Starting phenix.real_space_refine
on Tue Mar  3 18:33:18 2026 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/7xht_33198/03_2026/7xht_33198.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/7xht_33198/03_2026/7xht_33198.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=2.55
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/cci-nas-00/data/ceres_data/7xht_33198/03_2026/7xht_33198.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/7xht_33198/03_2026/7xht_33198.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/7xht_33198/03_2026/7xht_33198.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/7xht_33198/03_2026/7xht_33198.cif"
  }
  resolution = 2.55
  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=   0.177
Set stop_for_unknowns flag
  Set to: True
Assert model is a single copy model
Assert all atoms have isotropic ADPs
Construct map_model_manager
Extract box with map and model
Check model and map are aligned
Set scattering table
  Set to: electron
  Number of scattering types: 6
    Type Number    sf(0)   Gaussians
     P     220      5.49       5
     Mg      2      5.21       5
     S      19      5.16       5
     C    4108      2.51       5
     N    1449      2.21       5
     O    2041      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-dev-5986/lib/python3.9/site-packages/chem_data/mon_lib"
  Total number of atoms: 7839
  Number of models: 1
  Model: ""
    Number of chains: 6
    Chain: "B"
      Number of atoms: 3822
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 179, 3822
          Classifications: {'RNA': 179}
          Modifications used: {'rna2p_pur': 14, 'rna2p_pyr': 12, 'rna3p_pur': 84, 'rna3p_pyr': 69}
          Link IDs: {'rna2p': 26, 'rna3p': 152}
          Chain breaks: 3
    Chain: "C"
      Number of atoms: 595
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 29, 595
          Classifications: {'DNA': 29}
          Link IDs: {'rna3p': 28}
    Chain: "D"
      Number of atoms: 249
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 12, 249
          Classifications: {'DNA': 12}
          Link IDs: {'rna3p': 11}
    Chain: "A"
      Number of atoms: 3155
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 395, 3155
          Classifications: {'peptide': 395}
          Link IDs: {'PCIS': 1, 'PTRANS': 17, 'TRANS': 376}
          Chain breaks: 1
    Chain: "B"
      Number of atoms: 1
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 1, 1
          Unusual residues: {' MG': 1}
          Classifications: {'undetermined': 1}
    Chain: "A"
      Number of atoms: 17
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 2, 17
          Unusual residues: {' MG': 1, 'LDA': 1}
          Classifications: {'undetermined': 2}
          Link IDs: {None: 1}
  Time building chain proxies: 2.08, per 1000 atoms: 0.27
  Number of scatterers: 7839
  At special positions: 0
  Unit cell: (85.49, 110.39, 130.31, 90, 90, 90)
  Space group: P 1 (No. 1)
  Number of sites at special positions: 0
  Number of scattering types: 6
    Type Number    sf(0)
     S      19     16.00
     P     220     15.00
     Mg      2     11.99
     O    2041      8.00
     N    1449      7.00
     C    4108      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: 0.53
  Conformation dependent library (CDL) restraints added in 88.4 milliseconds
  

  782 Ramachandran restraints generated.
    391 Oldfield, 0 Emsley, 391 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  740

  Finding SS restraints...
    Secondary structure from input PDB file:
      12 helices and 6 sheets defined
      32.9% alpha, 21.0% beta
      82 base pairs and 138 stacking pairs defined.
    Time for finding SS restraints: 0.94
  Creating SS restraints...
    Processing helix  chain 'A' and resid 20 through 30
    Processing helix  chain 'A' and resid 89 through 109
      removed outlier: 4.419A  pdb=" N   LYS A  93 " --> pdb=" O   LYS A  89 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 110 through 122
    Processing helix  chain 'A' and resid 164 through 185
      removed outlier: 3.670A  pdb=" N   VAL A 178 " --> pdb=" O   HIS A 174 " (cutoff:3.500A)
      removed outlier: 3.833A  pdb=" N   ILE A 184 " --> pdb=" O   LYS A 180 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 298 through 315
      Proline residue:  A 305  - end of helix
    Processing helix  chain 'A' and resid 324 through 335
    Processing helix  chain 'A' and resid 339 through 341
      No H-bonds generated for 'chain 'A' and resid 339 through 341'
    Processing helix  chain 'A' and resid 342 through 349
    Processing helix  chain 'A' and resid 350 through 352
      No H-bonds generated for 'chain 'A' and resid 350 through 352'
    Processing helix  chain 'A' and resid 409 through 417
    Processing helix  chain 'A' and resid 418 through 424
    Processing helix  chain 'A' and resid 481 through 483
      No H-bonds generated for 'chain 'A' and resid 481 through 483'
    Processing sheet with id=AA1, first strand: chain 'A' and resid 6 through 8
      removed outlier: 6.254A  pdb=" N   TYR A   6 " --> pdb=" O   ILE A  43 " (cutoff:3.500A)
      removed outlier: 7.464A  pdb=" N   LEU A  45 " --> pdb=" O   TYR A   6 " (cutoff:3.500A)
      removed outlier: 7.194A  pdb=" N   ILE A   8 " --> pdb=" O   LEU A  45 " (cutoff:3.500A)
      removed outlier: 6.723A  pdb=" N   THR A  42 " --> pdb=" O   VAL A  36 " (cutoff:3.500A)
    Processing sheet with id=AA2, first strand: chain 'A' and resid 319 through 323
      removed outlier: 3.532A  pdb=" N   PHE A  80 " --> pdb=" O   VAL A  71 " (cutoff:3.500A)
      removed outlier: 6.591A  pdb=" N   THR A  73 " --> pdb=" O   SER A  78 " (cutoff:3.500A)
      removed outlier: 6.624A  pdb=" N   SER A  78 " --> pdb=" O   THR A  73 " (cutoff:3.500A)
    Processing sheet with id=AA3, first strand: chain 'A' and resid 129 through 132
    Processing sheet with id=AA4, first strand: chain 'A' and resid 379 through 381
      removed outlier: 6.375A  pdb=" N   GLN A 433 " --> pdb=" O   HIS A 380 " (cutoff:3.500A)
    Processing sheet with id=AA5, first strand: chain 'A' and resid 393 through 396
      removed outlier: 6.752A  pdb=" N   TYR A 388 " --> pdb=" O   VAL A 395 " (cutoff:3.500A)
    Processing sheet with id=AA6, first strand: chain 'A' and resid 477 through 479
      removed outlier: 6.789A  pdb=" N   VAL A 467 " --> pdb=" O   ARG A 462 " (cutoff:3.500A)
      removed outlier: 6.042A  pdb=" N   ARG A 462 " --> pdb=" O   VAL A 467 " (cutoff:3.500A)
      removed outlier: 6.438A  pdb=" N   ILE A 445 " --> pdb=" O   LEU A 486 " (cutoff:3.500A)

    132 hydrogen bonds defined for protein.
    375 hydrogen bond angles defined for protein.
    Restraints generated for nucleic acids:
      208 hydrogen bonds
      388 hydrogen bond angles
      0 basepair planarities
      82 basepair parallelities
      138 stacking parallelities
  Total time for adding SS restraints: 1.54

