set scattering table
  Set to: electron
  Number of scattering types: 5
    Type Number    sf(0)   Gaussians
     P       8      5.49       5
     S      16      5.16       5
     C    2240      2.51       5
     N     624      2.21       5
     O     693      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 1 residue(s): 0.00s

  Monomer Library directory:
    "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.2rc3-6140/lib/python3.11/site-packages/chem_data/mon_lib"
  Total number of atoms: 3581
  Number of models: 1
  Model: ""
    Number of chains: 2
    Chain: "A"
      Number of atoms: 3406
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 442, 3406
          Classifications: {'peptide': 442}
          Link IDs: {'PCIS': 2, 'PTRANS': 24, 'TRANS': 415}
    Chain: "B"
      Number of atoms: 175
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 8, 175
          Classifications: {'RNAv2': 8}
          Modifications used: {'rna3p_pur': 6, 'rna3p_pyr': 2}
          Link IDs: {'rna3p': 7}
  Residues with excluded nonbonded symmetry interactions: 1
    residue:
      pdb=" N   GLY A  50 " occ=0.00
      ... (2 atoms not shown)
      pdb=" O   GLY A  50 " occ=0.00
  Time building chain proxies: 0.90, per 1000 atoms: 0.25
  Number of scatterers: 3581
  At special positions: 0
  Unit cell: (65.934, 93.906, 67.932, 90, 90, 90)
  Space group: P 1 (No. 1)
  Number of sites at special positions: 0
  Number of scattering types: 5
    Type Number    sf(0)
     S      16     16.00
     P       8     15.00
     O     693      8.00
     N     624      7.00
     C    2240      6.00
    sf(0) = scattering factor at diffraction angle 0.

  Number of disulfides: simple=0, symmetry=0

  Automatic linking
    Parameters for automatic linking
      Linking & cutoffs
        Metal                : Auto  - 3.00
        Amino acid           : True  - 1.90
        Carbohydrate         : True  - 1.99
        Ligands              : True  - 1.99
        Small molecules      : False - 1.98
        Amino acid - RNA/DNA : False
      
  Number of custom bonds: simple=0, symmetry=0
  Time building additional restraints: 0.21
  Conformation dependent library (CDL) restraints added in 77.3 milliseconds
  

  880 Ramachandran restraints generated.
    440 Oldfield, 0 Emsley, 440 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  806

  Finding SS restraints...
    Secondary structure from input PDB file:
      11 helices and 5 sheets defined
      25.1% alpha, 33.3% beta
      1 base pairs and 4 stacking pairs defined.
    Time for finding SS restraints: 0.25
  Creating SS restraints...
    Processing helix  chain 'A' and resid 19 through 32
    Processing helix  chain 'A' and resid 35 through 50
    Processing helix  chain 'A' and resid 57 through 66
    Processing helix  chain 'A' and resid 97 through 105
    Processing helix  chain 'A' and resid 121 through 127
      removed outlier: 3.703A  pdb=" N   ILE A 127 " --> pdb=" O   PHE A 123 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 132 through 144
    Processing helix  chain 'A' and resid 154 through 158
      removed outlier: 3.836A  pdb=" N   SER A 157 " --> pdb=" O   LYS A 154 " (cutoff:3.500A)
      removed outlier: 3.701A  pdb=" N   THR A 158 " --> pdb=" O   MET A 155 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'A' and resid 154 through 158'
    Processing helix  chain 'A' and resid 163 through 182
      removed outlier: 3.601A  pdb=" N   TYR A 177 " --> pdb=" O   GLU A 173 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 184 through 188
    Processing helix  chain 'A' and resid 227 through 234
      removed outlier: 3.715A  pdb=" N   ALA A 231 " --> pdb=" O   SER A 227 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 418 through 421
    Processing sheet with id=AA1, first strand: chain 'A' and resid 79 through 81
      removed outlier: 6.557A  pdb=" N   ILE A   8 " --> pdb=" O   THR A  88 " (cutoff:3.500A)
      removed outlier: 7.069A  pdb=" N   ILE A  90 " --> pdb=" O   ILE A   8 " (cutoff:3.500A)
      removed outlier: 7.749A  pdb=" N   ILE A  10 " --> pdb=" O   ILE A  90 " (cutoff:3.500A)
      removed outlier: 8.782A  pdb=" N   CYS A 111 " --> pdb=" O   HIS A   7 " (cutoff:3.500A)
      removed outlier: 6.439A  pdb=" N   ASN A   9 " --> pdb=" O   CYS A 111 " (cutoff:3.500A)
      removed outlier: 7.652A  pdb=" N   VAL A 113 " --> pdb=" O   ASN A   9 " (cutoff:3.500A)
      removed outlier: 6.719A  pdb=" N   VAL A  11 " --> pdb=" O   VAL A 113 " (cutoff:3.500A)
      removed outlier: 7.513A  pdb=" N   ILE A 115 " --> pdb=" O   VAL A  11 " (cutoff:3.500A)
      removed outlier: 7.084A  pdb=" N   ILE A  13 " --> pdb=" O   ILE A 115 " (cutoff:3.500A)
      removed outlier: 8.207A  pdb=" N   ALA A 117 " --> pdb=" O   ILE A  13 " (cutoff:3.500A)
      removed outlier: 3.656A  pdb=" N   VAL A 191 " --> pdb=" O   VAL A 150 " (cutoff:3.500A)
    Processing sheet with id=AA2, first strand: chain 'A' and resid 214 through 216
    Processing sheet with id=AA3, first strand: chain 'A' and resid 247 through 249
      removed outlier: 6.659A  pdb=" N   ASN A 311 " --> pdb=" O   LYS A 290 " (cutoff:3.500A)
      removed outlier: 5.119A  pdb=" N   VAL A 292 " --> pdb=" O   GLY A 309 " (cutoff:3.500A)
      removed outlier: 7.009A  pdb=" N   GLY A 309 " --> pdb=" O   VAL A 292 " (cutoff:3.500A)
      removed outlier: 6.329A  pdb=" N   MET A 294 " --> pdb=" O   ASN A 307 " (cutoff:3.500A)
      removed outlier: 9.275A  pdb=" N   ASN A 307 " --> pdb=" O   MET A 294 " (cutoff:3.500A)
      removed outlier: 4.478A  pdb=" N   THR A 261 " --> pdb=" O   VAL A 312 " (cutoff:3.500A)
    Processing sheet with id=AA4, first strand: chain 'A' and resid 247 through 249
    Processing sheet with id=AA5, first strand: chain 'A' and resid 386 through 389
      removed outlier: 6.610A  pdb=" N   ALA A 373 " --> pdb=" O   VAL A 405 " (cutoff:3.500A)
      removed outlier: 7.959A  pdb=" N   VAL A 405 " --> pdb=" O   ALA A 373 " (cutoff:3.500A)
      removed outlier: 5.998A  pdb=" N   LEU A 375 " --> pdb=" O   GLU A 403 " (cutoff:3.500A)
      removed outlier: 7.207A  pdb=" N   GLU A 403 " --> pdb=" O   LEU A 375 " (cutoff:3.500A)
      removed outlier: 7.723A  pdb=" N   ALA A 338 " --> pdb=" O   PRO A 406 " (cutoff:3.500A)
      removed outlier: 3.708A  pdb=" N   GLN A 339 " --> pdb=" O   GLU A 442 " (cutoff:3.500A)
      removed outlier: 6.394A  pdb=" N   GLN A 343 " --> pdb=" O   ILE A 438 " (cutoff:3.500A)
      removed outlier: 5.515A  pdb=" N   ILE A 438 " --> pdb=" O   GLN A 343 " (cutoff:3.500A)
      removed outlier: 7.244A  pdb=" N   ILE A 345 " --> pdb=" O   GLY A 436 " (cutoff:3.500A)
      removed outlier: 5.617A  pdb=" N   GLY A 436 " --> pdb=" O   ILE A 345 " (cutoff:3.500A)
      removed outlier: 5.061A  pdb=" N   THR A 432 " --> pdb=" O   ASP A 428 " (cutoff:3.500A)
      removed outlier: 6.500A  pdb=" N   ASP A 428 " --> pdb=" O   THR A 432 " (cutoff:3.500A)
      removed outlier: 3.812A  pdb=" N   VAL A 360 " --> pdb=" O   ARG A 427 " (cutoff:3.500A)

