Starting phenix.real_space_refine
on Wed Jun  4 12:08:56 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/7ypg_33999/06_2025/7ypg_33999.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/7ypg_33999/06_2025/7ypg_33999.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=2.5
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/cci-nas-00/data/ceres_data/7ypg_33999/06_2025/7ypg_33999.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/7ypg_33999/06_2025/7ypg_33999.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/7ypg_33999/06_2025/7ypg_33999.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/7ypg_33999/06_2025/7ypg_33999.cif"
  }
  resolution = 2.5
  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=   0.004
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: 4
    Type Number    sf(0)   Gaussians
     S       6      5.16       5
     C    1668      2.51       5
     N     486      2.21       5
     O     516      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model
  Monomer Library directory:
    "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/chem_data/mon_lib"
  Total number of atoms: 2676
  Number of models: 1
  Model: ""
    Number of chains: 1
    Chain: "A"
      Number of atoms: 446
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 59, 446
          Classifications: {'peptide': 59}
          Link IDs: {'PTRANS': 2, 'TRANS': 56}
  Restraints were copied for chains:
    C, B, E, D, F
  Time building chain proxies: 1.52, per 1000 atoms: 0.57
  Number of scatterers: 2676
  At special positions: 0
  Unit cell: (99.6, 110.39, 34.86, 90, 90, 90)
  Space group: P 1 (No. 1)
  Number of sites at special positions: 0
  Number of scattering types: 4
    Type Number    sf(0)
     S       6     16.00
     O     516      8.00
     N     486      7.00
     C    1668      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: 0.54
  Conformation dependent library (CDL) restraints added in 298.5 milliseconds
  

  684 Ramachandran restraints generated.
    342 Oldfield, 0 Emsley, 342 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  624

  Finding SS restraints...
    Secondary structure from input PDB file:
      0 helices and 10 sheets defined
      0.0% alpha, 18.6% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 0.31
  Creating SS restraints...
    Processing sheet with id=AA1, first strand: chain 'B' and resid 308 through 310
      removed outlier: 6.673A  pdb=" N   VAL B 309 " --> pdb=" O   TYR D 310 " (cutoff:3.500A)
      removed outlier: 6.673A  pdb=" N   VAL D 309 " --> pdb=" O   TYR E 310 " (cutoff:3.500A)
  No H-bonds generated for sheet with id=AA1
    Processing sheet with id=AA2, first strand: chain 'B' and resid 316 through 320
    Processing sheet with id=AA3, first strand: chain 'B' and resid 328 through 330
      removed outlier: 6.409A  pdb=" N   HIS B 329 " --> pdb=" O   HIS D 330 " (cutoff:3.500A)
      removed outlier: 6.402A  pdb=" N   HIS D 329 " --> pdb=" O   HIS E 330 " (cutoff:3.500A)
  No H-bonds generated for sheet with id=AA3
    Processing sheet with id=AA4, first strand: chain 'B' and resid 338 through 340
      removed outlier: 6.652A  pdb=" N   GLU B 338 " --> pdb=" O   VAL D 339 " (cutoff:3.500A)
      removed outlier: 6.649A  pdb=" N   GLU D 338 " --> pdb=" O   VAL E 339 " (cutoff:3.500A)
  No H-bonds generated for sheet with id=AA4
    Processing sheet with id=AA5, first strand: chain 'B' and resid 349 through 350
    Processing sheet with id=AA6, first strand: chain 'F' and resid 308 through 310
      removed outlier: 6.673A  pdb=" N   VAL F 309 " --> pdb=" O   TYR A 310 " (cutoff:3.500A)
      removed outlier: 6.673A  pdb=" N   VAL A 309 " --> pdb=" O   TYR C 310 " (cutoff:3.500A)
  No H-bonds generated for sheet with id=AA6
    Processing sheet with id=AA7, first strand: chain 'F' and resid 316 through 320
    Processing sheet with id=AA8, first strand: chain 'F' and resid 328 through 330
      removed outlier: 6.410A  pdb=" N   HIS F 329 " --> pdb=" O   HIS A 330 " (cutoff:3.500A)
      removed outlier: 6.403A  pdb=" N   HIS A 329 " --> pdb=" O   HIS C 330 " (cutoff:3.500A)
  No H-bonds generated for sheet with id=AA8
    Processing sheet with id=AA9, first strand: chain 'F' and resid 338 through 340
      removed outlier: 6.651A  pdb=" N   GLU F 338 " --> pdb=" O   VAL A 339 " (cutoff:3.500A)
      removed outlier: 6.649A  pdb=" N   GLU A 338 " --> pdb=" O   VAL C 339 " (cutoff:3.500A)
  No H-bonds generated for sheet with id=AA9
    Processing sheet with id=AB1, first strand: chain 'F' and resid 349 through 350

    20 hydrogen bonds defined for protein.
    60 hydrogen bond angles defined for protein.
    Restraints generated for nucleic acids:
      0 hydrogen bonds
      0 hydrogen bond angles
      0 basepair planarities
      0 basepair parallelities
      0 stacking parallelities
  Total time for adding SS restraints: 0.49

  Time building geometry restraints manager: 0.66 seconds

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

  Histogram of bond lengths:
        1.22 -     1.33: 881
        1.33 -     1.45: 217
        1.45 -     1.56: 1608
        1.56 -     1.67: 0
        1.67 -     1.79: 6
  Bond restraints: 2712
  Sorted by residual:
  bond pdb=" CB  VAL D 306 "
       pdb=" CG2 VAL D 306 "
    ideal  model  delta    sigma   weight residual
    1.521  1.478  0.043 3.30e-02 9.18e+02 1.68e+00
  bond pdb=" CB  VAL A 306 "
       pdb=" CG2 VAL A 306 "
    ideal  model  delta    sigma   weight residual
    1.521  1.478  0.043 3.30e-02 9.18e+02 1.66e+00
  bond pdb=" CB  VAL E 306 "
       pdb=" CG2 VAL E 306 "
    ideal  model  delta    sigma   weight residual
    1.521  1.479  0.042 3.30e-02 9.18e+02 1.65e+00
  bond pdb=" CB  VAL C 306 "
       pdb=" CG2 VAL C 306 "
    ideal  model  delta    sigma   weight residual
    1.521  1.479  0.042 3.30e-02 9.18e+02 1.65e+00
  bond pdb=" CB  VAL F 306 "
       pdb=" CG2 VAL F 306 "
    ideal  model  delta    sigma   weight residual
    1.521  1.479  0.042 3.30e-02 9.18e+02 1.64e+00
  ... (remaining 2707 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     0.89: 2971
        0.89 -     1.78: 534
        1.78 -     2.67: 65
        2.67 -     3.55: 34
        3.55 -     4.44: 26
  Bond angle restraints: 3630
  Sorted by residual:
  angle pdb=" N   THR A 361 "
        pdb=" CA  THR A 361 "
        pdb=" C   THR A 361 "
      ideal   model   delta    sigma   weight residual
     111.17  114.75   -3.58 1.41e+00 5.03e-01 6.44e+00
  angle pdb=" N   THR F 361 "
        pdb=" CA  THR F 361 "
        pdb=" C   THR F 361 "
      ideal   model   delta    sigma   weight residual
     111.17  114.72   -3.55 1.41e+00 5.03e-01 6.35e+00
  angle pdb=" N   THR D 361 "
        pdb=" CA  THR D 361 "
        pdb=" C   THR D 361 "
      ideal   model   delta    sigma   weight residual
     111.17  114.71   -3.54 1.41e+00 5.03e-01 6.31e+00
  angle pdb=" N   THR C 361 "
        pdb=" CA  THR C 361 "
        pdb=" C   THR C 361 "
      ideal   model   delta    sigma   weight residual
     111.17  114.71   -3.54 1.41e+00 5.03e-01 6.31e+00
  angle pdb=" N   THR E 361 "
        pdb=" CA  THR E 361 "
        pdb=" C   THR E 361 "
      ideal   model   delta    sigma   weight residual
     111.17  114.70   -3.53 1.41e+00 5.03e-01 6.26e+00
  ... (remaining 3625 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    17.74: 1506
       17.74 -    35.47: 114
       35.47 -    53.21: 30
       53.21 -    70.95: 0
       70.95 -    88.68: 6
  Dihedral angle restraints: 1656
    sinusoidal: 678
      harmonic: 978
  Sorted by residual:
  dihedral pdb=" CB  GLU B 338 "
           pdb=" CG  GLU B 338 "
           pdb=" CD  GLU B 338 "
           pdb=" OE1 GLU B 338 "
      ideal   model   delta sinusoidal    sigma   weight residual
       0.00   88.68  -88.68     1      3.00e+01 1.11e-03 1.04e+01
  dihedral pdb=" CB  GLU D 338 "
           pdb=" CG  GLU D 338 "
           pdb=" CD  GLU D 338 "
           pdb=" OE1 GLU D 338 "
      ideal   model   delta sinusoidal    sigma   weight residual
       0.00   88.66  -88.66     1      3.00e+01 1.11e-03 1.04e+01
  dihedral pdb=" CB  GLU F 338 "
           pdb=" CG  GLU F 338 "
           pdb=" CD  GLU F 338 "
           pdb=" OE1 GLU F 338 "
      ideal   model   delta sinusoidal    sigma   weight residual
       0.00   88.65  -88.65     1      3.00e+01 1.11e-03 1.04e+01
  ... (remaining 1653 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.048: 296
       0.048 -    0.095: 64
       0.095 -    0.143: 36
       0.143 -    0.190: 6
       0.190 -    0.238: 12
  Chirality restraints: 414
  Sorted by residual:
  chirality pdb=" CB  THR D 361 "
            pdb=" CA  THR D 361 "
            pdb=" OG1 THR D 361 "
            pdb=" CG2 THR D 361 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.55    2.31    0.24 2.00e-01 2.50e+01 1.42e+00
  chirality pdb=" CB  THR E 361 "
            pdb=" CA  THR E 361 "
            pdb=" OG1 THR E 361 "
            pdb=" CG2 THR E 361 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.55    2.32    0.24 2.00e-01 2.50e+01 1.40e+00
  chirality pdb=" CB  THR A 361 "
            pdb=" CA  THR A 361 "
            pdb=" OG1 THR A 361 "
            pdb=" CG2 THR A 361 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.55    2.32    0.24 2.00e-01 2.50e+01 1.39e+00
  ... (remaining 411 not shown)