  Time building geometry restraints manager: 0.76 seconds

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

  Histogram of bond lengths:
        1.21 -     1.33: 1283
        1.33 -     1.45: 3178
        1.45 -     1.57: 3525
        1.57 -     1.69: 434
        1.69 -     1.81: 29
  Bond restraints: 8449
  Sorted by residual:
  bond pdb=" N1  LDA A 501 "
       pdb=" O1  LDA A 501 "
    ideal  model  delta    sigma   weight residual
    1.354  1.249  0.105 2.00e-02 2.50e+03 2.75e+01
  bond pdb=" C1  LDA A 501 "
       pdb=" N1  LDA A 501 "
    ideal  model  delta    sigma   weight residual
    1.503  1.454  0.049 2.00e-02 2.50e+03 6.03e+00
  bond pdb=" O3'  DC D   8 "
       pdb=" P    DC D   9 "
    ideal  model  delta    sigma   weight residual
    1.607  1.579  0.028 1.50e-02 4.44e+03 3.56e+00
  bond pdb=" O3'   A B 195 "
       pdb=" P     A B 196 "
    ideal  model  delta    sigma   weight residual
    1.607  1.579  0.028 1.50e-02 4.44e+03 3.42e+00
  bond pdb=" O3'  DG C  16 "
       pdb=" P    DC C  17 "
    ideal  model  delta    sigma   weight residual
    1.607  1.580  0.027 1.50e-02 4.44e+03 3.19e+00
  ... (remaining 8444 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     5.36: 12431
        5.36 -    10.72: 10
       10.72 -    16.08: 2
       16.08 -    21.44: 1
       21.44 -    26.80: 1
  Bond angle restraints: 12445
  Sorted by residual:
  angle pdb=" O3'  DT C  10 "
        pdb=" P    DT C  11 "
        pdb=" OP1  DT C  11 "
      ideal   model   delta    sigma   weight residual
     108.00   81.20   26.80 3.00e+00 1.11e-01 7.98e+01
  angle pdb=" O3'  DT C  10 "
        pdb=" P    DT C  11 "
        pdb=" O5'  DT C  11 "
      ideal   model   delta    sigma   weight residual
     104.00  115.97  -11.97 1.50e+00 4.44e-01 6.36e+01
  angle pdb=" O3'  DT C  11 "
        pdb=" P    DA C  12 "
        pdb=" OP1  DA C  12 "
      ideal   model   delta    sigma   weight residual
     108.00   89.06   18.94 3.00e+00 1.11e-01 3.99e+01
  angle pdb=" C3'  DT C  11 "
        pdb=" O3'  DT C  11 "
        pdb=" P    DA C  12 "
      ideal   model   delta    sigma   weight residual
     120.20  110.80    9.40 1.50e+00 4.44e-01 3.93e+01
  angle pdb=" O3'  DT C  11 "
        pdb=" P    DA C  12 "
        pdb=" O5'  DA C  12 "
      ideal   model   delta    sigma   weight residual
     104.00  113.30   -9.30 1.50e+00 4.44e-01 3.84e+01
  ... (remaining 12440 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    33.65: 4621
       33.65 -    67.30: 510
       67.30 -   100.95: 53
      100.95 -   134.60: 0
      134.60 -   168.25: 2
  Dihedral angle restraints: 5186
    sinusoidal: 4037
      harmonic: 1149
  Sorted by residual:
  dihedral pdb=" O4'   U B  92 "
           pdb=" C1'   U B  92 "
           pdb=" N1    U B  92 "
           pdb=" C2    U B  92 "
      ideal   model   delta sinusoidal    sigma   weight residual
     232.00   94.55  137.45     1      1.70e+01 3.46e-03 5.77e+01
  dihedral pdb=" C4'   G B  76 "
           pdb=" C3'   G B  76 "
           pdb=" O3'   G B  76 "
           pdb=" P     A B  77 "
      ideal   model   delta sinusoidal    sigma   weight residual
     220.00   51.75  168.25     1      3.50e+01 8.16e-04 1.55e+01
  dihedral pdb=" CA  ASN A 148 "
           pdb=" C   ASN A 148 "
           pdb=" N   LYS A 149 "
           pdb=" CA  LYS A 149 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  162.45   17.55     0      5.00e+00 4.00e-02 1.23e+01
  ... (remaining 5183 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.056: 1390
       0.056 -    0.112: 126
       0.112 -    0.168: 12
       0.168 -    0.224: 0
       0.224 -    0.280: 1
  Chirality restraints: 1529
  Sorted by residual:
  chirality pdb=" CB  ILE A 146 "
            pdb=" CA  ILE A 146 "
            pdb=" CG1 ILE A 146 "
            pdb=" CG2 ILE A 146 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.64    2.36    0.28 2.00e-01 2.50e+01 1.96e+00
  chirality pdb=" C1'   A B  81 "
            pdb=" O4'   A B  81 "
            pdb=" C2'   A B  81 "
            pdb=" N9    A B  81 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.46    2.30    0.15 2.00e-01 2.50e+01 5.84e-01
  chirality pdb=" C3'   G B  76 "
            pdb=" C4'   G B  76 "
            pdb=" O3'   G B  76 "
            pdb=" C2'   G B  76 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.48   -2.34   -0.14 2.00e-01 2.50e+01 4.96e-01
  ... (remaining 1526 not shown)

  Planarity restraints: 776
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C1'   A B  51 "    0.030 2.00e-02 2.50e+03   1.30e-02 4.66e+00
        pdb=" N9    A B  51 "   -0.027 2.00e-02 2.50e+03
        pdb=" C8    A B  51 "   -0.001 2.00e-02 2.50e+03
        pdb=" N7    A B  51 "   -0.001 2.00e-02 2.50e+03
        pdb=" C5    A B  51 "   -0.004 2.00e-02 2.50e+03
        pdb=" C6    A B  51 "    0.004 2.00e-02 2.50e+03
        pdb=" N6    A B  51 "    0.009 2.00e-02 2.50e+03
        pdb=" N1    A B  51 "    0.004 2.00e-02 2.50e+03
        pdb=" C2    A B  51 "   -0.001 2.00e-02 2.50e+03
        pdb=" N3    A B  51 "   -0.007 2.00e-02 2.50e+03
        pdb=" C4    A B  51 "   -0.006 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C1'   C B  -8 "   -0.028 2.00e-02 2.50e+03   1.41e-02 4.45e+00
        pdb=" N1    C B  -8 "    0.029 2.00e-02 2.50e+03
        pdb=" C2    C B  -8 "    0.004 2.00e-02 2.50e+03
        pdb=" O2    C B  -8 "    0.005 2.00e-02 2.50e+03
        pdb=" N3    C B  -8 "   -0.003 2.00e-02 2.50e+03
        pdb=" C4    C B  -8 "   -0.005 2.00e-02 2.50e+03
        pdb=" N4    C B  -8 "   -0.007 2.00e-02 2.50e+03
        pdb=" C5    C B  -8 "    0.001 2.00e-02 2.50e+03
        pdb=" C6    C B  -8 "    0.005 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C1'   A B 112 "   -0.022 2.00e-02 2.50e+03   1.08e-02 3.19e+00
        pdb=" N9    A B 112 "    0.027 2.00e-02 2.50e+03
        pdb=" C8    A B 112 "    0.000 2.00e-02 2.50e+03
        pdb=" N7    A B 112 "   -0.001 2.00e-02 2.50e+03
        pdb=" C5    A B 112 "   -0.001 2.00e-02 2.50e+03
        pdb=" C6    A B 112 "   -0.003 2.00e-02 2.50e+03
        pdb=" N6    A B 112 "   -0.004 2.00e-02 2.50e+03
        pdb=" N1    A B 112 "   -0.002 2.00e-02 2.50e+03
        pdb=" C2    A B 112 "    0.001 2.00e-02 2.50e+03
        pdb=" N3    A B 112 "    0.003 2.00e-02 2.50e+03
        pdb=" C4    A B 112 "    0.002 2.00e-02 2.50e+03
  ... (remaining 773 not shown)

