Starting phenix.real_space_refine
on Fri Jun 13 09:25:34 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/8t2s_40986/06_2025/8t2s_40986.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/8t2s_40986/06_2025/8t2s_40986.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=3.0
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/cci-nas-00/data/ceres_data/8t2s_40986/06_2025/8t2s_40986.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/8t2s_40986/06_2025/8t2s_40986.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/8t2s_40986/06_2025/8t2s_40986.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/8t2s_40986/06_2025/8t2s_40986.cif"
  }
  resolution = 3.0
  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=   0.032
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
     Ca     11      9.91       5
     P     551      5.49       5
     S      21      5.16       5
     C    7283      2.51       5
     N    2764      2.21       5
     O    4368      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 6 residue(s): 0.01s

  Monomer Library directory:
    "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/chem_data/mon_lib"
  Total number of atoms: 14998
  Number of models: 1
  Model: ""
    Number of chains: 3
    Chain: "D"
      Number of atoms: 3146
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 389, 3146
          Classifications: {'peptide': 389}
          Link IDs: {'PTRANS': 10, 'TRANS': 378}
          Chain breaks: 2
    Chain: "B"
      Number of atoms: 11839
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 551, 11839
          Classifications: {'RNA': 551}
          Modifications used: {'rna2p_pur': 46, 'rna2p_pyr': 17, 'rna3p_pur': 283, 'rna3p_pyr': 205}
          Link IDs: {'rna2p': 62, 'rna3p': 488}
          Chain breaks: 6
    Chain: "B"
      Number of atoms: 13
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 13, 13
          Unusual residues: {' CA': 11, 'NH4': 2}
          Classifications: {'undetermined': 13}
          Link IDs: {None: 12}
  Time building chain proxies: 10.12, per 1000 atoms: 0.67
  Number of scatterers: 14998
  At special positions: 0
  Unit cell: (110.564, 136.728, 160.36, 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)
     Ca     11     19.99
     S      21     16.00
     P     551     15.00
     O    4368      8.00
     N    2764      7.00
     C    7283      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=1, symmetry=0
  Number of additional bonds: simple=1, symmetry=0
  Coordination:
  Other bonds:
  Time building additional restraints: 3.73
  Conformation dependent library (CDL) restraints added in 460.2 milliseconds
  

  766 Ramachandran restraints generated.
    383 Oldfield, 0 Emsley, 383 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  728