    136 hydrogen bonds defined for protein.
    366 hydrogen bond angles defined for protein.
    Restraints generated for nucleic acids:
      2 hydrogen bonds
      4 hydrogen bond angles
      0 basepair planarities
      1 basepair parallelities
      4 stacking parallelities
  Total time for adding SS restraints: 0.34

  Time building geometry restraints manager: 0.29 seconds

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

  Histogram of bond lengths:
        1.22 -     1.34: 1126
        1.34 -     1.46: 522
        1.46 -     1.57: 1984
        1.57 -     1.69: 15
        1.69 -     1.81: 26
  Bond restraints: 3673
  Sorted by residual:
  bond pdb=" C   ILE A 235 "
       pdb=" N   LEU A 236 "
    ideal  model  delta    sigma   weight residual
    1.327  1.339 -0.012 1.39e-02 5.18e+03 7.88e-01
  bond pdb=" N   VAL A 152 "
       pdb=" CA  VAL A 152 "
    ideal  model  delta    sigma   weight residual
    1.465  1.476 -0.011 1.38e-02 5.25e+03 5.94e-01
  bond pdb=" CA  GLY A 351 "
       pdb=" C   GLY A 351 "
    ideal  model  delta    sigma   weight residual
    1.514  1.505  0.010 1.41e-02 5.03e+03 4.55e-01
  bond pdb=" CA  HIS A 364 "
       pdb=" CB  HIS A 364 "
    ideal  model  delta    sigma   weight residual
    1.530  1.541 -0.011 1.69e-02 3.50e+03 4.23e-01
  bond pdb=" C   LYS A 165 "
       pdb=" O   LYS A 165 "
    ideal  model  delta    sigma   weight residual
    1.236  1.228  0.008 1.26e-02 6.30e+03 4.09e-01
  ... (remaining 3668 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     1.47: 4896
        1.47 -     2.93: 90
        2.93 -     4.40: 20
        4.40 -     5.86: 1
        5.86 -     7.33: 1
  Bond angle restraints: 5008
  Sorted by residual:
  angle pdb=" N   GLY A 182 "
        pdb=" CA  GLY A 182 "
        pdb=" C   GLY A 182 "
      ideal   model   delta    sigma   weight residual
     113.18  120.51   -7.33 2.37e+00 1.78e-01 9.56e+00
  angle pdb=" N   SER A 157 "
        pdb=" CA  SER A 157 "
        pdb=" C   SER A 157 "
      ideal   model   delta    sigma   weight residual
     112.88  115.26   -2.38 1.29e+00 6.01e-01 3.40e+00
  angle pdb=" CB  LYS A 172 "
        pdb=" CG  LYS A 172 "
        pdb=" CD  LYS A 172 "
      ideal   model   delta    sigma   weight residual
     111.30  115.15   -3.85 2.30e+00 1.89e-01 2.80e+00
  angle pdb=" CA  GLY A 182 "
        pdb=" C   GLY A 182 "
        pdb=" N   TYR A 183 "
      ideal   model   delta    sigma   weight residual
     116.69  119.99   -3.30 2.04e+00 2.40e-01 2.62e+00
  angle pdb=" N   ASN A 200 "
        pdb=" CA  ASN A 200 "
        pdb=" CB  ASN A 200 "
      ideal   model   delta    sigma   weight residual
     113.15  110.58    2.57 1.63e+00 3.76e-01 2.48e+00
  ... (remaining 5003 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    17.77: 2100
       17.77 -    35.54: 78
       35.54 -    53.31: 27
       53.31 -    71.07: 4
       71.07 -    88.84: 1
  Dihedral angle restraints: 2210
    sinusoidal: 951
      harmonic: 1259
  Sorted by residual:
  dihedral pdb=" O5'   A B4607 "
           pdb=" C5'   A B4607 "
           pdb=" C4'   A B4607 "
           pdb=" C3'   A B4607 "
      ideal   model   delta sinusoidal    sigma   weight residual
     180.00  128.51   51.49     3      6.40e+00 2.44e-02 4.95e+01
  dihedral pdb=" O5'   A B4602 "
           pdb=" C5'   A B4602 "
           pdb=" C4'   A B4602 "
           pdb=" C3'   A B4602 "
      ideal   model   delta sinusoidal    sigma   weight residual
     180.00  148.83   31.17     3      6.40e+00 2.44e-02 2.76e+01
  dihedral pdb=" CA  VAL A 152 "
           pdb=" C   VAL A 152 "
           pdb=" N   ASN A 153 "
           pdb=" CA  ASN A 153 "
      ideal   model   delta  harmonic     sigma   weight residual
    -180.00 -161.01  -18.99     0      5.00e+00 4.00e-02 1.44e+01
  ... (remaining 2207 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.048: 436
       0.048 -    0.095: 81
       0.095 -    0.143: 44
       0.143 -    0.191: 0
       0.191 -    0.238: 8
  Chirality restraints: 569
  Sorted by residual:
  chirality pdb=" P     C B4603 "
            pdb=" OP1   C B4603 "
            pdb=" OP2   C B4603 "
            pdb=" O5'   C B4603 "
    both_signs  ideal   model   delta    sigma   weight residual
      True       2.17   -2.41   -0.24 2.00e-01 2.50e+01 1.42e+00
  chirality pdb=" P     A B4602 "
            pdb=" OP1   A B4602 "
            pdb=" OP2   A B4602 "
            pdb=" O5'   A B4602 "
    both_signs  ideal   model   delta    sigma   weight residual
      True       2.17   -2.41   -0.24 2.00e-01 2.50e+01 1.42e+00
  chirality pdb=" P     G B4604 "
            pdb=" OP1   G B4604 "
            pdb=" OP2   G B4604 "
            pdb=" O5'   G B4604 "
    both_signs  ideal   model   delta    sigma   weight residual
      True       2.17   -2.41   -0.23 2.00e-01 2.50e+01 1.35e+00
  ... (remaining 566 not shown)

  Planarity restraints: 613
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   PRO A 419 "    0.027 5.00e-02 4.00e+02   4.10e-02 2.69e+00
        pdb=" N   PRO A 420 "   -0.071 5.00e-02 4.00e+02
        pdb=" CA  PRO A 420 "    0.021 5.00e-02 4.00e+02
        pdb=" CD  PRO A 420 "    0.023 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   TYR A 418 "   -0.021 5.00e-02 4.00e+02   3.26e-02 1.70e+00
        pdb=" N   PRO A 419 "    0.056 5.00e-02 4.00e+02
        pdb=" CA  PRO A 419 "   -0.017 5.00e-02 4.00e+02
        pdb=" CD  PRO A 419 "   -0.018 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   SER A 358 "    0.016 5.00e-02 4.00e+02   2.43e-02 9.41e-01
        pdb=" N   PRO A 359 "   -0.042 5.00e-02 4.00e+02
        pdb=" CA  PRO A 359 "    0.013 5.00e-02 4.00e+02
        pdb=" CD  PRO A 359 "    0.013 5.00e-02 4.00e+02
  ... (remaining 610 not shown)