  Planarity restraints: 462
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  SER E 341 "   -0.004 2.00e-02 2.50e+03   7.23e-03 5.22e-01
        pdb=" C   SER E 341 "    0.013 2.00e-02 2.50e+03
        pdb=" O   SER E 341 "   -0.005 2.00e-02 2.50e+03
        pdb=" N   GLU E 342 "   -0.004 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  SER B 341 "   -0.004 2.00e-02 2.50e+03   7.11e-03 5.06e-01
        pdb=" C   SER B 341 "    0.012 2.00e-02 2.50e+03
        pdb=" O   SER B 341 "   -0.005 2.00e-02 2.50e+03
        pdb=" N   GLU B 342 "   -0.004 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  SER D 341 "   -0.003 2.00e-02 2.50e+03   6.96e-03 4.84e-01
        pdb=" C   SER D 341 "    0.012 2.00e-02 2.50e+03
        pdb=" O   SER D 341 "   -0.005 2.00e-02 2.50e+03
        pdb=" N   GLU D 342 "   -0.004 2.00e-02 2.50e+03
  ... (remaining 459 not shown)

  Histogram of nonbonded interaction distances:
        2.33 -     2.84: 799
        2.84 -     3.36: 2167
        3.36 -     3.87: 4389
        3.87 -     4.39: 4578
        4.39 -     4.90: 9317
  Nonbonded interactions: 21250
  Sorted by model distance:
  nonbonded pdb=" NE2 GLN D 336 "
            pdb=" O   GLN A 336 "
     model   vdw
     2.331 3.120
  nonbonded pdb=" O   GLN B 336 "
            pdb=" NE2 GLN A 336 "
     model   vdw
     2.343 3.120
  nonbonded pdb=" O   GLN D 336 "
            pdb=" NE2 GLN C 336 "
     model   vdw
     2.346 3.120
  nonbonded pdb=" NE2 GLN B 336 "
            pdb=" O   GLN F 336 "
     model   vdw
     2.355 3.120
  nonbonded pdb=" NE2 GLN E 336 "
            pdb=" O   GLN C 336 "
     model   vdw
     2.356 3.120
  ... (remaining 21245 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: 0.02
Found NCS groups:
ncs_group {
  reference = chain 'A'
  selection = chain 'C'
  selection = chain 'B'
  selection = chain 'E'
  selection = chain 'D'
  selection = chain 'F'
}

Set up NCS constraints
  No NCS constraints will be used in refinement.
Set refine NCS operators
Adjust number of macro_cycles
  Number of macro_cycles: 10
Reset NCS operators
Extract rigid body selections
Check and reset occupancies
  Occupancies: min=1.00 max=1.00 mean=1.00
Load rotamer database and sin/cos tables
Set ADP refinement strategy
  ADPs will be refined as individual isotropic
Make a string to write initial .geo file
Internal consistency checks
Time:
  Set random seed:                         0.000
  Set model cs if undefined:               0.000
  Decide on map wrapping:                  0.000
  Normalize map: mean=0, sd=1:             0.930
  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:          0.100
  Check model and map are aligned:         0.020
  Set scattering table:                    0.020
  Process input model:                     9.890
  Find NCS groups from input model:        0.060
  Set up NCS constraints:                  0.000
  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:13.170
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   24.190
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7901
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      :  0.008   0.047   2712  Z= 0.338
  Angle     :  0.796   4.443   3630  Z= 0.430
  Chirality :  0.064   0.238    414
  Planarity :  0.003   0.007    462
  Dihedral  : 14.504  88.683   1032
  Min Nonbonded Distance : 2.331

Molprobity Statistics.
  All-atom Clashscore : 9.02
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  : 12.28 %
    Favored  : 87.72 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  5.77 %
    Favored  : 94.23 %
  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: -5.97 (0.30), residues: 342
  helix:  None (None), residues: 0
  sheet:  None (None), residues: 0
  loop : -4.55 (0.23), residues: 342

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 HIS   0.002   0.001   HIS E 362 
 PHE   0.005   0.003   PHE F 346 
 TYR   0.009   0.003   TYR E 310 
 ARG   0.001   0.000   ARG B 349 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.17302 (   20)
  hydrogen bonds       : angle       6.43548 (   60)
  covalent geometry    : bond        0.00828 ( 2712)
  covalent geometry    : angle       0.79556 ( 3630)

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

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

  684 Ramachandran restraints generated.
    342 Oldfield, 0 Emsley, 342 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  684 Ramachandran restraints generated.
    342 Oldfield, 0 Emsley, 342 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  81 residues out of total 312 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 81
  time to evaluate  : 0.368 
Fit side-chains
REVERT: B  317 LYS cc_start: 0.7820 (ttmt) cc_final: 0.7519 (mtpm)
REVERT: B  343 LYS cc_start: 0.7919 (tttm) cc_final: 0.7707 (ttpt)
REVERT: B  349 ARG cc_start: 0.7178 (mtt-85) cc_final: 0.6597 (mtm-85)
REVERT: D  317 LYS cc_start: 0.7743 (ttmt) cc_final: 0.7464 (mtpp)
REVERT: D  340 LYS cc_start: 0.7845 (ttpt) cc_final: 0.7541 (ttpt)
REVERT: D  348 ASP cc_start: 0.7762 (m-30) cc_final: 0.7318 (m-30)
REVERT: D  349 ARG cc_start: 0.6921 (mtt-85) cc_final: 0.6352 (mtp85)
REVERT: D  353 LYS cc_start: 0.7983 (mtpt) cc_final: 0.7781 (mtpp)
REVERT: E  317 LYS cc_start: 0.7939 (ttmt) cc_final: 0.7712 (mtpt)
REVERT: E  340 LYS cc_start: 0.7980 (ttpt) cc_final: 0.7644 (ttpt)
REVERT: E  343 LYS cc_start: 0.7817 (tttm) cc_final: 0.7516 (ttmm)
REVERT: E  349 ARG cc_start: 0.6799 (mtt-85) cc_final: 0.6325 (mtp85)
REVERT: E  353 LYS cc_start: 0.8137 (mtpt) cc_final: 0.7282 (mttm)
REVERT: F  317 LYS cc_start: 0.7880 (ttmt) cc_final: 0.7551 (mtpm)
REVERT: F  348 ASP cc_start: 0.7820 (m-30) cc_final: 0.7565 (m-30)
REVERT: F  349 ARG cc_start: 0.7140 (mtt-85) cc_final: 0.6885 (mtt90)
REVERT: F  353 LYS cc_start: 0.8156 (mtpt) cc_final: 0.7451 (mttp)
REVERT: A  317 LYS cc_start: 0.7575 (ttmt) cc_final: 0.7144 (mtpt)
REVERT: A  349 ARG cc_start: 0.6752 (mtt-85) cc_final: 0.6532 (mtt90)
REVERT: A  353 LYS cc_start: 0.7834 (mtpt) cc_final: 0.7206 (tptt)
REVERT: C  317 LYS cc_start: 0.7976 (ttmt) cc_final: 0.7664 (tttt)
REVERT: C  343 LYS cc_start: 0.7674 (tttm) cc_final: 0.7455 (tttm)
REVERT: C  349 ARG cc_start: 0.6699 (mtt-85) cc_final: 0.6313 (mtt-85)
REVERT: C  353 LYS cc_start: 0.8039 (mtpt) cc_final: 0.7325 (mttp)
  outliers start: 0
  outliers final: 0
  residues processed: 81
  average time/residue: 1.4822
  time to fit residues: 122.2890
Evaluate side-chains
  56 residues out of total 312 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 56
  time to evaluate  : 0.332 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 30
   random chunks:
   chunk 25 optimal weight:    0.8980
   chunk 22 optimal weight:    0.8980
   chunk 12 optimal weight:    4.9990
   chunk 7 optimal weight:    0.9990
   chunk 15 optimal weight:    2.9990
   chunk 23 optimal weight:    5.9990
   chunk 9 optimal weight:    3.9990
   chunk 14 optimal weight:   10.0000
   chunk 17 optimal weight:    0.8980
   chunk 27 optimal weight:    4.9990
   chunk 8 optimal weight:    6.9990
   overall best weight:    1.3384