  Histogram of nonbonded interaction distances:
        2.01 -     2.59: 66
        2.59 -     3.17: 5661
        3.17 -     3.75: 15108
        3.75 -     4.32: 21418
        4.32 -     4.90: 28200
  Nonbonded interactions: 70453
  Sorted by model distance:
  nonbonded pdb=" OD1 ASP A  61 "
            pdb="MG    MG A 502 "
     model   vdw
     2.014 2.170
  nonbonded pdb=" O2'   A B  69 "
            pdb=" O4'   A B  70 "
     model   vdw
     2.139 3.040
  nonbonded pdb=" OP1   U B 190 "
            pdb=" OH  TYR A  47 "
     model   vdw
     2.204 3.040
  nonbonded pdb=" O2'   C B  82 "
            pdb=" O   ASN A 155 "
     model   vdw
     2.222 3.040
  nonbonded pdb=" O2'   G B  76 "
            pdb=" O5'   A B  77 "
     model   vdw
     2.230 3.040
  ... (remaining 70448 not shown)

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

  No NCS relation were found !!!

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

Found NCS groups:
  found none.
Set up NCS constraints
  No NCS constraints will be used in refinement.
Set refine NCS operators
Adjust number of macro_cycles
  Number of macro_cycles: 10
Reset NCS operators
Extract rigid body selections
Check and reset occupancies
  Occupancies: min=1.00 max=1.00 mean=1.00
Load rotamer database and sin/cos tables
Set ADP refinement strategy
  ADPs will be refined as individual isotropic
Make a string to write initial .geo file
Internal consistency checks
Time:
  Set random seed:                         0.000
  Set model cs if undefined:               0.000
  Decide on map wrapping:                  0.000
  Normalize map: mean=0, sd=1:             2.160
  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:          0.140
  Check model and map are aligned:         0.020
  Set scattering table:                    0.020
  Process input model:                     9.080
  Find NCS groups from input model:        0.020
  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:             0.010
  Load rotamer database and sin/cos tables:6.020
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   17.480
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8298
moved from start:          0.0000

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.105   8449  Z= 0.170
  Angle     :  0.680  26.798  12445  Z= 0.350
  Chirality :  0.033   0.280   1529
  Planarity :  0.005   0.038    776
  Dihedral  : 21.149 168.253   4446
  Min Nonbonded Distance : 2.014

Molprobity Statistics.
  All-atom Clashscore : 6.29
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.79 %
    Favored  : 98.21 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  0.00 %
    Favored  : 100.00 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 5.56 %
    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:  0.35 (0.42), residues: 391
  helix:  1.08 (0.50), residues: 120
  sheet:  0.76 (0.61), residues: 72
  loop : -0.45 (0.41), residues: 199

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.001   ARG A  38 
 TYR   0.017   0.002   TYR A   6 
 PHE   0.009   0.001   PHE A 315 
 TRP   0.003   0.001   TRP A 479 
 HIS   0.006   0.001   HIS A 105 

Details of bonding type rmsd
  covalent geometry    : bond        0.00337 ( 8449)
  covalent geometry    : angle       0.67969 (12445)
  hydrogen bonds       : bond        0.11751 (  340)
  hydrogen bonds       : angle       5.04033 (  763)

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

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

  782 Ramachandran restraints generated.
    391 Oldfield, 0 Emsley, 391 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  782 Ramachandran restraints generated.
    391 Oldfield, 0 Emsley, 391 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  74 residues out of total 342 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 74
  time to evaluate  : 0.157 
Fit side-chains
REVERT: A   77 GLU cc_start: 0.7378 (mt-10) cc_final: 0.7117 (tp30)
REVERT: A  100 GLN cc_start: 0.8038 (tt0) cc_final: 0.7788 (tt0)
REVERT: A  119 LYS cc_start: 0.8401 (mttt) cc_final: 0.8182 (mtmt)
REVERT: A  168 ASN cc_start: 0.8526 (m-40) cc_final: 0.8007 (t0)
REVERT: A  341 TYR cc_start: 0.7728 (p90) cc_final: 0.7521 (p90)
REVERT: A  466 GLN cc_start: 0.7799 (mt0) cc_final: 0.7595 (tp40)
REVERT: A  481 ARG cc_start: 0.7737 (mtt90) cc_final: 0.7510 (mtt90)
  outliers start: 0
  outliers final: 0
  residues processed: 74
  average time/residue: 0.7035
  time to fit residues: 54.4719
Evaluate side-chains
  50 residues out of total 342 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 50
  time to evaluate  : 0.144 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 59
   random chunks:
   chunk 54 optimal weight:    0.9990
   chunk 24 optimal weight:    2.9990
   chunk 48 optimal weight:    4.9990
   chunk 56 optimal weight:    3.9990
   chunk 26 optimal weight:    5.9990
   chunk 2 optimal weight:    5.9990
   chunk 16 optimal weight:   20.0000
   chunk 32 optimal weight:    1.9990
   chunk 31 optimal weight:    1.9990
   chunk 25 optimal weight:    1.9990
   chunk 58 optimal weight:    0.7980
   overall best weight:    1.5588

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

Flipped N/Q/H residues before XYZ refinement:
A  88 ASN
A 168 ASN
A 169 HIS
A 195 ASN

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3889 r_free = 0.3889 target = 0.174922 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 54)----------------|
| r_work = 0.3317 r_free = 0.3317 target = 0.121583 restraints weight = 5530.307|
|-----------------------------------------------------------------------------|
r_work (start): 0.3279 rms_B_bonded: 0.66
r_work: 0.3066 rms_B_bonded: 1.91 restraints_weight: 0.5000
r_work: 0.2945 rms_B_bonded: 3.02 restraints_weight: 0.2500
r_work (final): 0.2945
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8386
moved from start:          0.0931

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.033   8449  Z= 0.209
  Angle     :  0.595   7.103  12445  Z= 0.323
  Chirality :  0.036   0.206   1529
  Planarity :  0.005   0.044    776
  Dihedral  : 22.250 172.148   3639
  Min Nonbonded Distance : 2.006

Molprobity Statistics.
  All-atom Clashscore : 4.29
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.05 %
    Favored  : 97.95 %
  Rotamer:
    Outliers :  1.75 %
    Allowed  :  9.36 %
    Favored  : 88.89 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 5.56 %
    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:  0.46 (0.42), residues: 391
  helix:  1.32 (0.49), residues: 120
  sheet:  0.59 (0.61), residues: 72
  loop : -0.38 (0.41), residues: 199

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.001   ARG A  38 
 TYR   0.019   0.002   TYR A   6 
 PHE   0.009   0.002   PHE A 315 
 TRP   0.003   0.001   TRP A 479 
 HIS   0.005   0.001   HIS A 105 

Details of bonding type rmsd
  covalent geometry    : bond        0.00433 ( 8449)
  covalent geometry    : angle       0.59467 (12445)
  hydrogen bonds       : bond        0.04885 (  340)
  hydrogen bonds       : angle       3.69628 (  763)