  Histogram of nonbonded interaction distances:
        2.29 -     2.81: 924
        2.81 -     3.33: 3215
        3.33 -     3.85: 5926
        3.85 -     4.38: 6908
        4.38 -     4.90: 11870
  Nonbonded interactions: 28843
  Sorted by model distance:
  nonbonded pdb=" OD2 ASP A  74 "
            pdb=" OG  SER A  76 "
     model   vdw
     2.286 3.040
  nonbonded pdb=" O   ALA A 231 "
            pdb=" OG1 THR A 234 "
     model   vdw
     2.388 3.040
  nonbonded pdb=" O   VAL A 277 "
            pdb=" OG  SER A 329 "
     model   vdw
     2.390 3.040
  nonbonded pdb=" OH  TYR A  29 "
            pdb=" NE1 TRP A  58 "
     model   vdw
     2.391 3.120
  nonbonded pdb=" OE2 GLU A  68 "
            pdb=" N   ARG A  96 "
     model   vdw
     2.413 3.120
  ... (remaining 28838 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=0.00 max=1.00 mean=0.70
Load rotamer database and sin/cos tables
Set ADP refinement strategy
  ADPs will be refined as individual isotropic
Make a string to write initial .geo file
Internal consistency checks
Time:
  Set random seed:                         0.000
  Set model cs if undefined:               0.000
  Decide on map wrapping:                  0.000
  Normalize map: mean=0, sd=1:             6.870
  Set stop_for_unknowns flag:              0.000
  Assert model is a single copy model:     0.000
  Assert all atoms have isotropic ADPs:    0.000
  Construct map_model_manager:             0.000
  Extract box with map and model:          0.040
  Check model and map are aligned:         0.000
  Set scattering table:                    0.010
  Process input model:                     4.340
  Find NCS groups from input model:        0.010
  Set up NCS constraints:                  0.010
  Set refine NCS operators:                0.000
  Adjust number of macro_cycles:           0.000
  Reset NCS operators:                     0.000
  Extract rigid body selections:           0.000
  Check and reset occupancies:             0.000
  Load rotamer database and sin/cos tables:4.990
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   16.270
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.5551
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      :  0.002   0.023   3673  Z= 0.111
  Angle     :  0.533   7.329   5008  Z= 0.277
  Chirality :  0.052   0.238    569
  Planarity :  0.004   0.041    613
  Dihedral  : 11.141  88.842   1404
  Min Nonbonded Distance : 2.286

Molprobity Statistics.
  All-atom Clashscore : 0.59
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.36 %
    Favored  : 98.64 %
  Rotamer:
    Outliers :  0.27 %
    Allowed  :  2.14 %
    Favored  : 97.59 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 7.69 %
    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: -0.69 (0.37), residues: 440
  helix: -0.07 (0.48), residues: 93
  sheet: -0.11 (0.60), residues: 83
  loop : -0.67 (0.35), residues: 264

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG A 134 
 TYR   0.012   0.002   TYR A 167 
 PHE   0.005   0.001   PHE A 123 
 TRP   0.004   0.001   TRP A  78 
 HIS   0.005   0.001   HIS A 364 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00228 /  0.11 ( 3673)
  covalent geometry    : angle       0.53266 /  0.28 ( 5008)
  hydrogen bonds       : bond        0.21255 / 15.44 (  128)
  hydrogen bonds       : angle       8.23571 /  5.98 (  370)

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

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

  880 Ramachandran restraints generated.
    440 Oldfield, 0 Emsley, 440 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  880 Ramachandran restraints generated.
    440 Oldfield, 0 Emsley, 440 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  70 residues out of total 373 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 69
  time to evaluate  : 0.117 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   82 THR cc_start: 0.6986 (p) cc_final: 0.5496 (t)
REVERT: A  243 ASP cc_start: 0.5976 (m-30) cc_final: 0.5723 (t0)
REVERT: A  254 TYR cc_start: 0.4476 (m-80) cc_final: 0.4154 (m-80)
  outliers start: 1
  outliers final: 0
  residues processed: 70
  average time/residue: 0.5064
  time to fit residues: 36.3675
Evaluate side-chains
  34 residues out of total 373 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 34
  time to evaluate  : 0.079 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 44
   random chunks:
   chunk 24 optimal weight:   20.0000
   chunk 26 optimal weight:    8.9990
   chunk 2 optimal weight:    3.9990
   chunk 16 optimal weight:   30.0000
   chunk 32 optimal weight:    6.9990
   chunk 31 optimal weight:   30.0000
   chunk 25 optimal weight:   20.0000
   chunk 19 optimal weight:   30.0000
   chunk 30 optimal weight:    6.9990
   chunk 22 optimal weight:   50.0000
   chunk 37 optimal weight:   40.0000
   overall best weight:    9.3992

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
A 349 HIS

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4319 r_free = 0.4319 target = 0.105055 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 61)----------------|
| r_work = 0.3956 r_free = 0.3956 target = 0.087037 restraints weight = 14390.934|
|-----------------------------------------------------------------------------|
r_work (start): 0.3852 rms_B_bonded: 2.68
r_work: 0.3778 rms_B_bonded: 2.72 restraints_weight: 0.5000
r_work: 0.3715 rms_B_bonded: 4.43 restraints_weight: 0.2500
r_work (final): 0.3715
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3692
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3692 r_free = 0.3692    target_work(ls_wunit_k1) = 0.077         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:     1041 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3683 r_free = 0.3683    target_work(ls_wunit_k1) = 0.075         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:     1055 |
|-----------------------------------------------------------------------------|

Number of minimizer iterations: 7 (13 function evaluations)
r_final: 0.3683
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7540
moved from start:          0.3002

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.043   3673  Z= 0.195
  Angle     :  0.772  12.772   5008  Z= 0.377
  Chirality :  0.053   0.244    569
  Planarity :  0.005   0.042    613
  Dihedral  :  8.462  63.370    564
  Min Nonbonded Distance : 2.553

Molprobity Statistics.
  All-atom Clashscore : 5.15
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.73 %
    Favored  : 97.27 %
  Rotamer:
    Outliers :  2.14 %
    Allowed  : 13.14 %
    Favored  : 84.72 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 7.69 %
    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: -0.40 (0.39), residues: 440
  helix:  0.48 (0.53), residues: 96
  sheet:  0.09 (0.53), residues: 93
  loop : -0.66 (0.38), residues: 251

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.008   0.001   ARG A  37 
 TYR   0.017   0.002   TYR A 183 
 PHE   0.008   0.001   PHE A 310 
 TRP   0.006   0.002   TRP A 196 
 HIS   0.007   0.002   HIS A 295 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00430 /  0.19 ( 3673)
  covalent geometry    : angle       0.77157 /  0.38 ( 5008)
  hydrogen bonds       : bond        0.04862 /  3.36 (  128)
  hydrogen bonds       : angle       6.04107 /  4.16 (  370)