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

Flipped N/Q/H residues before XYZ refinement:
B 307 GLN
B 329 HIS
B 330 HIS
D 307 GLN
D 329 HIS
D 330 HIS
E 307 GLN
E 329 HIS
F 307 GLN
F 329 HIS
F 330 HIS
A 307 GLN
A 329 HIS
A 330 HIS
C 307 GLN
C 329 HIS

Total number of N/Q/H flips: 16

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4203 r_free = 0.4203 target = 0.136450 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 41)----------------|
| r_work = 0.3864 r_free = 0.3864 target = 0.108439 restraints weight = 3504.463|
|-----------------------------------------------------------------------------|
r_work (start): 0.3870 rms_B_bonded: 2.26
r_work: 0.3777 rms_B_bonded: 2.32 restraints_weight: 0.5000
r_work: 0.3679 rms_B_bonded: 3.80 restraints_weight: 0.2500
r_work (final): 0.3679
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8016
moved from start:          0.1911

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.017   2712  Z= 0.127
  Angle     :  0.579   4.521   3630  Z= 0.287
  Chirality :  0.053   0.144    414
  Planarity :  0.002   0.014    462
  Dihedral  :  4.155  10.510    360
  Min Nonbonded Distance : 2.633

Molprobity Statistics.
  All-atom Clashscore : 7.18
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.73 %
    Favored  : 93.27 %
  Rotamer:
    Outliers :  2.56 %
    Allowed  : 13.46 %
    Favored  : 83.97 %
  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: -5.54 (0.32), residues: 342
  helix:  None (None), residues: 0
  sheet:  None (None), residues: 0
  loop : -4.21 (0.24), residues: 342

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 HIS   0.002   0.001   HIS D 362 
 PHE   0.003   0.001   PHE E 346 
 TYR   0.004   0.001   TYR C 310 
 ARG   0.001   0.000   ARG E 349 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.02200 (   20)
  hydrogen bonds       : angle       4.52704 (   60)
  covalent geometry    : bond        0.00268 ( 2712)
  covalent geometry    : angle       0.57859 ( 3630)

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

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

  684 Ramachandran restraints generated.
    342 Oldfield, 0 Emsley, 342 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  684 Ramachandran restraints generated.
    342 Oldfield, 0 Emsley, 342 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  77 residues out of total 312 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 8
    poor density    : 69
  time to evaluate  : 0.331 
Fit side-chains
REVERT: B  340 LYS cc_start: 0.8024 (ttpt) cc_final: 0.7705 (ttmm)
REVERT: B  349 ARG cc_start: 0.7523 (mtt-85) cc_final: 0.7075 (mtm-85)
REVERT: D  317 LYS cc_start: 0.7949 (ttmt) cc_final: 0.7674 (ttpp)
REVERT: D  340 LYS cc_start: 0.8062 (ttpt) cc_final: 0.7843 (ttpt)
REVERT: D  348 ASP cc_start: 0.8038 (m-30) cc_final: 0.7734 (m-30)
REVERT: D  349 ARG cc_start: 0.7264 (mtt-85) cc_final: 0.6670 (mtp85)
REVERT: D  353 LYS cc_start: 0.8001 (mtpt) cc_final: 0.7151 (mppt)
REVERT: E  317 LYS cc_start: 0.8209 (ttmt) cc_final: 0.7824 (tttt)
REVERT: E  343 LYS cc_start: 0.7969 (tttm) cc_final: 0.7719 (ttmm)
REVERT: E  348 ASP cc_start: 0.7812 (OUTLIER) cc_final: 0.7553 (m-30)
REVERT: E  349 ARG cc_start: 0.7051 (mtt-85) cc_final: 0.6510 (mtp85)
REVERT: F  317 LYS cc_start: 0.8011 (ttmt) cc_final: 0.7768 (mtpm)
REVERT: F  348 ASP cc_start: 0.8241 (m-30) cc_final: 0.7935 (m-30)
REVERT: F  349 ARG cc_start: 0.7532 (mtt-85) cc_final: 0.7213 (mtm-85)
REVERT: F  353 LYS cc_start: 0.7981 (mtpt) cc_final: 0.7342 (mttp)
REVERT: A  340 LYS cc_start: 0.8085 (ttpt) cc_final: 0.7881 (ttpt)
REVERT: A  349 ARG cc_start: 0.7158 (mtt-85) cc_final: 0.6826 (mtt90)
REVERT: A  357 LEU cc_start: 0.7901 (tt) cc_final: 0.7587 (tp)
REVERT: C  317 LYS cc_start: 0.8272 (ttmt) cc_final: 0.7877 (tttt)
REVERT: C  348 ASP cc_start: 0.8025 (m-30) cc_final: 0.7711 (m-30)
REVERT: C  349 ARG cc_start: 0.6991 (mtt-85) cc_final: 0.6369 (mtp-110)
REVERT: C  353 LYS cc_start: 0.8127 (mtpt) cc_final: 0.7404 (mttp)
  outliers start: 8
  outliers final: 4
  residues processed: 72
  average time/residue: 1.5121
  time to fit residues: 110.9011
Evaluate side-chains
  60 residues out of total 312 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 5
    poor density    : 55
  time to evaluate  : 0.312 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue  316 SER
Chi-restraints excluded: chain E residue  320 SER
Chi-restraints excluded: chain E residue  348 ASP
Chi-restraints excluded: chain F residue  315 LEU
Chi-restraints excluded: chain A residue  348 ASP
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 30
   random chunks:
   chunk 17 optimal weight:    0.6980
   chunk 2 optimal weight:    0.0060
   chunk 29 optimal weight:    5.9990
   chunk 19 optimal weight:    4.9990
   chunk 21 optimal weight:    8.9990
   chunk 20 optimal weight:    5.9990
   chunk 28 optimal weight:    6.9990
   chunk 12 optimal weight:    9.9990
   chunk 8 optimal weight:    2.9990
   chunk 0 optimal weight:    8.9990
   chunk 14 optimal weight:    3.9990
   overall best weight:    2.5402

-------------------------------------------------------------------------------
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 = 0.4182 r_free = 0.4182 target = 0.134018 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 35)----------------|
| r_work = 0.3868 r_free = 0.3868 target = 0.106979 restraints weight = 3567.208|
|-----------------------------------------------------------------------------|
r_work (start): 0.3865 rms_B_bonded: 2.17
r_work: 0.3777 rms_B_bonded: 2.26 restraints_weight: 0.5000
r_work: 0.3682 rms_B_bonded: 3.71 restraints_weight: 0.2500
r_work (final): 0.3682
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8008
moved from start:          0.2106

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.029   2712  Z= 0.171
  Angle     :  0.616   5.369   3630  Z= 0.302
  Chirality :  0.053   0.146    414
  Planarity :  0.002   0.013    462
  Dihedral  :  4.366  11.445    360
  Min Nonbonded Distance : 2.638

Molprobity Statistics.
  All-atom Clashscore : 8.66
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  8.77 %
    Favored  : 91.23 %
  Rotamer:
    Outliers :  3.53 %
    Allowed  : 16.99 %
    Favored  : 79.49 %
  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: -5.62 (0.32), residues: 342
  helix:  None (None), residues: 0
  sheet:  None (None), residues: 0
  loop : -4.28 (0.24), residues: 342

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 HIS   0.002   0.001   HIS F 362 
 PHE   0.004   0.002   PHE E 346 
 TYR   0.007   0.002   TYR D 310 
 ARG   0.001   0.000   ARG E 349 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.02077 (   20)
  hydrogen bonds       : angle       4.30852 (   60)
  covalent geometry    : bond        0.00394 ( 2712)
  covalent geometry    : angle       0.61639 ( 3630)