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

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

  782 Ramachandran restraints generated.
    391 Oldfield, 0 Emsley, 391 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  782 Ramachandran restraints generated.
    391 Oldfield, 0 Emsley, 391 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  48 residues out of total 342 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 6
    poor density    : 42
  time to evaluate  : 0.198 
Fit side-chains
REVERT: A   77 GLU cc_start: 0.7710 (mt-10) cc_final: 0.7006 (tp30)
REVERT: A   96 LYS cc_start: 0.8541 (OUTLIER) cc_final: 0.8318 (ttpt)
REVERT: A  119 LYS cc_start: 0.8369 (mttt) cc_final: 0.7957 (mtmt)
REVERT: A  127 GLU cc_start: 0.7723 (OUTLIER) cc_final: 0.6870 (mp0)
REVERT: A  168 ASN cc_start: 0.8547 (m110) cc_final: 0.7888 (t0)
REVERT: A  301 ASN cc_start: 0.8044 (OUTLIER) cc_final: 0.7736 (m110)
REVERT: A  341 TYR cc_start: 0.7742 (p90) cc_final: 0.7269 (p90)
REVERT: A  466 GLN cc_start: 0.7888 (mt0) cc_final: 0.7506 (tp40)
  outliers start: 6
  outliers final: 3
  residues processed: 45
  average time/residue: 0.6897
  time to fit residues: 32.4806
Evaluate side-chains
  46 residues out of total 342 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 6
    poor density    : 40
  time to evaluate  : 0.171 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   69 MET
Chi-restraints excluded: chain A residue   75 SER
Chi-restraints excluded: chain A residue   96 LYS
Chi-restraints excluded: chain A residue  127 GLU
Chi-restraints excluded: chain A residue  301 ASN
Chi-restraints excluded: chain A residue  321 VAL
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 59
   random chunks:
   chunk 11 optimal weight:    3.9990
   chunk 44 optimal weight:    0.5980
   chunk 7 optimal weight:    6.9990
   chunk 51 optimal weight:    2.9990
   chunk 21 optimal weight:    6.9990
   chunk 53 optimal weight:    0.6980
   chunk 37 optimal weight:    0.9980
   chunk 4 optimal weight:    3.9990
   chunk 45 optimal weight:    5.9990
   chunk 16 optimal weight:   20.0000
   chunk 48 optimal weight:    2.9990
   overall best weight:    1.6584

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

Flipped N/Q/H residues before XYZ refinement:
A 100 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3874 r_free = 0.3874 target = 0.173631 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 58)----------------|
| r_work = 0.3312 r_free = 0.3312 target = 0.121360 restraints weight = 5461.970|
|-----------------------------------------------------------------------------|
r_work (start): 0.3278 rms_B_bonded: 0.64
r_work: 0.3062 rms_B_bonded: 1.83 restraints_weight: 0.5000
r_work: 0.2943 rms_B_bonded: 2.89 restraints_weight: 0.2500
r_work (final): 0.2943
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8384
moved from start:          0.1186

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.033   8449  Z= 0.217
  Angle     :  0.599   7.217  12445  Z= 0.325
  Chirality :  0.036   0.177   1529
  Planarity :  0.005   0.045    776
  Dihedral  : 22.199 171.024   3639
  Min Nonbonded Distance : 2.029

Molprobity Statistics.
  All-atom Clashscore : 4.07
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.05 %
    Favored  : 97.95 %
  Rotamer:
    Outliers :  2.05 %
    Allowed  : 10.53 %
    Favored  : 87.43 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 5.56 %
    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 (0.42), residues: 391
  helix:  1.59 (0.48), residues: 120
  sheet:  0.42 (0.60), residues: 72
  loop : -0.28 (0.42), residues: 199

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.001   ARG A 481 
 TYR   0.018   0.002   TYR A   6 
 PHE   0.007   0.002   PHE A 315 
 TRP   0.005   0.002   TRP A 162 
 HIS   0.004   0.001   HIS A 105 

Details of bonding type rmsd
  covalent geometry    : bond        0.00449 ( 8449)
  covalent geometry    : angle       0.59885 (12445)
  hydrogen bonds       : bond        0.04894 (  340)
  hydrogen bonds       : angle       3.60226 (  763)

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

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

  782 Ramachandran restraints generated.
    391 Oldfield, 0 Emsley, 391 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  782 Ramachandran restraints generated.
    391 Oldfield, 0 Emsley, 391 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  51 residues out of total 342 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 7
    poor density    : 44
  time to evaluate  : 0.167 
Fit side-chains
REVERT: A   77 GLU cc_start: 0.7766 (mt-10) cc_final: 0.7362 (tt0)
REVERT: A   96 LYS cc_start: 0.8538 (OUTLIER) cc_final: 0.8281 (ttpt)
REVERT: A  119 LYS cc_start: 0.8373 (mttt) cc_final: 0.7963 (mtmt)
REVERT: A  126 GLU cc_start: 0.7590 (mm-30) cc_final: 0.6930 (mp0)
REVERT: A  168 ASN cc_start: 0.8577 (m110) cc_final: 0.7920 (t0)
REVERT: A  301 ASN cc_start: 0.8237 (OUTLIER) cc_final: 0.7873 (m110)
REVERT: A  341 TYR cc_start: 0.7757 (p90) cc_final: 0.7354 (p90)
REVERT: A  466 GLN cc_start: 0.7777 (mt0) cc_final: 0.7400 (tp40)
  outliers start: 7
  outliers final: 4
  residues processed: 47
  average time/residue: 0.6720
  time to fit residues: 33.1565
Evaluate side-chains
  48 residues out of total 342 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 6
    poor density    : 42
  time to evaluate  : 0.172 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   36 VAL
Chi-restraints excluded: chain A residue   69 MET
Chi-restraints excluded: chain A residue   75 SER
Chi-restraints excluded: chain A residue   96 LYS
Chi-restraints excluded: chain A residue  301 ASN
Chi-restraints excluded: chain A residue  321 VAL
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 59
   random chunks:
   chunk 13 optimal weight:    6.9990
   chunk 54 optimal weight:    0.7980
   chunk 32 optimal weight:    1.9990
   chunk 29 optimal weight:    0.8980
   chunk 34 optimal weight:    1.9990
   chunk 23 optimal weight:    0.3980
   chunk 19 optimal weight:    3.9990
   chunk 41 optimal weight:    1.9990
   chunk 43 optimal weight:    0.9990
   chunk 8 optimal weight:    4.9990
   chunk 5 optimal weight:    1.9990
   overall best weight:    1.0184

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

Flipped N/Q/H residues before XYZ refinement:
A 100 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3887 r_free = 0.3887 target = 0.174975 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 49)----------------|
| r_work = 0.3324 r_free = 0.3324 target = 0.122229 restraints weight = 5569.122|
|-----------------------------------------------------------------------------|
r_work (start): 0.3289 rms_B_bonded: 0.66
r_work: 0.3065 rms_B_bonded: 1.96 restraints_weight: 0.5000
r_work: 0.2944 rms_B_bonded: 3.12 restraints_weight: 0.2500
r_work (final): 0.2944
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8381
moved from start:          0.1195

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.025   8449  Z= 0.157
  Angle     :  0.557   7.263  12445  Z= 0.306
  Chirality :  0.034   0.162   1529
  Planarity :  0.005   0.044    776
  Dihedral  : 22.173 170.296   3639
  Min Nonbonded Distance : 2.015