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

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

  880 Ramachandran restraints generated.
    440 Oldfield, 0 Emsley, 440 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  880 Ramachandran restraints generated.
    440 Oldfield, 0 Emsley, 440 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  38 residues out of total 373 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 8
    poor density    : 30
  time to evaluate  : 0.131 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   49 MET cc_start: -0.2440 (mmt) cc_final: -0.2784 (mmm)
REVERT: A  243 ASP cc_start: 0.7174 (m-30) cc_final: 0.6958 (t0)
REVERT: A  276 MET cc_start: 0.5872 (mtp) cc_final: 0.5240 (ttm)
REVERT: A  294 MET cc_start: 0.5200 (tpt) cc_final: 0.4959 (tmm)
  outliers start: 8
  outliers final: 2
  residues processed: 37
  average time/residue: 0.5216
  time to fit residues: 19.8366
Evaluate side-chains
  24 residues out of total 373 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 2
    poor density    : 22
  time to evaluate  : 0.079 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  315 VAL
Chi-restraints excluded: chain A residue  330 LYS
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 44
   random chunks:
   chunk 22 optimal weight:   50.0000
   chunk 13 optimal weight:   50.0000
   chunk 41 optimal weight:   20.0000
   chunk 2 optimal weight:   50.0000
   chunk 12 optimal weight:   30.0000
   chunk 28 optimal weight:   30.0000
   chunk 33 optimal weight:    9.9990
   chunk 43 optimal weight:    9.9990
   chunk 0 optimal weight:   50.0000
   chunk 9 optimal weight:   40.0000
   chunk 15 optimal weight:    7.9990
   overall best weight:   15.5994

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
A 147 GLN
A 314 ASN
A 339 GLN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4289 r_free = 0.4289 target = 0.101669 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 70)----------------|
| r_work = 0.3901 r_free = 0.3901 target = 0.083494 restraints weight = 13751.866|
|-----------------------------------------------------------------------------|
r_work (start): 0.3798 rms_B_bonded: 2.52
r_work: 0.3722 rms_B_bonded: 2.70 restraints_weight: 0.5000
r_work: 0.3662 rms_B_bonded: 4.39 restraints_weight: 0.2500
r_work (final): 0.3662
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3636
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3636 r_free = 0.3636    target_work(ls_wunit_k1) = 0.074         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:     1055 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3636 r_free = 0.3636    target_work(ls_wunit_k1) = 0.074         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:     1057 |
|-----------------------------------------------------------------------------|

Number of minimizer iterations: 4 (10 function evaluations)
r_final: 0.3636
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7626
moved from start:          0.4293

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.006   0.046   3673  Z= 0.277
  Angle     :  0.831  14.440   5008  Z= 0.408
  Chirality :  0.053   0.238    569
  Planarity :  0.006   0.054    613
  Dihedral  :  8.907  63.427    564
  Min Nonbonded Distance : 2.523

Molprobity Statistics.
  All-atom Clashscore : 5.76
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.18 %
    Favored  : 96.82 %
  Rotamer:
    Outliers :  1.88 %
    Allowed  : 15.55 %
    Favored  : 82.57 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 7.69 %
    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: -0.73 (0.37), residues: 440
  helix:  0.38 (0.50), residues: 95
  sheet: -0.19 (0.56), residues: 83
  loop : -0.90 (0.35), residues: 262

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.001   ARG A 266 
 TYR   0.016   0.003   TYR A 183 
 PHE   0.029   0.003   PHE A 211 
 TRP   0.007   0.002   TRP A 196 
 HIS   0.007   0.002   HIS A 295 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00591 /  0.28 ( 3673)
  covalent geometry    : angle       0.83057 /  0.41 ( 5008)
  hydrogen bonds       : bond        0.05256 /  3.70 (  128)
  hydrogen bonds       : angle       5.82819 /  4.06 (  370)

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

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

  880 Ramachandran restraints generated.
    440 Oldfield, 0 Emsley, 440 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  880 Ramachandran restraints generated.
    440 Oldfield, 0 Emsley, 440 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  31 residues out of total 373 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 7
    poor density    : 24
  time to evaluate  : 0.080 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  290 LYS cc_start: 0.6256 (OUTLIER) cc_final: 0.4869 (tppt)
REVERT: A  294 MET cc_start: 0.5488 (tpt) cc_final: 0.5191 (tmm)
REVERT: A  310 PHE cc_start: 0.8748 (p90) cc_final: 0.7875 (p90)
  outliers start: 7
  outliers final: 1
  residues processed: 31
  average time/residue: 0.3922
  time to fit residues: 12.5745
Evaluate side-chains
  22 residues out of total 373 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 2
    poor density    : 20
  time to evaluate  : 0.078 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  290 LYS
Chi-restraints excluded: chain A residue  330 LYS
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 44
   random chunks:
   chunk 3 optimal weight:   30.0000
   chunk 43 optimal weight:    9.9990
   chunk 6 optimal weight:   40.0000
   chunk 24 optimal weight:   20.0000
   chunk 26 optimal weight:   10.0000
   chunk 8 optimal weight:   40.0000
   chunk 30 optimal weight:   10.0000
   chunk 36 optimal weight:    0.0870
   chunk 19 optimal weight:   20.0000
   chunk 0 optimal weight:   40.0000
   chunk 34 optimal weight:    6.9990
   overall best weight:    7.4170

-------------------------------------------------------------------------------
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 = 0.4297 r_free = 0.4297 target = 0.101867 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 65)----------------|
| r_work = 0.3918 r_free = 0.3918 target = 0.083914 restraints weight = 13937.399|
|-----------------------------------------------------------------------------|
r_work (start): 0.3808 rms_B_bonded: 2.60
r_work: 0.3736 rms_B_bonded: 2.72 restraints_weight: 0.5000
r_work: 0.3675 rms_B_bonded: 4.44 restraints_weight: 0.2500
r_work (final): 0.3675
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3650
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3650 r_free = 0.3650    target_work(ls_wunit_k1) = 0.074         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:     1057 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3651 r_free = 0.3651    target_work(ls_wunit_k1) = 0.074         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:     1057 |
|-----------------------------------------------------------------------------|

Number of minimizer iterations: 5 (11 function evaluations)
r_final: 0.3651
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7617
moved from start:          0.4730

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.036   3673  Z= 0.154
  Angle     :  0.702   9.580   5008  Z= 0.345
  Chirality :  0.049   0.169    569
  Planarity :  0.005   0.056    613
  Dihedral  :  8.566  72.461    564
  Min Nonbonded Distance : 2.535

Molprobity Statistics.
  All-atom Clashscore : 4.57
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.50 %
    Favored  : 97.50 %
  Rotamer:
    Outliers :  0.80 %
    Allowed  : 16.09 %
    Favored  : 83.11 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 7.69 %
    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: -0.64 (0.37), residues: 440
  helix:  0.37 (0.50), residues: 95
  sheet: -0.07 (0.57), residues: 86
  loop : -0.84 (0.35), residues: 259

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG A  37 
 TYR   0.011   0.002   TYR A 183 
 PHE   0.030   0.002   PHE A 211 
 TRP   0.015   0.002   TRP A  58 
 HIS   0.005   0.001   HIS A 364 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00341 /  0.15 ( 3673)
  covalent geometry    : angle       0.70196 /  0.34 ( 5008)
  hydrogen bonds       : bond        0.04200 /  3.00 (  128)
  hydrogen bonds       : angle       5.32769 /  3.71 (  370)