  Finding SS restraints...
    Secondary structure from input PDB file:
      20 helices and 2 sheets defined
      65.8% alpha, 6.2% beta
      181 base pairs and 323 stacking pairs defined.
    Time for finding SS restraints: 8.80
  Creating SS restraints...
    Processing helix  chain 'D' and resid 5 through 11
      removed outlier: 3.886A  pdb=" N   GLN D   9 " --> pdb=" O   ASN D   5 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 12 through 27
    Processing helix  chain 'D' and resid 39 through 57
      removed outlier: 5.712A  pdb=" N   GLU D  49 " --> pdb=" O   ALA D  45 " (cutoff:3.500A)
      removed outlier: 5.361A  pdb=" N   THR D  50 " --> pdb=" O   LYS D  46 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 84 through 96
    Processing helix  chain 'D' and resid 97 through 104
      removed outlier: 4.251A  pdb=" N   ILE D 101 " --> pdb=" O   VAL D  97 " (cutoff:3.500A)
      removed outlier: 4.055A  pdb=" N   GLU D 104 " --> pdb=" O   PRO D 100 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 118 through 133
      removed outlier: 3.671A  pdb=" N   ALA D 122 " --> pdb=" O   CYS D 118 " (cutoff:3.500A)
      removed outlier: 3.675A  pdb=" N   GLY D 133 " --> pdb=" O   ILE D 129 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 144 through 149
      removed outlier: 3.532A  pdb=" N   VAL D 149 " --> pdb=" O   PHE D 145 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 150 through 160
    Processing helix  chain 'D' and resid 166 through 176
      removed outlier: 4.359A  pdb=" N   ILE D 170 " --> pdb=" O   ASP D 166 " (cutoff:3.500A)
      removed outlier: 3.861A  pdb=" N   LEU D 175 " --> pdb=" O   VAL D 171 " (cutoff:3.500A)
      removed outlier: 3.529A  pdb=" N   VAL D 176 " --> pdb=" O   ARG D 172 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 198 through 217
      removed outlier: 3.863A  pdb=" N   GLU D 209 " --> pdb=" O   ILE D 205 " (cutoff:3.500A)
      removed outlier: 4.396A  pdb=" N   LEU D 210 " --> pdb=" O   MET D 206 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 234 through 252
    Processing helix  chain 'D' and resid 291 through 306
      removed outlier: 3.577A  pdb=" N   LYS D 297 " --> pdb=" O   LYS D 293 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 313 through 330
      removed outlier: 3.985A  pdb=" N   ASN D 330 " --> pdb=" O   ARG D 326 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 337 through 361
      removed outlier: 3.663A  pdb=" N   LYS D 361 " --> pdb=" O   TRP D 357 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 362 through 372
    Processing helix  chain 'D' and resid 376 through 385
    Processing helix  chain 'D' and resid 389 through 394
    Processing helix  chain 'D' and resid 397 through 403
    Processing helix  chain 'D' and resid 404 through 410
    Processing helix  chain 'D' and resid 415 through 424
    Processing sheet with id=AA1, first strand: chain 'D' and resid 220 through 224
      removed outlier: 4.133A  pdb=" N   ASN D 220 " --> pdb=" O   MET D 231 " (cutoff:3.500A)
      removed outlier: 4.251A  pdb=" N   CYS D 228 " --> pdb=" O   ILE D 140 " (cutoff:3.500A)
    Processing sheet with id=AA2, first strand: chain 'D' and resid 271 through 272

    178 hydrogen bonds defined for protein.
    525 hydrogen bond angles defined for protein.
    Restraints generated for nucleic acids:
      447 hydrogen bonds
      708 hydrogen bond angles
      0 basepair planarities
      181 basepair parallelities
      323 stacking parallelities
  Total time for adding SS restraints: 10.51