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

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

  684 Ramachandran restraints generated.
    342 Oldfield, 0 Emsley, 342 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  684 Ramachandran restraints generated.
    342 Oldfield, 0 Emsley, 342 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  71 residues out of total 312 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 60
  time to evaluate  : 0.298 
Fit side-chains
REVERT: B  340 LYS cc_start: 0.7941 (ttpt) cc_final: 0.7739 (ttpp)
REVERT: B  349 ARG cc_start: 0.7549 (mtt-85) cc_final: 0.7141 (mtm-85)
REVERT: D  317 LYS cc_start: 0.7928 (ttmt) cc_final: 0.7620 (ttpp)
REVERT: D  340 LYS cc_start: 0.7914 (ttpt) cc_final: 0.7669 (ttpt)
REVERT: D  348 ASP cc_start: 0.8013 (m-30) cc_final: 0.7710 (m-30)
REVERT: D  349 ARG cc_start: 0.7184 (mtt-85) cc_final: 0.6511 (mtp85)
REVERT: D  353 LYS cc_start: 0.7958 (mtpt) cc_final: 0.7086 (mppt)
REVERT: D  358 ASP cc_start: 0.6344 (m-30) cc_final: 0.5529 (p0)
REVERT: E  317 LYS cc_start: 0.8106 (ttmt) cc_final: 0.7822 (ttpp)
REVERT: E  343 LYS cc_start: 0.8077 (tttm) cc_final: 0.7768 (ttmm)
REVERT: E  348 ASP cc_start: 0.7851 (OUTLIER) cc_final: 0.7575 (m-30)
REVERT: E  349 ARG cc_start: 0.6980 (mtt-85) cc_final: 0.6430 (mtp85)
REVERT: F  317 LYS cc_start: 0.7962 (ttmt) cc_final: 0.7663 (mtpm)
REVERT: F  348 ASP cc_start: 0.8262 (m-30) cc_final: 0.8017 (m-30)
REVERT: F  349 ARG cc_start: 0.7539 (mtt-85) cc_final: 0.7285 (mtm-85)
REVERT: A  317 LYS cc_start: 0.7853 (ttmt) cc_final: 0.7477 (mtpt)
REVERT: A  349 ARG cc_start: 0.7122 (mtt-85) cc_final: 0.6503 (mtp-110)
REVERT: A  357 LEU cc_start: 0.7775 (tt) cc_final: 0.7347 (tp)
REVERT: A  358 ASP cc_start: 0.6848 (m-30) cc_final: 0.6525 (m-30)
REVERT: C  317 LYS cc_start: 0.8172 (ttmt) cc_final: 0.7711 (ttmm)
REVERT: C  349 ARG cc_start: 0.6927 (mtt-85) cc_final: 0.6307 (mtp-110)
REVERT: C  353 LYS cc_start: 0.8171 (mtpt) cc_final: 0.7435 (mttp)
  outliers start: 11
  outliers final: 7
  residues processed: 68
  average time/residue: 1.4179
  time to fit residues: 98.3380
Evaluate side-chains
  67 residues out of total 312 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 8
    poor density    : 59
  time to evaluate  : 0.337 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue  316 SER
Chi-restraints excluded: chain D residue  316 SER
Chi-restraints excluded: chain E residue  320 SER
Chi-restraints excluded: chain E residue  348 ASP
Chi-restraints excluded: chain F residue  315 LEU
Chi-restraints excluded: chain A residue  316 SER
Chi-restraints excluded: chain A residue  348 ASP
Chi-restraints excluded: chain C residue  311 LYS
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 30
   random chunks:
   chunk 2 optimal weight:    4.9990
   chunk 14 optimal weight:    8.9990
   chunk 8 optimal weight:    5.9990
   chunk 1 optimal weight:    2.9990
   chunk 10 optimal weight:    7.9990
   chunk 26 optimal weight:   10.0000
   chunk 16 optimal weight:    4.9990
   chunk 7 optimal weight:    6.9990
   chunk 9 optimal weight:    7.9990
   chunk 15 optimal weight:    7.9990
   chunk 29 optimal weight:   10.0000
   overall best weight:    5.1990

-------------------------------------------------------------------------------
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 = 0.4173 r_free = 0.4173 target = 0.132988 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 32)----------------|
| r_work = 0.3853 r_free = 0.3853 target = 0.105902 restraints weight = 3618.484|
|-----------------------------------------------------------------------------|
r_work (start): 0.3852 rms_B_bonded: 2.17
r_work: 0.3762 rms_B_bonded: 2.25 restraints_weight: 0.5000
r_work: 0.3664 rms_B_bonded: 3.71 restraints_weight: 0.2500
r_work (final): 0.3664
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8011
moved from start:          0.2261

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.007   0.045   2712  Z= 0.279
  Angle     :  0.752   6.757   3630  Z= 0.372
  Chirality :  0.055   0.151    414
  Planarity :  0.004   0.014    462
  Dihedral  :  5.092  13.941    360
  Min Nonbonded Distance : 2.647

Molprobity Statistics.
  All-atom Clashscore : 10.50
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  : 13.16 %
    Favored  : 86.84 %
  Rotamer:
    Outliers :  7.69 %
    Allowed  : 14.42 %
    Favored  : 77.88 %
  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: -5.76 (0.31), residues: 342
  helix:  None (None), residues: 0
  sheet:  None (None), residues: 0
  loop : -4.38 (0.23), residues: 342

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 HIS   0.003   0.001   HIS F 362 
 PHE   0.007   0.003   PHE F 346 
 TYR   0.011   0.003   TYR C 310 
 ARG   0.003   0.001   ARG E 349 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.01956 (   20)
  hydrogen bonds       : angle       4.14610 (   60)
  covalent geometry    : bond        0.00664 ( 2712)
  covalent geometry    : angle       0.75153 ( 3630)

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

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

  684 Ramachandran restraints generated.
    342 Oldfield, 0 Emsley, 342 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  684 Ramachandran restraints generated.
    342 Oldfield, 0 Emsley, 342 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  84 residues out of total 312 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 24
    poor density    : 60
  time to evaluate  : 0.305 
Fit side-chains
REVERT: B  340 LYS cc_start: 0.7874 (ttpt) cc_final: 0.7616 (ttpp)
REVERT: B  348 ASP cc_start: 0.8221 (m-30) cc_final: 0.7719 (m-30)
REVERT: B  349 ARG cc_start: 0.7575 (mtt-85) cc_final: 0.7168 (mtm-85)
REVERT: B  353 LYS cc_start: 0.8091 (OUTLIER) cc_final: 0.7637 (mtpt)
REVERT: D  317 LYS cc_start: 0.7950 (ttmt) cc_final: 0.7635 (ttpp)
REVERT: D  349 ARG cc_start: 0.7123 (mtt-85) cc_final: 0.6445 (mtp85)
REVERT: D  353 LYS cc_start: 0.8022 (mtpt) cc_final: 0.7757 (mtpp)
REVERT: D  358 ASP cc_start: 0.6198 (m-30) cc_final: 0.5960 (t0)
REVERT: E  317 LYS cc_start: 0.8131 (ttmt) cc_final: 0.7845 (ttpp)
REVERT: E  325 LEU cc_start: 0.8520 (OUTLIER) cc_final: 0.8291 (pp)
REVERT: E  343 LYS cc_start: 0.7987 (tttm) cc_final: 0.7688 (ttmm)
REVERT: E  348 ASP cc_start: 0.7918 (OUTLIER) cc_final: 0.7633 (m-30)
REVERT: E  349 ARG cc_start: 0.7083 (mtt-85) cc_final: 0.6432 (mtp85)
REVERT: F  317 LYS cc_start: 0.8010 (ttmt) cc_final: 0.7712 (mtpm)
REVERT: F  348 ASP cc_start: 0.8307 (m-30) cc_final: 0.8058 (m-30)
REVERT: F  349 ARG cc_start: 0.7509 (mtt-85) cc_final: 0.7082 (mtm-85)
REVERT: F  353 LYS cc_start: 0.7979 (mtpt) cc_final: 0.7350 (mttp)
REVERT: A  317 LYS cc_start: 0.7795 (ttmt) cc_final: 0.7324 (mttt)
REVERT: A  349 ARG cc_start: 0.7059 (mtt-85) cc_final: 0.6386 (mtp-110)
REVERT: A  357 LEU cc_start: 0.8035 (tt) cc_final: 0.7646 (tp)
REVERT: C  317 LYS cc_start: 0.8178 (ttmt) cc_final: 0.7728 (ttmm)
REVERT: C  349 ARG cc_start: 0.7016 (mtt-85) cc_final: 0.6461 (mtt-85)
  outliers start: 24
  outliers final: 15
  residues processed: 80
  average time/residue: 1.3806
  time to fit residues: 112.7908
Evaluate side-chains
  73 residues out of total 312 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 18
    poor density    : 55
  time to evaluate  : 0.306 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue  316 SER
Chi-restraints excluded: chain B residue  353 LYS
Chi-restraints excluded: chain D residue  306 VAL
Chi-restraints excluded: chain D residue  315 LEU
Chi-restraints excluded: chain D residue  316 SER
Chi-restraints excluded: chain E residue  316 SER
Chi-restraints excluded: chain E residue  320 SER
Chi-restraints excluded: chain E residue  325 LEU
Chi-restraints excluded: chain E residue  348 ASP
Chi-restraints excluded: chain F residue  315 LEU
Chi-restraints excluded: chain A residue  306 VAL
Chi-restraints excluded: chain A residue  316 SER
Chi-restraints excluded: chain A residue  322 CYS
Chi-restraints excluded: chain A residue  340 LYS
Chi-restraints excluded: chain A residue  348 ASP
Chi-restraints excluded: chain C residue  311 LYS
Chi-restraints excluded: chain C residue  316 SER
Chi-restraints excluded: chain C residue  348 ASP
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 30
   random chunks:
   chunk 28 optimal weight:    5.9990
   chunk 0 optimal weight:    5.9990
   chunk 29 optimal weight:    9.9990
   chunk 11 optimal weight:    6.9990
   chunk 8 optimal weight:    8.9990
   chunk 20 optimal weight:    0.9990
   chunk 6 optimal weight:    6.9990
   chunk 21 optimal weight:   10.0000
   chunk 17 optimal weight:    1.9990
   chunk 19 optimal weight:    9.9990
   chunk 26 optimal weight:    9.9990
   overall best weight:    4.3990

-------------------------------------------------------------------------------
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 = 0.4180 r_free = 0.4180 target = 0.133890 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 37)----------------|
| r_work = 0.3862 r_free = 0.3862 target = 0.106589 restraints weight = 3552.013|
|-----------------------------------------------------------------------------|
r_work (start): 0.3863 rms_B_bonded: 2.15
r_work: 0.3773 rms_B_bonded: 2.26 restraints_weight: 0.5000
r_work: 0.3677 rms_B_bonded: 3.71 restraints_weight: 0.2500
r_work (final): 0.3677
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8003
moved from start:          0.2467