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

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

  880 Ramachandran restraints generated.
    440 Oldfield, 0 Emsley, 440 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  880 Ramachandran restraints generated.
    440 Oldfield, 0 Emsley, 440 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  24 residues out of total 373 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 3
    poor density    : 21
  time to evaluate  : 0.083 
Fit side-chains
   revert: symmetry clash
REVERT: A   49 MET cc_start: -0.2303 (mmt) cc_final: -0.2760 (mmm)
REVERT: A  155 MET cc_start: 0.6830 (mtm) cc_final: 0.6494 (pmm)
REVERT: A  276 MET cc_start: 0.6163 (mtp) cc_final: 0.5470 (ttm)
REVERT: A  290 LYS cc_start: 0.6007 (OUTLIER) cc_final: 0.4715 (tppt)
REVERT: A  294 MET cc_start: 0.5368 (tpt) cc_final: 0.5094 (tmm)
REVERT: A  310 PHE cc_start: 0.8748 (p90) cc_final: 0.7930 (p90)
REVERT: A  404 MET cc_start: 0.7608 (OUTLIER) cc_final: 0.7242 (mmm)
  outliers start: 3
  outliers final: 1
  residues processed: 23
  average time/residue: 0.3923
  time to fit residues: 9.3698
Evaluate side-chains
  21 residues out of total 373 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 3
    poor density    : 18
  time to evaluate  : 0.080 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   83 THR
Chi-restraints excluded: chain A residue  290 LYS
Chi-restraints excluded: chain A residue  404 MET
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 44
   random chunks:
   chunk 2 optimal weight:   40.0000
   chunk 10 optimal weight:    6.9990
   chunk 28 optimal weight:   30.0000
   chunk 15 optimal weight:    0.0270
   chunk 30 optimal weight:    8.9990
   chunk 6 optimal weight:   50.0000
   chunk 42 optimal weight:    6.9990
   chunk 20 optimal weight:   20.0000
   chunk 43 optimal weight:   20.0000
   chunk 34 optimal weight:   20.0000
   chunk 27 optimal weight:    7.9990
   overall best weight:    6.2046

-------------------------------------------------------------------------------
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 = 0.4291 r_free = 0.4291 target = 0.101390 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 73)----------------|
| r_work = 0.3905 r_free = 0.3905 target = 0.083175 restraints weight = 13808.972|
|-----------------------------------------------------------------------------|
r_work (start): 0.3801 rms_B_bonded: 2.61
r_work: 0.3730 rms_B_bonded: 2.75 restraints_weight: 0.5000
r_work: 0.3670 rms_B_bonded: 4.49 restraints_weight: 0.2500
r_work (final): 0.3670
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3643
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3643 r_free = 0.3643    target_work(ls_wunit_k1) = 0.073         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:     1057 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3643 r_free = 0.3643    target_work(ls_wunit_k1) = 0.073         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:     1058 |
|-----------------------------------------------------------------------------|

Number of minimizer iterations: 3 (11 function evaluations)
r_final: 0.3643
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7621
moved from start:          0.5072

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.033   3673  Z= 0.140
  Angle     :  0.666   9.387   5008  Z= 0.324
  Chirality :  0.048   0.151    569
  Planarity :  0.005   0.055    613
  Dihedral  :  8.252  71.551    564
  Min Nonbonded Distance : 2.577

Molprobity Statistics.
  All-atom Clashscore : 5.76
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.50 %
    Favored  : 97.50 %
  Rotamer:
    Outliers :  1.07 %
    Allowed  : 15.82 %
    Favored  : 83.11 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 7.69 %
    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: -0.44 (0.38), residues: 440
  helix:  0.67 (0.51), residues: 95
  sheet: -0.20 (0.55), residues: 92
  loop : -0.67 (0.36), residues: 253

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG A  37 
 TYR   0.011   0.001   TYR A 162 
 PHE   0.036   0.002   PHE A 211 
 TRP   0.007   0.001   TRP A 210 
 HIS   0.005   0.001   HIS A 364 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00308 /  0.14 ( 3673)
  covalent geometry    : angle       0.66576 /  0.32 ( 5008)
  hydrogen bonds       : bond        0.03775 /  2.67 (  128)
  hydrogen bonds       : angle       5.17947 /  3.63 (  370)

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

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

  880 Ramachandran restraints generated.
    440 Oldfield, 0 Emsley, 440 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  880 Ramachandran restraints generated.
    440 Oldfield, 0 Emsley, 440 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  24 residues out of total 373 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 4
    poor density    : 20
  time to evaluate  : 0.091 
Fit side-chains
   revert: symmetry clash
REVERT: A  113 VAL cc_start: 0.8978 (t) cc_final: 0.8426 (m)
REVERT: A  155 MET cc_start: 0.6523 (OUTLIER) cc_final: 0.6067 (pmm)
REVERT: A  165 LYS cc_start: 0.8511 (mmpt) cc_final: 0.8164 (pmtt)
REVERT: A  276 MET cc_start: 0.6196 (mtp) cc_final: 0.5554 (ttm)
REVERT: A  290 LYS cc_start: 0.6125 (OUTLIER) cc_final: 0.4647 (tppt)
REVERT: A  294 MET cc_start: 0.5436 (tpt) cc_final: 0.5085 (tmm)
REVERT: A  310 PHE cc_start: 0.8728 (p90) cc_final: 0.7799 (p90)
REVERT: A  404 MET cc_start: 0.7370 (OUTLIER) cc_final: 0.7016 (mmm)
  outliers start: 4
  outliers final: 0
  residues processed: 22
  average time/residue: 0.5032
  time to fit residues: 11.4857
Evaluate side-chains
  21 residues out of total 373 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 3
    poor density    : 18
  time to evaluate  : 0.079 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  155 MET
Chi-restraints excluded: chain A residue  290 LYS
Chi-restraints excluded: chain A residue  404 MET
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 44
   random chunks:
   chunk 18 optimal weight:    8.9990
   chunk 41 optimal weight:    6.9990
   chunk 29 optimal weight:   10.0000
   chunk 6 optimal weight:   50.0000
   chunk 28 optimal weight:   40.0000
   chunk 30 optimal weight:   20.0000
   chunk 3 optimal weight:   30.0000
   chunk 1 optimal weight:   50.0000
   chunk 8 optimal weight:    9.9990
   chunk 26 optimal weight:    7.9990
   chunk 11 optimal weight:   50.0000
   overall best weight:    8.7992

-------------------------------------------------------------------------------
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 = 0.4287 r_free = 0.4287 target = 0.101068 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 68)----------------|
| r_work = 0.3886 r_free = 0.3886 target = 0.082713 restraints weight = 13767.717|
|-----------------------------------------------------------------------------|
r_work (start): 0.3788 rms_B_bonded: 2.55
r_work: 0.3718 rms_B_bonded: 2.71 restraints_weight: 0.5000
r_work: 0.3658 rms_B_bonded: 4.39 restraints_weight: 0.2500
r_work (final): 0.3658
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3634
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3634 r_free = 0.3634    target_work(ls_wunit_k1) = 0.073         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:     1058 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3634 r_free = 0.3634    target_work(ls_wunit_k1) = 0.073         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:     1058 |
|-----------------------------------------------------------------------------|

Number of minimizer iterations: 3 (9 function evaluations)
r_final: 0.3634
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7638
moved from start:          0.5442

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.035   3673  Z= 0.168
  Angle     :  0.690   9.306   5008  Z= 0.337
  Chirality :  0.048   0.169    569
  Planarity :  0.005   0.058    613
  Dihedral  :  8.190  68.875    564
  Min Nonbonded Distance : 2.550