  Time building geometry restraints manager: 4.38 seconds

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

  Histogram of bond lengths:
        1.20 -     1.32: 1521
        1.32 -     1.45: 7659
        1.45 -     1.57: 6151
        1.57 -     1.69: 1096
        1.69 -     1.82: 35
  Bond restraints: 16462
  Sorted by residual:
  bond pdb=" C   THR D  99 "
       pdb=" N   PRO D 100 "
    ideal  model  delta    sigma   weight residual
    1.335  1.361 -0.026 1.28e-02 6.10e+03 4.24e+00
  bond pdb=" CG  GLN D  63 "
       pdb=" CD  GLN D  63 "
    ideal  model  delta    sigma   weight residual
    1.516  1.566 -0.050 2.50e-02 1.60e+03 3.98e+00
  bond pdb=" CB  GLN D  63 "
       pdb=" CG  GLN D  63 "
    ideal  model  delta    sigma   weight residual
    1.520  1.574 -0.054 3.00e-02 1.11e+03 3.27e+00
  bond pdb=" C3'   G B 369 "
       pdb=" O3'   G B 369 "
    ideal  model  delta    sigma   weight residual
    1.427  1.453 -0.026 1.50e-02 4.44e+03 2.98e+00
  bond pdb=" CB  ASP D 226 "
       pdb=" CG  ASP D 226 "
    ideal  model  delta    sigma   weight residual
    1.516  1.559 -0.043 2.50e-02 1.60e+03 2.93e+00
  ... (remaining 16457 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     2.76: 24506
        2.76 -     5.51: 379
        5.51 -     8.27: 62
        8.27 -    11.02: 13
       11.02 -    13.78: 4
  Bond angle restraints: 24964
  Sorted by residual:
  angle pdb=" CA  MET D   7 "
        pdb=" CB  MET D   7 "
        pdb=" CG  MET D   7 "
      ideal   model   delta    sigma   weight residual
     114.10  124.56  -10.46 2.00e+00 2.50e-01 2.73e+01
  angle pdb=" CA  GLU D 235 "
        pdb=" CB  GLU D 235 "
        pdb=" CG  GLU D 235 "
      ideal   model   delta    sigma   weight residual
     114.10  124.39  -10.29 2.00e+00 2.50e-01 2.65e+01
  angle pdb=" C3'   G B 369 "
        pdb=" O3'   G B 369 "
        pdb=" P     A B 370 "
      ideal   model   delta    sigma   weight residual
     120.20  127.87   -7.67 1.50e+00 4.44e-01 2.62e+01
  angle pdb=" C3'   A B 551 "
        pdb=" O3'   A B 551 "
        pdb=" P     U B 552 "
      ideal   model   delta    sigma   weight residual
     120.20  127.62   -7.42 1.50e+00 4.44e-01 2.44e+01
  angle pdb=" C3'   A B  67 "
        pdb=" O3'   A B  67 "
        pdb=" P     U B  68 "
      ideal   model   delta    sigma   weight residual
     120.20  127.32   -7.12 1.50e+00 4.44e-01 2.25e+01
  ... (remaining 24959 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    35.46: 8923
       35.46 -    70.92: 1328
       70.92 -   106.37: 142
      106.37 -   141.83: 7
      141.83 -   177.29: 10
  Dihedral angle restraints: 10410
    sinusoidal: 9280
      harmonic: 1130
  Sorted by residual:
  dihedral pdb=" O4'   C B 581 "
           pdb=" C1'   C B 581 "
           pdb=" N1    C B 581 "
           pdb=" C2    C B 581 "
      ideal   model   delta sinusoidal    sigma   weight residual
    -160.00   12.10 -172.10     1      1.50e+01 4.44e-03 8.49e+01
  dihedral pdb=" O4'   U B 172 "
           pdb=" C1'   U B 172 "
           pdb=" N1    U B 172 "
           pdb=" C2    U B 172 "
      ideal   model   delta sinusoidal    sigma   weight residual
     200.00   31.97  168.03     1      1.50e+01 4.44e-03 8.44e+01
  dihedral pdb=" O4'   C B 439 "
           pdb=" C1'   C B 439 "
           pdb=" N1    C B 439 "
           pdb=" C2    C B 439 "
      ideal   model   delta sinusoidal    sigma   weight residual
     200.00   43.48  156.52     1      1.50e+01 4.44e-03 8.18e+01
  ... (remaining 10407 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.068: 2939
       0.068 -    0.135: 241
       0.135 -    0.203: 25
       0.203 -    0.271: 10
       0.271 -    0.338: 8
  Chirality restraints: 3223
  Sorted by residual:
  chirality pdb=" C3'   C B 206 "
            pdb=" C4'   C B 206 "
            pdb=" O3'   C B 206 "
            pdb=" C2'   C B 206 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.48   -2.14   -0.34 2.00e-01 2.50e+01 2.86e+00
  chirality pdb=" C3'   G B 369 "
            pdb=" C4'   G B 369 "
            pdb=" O3'   G B 369 "
            pdb=" C2'   G B 369 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.74   -2.42   -0.33 2.00e-01 2.50e+01 2.64e+00
  chirality pdb=" C3'   C B  39 "
            pdb=" C4'   C B  39 "
            pdb=" O3'   C B  39 "
            pdb=" C2'   C B  39 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.48   -2.16   -0.32 2.00e-01 2.50e+01 2.56e+00
  ... (remaining 3220 not shown)