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.006   0.040   2712  Z= 0.246
  Angle     :  0.711   6.241   3630  Z= 0.352
  Chirality :  0.054   0.147    414
  Planarity :  0.003   0.015    462
  Dihedral  :  5.014  13.592    360
  Min Nonbonded Distance : 2.649

Molprobity Statistics.
  All-atom Clashscore : 9.94
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  : 11.99 %
    Favored  : 88.01 %
  Rotamer:
    Outliers :  8.33 %
    Allowed  : 16.35 %
    Favored  : 75.32 %
  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: -5.68 (0.31), residues: 342
  helix:  None (None), residues: 0
  sheet:  None (None), residues: 0
  loop : -4.32 (0.24), residues: 342

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 HIS   0.003   0.001   HIS F 362 
 PHE   0.006   0.003   PHE F 346 
 TYR   0.009   0.003   TYR C 310 
 ARG   0.002   0.001   ARG C 349 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.01810 (   20)
  hydrogen bonds       : angle       4.12817 (   60)
  covalent geometry    : bond        0.00579 ( 2712)
  covalent geometry    : angle       0.71108 ( 3630)

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

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

  684 Ramachandran restraints generated.
    342 Oldfield, 0 Emsley, 342 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  684 Ramachandran restraints generated.
    342 Oldfield, 0 Emsley, 342 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  79 residues out of total 312 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 26
    poor density    : 53
  time to evaluate  : 0.330 
Fit side-chains
REVERT: B  348 ASP cc_start: 0.8213 (m-30) cc_final: 0.7715 (m-30)
REVERT: B  349 ARG cc_start: 0.7646 (mtt-85) cc_final: 0.7217 (mtm-85)
REVERT: B  353 LYS cc_start: 0.8056 (OUTLIER) cc_final: 0.7591 (mtpt)
REVERT: D  311 LYS cc_start: 0.8223 (OUTLIER) cc_final: 0.8002 (mmtp)
REVERT: D  317 LYS cc_start: 0.7952 (ttmt) cc_final: 0.7646 (ttpp)
REVERT: D  349 ARG cc_start: 0.7137 (mtt-85) cc_final: 0.6506 (mtp85)
REVERT: D  353 LYS cc_start: 0.8044 (mtpt) cc_final: 0.7772 (mtpp)
REVERT: E  317 LYS cc_start: 0.8113 (ttmt) cc_final: 0.7820 (ttpp)
REVERT: E  325 LEU cc_start: 0.8553 (OUTLIER) cc_final: 0.8269 (pp)
REVERT: E  342 GLU cc_start: 0.8054 (pt0) cc_final: 0.7582 (pt0)
REVERT: E  343 LYS cc_start: 0.8008 (tttm) cc_final: 0.7698 (ttmm)
REVERT: E  348 ASP cc_start: 0.7916 (OUTLIER) cc_final: 0.7616 (m-30)
REVERT: E  349 ARG cc_start: 0.7145 (mtt-85) cc_final: 0.6436 (mtp85)
REVERT: F  317 LYS cc_start: 0.8023 (ttmt) cc_final: 0.7747 (mtpm)
REVERT: F  348 ASP cc_start: 0.8264 (m-30) cc_final: 0.8028 (m-30)
REVERT: F  349 ARG cc_start: 0.7463 (mtt-85) cc_final: 0.7059 (mtm-85)
REVERT: F  353 LYS cc_start: 0.7940 (mtpt) cc_final: 0.7306 (mttp)
REVERT: A  317 LYS cc_start: 0.7817 (ttmt) cc_final: 0.7444 (mtpt)
REVERT: A  349 ARG cc_start: 0.7101 (mtt-85) cc_final: 0.6438 (mtp-110)
REVERT: A  357 LEU cc_start: 0.8000 (tt) cc_final: 0.7579 (tp)
REVERT: C  317 LYS cc_start: 0.8187 (ttmt) cc_final: 0.7740 (ttmm)
REVERT: C  349 ARG cc_start: 0.7044 (mtt-85) cc_final: 0.6478 (mtp-110)
  outliers start: 26
  outliers final: 17
  residues processed: 73
  average time/residue: 1.3004
  time to fit residues: 96.9222
Evaluate side-chains
  72 residues out of total 312 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 21
    poor density    : 51
  time to evaluate  : 0.302 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue  316 SER
Chi-restraints excluded: chain B residue  353 LYS
Chi-restraints excluded: chain D residue  306 VAL
Chi-restraints excluded: chain D residue  311 LYS
Chi-restraints excluded: chain D residue  315 LEU
Chi-restraints excluded: chain D residue  316 SER
Chi-restraints excluded: chain D residue  348 ASP
Chi-restraints excluded: chain E residue  306 VAL
Chi-restraints excluded: chain E residue  320 SER
Chi-restraints excluded: chain E residue  325 LEU
Chi-restraints excluded: chain E residue  348 ASP
Chi-restraints excluded: chain F residue  315 LEU
Chi-restraints excluded: chain F residue  325 LEU
Chi-restraints excluded: chain A residue  306 VAL
Chi-restraints excluded: chain A residue  316 SER
Chi-restraints excluded: chain A residue  322 CYS
Chi-restraints excluded: chain A residue  340 LYS
Chi-restraints excluded: chain A residue  348 ASP
Chi-restraints excluded: chain C residue  306 VAL
Chi-restraints excluded: chain C residue  311 LYS
Chi-restraints excluded: chain C residue  348 ASP
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 30
   random chunks:
   chunk 12 optimal weight:    0.5980
   chunk 6 optimal weight:   10.0000
   chunk 28 optimal weight:    8.9990
   chunk 8 optimal weight:    4.9990
   chunk 1 optimal weight:    1.9990
   chunk 3 optimal weight:    1.9990
   chunk 10 optimal weight:    0.0270
   chunk 4 optimal weight:    0.0980
   chunk 15 optimal weight:    6.9990
   chunk 29 optimal weight:   10.0000
   chunk 9 optimal weight:   10.0000
   overall best weight:    0.9442

-------------------------------------------------------------------------------
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 = 0.4253 r_free = 0.4253 target = 0.142125 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 33)----------------|
| r_work = 0.3941 r_free = 0.3941 target = 0.114329 restraints weight = 3452.955|
|-----------------------------------------------------------------------------|
r_work (start): 0.3952 rms_B_bonded: 2.15
r_work: 0.3865 rms_B_bonded: 2.27 restraints_weight: 0.5000
r_work: 0.3772 rms_B_bonded: 3.74 restraints_weight: 0.2500
r_work (final): 0.3772
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7955
moved from start:          0.2837

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.015   2712  Z= 0.111
  Angle     :  0.546   4.715   3630  Z= 0.267
  Chirality :  0.051   0.136    414
  Planarity :  0.002   0.017    462
  Dihedral  :  4.049  10.948    360
  Min Nonbonded Distance : 2.635

Molprobity Statistics.
  All-atom Clashscore : 8.47
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.14 %
    Favored  : 93.86 %
  Rotamer:
    Outliers :  4.81 %
    Allowed  : 20.19 %
    Favored  : 75.00 %
  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: -5.31 (0.33), residues: 342
  helix:  None (None), residues: 0
  sheet:  None (None), residues: 0
  loop : -4.04 (0.25), residues: 342

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 HIS   0.003   0.001   HIS E 362 
 PHE   0.003   0.001   PHE C 346 
 TYR   0.004   0.001   TYR C 310 
 ARG   0.001   0.000   ARG C 349 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.01725 (   20)
  hydrogen bonds       : angle       4.13453 (   60)
  covalent geometry    : bond        0.00234 ( 2712)
  covalent geometry    : angle       0.54573 ( 3630)