Molprobity Statistics.
  All-atom Clashscore : 6.16
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.95 %
    Favored  : 97.05 %
  Rotamer:
    Outliers :  2.41 %
    Allowed  : 15.28 %
    Favored  : 82.31 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 7.69 %
    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: -0.61 (0.38), residues: 440
  helix:  0.46 (0.51), residues: 97
  sheet: -0.22 (0.56), residues: 90
  loop : -0.79 (0.36), residues: 253

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.001   ARG A  37 
 TYR   0.011   0.002   TYR A 162 
 PHE   0.011   0.002   PHE A 340 
 TRP   0.005   0.001   TRP A 214 
 HIS   0.005   0.001   HIS A 295 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00366 /  0.17 ( 3673)
  covalent geometry    : angle       0.68988 /  0.34 ( 5008)
  hydrogen bonds       : bond        0.04063 /  2.80 (  128)
  hydrogen bonds       : angle       5.15122 /  3.63 (  370)

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

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

  880 Ramachandran restraints generated.
    440 Oldfield, 0 Emsley, 440 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  880 Ramachandran restraints generated.
    440 Oldfield, 0 Emsley, 440 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  26 residues out of total 373 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 9
    poor density    : 17
  time to evaluate  : 0.090 
Fit side-chains
   revert: symmetry clash
REVERT: A  165 LYS cc_start: 0.8446 (mmpt) cc_final: 0.7992 (ptpp)
REVERT: A  276 MET cc_start: 0.6059 (mtp) cc_final: 0.5318 (ttm)
REVERT: A  290 LYS cc_start: 0.6194 (OUTLIER) cc_final: 0.4617 (tppt)
REVERT: A  294 MET cc_start: 0.5370 (tpt) cc_final: 0.5001 (tmm)
REVERT: A  310 PHE cc_start: 0.8713 (p90) cc_final: 0.7913 (p90)
REVERT: A  404 MET cc_start: 0.7358 (OUTLIER) cc_final: 0.7009 (mmm)
  outliers start: 9
  outliers final: 1
  residues processed: 23
  average time/residue: 0.4559
  time to fit residues: 10.8534
Evaluate side-chains
  20 residues out of total 373 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 3
    poor density    : 17
  time to evaluate  : 0.129 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   83 THR
Chi-restraints excluded: chain A residue  290 LYS
Chi-restraints excluded: chain A residue  404 MET
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 44
   random chunks:
   chunk 40 optimal weight:   10.0000
   chunk 29 optimal weight:   40.0000
   chunk 20 optimal weight:    5.9990
   chunk 21 optimal weight:   20.0000
   chunk 7 optimal weight:   20.0000
   chunk 31 optimal weight:    7.9990
   chunk 8 optimal weight:    8.9990
   chunk 9 optimal weight:    8.9990
   chunk 18 optimal weight:    8.9990
   chunk 38 optimal weight:    0.6980
   chunk 19 optimal weight:    9.9990
   overall best weight:    6.5388

-------------------------------------------------------------------------------
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 = 0.4292 r_free = 0.4292 target = 0.101151 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 65)----------------|
| r_work = 0.3899 r_free = 0.3899 target = 0.083058 restraints weight = 13977.421|
|-----------------------------------------------------------------------------|
r_work (start): 0.3800 rms_B_bonded: 2.50
r_work: 0.3727 rms_B_bonded: 2.65 restraints_weight: 0.5000
r_work: 0.3670 rms_B_bonded: 4.27 restraints_weight: 0.2500
r_work (final): 0.3670
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3647
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3647 r_free = 0.3647    target_work(ls_wunit_k1) = 0.074         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:     1058 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3647 r_free = 0.3647    target_work(ls_wunit_k1) = 0.074         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:     1058 |
|-----------------------------------------------------------------------------|

Number of minimizer iterations: 3 (9 function evaluations)
r_final: 0.3647
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7619
moved from start:          0.5670

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.032   3673  Z= 0.139
  Angle     :  0.651   8.299   5008  Z= 0.319
  Chirality :  0.047   0.155    569
  Planarity :  0.005   0.056    613
  Dihedral  :  8.153  72.585    564
  Min Nonbonded Distance : 2.564

Molprobity Statistics.
  All-atom Clashscore : 5.37
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.95 %
    Favored  : 97.05 %
  Rotamer:
    Outliers :  1.88 %
    Allowed  : 16.09 %
    Favored  : 82.04 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 7.69 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -0.60 (0.38), residues: 440
  helix:  0.56 (0.52), residues: 97
  sheet: -0.26 (0.56), residues: 90
  loop : -0.81 (0.36), residues: 253

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG A  37 
 TYR   0.009   0.001   TYR A 162 
 PHE   0.012   0.001   PHE A 340 
 TRP   0.007   0.001   TRP A 210 
 HIS   0.004   0.001   HIS A 364 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00306 /  0.14 ( 3673)
  covalent geometry    : angle       0.65088 /  0.32 ( 5008)
  hydrogen bonds       : bond        0.03704 /  2.55 (  128)
  hydrogen bonds       : angle       5.04991 /  3.54 (  370)

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

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

  880 Ramachandran restraints generated.
    440 Oldfield, 0 Emsley, 440 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  880 Ramachandran restraints generated.
    440 Oldfield, 0 Emsley, 440 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  26 residues out of total 373 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 7
    poor density    : 19
  time to evaluate  : 0.082 
Fit side-chains
   revert: symmetry clash
REVERT: A  146 LYS cc_start: 0.8441 (OUTLIER) cc_final: 0.7857 (pptt)
REVERT: A  165 LYS cc_start: 0.8517 (mmpt) cc_final: 0.8190 (pmtt)
REVERT: A  276 MET cc_start: 0.6034 (mtp) cc_final: 0.5349 (ttm)
REVERT: A  290 LYS cc_start: 0.6167 (OUTLIER) cc_final: 0.4621 (tppt)
REVERT: A  294 MET cc_start: 0.5380 (tpt) cc_final: 0.5016 (tmm)
REVERT: A  310 PHE cc_start: 0.8698 (p90) cc_final: 0.7889 (p90)
REVERT: A  404 MET cc_start: 0.7228 (OUTLIER) cc_final: 0.6891 (mmm)
  outliers start: 7
  outliers final: 2
  residues processed: 24
  average time/residue: 0.4060
  time to fit residues: 10.1184
Evaluate side-chains
  24 residues out of total 373 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 5
    poor density    : 19
  time to evaluate  : 0.126 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   83 THR
Chi-restraints excluded: chain A residue  146 LYS
Chi-restraints excluded: chain A residue  290 LYS
Chi-restraints excluded: chain A residue  303 LEU
Chi-restraints excluded: chain A residue  404 MET
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 44
   random chunks:
   chunk 24 optimal weight:    5.9990
   chunk 0 optimal weight:   60.0000
   chunk 39 optimal weight:    9.9990
   chunk 5 optimal weight:    6.9990
   chunk 37 optimal weight:    7.9990
   chunk 10 optimal weight:   30.0000
   chunk 26 optimal weight:    6.9990
   chunk 27 optimal weight:    0.0000
   chunk 11 optimal weight:   50.0000
   chunk 28 optimal weight:    9.9990
   chunk 13 optimal weight:    8.9990
   overall best weight:    5.5992