  Planarity restraints: 1096
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C1'   A B 185 "   -0.043 2.00e-02 2.50e+03   1.91e-02 1.01e+01
        pdb=" N9    A B 185 "    0.042 2.00e-02 2.50e+03
        pdb=" C8    A B 185 "    0.003 2.00e-02 2.50e+03
        pdb=" N7    A B 185 "    0.000 2.00e-02 2.50e+03
        pdb=" C5    A B 185 "   -0.003 2.00e-02 2.50e+03
        pdb=" C6    A B 185 "   -0.006 2.00e-02 2.50e+03
        pdb=" N6    A B 185 "   -0.009 2.00e-02 2.50e+03
        pdb=" N1    A B 185 "   -0.004 2.00e-02 2.50e+03
        pdb=" C2    A B 185 "   -0.002 2.00e-02 2.50e+03
        pdb=" N3    A B 185 "    0.013 2.00e-02 2.50e+03
        pdb=" C4    A B 185 "    0.009 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   ARG D 266 "    0.042 5.00e-02 4.00e+02   6.40e-02 6.55e+00
        pdb=" N   PRO D 267 "   -0.111 5.00e-02 4.00e+02
        pdb=" CA  PRO D 267 "    0.033 5.00e-02 4.00e+02
        pdb=" CD  PRO D 267 "    0.036 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C1'   U B 175 "    0.033 2.00e-02 2.50e+03   1.66e-02 6.18e+00
        pdb=" N1    U B 175 "   -0.033 2.00e-02 2.50e+03
        pdb=" C2    U B 175 "   -0.001 2.00e-02 2.50e+03
        pdb=" O2    U B 175 "   -0.006 2.00e-02 2.50e+03
        pdb=" N3    U B 175 "    0.002 2.00e-02 2.50e+03
        pdb=" C4    U B 175 "    0.007 2.00e-02 2.50e+03
        pdb=" O4    U B 175 "    0.011 2.00e-02 2.50e+03
        pdb=" C5    U B 175 "   -0.007 2.00e-02 2.50e+03
        pdb=" C6    U B 175 "   -0.006 2.00e-02 2.50e+03
  ... (remaining 1093 not shown)

  Histogram of nonbonded interaction distances:
        2.25 -     2.78: 2986
        2.78 -     3.31: 12012
        3.31 -     3.84: 33245
        3.84 -     4.37: 38293
        4.37 -     4.90: 49211
  Nonbonded interactions: 135747
  Sorted by model distance:
  nonbonded pdb=" OP2   A B 137 "
            pdb=" O2'   A B 147 "
     model   vdw
     2.251 3.040
  nonbonded pdb=" O2'   G B 276 "
            pdb=" O4    U B 325 "
     model   vdw
     2.259 3.040
  nonbonded pdb=" O2'   G B 136 "
            pdb=" OP1   U B 148 "
     model   vdw
     2.277 3.040
  nonbonded pdb=" OD1 ASN D 395 "
            pdb=" O2'   A B -33 "
     model   vdw
     2.287 3.040
  nonbonded pdb=" N2    G B 287 "
            pdb=" O2    C B 315 "
     model   vdw
     2.304 2.496
  ... (remaining 135742 not shown)

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

  No NCS relation were found !!!

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

Found NCS groups:
  found none.
Set up NCS constraints
  No NCS constraints will be used in refinement.
Set refine NCS operators
Adjust number of macro_cycles
  Number of macro_cycles: 10
Reset NCS operators
Extract rigid body selections
Check and reset occupancies
  Occupancies: min=0.00 max=1.00 mean=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:             4.520
  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:             0.020
  Extract box with map and model:          0.590
  Check model and map are aligned:         0.110
  Set scattering table:                    0.130
  Process input model:                     46.400
  Find NCS groups from input model:        0.130
  Set up NCS constraints:                  0.060
  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:46.380
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   98.340
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8028
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      :  0.004   0.054  16463  Z= 0.201
  Angle     :  0.889  13.780  24964  Z= 0.433
  Chirality :  0.042   0.338   3223
  Planarity :  0.006   0.064   1096
  Dihedral  : 24.681 177.289   9682
  Min Nonbonded Distance : 2.251