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

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

  684 Ramachandran restraints generated.
    342 Oldfield, 0 Emsley, 342 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  684 Ramachandran restraints generated.
    342 Oldfield, 0 Emsley, 342 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  71 residues out of total 312 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 15
    poor density    : 56
  time to evaluate  : 0.326 
Fit side-chains
REVERT: B  348 ASP cc_start: 0.8149 (m-30) cc_final: 0.7745 (m-30)
REVERT: B  349 ARG cc_start: 0.7615 (mtt-85) cc_final: 0.7182 (mtm-85)
REVERT: B  357 LEU cc_start: 0.7940 (tt) cc_final: 0.7577 (tp)
REVERT: D  317 LYS cc_start: 0.8028 (ttmt) cc_final: 0.7769 (ttpp)
REVERT: D  349 ARG cc_start: 0.7227 (mtt-85) cc_final: 0.6655 (mtp85)
REVERT: D  353 LYS cc_start: 0.8039 (mtpt) cc_final: 0.7195 (mppt)
REVERT: E  317 LYS cc_start: 0.8080 (ttmt) cc_final: 0.7561 (ttmm)
REVERT: E  342 GLU cc_start: 0.7882 (pt0) cc_final: 0.7479 (pt0)
REVERT: E  343 LYS cc_start: 0.8098 (tttm) cc_final: 0.7799 (ttmm)
REVERT: E  348 ASP cc_start: 0.7728 (OUTLIER) cc_final: 0.7498 (m-30)
REVERT: E  349 ARG cc_start: 0.7087 (mtt-85) cc_final: 0.6564 (mtp85)
REVERT: F  317 LYS cc_start: 0.7955 (ttmt) cc_final: 0.7720 (mtpm)
REVERT: F  348 ASP cc_start: 0.8290 (m-30) cc_final: 0.8027 (m-30)
REVERT: F  349 ARG cc_start: 0.7455 (mtt-85) cc_final: 0.6042 (mpp-170)
REVERT: A  317 LYS cc_start: 0.7918 (ttmt) cc_final: 0.7587 (mtpt)
REVERT: A  349 ARG cc_start: 0.7161 (mtt-85) cc_final: 0.6630 (mtp-110)
REVERT: A  357 LEU cc_start: 0.7850 (tt) cc_final: 0.7417 (tp)
REVERT: C  317 LYS cc_start: 0.8183 (ttmt) cc_final: 0.7790 (ttmm)
REVERT: C  349 ARG cc_start: 0.7053 (mtt-85) cc_final: 0.6530 (mtp-110)
  outliers start: 15
  outliers final: 6
  residues processed: 66
  average time/residue: 1.3830
  time to fit residues: 93.1602
Evaluate side-chains
  59 residues out of total 312 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 7
    poor density    : 52
  time to evaluate  : 0.333 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue  316 SER
Chi-restraints excluded: chain D residue  348 ASP
Chi-restraints excluded: chain E residue  306 VAL
Chi-restraints excluded: chain E residue  320 SER
Chi-restraints excluded: chain E residue  348 ASP
Chi-restraints excluded: chain A residue  306 VAL
Chi-restraints excluded: chain A residue  348 ASP
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 30
   random chunks:
   chunk 19 optimal weight:    5.9990
   chunk 29 optimal weight:    9.9990
   chunk 20 optimal weight:   10.0000
   chunk 27 optimal weight:    2.9990
   chunk 21 optimal weight:   10.0000
   chunk 25 optimal weight:    0.8980
   chunk 13 optimal weight:    9.9990
   chunk 6 optimal weight:    8.9990
   chunk 14 optimal weight:    4.9990
   chunk 24 optimal weight:    4.9990
   chunk 1 optimal weight:    3.9990
   overall best weight:    3.5788

-------------------------------------------------------------------------------
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 = 0.4197 r_free = 0.4197 target = 0.134872 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.3872 r_free = 0.3872 target = 0.107419 restraints weight = 3720.076|
|-----------------------------------------------------------------------------|
r_work (start): 0.3874 rms_B_bonded: 2.22
r_work: 0.3786 rms_B_bonded: 2.31 restraints_weight: 0.5000
r_work: 0.3689 rms_B_bonded: 3.81 restraints_weight: 0.2500
r_work (final): 0.3689
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7994
moved from start:          0.2727

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.035   2712  Z= 0.211
  Angle     :  0.672   6.830   3630  Z= 0.327
  Chirality :  0.054   0.146    414
  Planarity :  0.003   0.014    462
  Dihedral  :  4.739  13.029    360
  Min Nonbonded Distance : 2.646

Molprobity Statistics.
  All-atom Clashscore : 9.94
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  : 13.16 %
    Favored  : 86.84 %
  Rotamer:
    Outliers :  6.41 %
    Allowed  : 19.87 %
    Favored  : 73.72 %
  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: -5.46 (0.32), residues: 342
  helix:  None (None), residues: 0
  sheet:  None (None), residues: 0
  loop : -4.16 (0.25), residues: 342

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 HIS   0.003   0.001   HIS F 362 
 PHE   0.005   0.002   PHE C 346 
 TYR   0.008   0.002   TYR C 310 
 ARG   0.002   0.001   ARG C 349 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.01948 (   20)
  hydrogen bonds       : angle       4.03103 (   60)
  covalent geometry    : bond        0.00498 ( 2712)
  covalent geometry    : angle       0.67165 ( 3630)

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

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

  684 Ramachandran restraints generated.
    342 Oldfield, 0 Emsley, 342 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  684 Ramachandran restraints generated.
    342 Oldfield, 0 Emsley, 342 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  70 residues out of total 312 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 20
    poor density    : 50
  time to evaluate  : 0.336 
Fit side-chains
REVERT: B  348 ASP cc_start: 0.8245 (m-30) cc_final: 0.7739 (m-30)
REVERT: B  349 ARG cc_start: 0.7658 (mtt-85) cc_final: 0.7323 (mtp85)
REVERT: B  353 LYS cc_start: 0.8038 (OUTLIER) cc_final: 0.7553 (mtpt)
REVERT: D  317 LYS cc_start: 0.7984 (ttmt) cc_final: 0.7697 (ttpp)
REVERT: D  349 ARG cc_start: 0.7188 (mtt-85) cc_final: 0.6735 (mtt-85)
REVERT: D  353 LYS cc_start: 0.8045 (mtpt) cc_final: 0.7133 (mppt)
REVERT: E  317 LYS cc_start: 0.8104 (ttmt) cc_final: 0.7813 (ttpp)
REVERT: E  342 GLU cc_start: 0.8037 (pt0) cc_final: 0.7534 (pt0)
REVERT: E  343 LYS cc_start: 0.8137 (tttm) cc_final: 0.7795 (ttmm)
REVERT: E  348 ASP cc_start: 0.7902 (OUTLIER) cc_final: 0.7600 (m-30)
REVERT: E  349 ARG cc_start: 0.7082 (mtt-85) cc_final: 0.6364 (mtp85)
REVERT: F  317 LYS cc_start: 0.7959 (ttmt) cc_final: 0.7695 (mtpm)
REVERT: F  348 ASP cc_start: 0.8300 (m-30) cc_final: 0.8048 (m-30)
REVERT: F  349 ARG cc_start: 0.7427 (mtt-85) cc_final: 0.7108 (mtm-85)
REVERT: A  317 LYS cc_start: 0.7815 (ttmt) cc_final: 0.7483 (mtpt)
REVERT: A  349 ARG cc_start: 0.7013 (mtt-85) cc_final: 0.6402 (mtp-110)
REVERT: A  357 LEU cc_start: 0.7950 (tt) cc_final: 0.7496 (tp)
REVERT: C  317 LYS cc_start: 0.8199 (ttmt) cc_final: 0.7742 (ttmm)
REVERT: C  349 ARG cc_start: 0.6982 (mtt-85) cc_final: 0.6441 (mtt-85)
  outliers start: 20
  outliers final: 16
  residues processed: 65
  average time/residue: 1.2737
  time to fit residues: 84.6488
Evaluate side-chains
  67 residues out of total 312 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 18
    poor density    : 49
  time to evaluate  : 0.331 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue  316 SER
Chi-restraints excluded: chain B residue  353 LYS
Chi-restraints excluded: chain D residue  306 VAL
Chi-restraints excluded: chain D residue  316 SER
Chi-restraints excluded: chain D residue  325 LEU
Chi-restraints excluded: chain D residue  348 ASP
Chi-restraints excluded: chain E residue  306 VAL
Chi-restraints excluded: chain E residue  316 SER
Chi-restraints excluded: chain E residue  318 VAL
Chi-restraints excluded: chain E residue  320 SER
Chi-restraints excluded: chain E residue  348 ASP
Chi-restraints excluded: chain F residue  315 LEU
Chi-restraints excluded: chain A residue  306 VAL
Chi-restraints excluded: chain A residue  316 SER
Chi-restraints excluded: chain A residue  340 LYS
Chi-restraints excluded: chain A residue  348 ASP
Chi-restraints excluded: chain C residue  306 VAL
Chi-restraints excluded: chain C residue  348 ASP
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 30
   random chunks:
   chunk 0 optimal weight:    7.9990
   chunk 14 optimal weight:    0.1980
   chunk 18 optimal weight:    9.9990
   chunk 6 optimal weight:    5.9990
   chunk 13 optimal weight:    4.9990
   chunk 29 optimal weight:    6.9990
   chunk 8 optimal weight:   10.0000
   chunk 20 optimal weight:    5.9990
   chunk 26 optimal weight:    3.9990
   chunk 4 optimal weight:    8.9990
   chunk 10 optimal weight:    5.9990
   overall best weight:    4.2388

-------------------------------------------------------------------------------
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 = 0.4191 r_free = 0.4191 target = 0.134323 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 36)----------------|
| r_work = 0.3870 r_free = 0.3870 target = 0.107188 restraints weight = 3563.527|
|-----------------------------------------------------------------------------|
r_work (start): 0.3871 rms_B_bonded: 2.16
r_work: 0.3782 rms_B_bonded: 2.26 restraints_weight: 0.5000
r_work: 0.3686 rms_B_bonded: 3.73 restraints_weight: 0.2500
r_work (final): 0.3686
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7996
moved from start:          0.2752

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.006   0.038   2712  Z= 0.237
  Angle     :  0.709   6.781   3630  Z= 0.347
  Chirality :  0.055   0.147    414
  Planarity :  0.003   0.014    462
  Dihedral  :  4.976  13.599    360
  Min Nonbonded Distance : 2.649

Molprobity Statistics.
  All-atom Clashscore : 10.31
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  : 10.82 %
    Favored  : 89.18 %
  Rotamer:
    Outliers :  6.41 %
    Allowed  : 20.19 %
    Favored  : 73.40 %
  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: -5.50 (0.32), residues: 342
  helix:  None (None), residues: 0
  sheet:  None (None), residues: 0
  loop : -4.19 (0.24), residues: 342