Molprobity Statistics.
  All-atom Clashscore : 4.59
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.79 %
    Favored  : 98.21 %
  Rotamer:
    Outliers :  2.63 %
    Allowed  : 11.11 %
    Favored  : 86.26 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 5.56 %
    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:  0.76 (0.42), residues: 391
  helix:  1.91 (0.48), residues: 120
  sheet:  0.31 (0.59), residues: 72
  loop : -0.24 (0.42), residues: 199

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.001   ARG A 414 
 TYR   0.015   0.002   TYR A   6 
 PHE   0.006   0.001   PHE A 315 
 TRP   0.004   0.001   TRP A 162 
 HIS   0.003   0.001   HIS A 105 

Details of bonding type rmsd
  covalent geometry    : bond        0.00316 ( 8449)
  covalent geometry    : angle       0.55738 (12445)
  hydrogen bonds       : bond        0.04311 (  340)
  hydrogen bonds       : angle       3.52400 (  763)

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

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

  782 Ramachandran restraints generated.
    391 Oldfield, 0 Emsley, 391 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  782 Ramachandran restraints generated.
    391 Oldfield, 0 Emsley, 391 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  51 residues out of total 342 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 9
    poor density    : 42
  time to evaluate  : 0.183 
Fit side-chains
REVERT: A   77 GLU cc_start: 0.7810 (mt-10) cc_final: 0.7287 (tt0)
REVERT: A  119 LYS cc_start: 0.8369 (mttt) cc_final: 0.7948 (mtmt)
REVERT: A  126 GLU cc_start: 0.7608 (mm-30) cc_final: 0.6899 (mp0)
REVERT: A  168 ASN cc_start: 0.8588 (m110) cc_final: 0.7945 (t0)
REVERT: A  301 ASN cc_start: 0.8163 (OUTLIER) cc_final: 0.7815 (m110)
REVERT: A  341 TYR cc_start: 0.7732 (p90) cc_final: 0.7281 (p90)
REVERT: A  466 GLN cc_start: 0.7804 (mt0) cc_final: 0.7407 (tp40)
  outliers start: 9
  outliers final: 7
  residues processed: 46
  average time/residue: 0.7102
  time to fit residues: 34.2856
Evaluate side-chains
  48 residues out of total 342 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 8
    poor density    : 40
  time to evaluate  : 0.184 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   36 VAL
Chi-restraints excluded: chain A residue   69 MET
Chi-restraints excluded: chain A residue   75 SER
Chi-restraints excluded: chain A residue   86 THR
Chi-restraints excluded: chain A residue  189 LYS
Chi-restraints excluded: chain A residue  301 ASN
Chi-restraints excluded: chain A residue  321 VAL
Chi-restraints excluded: chain A residue  421 ASP
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 59
   random chunks:
   chunk 46 optimal weight:    0.9990
   chunk 44 optimal weight:    0.9980
   chunk 54 optimal weight:    0.8980
   chunk 42 optimal weight:    4.9990
   chunk 36 optimal weight:    1.9990
   chunk 23 optimal weight:    6.9990
   chunk 10 optimal weight:    4.9990
   chunk 9 optimal weight:    2.9990
   chunk 24 optimal weight:    0.9990
   chunk 56 optimal weight:    0.7980
   chunk 14 optimal weight:    3.9990
   overall best weight:    0.9384

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

Flipped N/Q/H residues before XYZ refinement:
A 100 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3894 r_free = 0.3894 target = 0.175781 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 81)----------------|
| r_work = 0.3320 r_free = 0.3320 target = 0.122233 restraints weight = 5521.477|
|-----------------------------------------------------------------------------|
r_work (start): 0.3285 rms_B_bonded: 0.65
r_work: 0.3096 rms_B_bonded: 1.84 restraints_weight: 0.5000
r_work: 0.2975 rms_B_bonded: 2.94 restraints_weight: 0.2500
r_work (final): 0.2975
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8364
moved from start:          0.1205

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.023   8449  Z= 0.154
  Angle     :  0.547   7.112  12445  Z= 0.299
  Chirality :  0.033   0.169   1529
  Planarity :  0.005   0.045    776
  Dihedral  : 22.130 170.193   3639
  Min Nonbonded Distance : 2.009

Molprobity Statistics.
  All-atom Clashscore : 4.59
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.79 %
    Favored  : 98.21 %
  Rotamer:
    Outliers :  2.63 %
    Allowed  : 11.40 %
    Favored  : 85.96 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 5.56 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  0.81 (0.42), residues: 391
  helix:  2.03 (0.48), residues: 120
  sheet:  0.20 (0.59), residues: 72
  loop : -0.21 (0.42), residues: 199

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.001   ARG A 331 
 TYR   0.014   0.002   TYR A   6 
 PHE   0.006   0.001   PHE A  41 
 TRP   0.004   0.001   TRP A 162 
 HIS   0.003   0.001   HIS A 105 

Details of bonding type rmsd
  covalent geometry    : bond        0.00314 ( 8449)
  covalent geometry    : angle       0.54659 (12445)
  hydrogen bonds       : bond        0.04180 (  340)
  hydrogen bonds       : angle       3.42497 (  763)

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

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

  782 Ramachandran restraints generated.
    391 Oldfield, 0 Emsley, 391 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  782 Ramachandran restraints generated.
    391 Oldfield, 0 Emsley, 391 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  52 residues out of total 342 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 9
    poor density    : 43
  time to evaluate  : 0.181 
Fit side-chains
REVERT: A   77 GLU cc_start: 0.7792 (mt-10) cc_final: 0.7306 (tt0)
REVERT: A  119 LYS cc_start: 0.8354 (mttt) cc_final: 0.7936 (mtmt)
REVERT: A  126 GLU cc_start: 0.7595 (mm-30) cc_final: 0.6943 (mp0)
REVERT: A  168 ASN cc_start: 0.8579 (m110) cc_final: 0.7928 (t0)
REVERT: A  301 ASN cc_start: 0.8137 (OUTLIER) cc_final: 0.7809 (m110)
REVERT: A  341 TYR cc_start: 0.7675 (p90) cc_final: 0.7271 (p90)
REVERT: A  466 GLN cc_start: 0.7798 (mt0) cc_final: 0.7416 (tp40)
  outliers start: 9
  outliers final: 6
  residues processed: 46
  average time/residue: 0.6879
  time to fit residues: 33.2617
Evaluate side-chains
  48 residues out of total 342 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 7
    poor density    : 41
  time to evaluate  : 0.184 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   36 VAL
Chi-restraints excluded: chain A residue   69 MET
Chi-restraints excluded: chain A residue   75 SER
Chi-restraints excluded: chain A residue   81 ASN
Chi-restraints excluded: chain A residue  301 ASN
Chi-restraints excluded: chain A residue  321 VAL
Chi-restraints excluded: chain A residue  421 ASP
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 59
   random chunks:
   chunk 43 optimal weight:    3.9990
   chunk 39 optimal weight:    0.8980
   chunk 29 optimal weight:    0.6980
   chunk 52 optimal weight:    0.6980
   chunk 21 optimal weight:    3.9990
   chunk 51 optimal weight:    0.9990
   chunk 35 optimal weight:    1.9990
   chunk 6 optimal weight:    5.9990
   chunk 58 optimal weight:    3.9990
   chunk 14 optimal weight:    3.9990
   chunk 38 optimal weight:    1.9990
   overall best weight:    1.0584