Molprobity Statistics.
  All-atom Clashscore : 3.85
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.87 %
    Favored  : 97.13 %
  Rotamer:
    Outliers :  2.04 %
    Allowed  : 24.49 %
    Favored  : 73.47 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.27 %

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: -2.71 (0.36), residues: 383
  helix: -1.32 (0.28), residues: 246
  sheet: -1.07 (0.98), residues: 24
  loop : -2.72 (0.45), residues: 113

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.016   0.002   TRP D 357 
 HIS   0.008   0.002   HIS D  43 
 PHE   0.019   0.003   PHE D  89 
 TYR   0.019   0.002   TYR D  60 
 ARG   0.005   0.001   ARG D 347 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.10370 (  625)
  hydrogen bonds       : angle       4.99506 ( 1233)
  covalent geometry    : bond        0.00379 (16462)
  covalent geometry    : angle       0.88888 (24964)
  Misc. bond           : bond        0.00023 (    1)

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

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

  766 Ramachandran restraints generated.
    383 Oldfield, 0 Emsley, 383 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  766 Ramachandran restraints generated.
    383 Oldfield, 0 Emsley, 383 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  39 residues out of total 343 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 7
    poor density    : 32
  time to evaluate  : 0.725 
Fit side-chains
REVERT: D  130 MET cc_start: 0.7844 (mtt) cc_final: 0.7623 (mtt)
REVERT: D  236 MET cc_start: 0.7785 (ppp) cc_final: 0.7583 (ppp)
REVERT: D  266 ARG cc_start: 0.8347 (mmt90) cc_final: 0.7959 (mmm-85)
REVERT: D  406 LYS cc_start: 0.8059 (mtmm) cc_final: 0.7592 (mppt)
  outliers start: 7
  outliers final: 2
  residues processed: 38
  average time/residue: 1.4755
  time to fit residues: 62.0129
Evaluate side-chains
  29 residues out of total 343 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 2
    poor density    : 27
  time to evaluate  : 0.657 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain D residue  149 VAL
Chi-restraints excluded: chain D residue  166 ASP
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 93
   random chunks:
   chunk 78 optimal weight:   20.0000
   chunk 70 optimal weight:    4.9990
   chunk 39 optimal weight:    3.9990
   chunk 24 optimal weight:    0.7980
   chunk 47 optimal weight:    3.9990
   chunk 37 optimal weight:    1.9990
   chunk 72 optimal weight:    8.9990
   chunk 28 optimal weight:    0.9990
   chunk 44 optimal weight:   10.0000
   chunk 54 optimal weight:    3.9990
   chunk 84 optimal weight:   20.0000
   overall best weight:    2.3588

-------------------------------------------------------------------------------
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 = 0.4031 r_free = 0.4031 target = 0.176571 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 73)----------------|
| r_work = 0.3159 r_free = 0.3159 target = 0.103512 restraints weight = 17954.472|
|-----------------------------------------------------------------------------|
r_work (start): 0.3107 rms_B_bonded: 0.99
r_work: 0.2955 rms_B_bonded: 2.52 restraints_weight: 0.5000
r_work: 0.2831 rms_B_bonded: 3.92 restraints_weight: 0.2500
r_work (final): 0.2831
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8584
moved from start:          0.1645

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.006   0.068  16463  Z= 0.322
  Angle     :  0.703   7.499  24964  Z= 0.360
  Chirality :  0.040   0.288   3223
  Planarity :  0.005   0.041   1096
  Dihedral  : 24.623 176.244   8878
  Min Nonbonded Distance : 2.104

Molprobity Statistics.
  All-atom Clashscore : 6.16
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.96 %
    Favored  : 95.04 %
  Rotamer:
    Outliers :  6.41 %
    Allowed  : 18.08 %
    Favored  : 75.51 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -1.53 (0.40), residues: 383
  helix: -0.20 (0.32), residues: 249
  sheet: -1.50 (0.93), residues: 24
  loop : -2.63 (0.48), residues: 110