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 HIS   0.003   0.001   HIS F 362 
 PHE   0.005   0.002   PHE F 346 
 TYR   0.010   0.003   TYR C 310 
 ARG   0.002   0.001   ARG A 349 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.01844 (   20)
  hydrogen bonds       : angle       4.03027 (   60)
  covalent geometry    : bond        0.00557 ( 2712)
  covalent geometry    : angle       0.70922 ( 3630)

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

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

  684 Ramachandran restraints generated.
    342 Oldfield, 0 Emsley, 342 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  684 Ramachandran restraints generated.
    342 Oldfield, 0 Emsley, 342 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  72 residues out of total 312 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 20
    poor density    : 52
  time to evaluate  : 0.324 
Fit side-chains
REVERT: B  348 ASP cc_start: 0.8235 (m-30) cc_final: 0.7728 (m-30)
REVERT: B  349 ARG cc_start: 0.7624 (mtt-85) cc_final: 0.7287 (mtp85)
REVERT: B  353 LYS cc_start: 0.8059 (OUTLIER) cc_final: 0.7584 (mtpt)
REVERT: D  317 LYS cc_start: 0.7987 (ttmt) cc_final: 0.7692 (ttpp)
REVERT: D  349 ARG cc_start: 0.7222 (mtt-85) cc_final: 0.6796 (mtp85)
REVERT: D  353 LYS cc_start: 0.8007 (mtpt) cc_final: 0.7107 (mppt)
REVERT: E  317 LYS cc_start: 0.8095 (ttmt) cc_final: 0.7802 (ttpp)
REVERT: E  325 LEU cc_start: 0.8536 (OUTLIER) cc_final: 0.8243 (pp)
REVERT: E  343 LYS cc_start: 0.8064 (tttm) cc_final: 0.7753 (ttmm)
REVERT: E  348 ASP cc_start: 0.7921 (OUTLIER) cc_final: 0.7604 (m-30)
REVERT: E  349 ARG cc_start: 0.7125 (mtt-85) cc_final: 0.6684 (mtt90)
REVERT: F  317 LYS cc_start: 0.8024 (ttmt) cc_final: 0.7765 (mtpm)
REVERT: F  348 ASP cc_start: 0.8302 (m-30) cc_final: 0.8050 (m-30)
REVERT: F  349 ARG cc_start: 0.7434 (mtt-85) cc_final: 0.7047 (mtm-85)
REVERT: A  317 LYS cc_start: 0.7799 (ttmt) cc_final: 0.7464 (mtpt)
REVERT: A  349 ARG cc_start: 0.7117 (mtt-85) cc_final: 0.6419 (mtp-110)
REVERT: A  353 LYS cc_start: 0.7710 (mtpt) cc_final: 0.7157 (tptt)
REVERT: A  357 LEU cc_start: 0.7943 (tt) cc_final: 0.7499 (tp)
REVERT: C  317 LYS cc_start: 0.8181 (ttmt) cc_final: 0.7730 (ttmm)
REVERT: C  349 ARG cc_start: 0.7024 (mtt-85) cc_final: 0.6416 (mtp-110)
  outliers start: 20
  outliers final: 18
  residues processed: 67
  average time/residue: 1.2199
  time to fit residues: 83.5978
Evaluate side-chains
  73 residues out of total 312 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 21
    poor density    : 52
  time to evaluate  : 0.352 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue  316 SER
Chi-restraints excluded: chain B residue  353 LYS
Chi-restraints excluded: chain D residue  306 VAL
Chi-restraints excluded: chain D residue  316 SER
Chi-restraints excluded: chain D residue  325 LEU
Chi-restraints excluded: chain D residue  348 ASP
Chi-restraints excluded: chain E residue  306 VAL
Chi-restraints excluded: chain E residue  316 SER
Chi-restraints excluded: chain E residue  318 VAL
Chi-restraints excluded: chain E residue  320 SER
Chi-restraints excluded: chain E residue  325 LEU
Chi-restraints excluded: chain E residue  348 ASP
Chi-restraints excluded: chain F residue  315 LEU
Chi-restraints excluded: chain A residue  306 VAL
Chi-restraints excluded: chain A residue  316 SER
Chi-restraints excluded: chain A residue  322 CYS
Chi-restraints excluded: chain A residue  340 LYS
Chi-restraints excluded: chain A residue  348 ASP
Chi-restraints excluded: chain C residue  306 VAL
Chi-restraints excluded: chain C residue  316 SER
Chi-restraints excluded: chain C residue  348 ASP
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 30
   random chunks:
   chunk 14 optimal weight:   10.0000
   chunk 21 optimal weight:   10.0000
   chunk 11 optimal weight:    5.9990
   chunk 0 optimal weight:    7.9990
   chunk 23 optimal weight:    4.9990
   chunk 20 optimal weight:    0.9990
   chunk 8 optimal weight:    6.9990
   chunk 29 optimal weight:   10.0000
   chunk 26 optimal weight:    0.5980
   chunk 27 optimal weight:    8.9990
   chunk 15 optimal weight:    3.9990
   overall best weight:    3.3188

-------------------------------------------------------------------------------
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 = 0.4201 r_free = 0.4201 target = 0.135088 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.3876 r_free = 0.3876 target = 0.107689 restraints weight = 3581.162|
|-----------------------------------------------------------------------------|
r_work (start): 0.3877 rms_B_bonded: 2.17
r_work: 0.3789 rms_B_bonded: 2.28 restraints_weight: 0.5000
r_work: 0.3693 rms_B_bonded: 3.75 restraints_weight: 0.2500
r_work (final): 0.3693
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7988
moved from start:          0.2813

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.032   2712  Z= 0.200
  Angle     :  0.669   6.990   3630  Z= 0.325
  Chirality :  0.053   0.144    414
  Planarity :  0.003   0.015    462
  Dihedral  :  4.797  13.239    360
  Min Nonbonded Distance : 2.645

Molprobity Statistics.
  All-atom Clashscore : 10.68
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  : 10.82 %
    Favored  : 89.18 %
  Rotamer:
    Outliers :  6.41 %
    Allowed  : 20.51 %
    Favored  : 73.08 %
  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: -5.44 (0.33), residues: 342
  helix:  None (None), residues: 0
  sheet:  None (None), residues: 0
  loop : -4.14 (0.25), residues: 342

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 HIS   0.002   0.001   HIS F 362 
 PHE   0.004   0.002   PHE C 346 
 TYR   0.008   0.002   TYR C 310 
 ARG   0.002   0.001   ARG A 349 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.01757 (   20)
  hydrogen bonds       : angle       4.00902 (   60)
  covalent geometry    : bond        0.00464 ( 2712)
  covalent geometry    : angle       0.66914 ( 3630)

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

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

  684 Ramachandran restraints generated.
    342 Oldfield, 0 Emsley, 342 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  684 Ramachandran restraints generated.
    342 Oldfield, 0 Emsley, 342 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  72 residues out of total 312 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 20
    poor density    : 52
  time to evaluate  : 0.351 
Fit side-chains
REVERT: B  348 ASP cc_start: 0.8240 (m-30) cc_final: 0.7730 (m-30)
REVERT: B  349 ARG cc_start: 0.7631 (mtt-85) cc_final: 0.7297 (mtp85)
REVERT: B  353 LYS cc_start: 0.8033 (OUTLIER) cc_final: 0.7553 (mtpt)
REVERT: D  317 LYS cc_start: 0.7982 (ttmt) cc_final: 0.7692 (ttpp)
REVERT: D  349 ARG cc_start: 0.7208 (mtt-85) cc_final: 0.6788 (mtp85)
REVERT: D  353 LYS cc_start: 0.7985 (mtpt) cc_final: 0.7062 (mppt)
REVERT: E  317 LYS cc_start: 0.8099 (ttmt) cc_final: 0.7806 (ttpp)
REVERT: E  325 LEU cc_start: 0.8520 (OUTLIER) cc_final: 0.8198 (pp)
REVERT: E  343 LYS cc_start: 0.8078 (tttm) cc_final: 0.7755 (ttmm)
REVERT: E  348 ASP cc_start: 0.7899 (OUTLIER) cc_final: 0.7578 (m-30)
REVERT: E  349 ARG cc_start: 0.7119 (mtt-85) cc_final: 0.6720 (mtt90)
REVERT: F  317 LYS cc_start: 0.7987 (ttmt) cc_final: 0.7725 (mtpm)
REVERT: F  348 ASP cc_start: 0.8294 (m-30) cc_final: 0.8037 (m-30)
REVERT: F  349 ARG cc_start: 0.7445 (mtt-85) cc_final: 0.7060 (mtm-85)
REVERT: A  317 LYS cc_start: 0.7850 (ttmt) cc_final: 0.7521 (mtpt)
REVERT: A  349 ARG cc_start: 0.7126 (mtt-85) cc_final: 0.6450 (mtp-110)
REVERT: A  357 LEU cc_start: 0.7913 (tt) cc_final: 0.7431 (tp)
REVERT: C  317 LYS cc_start: 0.8184 (ttmt) cc_final: 0.7730 (ttmm)
REVERT: C  349 ARG cc_start: 0.7011 (mtt-85) cc_final: 0.6400 (mtp-110)
  outliers start: 20
  outliers final: 16
  residues processed: 66
  average time/residue: 1.1934
  time to fit residues: 80.6428
Evaluate side-chains
  69 residues out of total 312 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 19
    poor density    : 50
  time to evaluate  : 0.330 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue  316 SER
Chi-restraints excluded: chain B residue  353 LYS
Chi-restraints excluded: chain D residue  306 VAL
Chi-restraints excluded: chain D residue  316 SER
Chi-restraints excluded: chain D residue  325 LEU
Chi-restraints excluded: chain D residue  348 ASP
Chi-restraints excluded: chain E residue  306 VAL
Chi-restraints excluded: chain E residue  318 VAL
Chi-restraints excluded: chain E residue  320 SER
Chi-restraints excluded: chain E residue  325 LEU
Chi-restraints excluded: chain E residue  348 ASP
Chi-restraints excluded: chain F residue  315 LEU
Chi-restraints excluded: chain A residue  306 VAL
Chi-restraints excluded: chain A residue  316 SER
Chi-restraints excluded: chain A residue  340 LYS
Chi-restraints excluded: chain A residue  348 ASP
Chi-restraints excluded: chain C residue  306 VAL
Chi-restraints excluded: chain C residue  316 SER
Chi-restraints excluded: chain C residue  348 ASP
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 30
   random chunks:
   chunk 17 optimal weight:    0.9980
   chunk 11 optimal weight:    6.9990
   chunk 9 optimal weight:    7.9990
   chunk 4 optimal weight:    4.9990
   chunk 14 optimal weight:    1.9990
   chunk 10 optimal weight:    0.9990
   chunk 21 optimal weight:   10.0000
   chunk 15 optimal weight:    7.9990
   chunk 8 optimal weight:   10.0000
   chunk 25 optimal weight:    0.0470
   chunk 24 optimal weight:   10.0000
   overall best weight:    1.8084