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

Flipped N/Q/H residues before XYZ refinement:
A 100 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3895 r_free = 0.3895 target = 0.175789 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 67)----------------|
| r_work = 0.3301 r_free = 0.3301 target = 0.120240 restraints weight = 5540.914|
|-----------------------------------------------------------------------------|
r_work (start): 0.3266 rms_B_bonded: 0.70
r_work: 0.3103 rms_B_bonded: 1.84 restraints_weight: 0.5000
r_work: 0.2980 rms_B_bonded: 2.92 restraints_weight: 0.2500
r_work (final): 0.2980
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8337
moved from start:          0.1221

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.025   8449  Z= 0.160
  Angle     :  0.540   6.963  12445  Z= 0.296
  Chirality :  0.033   0.159   1529
  Planarity :  0.005   0.045    776
  Dihedral  : 22.102 170.016   3639
  Min Nonbonded Distance : 2.003

Molprobity Statistics.
  All-atom Clashscore : 4.29
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.05 %
    Favored  : 97.95 %
  Rotamer:
    Outliers :  3.22 %
    Allowed  : 11.40 %
    Favored  : 85.38 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 5.56 %
    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:  0.87 (0.42), residues: 391
  helix:  2.05 (0.48), residues: 120
  sheet:  0.25 (0.60), residues: 72
  loop : -0.17 (0.42), residues: 199

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG A 414 
 TYR   0.015   0.002   TYR A   6 
 PHE   0.006   0.001   PHE A 315 
 TRP   0.003   0.001   TRP A 162 
 HIS   0.003   0.001   HIS A 105 

Details of bonding type rmsd
  covalent geometry    : bond        0.00327 ( 8449)
  covalent geometry    : angle       0.54035 (12445)
  hydrogen bonds       : bond        0.04170 (  340)
  hydrogen bonds       : angle       3.39608 (  763)

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

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

  782 Ramachandran restraints generated.
    391 Oldfield, 0 Emsley, 391 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  782 Ramachandran restraints generated.
    391 Oldfield, 0 Emsley, 391 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  53 residues out of total 342 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 42
  time to evaluate  : 0.149 
Fit side-chains
REVERT: A   77 GLU cc_start: 0.7760 (mt-10) cc_final: 0.7249 (tt0)
REVERT: A   96 LYS cc_start: 0.8487 (OUTLIER) cc_final: 0.8264 (ttpt)
REVERT: A  119 LYS cc_start: 0.8331 (mttt) cc_final: 0.7898 (mtmt)
REVERT: A  126 GLU cc_start: 0.7550 (mm-30) cc_final: 0.6879 (mp0)
REVERT: A  301 ASN cc_start: 0.8082 (OUTLIER) cc_final: 0.7776 (m110)
REVERT: A  341 TYR cc_start: 0.7643 (p90) cc_final: 0.7255 (p90)
REVERT: A  466 GLN cc_start: 0.7747 (mt0) cc_final: 0.7353 (tp40)
  outliers start: 11
  outliers final: 7
  residues processed: 48
  average time/residue: 0.7106
  time to fit residues: 35.6950
Evaluate side-chains
  50 residues out of total 342 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 9
    poor density    : 41
  time to evaluate  : 0.174 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   36 VAL
Chi-restraints excluded: chain A residue   69 MET
Chi-restraints excluded: chain A residue   75 SER
Chi-restraints excluded: chain A residue   86 THR
Chi-restraints excluded: chain A residue   96 LYS
Chi-restraints excluded: chain A residue  189 LYS
Chi-restraints excluded: chain A residue  301 ASN
Chi-restraints excluded: chain A residue  321 VAL
Chi-restraints excluded: chain A residue  421 ASP
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 59
   random chunks:
   chunk 30 optimal weight:    3.9990
   chunk 25 optimal weight:    0.9990
   chunk 4 optimal weight:    3.9990
   chunk 8 optimal weight:    4.9990
   chunk 17 optimal weight:    6.9990
   chunk 9 optimal weight:    3.9990
   chunk 51 optimal weight:    2.9990
   chunk 55 optimal weight:    3.9990
   chunk 18 optimal weight:    3.9990
   chunk 22 optimal weight:    8.9990
   chunk 31 optimal weight:    2.9990
   overall best weight:    2.9990

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

Flipped N/Q/H residues before XYZ refinement:
A 100 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3842 r_free = 0.3842 target = 0.170527 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 96)----------------|
| r_work = 0.3243 r_free = 0.3243 target = 0.115099 restraints weight = 5563.024|
|-----------------------------------------------------------------------------|
r_work (start): 0.3180 rms_B_bonded: 0.82
r_work: 0.3014 rms_B_bonded: 1.81 restraints_weight: 0.5000
r_work: 0.2892 rms_B_bonded: 2.86 restraints_weight: 0.2500
r_work (final): 0.2892
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8410
moved from start:          0.1483

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.007   0.050   8449  Z= 0.352
  Angle     :  0.724   7.709  12445  Z= 0.384
  Chirality :  0.042   0.172   1529
  Planarity :  0.007   0.046    776
  Dihedral  : 22.338 172.580   3639
  Min Nonbonded Distance : 2.065

Molprobity Statistics.
  All-atom Clashscore : 4.22
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.30 %
    Favored  : 97.70 %
  Rotamer:
    Outliers :  3.80 %
    Allowed  : 11.11 %
    Favored  : 85.09 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 5.56 %
    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:  0.55 (0.42), residues: 391
  helix:  1.57 (0.48), residues: 120
  sheet:  0.29 (0.61), residues: 72
  loop : -0.30 (0.42), residues: 199

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.007   0.001   ARG A  87 
 TYR   0.021   0.003   TYR A   6 
 PHE   0.009   0.002   PHE A 319 
 TRP   0.004   0.002   TRP A 479 
 HIS   0.005   0.001   HIS A 429 

Details of bonding type rmsd
  covalent geometry    : bond        0.00738 ( 8449)
  covalent geometry    : angle       0.72378 (12445)
  hydrogen bonds       : bond        0.06033 (  340)
  hydrogen bonds       : angle       3.76096 (  763)

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

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

  782 Ramachandran restraints generated.
    391 Oldfield, 0 Emsley, 391 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  782 Ramachandran restraints generated.
    391 Oldfield, 0 Emsley, 391 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  55 residues out of total 342 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 42
  time to evaluate  : 0.139 
Fit side-chains
REVERT: A   52 GLU cc_start: 0.7439 (OUTLIER) cc_final: 0.6349 (mp0)
REVERT: A   77 GLU cc_start: 0.7845 (mt-10) cc_final: 0.7255 (tt0)
REVERT: A   96 LYS cc_start: 0.8563 (OUTLIER) cc_final: 0.8225 (ttpt)
REVERT: A  119 LYS cc_start: 0.8419 (mttt) cc_final: 0.7975 (mtmt)
REVERT: A  126 GLU cc_start: 0.7594 (mm-30) cc_final: 0.6885 (mp0)
REVERT: A  301 ASN cc_start: 0.8270 (OUTLIER) cc_final: 0.7871 (m110)
REVERT: A  341 TYR cc_start: 0.7738 (p90) cc_final: 0.7302 (p90)
REVERT: A  466 GLN cc_start: 0.7757 (mt0) cc_final: 0.7327 (tp40)
  outliers start: 13
  outliers final: 8
  residues processed: 49
  average time/residue: 0.6225
  time to fit residues: 32.1140
Evaluate side-chains
  52 residues out of total 342 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 41
  time to evaluate  : 0.123 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   36 VAL
Chi-restraints excluded: chain A residue   52 GLU
Chi-restraints excluded: chain A residue   75 SER
Chi-restraints excluded: chain A residue   86 THR
Chi-restraints excluded: chain A residue   96 LYS
Chi-restraints excluded: chain A residue  189 LYS
Chi-restraints excluded: chain A residue  301 ASN
Chi-restraints excluded: chain A residue  320 CYS
Chi-restraints excluded: chain A residue  321 VAL
Chi-restraints excluded: chain A residue  360 SER
Chi-restraints excluded: chain A residue  421 ASP
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 59
   random chunks:
   chunk 37 optimal weight:    0.9980
   chunk 20 optimal weight:    1.9990
   chunk 24 optimal weight:    8.9990
   chunk 43 optimal weight:    2.9990
   chunk 57 optimal weight:    0.8980
   chunk 36 optimal weight:    0.8980
   chunk 39 optimal weight:    0.0770
   chunk 16 optimal weight:   10.0000
   chunk 45 optimal weight:    4.9990
   chunk 54 optimal weight:    0.9990
   chunk 3 optimal weight:    5.9990
   overall best weight:    0.7740