-------------------------------------------------------------------------------
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 = 0.4297 r_free = 0.4297 target = 0.101150 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 66)----------------|
| r_work = 0.3902 r_free = 0.3902 target = 0.083203 restraints weight = 13988.771|
|-----------------------------------------------------------------------------|
r_work (start): 0.3802 rms_B_bonded: 2.43
r_work: 0.3731 rms_B_bonded: 2.60 restraints_weight: 0.5000
r_work: 0.3671 rms_B_bonded: 4.26 restraints_weight: 0.2500
r_work (final): 0.3671
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3649
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3649 r_free = 0.3649    target_work(ls_wunit_k1) = 0.074         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:     1058 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3649 r_free = 0.3649    target_work(ls_wunit_k1) = 0.074         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:     1058 |
|-----------------------------------------------------------------------------|

Number of minimizer iterations: 3 (9 function evaluations)
r_final: 0.3649
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7618
moved from start:          0.5888

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.031   3673  Z= 0.130
  Angle     :  0.646   8.780   5008  Z= 0.316
  Chirality :  0.047   0.150    569
  Planarity :  0.005   0.057    613
  Dihedral  :  8.098  72.624    564
  Min Nonbonded Distance : 2.578

Molprobity Statistics.
  All-atom Clashscore : 6.16
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.18 %
    Favored  : 96.82 %
  Rotamer:
    Outliers :  1.61 %
    Allowed  : 16.89 %
    Favored  : 81.50 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 7.69 %
    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: -0.61 (0.39), residues: 440
  helix:  0.63 (0.53), residues: 97
  sheet: -0.11 (0.58), residues: 87
  loop : -0.91 (0.36), residues: 256

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG A  37 
 TYR   0.010   0.001   TYR A 162 
 PHE   0.015   0.002   PHE A 211 
 TRP   0.006   0.001   TRP A  58 
 HIS   0.004   0.001   HIS A 364 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00287 /  0.13 ( 3673)
  covalent geometry    : angle       0.64550 /  0.32 ( 5008)
  hydrogen bonds       : bond        0.03616 /  2.46 (  128)
  hydrogen bonds       : angle       4.93298 /  3.44 (  370)

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

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

  880 Ramachandran restraints generated.
    440 Oldfield, 0 Emsley, 440 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  880 Ramachandran restraints generated.
    440 Oldfield, 0 Emsley, 440 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  26 residues out of total 373 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 6
    poor density    : 20
  time to evaluate  : 0.085 
Fit side-chains
   revert: symmetry clash
REVERT: A  113 VAL cc_start: 0.8829 (t) cc_final: 0.8193 (m)
REVERT: A  165 LYS cc_start: 0.8486 (mmpt) cc_final: 0.8159 (pmtt)
REVERT: A  276 MET cc_start: 0.6021 (mtp) cc_final: 0.5320 (ttm)
REVERT: A  290 LYS cc_start: 0.6170 (OUTLIER) cc_final: 0.4522 (tppt)
REVERT: A  294 MET cc_start: 0.5429 (tpt) cc_final: 0.5037 (tmm)
REVERT: A  310 PHE cc_start: 0.8732 (p90) cc_final: 0.7961 (p90)
REVERT: A  404 MET cc_start: 0.7174 (OUTLIER) cc_final: 0.6858 (mmm)
  outliers start: 6
  outliers final: 1
  residues processed: 24
  average time/residue: 0.5007
  time to fit residues: 12.4575
Evaluate side-chains
  23 residues out of total 373 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 3
    poor density    : 20
  time to evaluate  : 0.104 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  290 LYS
Chi-restraints excluded: chain A residue  330 LYS
Chi-restraints excluded: chain A residue  404 MET
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 44
   random chunks:
   chunk 11 optimal weight:    0.0870
   chunk 40 optimal weight:    7.9990
   chunk 2 optimal weight:   40.0000
   chunk 10 optimal weight:    7.9990
   chunk 8 optimal weight:    8.9990
   chunk 43 optimal weight:    9.9990
   chunk 16 optimal weight:   10.0000
   chunk 25 optimal weight:   30.0000
   chunk 6 optimal weight:   40.0000
   chunk 23 optimal weight:    8.9990
   chunk 5 optimal weight:   30.0000
   overall best weight:    6.8166

-------------------------------------------------------------------------------
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 = 0.4294 r_free = 0.4294 target = 0.100984 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 68)----------------|
| r_work = 0.3890 r_free = 0.3890 target = 0.082705 restraints weight = 13919.291|
|-----------------------------------------------------------------------------|
r_work (start): 0.3785 rms_B_bonded: 2.55
r_work: 0.3717 rms_B_bonded: 2.67 restraints_weight: 0.5000
r_work: 0.3657 rms_B_bonded: 4.34 restraints_weight: 0.2500
r_work (final): 0.3657
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3634
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3634 r_free = 0.3634    target_work(ls_wunit_k1) = 0.073         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:     1058 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3634 r_free = 0.3634    target_work(ls_wunit_k1) = 0.073         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:     1058 |
|-----------------------------------------------------------------------------|

Number of minimizer iterations: 3 (9 function evaluations)
r_final: 0.3634
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7633
moved from start:          0.6082

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.032   3673  Z= 0.145
  Angle     :  0.695  11.364   5008  Z= 0.333
  Chirality :  0.048   0.155    569
  Planarity :  0.005   0.058    613
  Dihedral  :  8.135  71.150    564
  Min Nonbonded Distance : 2.564

Molprobity Statistics.
  All-atom Clashscore : 5.56
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.18 %
    Favored  : 96.82 %
  Rotamer:
    Outliers :  0.80 %
    Allowed  : 17.43 %
    Favored  : 81.77 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 7.69 %
    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: -0.47 (0.39), residues: 440
  helix:  0.52 (0.53), residues: 97
  sheet: -0.02 (0.52), residues: 108
  loop : -0.77 (0.39), residues: 235

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG A  37 
 TYR   0.010   0.001   TYR A 162 
 PHE   0.011   0.001   PHE A 340 
 TRP   0.005   0.001   TRP A  58 
 HIS   0.006   0.002   HIS A  26 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00314 /  0.14 ( 3673)
  covalent geometry    : angle       0.69477 /  0.33 ( 5008)
  hydrogen bonds       : bond        0.03724 /  2.53 (  128)
  hydrogen bonds       : angle       5.15832 /  3.61 (  370)

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

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

  880 Ramachandran restraints generated.
    440 Oldfield, 0 Emsley, 440 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  880 Ramachandran restraints generated.
    440 Oldfield, 0 Emsley, 440 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  24 residues out of total 373 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 3
    poor density    : 21
  time to evaluate  : 0.080 
Fit side-chains
   revert: symmetry clash
REVERT: A   26 HIS cc_start: 0.8089 (t70) cc_final: 0.7663 (t-90)
REVERT: A  113 VAL cc_start: 0.8864 (t) cc_final: 0.8229 (m)
REVERT: A  165 LYS cc_start: 0.8506 (mmpt) cc_final: 0.8193 (pmtt)
REVERT: A  276 MET cc_start: 0.6105 (mtp) cc_final: 0.5440 (ttm)
REVERT: A  290 LYS cc_start: 0.6110 (OUTLIER) cc_final: 0.4349 (tppt)
REVERT: A  294 MET cc_start: 0.5435 (tpt) cc_final: 0.5057 (tmm)
REVERT: A  310 PHE cc_start: 0.8703 (p90) cc_final: 0.7928 (p90)
REVERT: A  404 MET cc_start: 0.7103 (OUTLIER) cc_final: 0.6759 (mmm)
  outliers start: 3
  outliers final: 1
  residues processed: 23
  average time/residue: 0.4124
  time to fit residues: 9.8466
Evaluate side-chains
  23 residues out of total 373 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 3
    poor density    : 20
  time to evaluate  : 0.078 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  290 LYS
Chi-restraints excluded: chain A residue  330 LYS
Chi-restraints excluded: chain A residue  404 MET
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 44
   random chunks:
   chunk 17 optimal weight:   50.0000
   chunk 39 optimal weight:   30.0000
   chunk 3 optimal weight:    7.9990
   chunk 11 optimal weight:    1.9990
   chunk 0 optimal weight:    6.9990
   chunk 40 optimal weight:   30.0000
   chunk 30 optimal weight:    0.9990
   chunk 5 optimal weight:    9.9990
   chunk 24 optimal weight:    5.9990
   chunk 35 optimal weight:   30.0000
   chunk 10 optimal weight:    7.9990
   overall best weight:    4.7990