-------------------------------------------------------------------------------
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 = 0.4234 r_free = 0.4234 target = 0.139933 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 30)----------------|
| r_work = 0.3917 r_free = 0.3917 target = 0.112326 restraints weight = 3456.953|
|-----------------------------------------------------------------------------|
r_work (start): 0.3920 rms_B_bonded: 2.14
r_work: 0.3831 rms_B_bonded: 2.27 restraints_weight: 0.5000
r_work: 0.3736 rms_B_bonded: 3.73 restraints_weight: 0.2500
r_work (final): 0.3736
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7967
moved from start:          0.2946

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.021   2712  Z= 0.140
  Angle     :  0.613   6.949   3630  Z= 0.293
  Chirality :  0.052   0.140    414
  Planarity :  0.002   0.017    462
  Dihedral  :  4.369  12.167    360
  Min Nonbonded Distance : 2.640

Molprobity Statistics.
  All-atom Clashscore : 9.21
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  7.60 %
    Favored  : 92.40 %
  Rotamer:
    Outliers :  4.49 %
    Allowed  : 22.44 %
    Favored  : 73.08 %
  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: -5.28 (0.34), residues: 342
  helix:  None (None), residues: 0
  sheet:  None (None), residues: 0
  loop : -4.02 (0.26), residues: 342

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 HIS   0.002   0.001   HIS E 362 
 PHE   0.003   0.001   PHE C 346 
 TYR   0.006   0.001   TYR D 310 
 ARG   0.001   0.000   ARG C 349 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.01667 (   20)
  hydrogen bonds       : angle       3.99231 (   60)
  covalent geometry    : bond        0.00311 ( 2712)
  covalent geometry    : angle       0.61349 ( 3630)

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

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

  684 Ramachandran restraints generated.
    342 Oldfield, 0 Emsley, 342 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  684 Ramachandran restraints generated.
    342 Oldfield, 0 Emsley, 342 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  66 residues out of total 312 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 52
  time to evaluate  : 0.352 
Fit side-chains
REVERT: B  348 ASP cc_start: 0.8171 (m-30) cc_final: 0.7694 (m-30)
REVERT: B  349 ARG cc_start: 0.7600 (mtt-85) cc_final: 0.7287 (mtp85)
REVERT: D  317 LYS cc_start: 0.8041 (ttmt) cc_final: 0.7773 (ttpp)
REVERT: D  349 ARG cc_start: 0.7208 (mtt-85) cc_final: 0.6753 (mtp85)
REVERT: D  353 LYS cc_start: 0.8002 (mtpt) cc_final: 0.7152 (mppt)
REVERT: E  317 LYS cc_start: 0.8082 (ttmt) cc_final: 0.7569 (ttmm)
REVERT: E  325 LEU cc_start: 0.8574 (OUTLIER) cc_final: 0.8265 (pp)
REVERT: E  342 GLU cc_start: 0.7969 (pt0) cc_final: 0.7566 (pt0)
REVERT: E  343 LYS cc_start: 0.8145 (tttm) cc_final: 0.7802 (ttmm)
REVERT: E  348 ASP cc_start: 0.7831 (OUTLIER) cc_final: 0.7555 (m-30)
REVERT: E  349 ARG cc_start: 0.7131 (mtt-85) cc_final: 0.6831 (mtt90)
REVERT: F  317 LYS cc_start: 0.7952 (ttmt) cc_final: 0.7713 (mtpm)
REVERT: F  348 ASP cc_start: 0.8310 (m-30) cc_final: 0.8036 (m-30)
REVERT: F  349 ARG cc_start: 0.7465 (mtt-85) cc_final: 0.5997 (mpp-170)
REVERT: A  317 LYS cc_start: 0.7923 (ttmt) cc_final: 0.7622 (mtpt)
REVERT: A  343 LYS cc_start: 0.7765 (OUTLIER) cc_final: 0.7558 (tttm)
REVERT: A  349 ARG cc_start: 0.7235 (mtt-85) cc_final: 0.6625 (mtp-110)
REVERT: A  357 LEU cc_start: 0.7882 (tt) cc_final: 0.7412 (tp)
REVERT: C  317 LYS cc_start: 0.8196 (ttmt) cc_final: 0.7948 (tttt)
REVERT: C  349 ARG cc_start: 0.7061 (mtt-85) cc_final: 0.6524 (mtp-110)
  outliers start: 14
  outliers final: 11
  residues processed: 60
  average time/residue: 1.3233
  time to fit residues: 81.2064
Evaluate side-chains
  64 residues out of total 312 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 50
  time to evaluate  : 0.348 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue  316 SER
Chi-restraints excluded: chain D residue  306 VAL
Chi-restraints excluded: chain D residue  325 LEU
Chi-restraints excluded: chain D residue  348 ASP
Chi-restraints excluded: chain E residue  306 VAL
Chi-restraints excluded: chain E residue  318 VAL
Chi-restraints excluded: chain E residue  320 SER
Chi-restraints excluded: chain E residue  325 LEU
Chi-restraints excluded: chain E residue  348 ASP
Chi-restraints excluded: chain F residue  315 LEU
Chi-restraints excluded: chain A residue  306 VAL
Chi-restraints excluded: chain A residue  343 LYS
Chi-restraints excluded: chain A residue  348 ASP
Chi-restraints excluded: chain C residue  348 ASP
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 30
   random chunks:
   chunk 5 optimal weight:    1.9990
   chunk 19 optimal weight:    7.9990
   chunk 27 optimal weight:    0.0370
   chunk 28 optimal weight:    3.9990
   chunk 12 optimal weight:    9.9990
   chunk 10 optimal weight:    5.9990
   chunk 9 optimal weight:    6.9990
   chunk 2 optimal weight:    2.9990
   chunk 29 optimal weight:    3.9990
   chunk 15 optimal weight:   10.0000
   chunk 1 optimal weight:    1.9990
   overall best weight:    2.2066

-------------------------------------------------------------------------------
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 = 0.4229 r_free = 0.4229 target = 0.139552 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 35)----------------|
| r_work = 0.3911 r_free = 0.3911 target = 0.111966 restraints weight = 3435.667|
|-----------------------------------------------------------------------------|
r_work (start): 0.3919 rms_B_bonded: 2.14
r_work: 0.3829 rms_B_bonded: 2.26 restraints_weight: 0.5000
r_work: 0.3734 rms_B_bonded: 3.72 restraints_weight: 0.2500
r_work (final): 0.3734
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7972
moved from start:          0.2933

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.025   2712  Z= 0.155
  Angle     :  0.623   6.910   3630  Z= 0.298
  Chirality :  0.052   0.141    414
  Planarity :  0.002   0.015    462
  Dihedral  :  4.406  12.374    360
  Min Nonbonded Distance : 2.640

Molprobity Statistics.
  All-atom Clashscore : 9.02
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  8.48 %
    Favored  : 91.52 %
  Rotamer:
    Outliers :  4.81 %
    Allowed  : 22.12 %
    Favored  : 73.08 %
  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: -5.28 (0.34), residues: 342
  helix:  None (None), residues: 0
  sheet:  None (None), residues: 0
  loop : -4.02 (0.26), residues: 342

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 HIS   0.002   0.001   HIS E 362 
 PHE   0.003   0.001   PHE C 346 
 TYR   0.005   0.002   TYR A 310 
 ARG   0.001   0.000   ARG A 349 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.01725 (   20)
  hydrogen bonds       : angle       3.96424 (   60)
  covalent geometry    : bond        0.00353 ( 2712)
  covalent geometry    : angle       0.62309 ( 3630)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 3008.25 seconds
wall clock time: 52 minutes 12.08 seconds (3132.08 seconds total)