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

Flipped N/Q/H residues before XYZ refinement:
A 100 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3901 r_free = 0.3901 target = 0.176654 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 83)----------------|
| r_work = 0.3331 r_free = 0.3331 target = 0.123269 restraints weight = 5580.225|
|-----------------------------------------------------------------------------|
r_work (start): 0.3313 rms_B_bonded: 0.67
r_work: 0.3122 rms_B_bonded: 1.87 restraints_weight: 0.5000
r_work: 0.3002 rms_B_bonded: 2.99 restraints_weight: 0.2500
r_work (final): 0.3002
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8338
moved from start:          0.1363

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.022   8449  Z= 0.139
  Angle     :  0.526   6.840  12445  Z= 0.289
  Chirality :  0.033   0.176   1529
  Planarity :  0.005   0.047    776
  Dihedral  : 22.118 170.752   3639
  Min Nonbonded Distance : 2.002

Molprobity Statistics.
  All-atom Clashscore : 5.33
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.28 %
    Favored  : 98.72 %
  Rotamer:
    Outliers :  2.92 %
    Allowed  : 12.28 %
    Favored  : 84.80 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 5.56 %
    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:  0.88 (0.42), residues: 391
  helix:  2.01 (0.48), residues: 120
  sheet:  0.36 (0.61), residues: 71
  loop : -0.17 (0.42), residues: 200

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG A 414 
 TYR   0.014   0.002   TYR A   6 
 PHE   0.005   0.001   PHE A 315 
 TRP   0.003   0.001   TRP A 479 
 HIS   0.004   0.001   HIS A 105 

Details of bonding type rmsd
  covalent geometry    : bond        0.00279 ( 8449)
  covalent geometry    : angle       0.52634 (12445)
  hydrogen bonds       : bond        0.03981 (  340)
  hydrogen bonds       : angle       3.37804 (  763)

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

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

  782 Ramachandran restraints generated.
    391 Oldfield, 0 Emsley, 391 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  782 Ramachandran restraints generated.
    391 Oldfield, 0 Emsley, 391 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  51 residues out of total 342 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 41
  time to evaluate  : 0.187 
Fit side-chains
REVERT: A   77 GLU cc_start: 0.7860 (mt-10) cc_final: 0.7253 (tt0)
REVERT: A  119 LYS cc_start: 0.8345 (mttt) cc_final: 0.7922 (mtmt)
REVERT: A  126 GLU cc_start: 0.7595 (mm-30) cc_final: 0.7003 (mp0)
REVERT: A  301 ASN cc_start: 0.8129 (OUTLIER) cc_final: 0.7813 (m110)
REVERT: A  341 TYR cc_start: 0.7664 (p90) cc_final: 0.7305 (p90)
REVERT: A  466 GLN cc_start: 0.7771 (mt0) cc_final: 0.7401 (tp40)
  outliers start: 10
  outliers final: 6
  residues processed: 47
  average time/residue: 0.6597
  time to fit residues: 32.6006
Evaluate side-chains
  47 residues out of total 342 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 7
    poor density    : 40
  time to evaluate  : 0.139 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   36 VAL
Chi-restraints excluded: chain A residue   75 SER
Chi-restraints excluded: chain A residue   86 THR
Chi-restraints excluded: chain A residue  301 ASN
Chi-restraints excluded: chain A residue  321 VAL
Chi-restraints excluded: chain A residue  360 SER
Chi-restraints excluded: chain A residue  421 ASP
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 59
   random chunks:
   chunk 36 optimal weight:    4.9990
   chunk 11 optimal weight:    3.9990
   chunk 40 optimal weight:    0.9980
   chunk 27 optimal weight:    0.0970
   chunk 10 optimal weight:    4.9990
   chunk 37 optimal weight:    1.9990
   chunk 53 optimal weight:    1.9990
   chunk 49 optimal weight:    1.9990
   chunk 54 optimal weight:    0.8980
   chunk 20 optimal weight:    0.0870
   chunk 43 optimal weight:    5.9990
   overall best weight:    0.8158

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

Flipped N/Q/H residues before XYZ refinement:
A 100 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3908 r_free = 0.3908 target = 0.177315 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 70)----------------|
| r_work = 0.3330 r_free = 0.3330 target = 0.122453 restraints weight = 5511.719|
|-----------------------------------------------------------------------------|
r_work (start): 0.3301 rms_B_bonded: 0.66
r_work: 0.3136 rms_B_bonded: 1.82 restraints_weight: 0.5000
r_work: 0.3013 rms_B_bonded: 2.89 restraints_weight: 0.2500
r_work (final): 0.3013
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8309
moved from start:          0.1417

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.022   8449  Z= 0.137
  Angle     :  0.507   6.456  12445  Z= 0.279
  Chirality :  0.032   0.168   1529
  Planarity :  0.004   0.047    776
  Dihedral  : 22.052 168.209   3639
  Min Nonbonded Distance : 2.019

Molprobity Statistics.
  All-atom Clashscore : 4.81
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.30 %
    Favored  : 97.70 %
  Rotamer:
    Outliers :  2.34 %
    Allowed  : 12.57 %
    Favored  : 85.09 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 5.56 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  0.98 (0.42), residues: 391
  helix:  2.12 (0.48), residues: 120
  sheet:  0.32 (0.60), residues: 71
  loop : -0.09 (0.43), residues: 200

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG A 414 
 TYR   0.013   0.001   TYR A   6 
 PHE   0.004   0.001   PHE A  41 
 TRP   0.003   0.001   TRP A 162 
 HIS   0.003   0.001   HIS A 105 

Details of bonding type rmsd
  covalent geometry    : bond        0.00277 ( 8449)
  covalent geometry    : angle       0.50681 (12445)
  hydrogen bonds       : bond        0.03840 (  340)
  hydrogen bonds       : angle       3.27500 (  763)