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
A 200 ASN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4294 r_free = 0.4294 target = 0.101087 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 60)----------------|
| r_work = 0.3902 r_free = 0.3902 target = 0.083167 restraints weight = 13985.170|
|-----------------------------------------------------------------------------|
r_work (start): 0.3796 rms_B_bonded: 2.58
r_work: 0.3730 rms_B_bonded: 2.68 restraints_weight: 0.5000
r_work: 0.3667 rms_B_bonded: 4.40 restraints_weight: 0.2500
r_work (final): 0.3667
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3645
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3645 r_free = 0.3645    target_work(ls_wunit_k1) = 0.073         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:     1058 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3645 r_free = 0.3645    target_work(ls_wunit_k1) = 0.073         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:     1058 |
|-----------------------------------------------------------------------------|

Number of minimizer iterations: 3 (9 function evaluations)
r_final: 0.3645
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7619
moved from start:          0.6274

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.030   3673  Z= 0.121
  Angle     :  0.672  13.633   5008  Z= 0.321
  Chirality :  0.048   0.147    569
  Planarity :  0.005   0.057    613
  Dihedral  :  8.055  74.995    564
  Min Nonbonded Distance : 2.588

Molprobity Statistics.
  All-atom Clashscore : 5.56
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.18 %
    Favored  : 96.82 %
  Rotamer:
    Outliers :  0.80 %
    Allowed  : 17.96 %
    Favored  : 81.23 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 7.69 %
    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: -0.49 (0.39), residues: 440
  helix:  0.53 (0.54), residues: 97
  sheet: -0.01 (0.56), residues: 93
  loop : -0.76 (0.37), residues: 250

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG A 423 
 TYR   0.008   0.001   TYR A 357 
 PHE   0.012   0.001   PHE A 340 
 TRP   0.009   0.001   TRP A 214 
 HIS   0.005   0.001   HIS A 364 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00264 /  0.12 ( 3673)
  covalent geometry    : angle       0.67217 /  0.32 ( 5008)
  hydrogen bonds       : bond        0.03506 /  2.38 (  128)
  hydrogen bonds       : angle       5.18282 /  3.64 (  370)

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

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

  880 Ramachandran restraints generated.
    440 Oldfield, 0 Emsley, 440 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  880 Ramachandran restraints generated.
    440 Oldfield, 0 Emsley, 440 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  20 residues out of total 373 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 3
    poor density    : 17
  time to evaluate  : 0.081 
Fit side-chains
   revert: symmetry clash
REVERT: A   26 HIS cc_start: 0.8105 (t70) cc_final: 0.7661 (t-90)
REVERT: A  165 LYS cc_start: 0.8495 (mmpt) cc_final: 0.8214 (pmtt)
REVERT: A  276 MET cc_start: 0.5936 (mtp) cc_final: 0.5250 (ttm)
REVERT: A  290 LYS cc_start: 0.6012 (OUTLIER) cc_final: 0.4070 (tppt)
REVERT: A  294 MET cc_start: 0.5465 (tpt) cc_final: 0.5087 (tmm)
REVERT: A  310 PHE cc_start: 0.8735 (p90) cc_final: 0.7975 (p90)
REVERT: A  404 MET cc_start: 0.7121 (OUTLIER) cc_final: 0.6845 (mmm)
  outliers start: 3
  outliers final: 1
  residues processed: 19
  average time/residue: 0.4734
  time to fit residues: 9.2984
Evaluate side-chains
  20 residues out of total 373 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 3
    poor density    : 17
  time to evaluate  : 0.079 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  290 LYS
Chi-restraints excluded: chain A residue  330 LYS
Chi-restraints excluded: chain A residue  404 MET
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 44
   random chunks:
   chunk 29 optimal weight:   30.0000
   chunk 34 optimal weight:   30.0000
   chunk 8 optimal weight:    8.9990
   chunk 32 optimal weight:    9.9990
   chunk 1 optimal weight:   20.0000
   chunk 2 optimal weight:   30.0000
   chunk 3 optimal weight:   20.0000
   chunk 13 optimal weight:   50.0000
   chunk 16 optimal weight:   20.0000
   chunk 14 optimal weight:   10.0000
   chunk 35 optimal weight:   40.0000
   overall best weight:   13.7996

-------------------------------------------------------------------------------
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 = 0.4275 r_free = 0.4275 target = 0.100161 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 65)----------------|
| r_work = 0.3867 r_free = 0.3867 target = 0.081821 restraints weight = 13503.736|
|-----------------------------------------------------------------------------|
r_work (start): 0.3754 rms_B_bonded: 2.47
r_work: 0.3686 rms_B_bonded: 2.56 restraints_weight: 0.5000
r_work: 0.3627 rms_B_bonded: 4.19 restraints_weight: 0.2500
r_work (final): 0.3627
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3604
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3604 r_free = 0.3604    target_work(ls_wunit_k1) = 0.072         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:     1058 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3604 r_free = 0.3604    target_work(ls_wunit_k1) = 0.072         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:     1057 |
|-----------------------------------------------------------------------------|

Number of minimizer iterations: 4 (10 function evaluations)
r_final: 0.3604
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7686
moved from start:          0.6625

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.035   3673  Z= 0.239
  Angle     :  0.766  11.772   5008  Z= 0.372
  Chirality :  0.050   0.214    569
  Planarity :  0.006   0.063    613
  Dihedral  :  8.451  63.936    564
  Min Nonbonded Distance : 2.495

Molprobity Statistics.
  All-atom Clashscore : 7.94
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.32 %
    Favored  : 95.68 %
  Rotamer:
    Outliers :  0.54 %
    Allowed  : 18.23 %
    Favored  : 81.23 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 7.69 %
    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: -0.52 (0.39), residues: 440
  helix:  0.51 (0.52), residues: 97
  sheet:  0.04 (0.53), residues: 106
  loop : -0.86 (0.38), residues: 237

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.001   ARG A 427 
 TYR   0.013   0.002   TYR A 162 
 PHE   0.010   0.002   PHE A 340 
 TRP   0.005   0.001   TRP A  78 
 HIS   0.007   0.002   HIS A 295 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00510 /  0.24 ( 3673)
  covalent geometry    : angle       0.76618 /  0.37 ( 5008)
  hydrogen bonds       : bond        0.04615 /  3.12 (  128)
  hydrogen bonds       : angle       5.38878 /  3.79 (  370)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 1411.14 seconds
wall clock time: 24 minutes 35.86 seconds (1475.86 seconds total)