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

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

  782 Ramachandran restraints generated.
    391 Oldfield, 0 Emsley, 391 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  782 Ramachandran restraints generated.
    391 Oldfield, 0 Emsley, 391 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  49 residues out of total 342 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 8
    poor density    : 41
  time to evaluate  : 0.144 
Fit side-chains
REVERT: A   77 GLU cc_start: 0.7785 (mt-10) cc_final: 0.7191 (tt0)
REVERT: A  119 LYS cc_start: 0.8307 (mttt) cc_final: 0.7876 (mtmt)
REVERT: A  126 GLU cc_start: 0.7576 (mm-30) cc_final: 0.6971 (mp0)
REVERT: A  301 ASN cc_start: 0.8042 (OUTLIER) cc_final: 0.7752 (m110)
REVERT: A  341 TYR cc_start: 0.7648 (p90) cc_final: 0.7271 (p90)
REVERT: A  466 GLN cc_start: 0.7746 (mt0) cc_final: 0.7364 (tp40)
  outliers start: 8
  outliers final: 6
  residues processed: 46
  average time/residue: 0.6195
  time to fit residues: 29.9238
Evaluate side-chains
  47 residues out of total 342 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 7
    poor density    : 40
  time to evaluate  : 0.225 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   36 VAL
Chi-restraints excluded: chain A residue   75 SER
Chi-restraints excluded: chain A residue   86 THR
Chi-restraints excluded: chain A residue  301 ASN
Chi-restraints excluded: chain A residue  320 CYS
Chi-restraints excluded: chain A residue  321 VAL
Chi-restraints excluded: chain A residue  360 SER
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 59
   random chunks:
   chunk 29 optimal weight:    0.9980
   chunk 0 optimal weight:    5.9990
   chunk 6 optimal weight:    5.9990
   chunk 44 optimal weight:    0.9980
   chunk 37 optimal weight:    3.9990
   chunk 24 optimal weight:    0.9980
   chunk 57 optimal weight:    0.8980
   chunk 52 optimal weight:    4.9990
   chunk 31 optimal weight:    3.9990
   chunk 23 optimal weight:    0.7980
   chunk 40 optimal weight:    0.9990
   overall best weight:    0.9380

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

Flipped N/Q/H residues before XYZ refinement:
A 100 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3905 r_free = 0.3905 target = 0.176943 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 92)----------------|
| r_work = 0.3318 r_free = 0.3318 target = 0.121569 restraints weight = 5551.269|
|-----------------------------------------------------------------------------|
r_work (start): 0.3278 rms_B_bonded: 0.74
r_work: 0.3119 rms_B_bonded: 1.85 restraints_weight: 0.5000
r_work: 0.2998 rms_B_bonded: 2.93 restraints_weight: 0.2500
r_work (final): 0.2998
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8302
moved from start:          0.1415

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.022   8449  Z= 0.146
  Angle     :  0.511   6.570  12445  Z= 0.281
  Chirality :  0.032   0.162   1529
  Planarity :  0.004   0.047    776
  Dihedral  : 22.038 168.640   3639
  Min Nonbonded Distance : 2.013

Molprobity Statistics.
  All-atom Clashscore : 4.59
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.05 %
    Favored  : 97.95 %
  Rotamer:
    Outliers :  2.34 %
    Allowed  : 12.28 %
    Favored  : 85.38 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 5.56 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  0.98 (0.42), residues: 391
  helix:  2.15 (0.48), residues: 120
  sheet:  0.33 (0.60), residues: 71
  loop : -0.11 (0.42), residues: 200

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG A 414 
 TYR   0.014   0.002   TYR A   6 
 PHE   0.005   0.001   PHE A  41 
 TRP   0.003   0.001   TRP A 162 
 HIS   0.002   0.001   HIS A 105 

Details of bonding type rmsd
  covalent geometry    : bond        0.00294 ( 8449)
  covalent geometry    : angle       0.51071 (12445)
  hydrogen bonds       : bond        0.03901 (  340)
  hydrogen bonds       : angle       3.30676 (  763)

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

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

  782 Ramachandran restraints generated.
    391 Oldfield, 0 Emsley, 391 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  782 Ramachandran restraints generated.
    391 Oldfield, 0 Emsley, 391 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  47 residues out of total 342 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 8
    poor density    : 39
  time to evaluate  : 0.163 
Fit side-chains
REVERT: A   77 GLU cc_start: 0.7767 (mt-10) cc_final: 0.7162 (tt0)
REVERT: A  119 LYS cc_start: 0.8310 (mttt) cc_final: 0.7868 (mtmt)
REVERT: A  126 GLU cc_start: 0.7562 (mm-30) cc_final: 0.6917 (mp0)
REVERT: A  301 ASN cc_start: 0.8037 (OUTLIER) cc_final: 0.7743 (m110)
REVERT: A  341 TYR cc_start: 0.7629 (p90) cc_final: 0.7240 (p90)
REVERT: A  466 GLN cc_start: 0.7746 (mt0) cc_final: 0.7328 (tp40)
  outliers start: 8
  outliers final: 6
  residues processed: 44
  average time/residue: 0.6148
  time to fit residues: 28.5382
Evaluate side-chains
  46 residues out of total 342 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 7
    poor density    : 39
  time to evaluate  : 0.169 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   36 VAL
Chi-restraints excluded: chain A residue   75 SER
Chi-restraints excluded: chain A residue   86 THR
Chi-restraints excluded: chain A residue  301 ASN
Chi-restraints excluded: chain A residue  320 CYS
Chi-restraints excluded: chain A residue  321 VAL
Chi-restraints excluded: chain A residue  360 SER
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 59
   random chunks:
   chunk 2 optimal weight:    5.9990
   chunk 29 optimal weight:    0.8980
   chunk 19 optimal weight:    3.9990
   chunk 36 optimal weight:    0.6980
   chunk 7 optimal weight:    7.9990
   chunk 6 optimal weight:    3.9990
   chunk 9 optimal weight:    3.9990
   chunk 30 optimal weight:    2.9990
   chunk 52 optimal weight:    2.9990
   chunk 56 optimal weight:    0.9980
   chunk 46 optimal weight:    4.9990
   overall best weight:    1.7184

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

Flipped N/Q/H residues before XYZ refinement:
A 100 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3874 r_free = 0.3874 target = 0.173731 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 81)----------------|
| r_work = 0.3278 r_free = 0.3278 target = 0.118104 restraints weight = 5551.574|
|-----------------------------------------------------------------------------|
r_work (start): 0.3217 rms_B_bonded: 0.74
r_work: 0.3050 rms_B_bonded: 1.85 restraints_weight: 0.5000
r_work: 0.2927 rms_B_bonded: 2.94 restraints_weight: 0.2500
r_work (final): 0.2927
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8371
moved from start:          0.1428

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.033   8449  Z= 0.220
  Angle     :  0.588   7.200  12445  Z= 0.319
  Chirality :  0.035   0.151   1529
  Planarity :  0.005   0.046    776
  Dihedral  : 22.126 169.596   3639
  Min Nonbonded Distance : 2.028

Molprobity Statistics.
  All-atom Clashscore : 4.44
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.56 %
    Favored  : 97.44 %
  Rotamer:
    Outliers :  2.05 %
    Allowed  : 12.57 %
    Favored  : 85.38 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 5.56 %
    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:  0.84 (0.42), residues: 391
  helix:  1.95 (0.48), residues: 120
  sheet:  0.31 (0.61), residues: 71
  loop : -0.16 (0.42), residues: 200

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.001   ARG A 414 
 TYR   0.017   0.002   TYR A   6 
 PHE   0.007   0.002   PHE A 315 
 TRP   0.004   0.001   TRP A 162 
 HIS   0.003   0.001   HIS A 429 

Details of bonding type rmsd
  covalent geometry    : bond        0.00454 ( 8449)
  covalent geometry    : angle       0.58844 (12445)
  hydrogen bonds       : bond        0.04762 (  340)
  hydrogen bonds       : angle       3.49719 (  763)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 3022.33 seconds
wall clock time: 52 minutes 2.01 seconds (3122.01 seconds total)