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.010   0.002   TRP D 357 
 HIS   0.005   0.001   HIS D 109 
 PHE   0.013   0.003   PHE D 298 
 TYR   0.023   0.002   TYR D 385 
 ARG   0.003   0.001   ARG D 243 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.06931 (  625)
  hydrogen bonds       : angle       3.44961 ( 1233)
  covalent geometry    : bond        0.00624 (16462)
  covalent geometry    : angle       0.70260 (24964)
  Misc. bond           : bond        0.00082 (    1)

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

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

  766 Ramachandran restraints generated.
    383 Oldfield, 0 Emsley, 383 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  766 Ramachandran restraints generated.
    383 Oldfield, 0 Emsley, 383 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  52 residues out of total 343 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 22
    poor density    : 30
  time to evaluate  : 0.682 
Fit side-chains
REVERT: D   59 LYS cc_start: 0.7642 (OUTLIER) cc_final: 0.7282 (mtmp)
REVERT: D  251 GLU cc_start: 0.8231 (OUTLIER) cc_final: 0.7667 (mt-10)
REVERT: D  347 ARG cc_start: 0.8097 (mtt-85) cc_final: 0.7634 (mtp180)
REVERT: D  364 GLN cc_start: 0.8381 (OUTLIER) cc_final: 0.7500 (mm-40)
REVERT: D  406 LYS cc_start: 0.8485 (mtmm) cc_final: 0.8218 (mppt)
  outliers start: 22
  outliers final: 5
  residues processed: 47
  average time/residue: 1.3161
  time to fit residues: 68.2398
Evaluate side-chains
  37 residues out of total 343 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 8
    poor density    : 29
  time to evaluate  : 0.646 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain D residue   59 LYS
Chi-restraints excluded: chain D residue  149 VAL
Chi-restraints excluded: chain D residue  161 THR
Chi-restraints excluded: chain D residue  166 ASP
Chi-restraints excluded: chain D residue  251 GLU
Chi-restraints excluded: chain D residue  255 LEU
Chi-restraints excluded: chain D residue  262 SER
Chi-restraints excluded: chain D residue  364 GLN
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 93
   random chunks:
   chunk 70 optimal weight:    3.9990
   chunk 78 optimal weight:   20.0000
   chunk 20 optimal weight:    0.7980
   chunk 41 optimal weight:    5.9990
   chunk 54 optimal weight:    3.9990
   chunk 31 optimal weight:    0.5980
   chunk 36 optimal weight:    0.7980
   chunk 60 optimal weight:    2.9990
   chunk 86 optimal weight:    2.9990
   chunk 58 optimal weight:    2.9990
   chunk 81 optimal weight:   10.0000
   overall best weight:    1.6384

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

Flipped N/Q/H residues before XYZ refinement:
D  96 GLN
D 369 ASN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4044 r_free = 0.4044 target = 0.178155 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 65)----------------|
| r_work = 0.3182 r_free = 0.3182 target = 0.105442 restraints weight = 17911.310|
|-----------------------------------------------------------------------------|
r_work (start): 0.3134 rms_B_bonded: 0.89
r_work: 0.2985 rms_B_bonded: 2.46 restraints_weight: 0.5000
r_work: 0.2864 rms_B_bonded: 3.81 restraints_weight: 0.2500
r_work (final): 0.2864
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8529
moved from start:          0.1803

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.050  16463  Z= 0.233
  Angle     :  0.638   7.538  24964  Z= 0.327
  Chirality :  0.036   0.284   3223
  Planarity :  0.005   0.040   1096
  Dihedral  : 24.572 175.061   8878
  Min Nonbonded Distance : 2.127

Molprobity Statistics.
  All-atom Clashscore : 7.03
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.92 %
    Favored  : 96.08 %
  Rotamer:
    Outliers :  6.12 %
    Allowed  : 19.24 %
    Favored  : 74.64 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -0.79 (0.42), residues: 383
  helix:  0.48 (0.33), residues: 249
  sheet: -1.64 (0.94), residues: 24
  loop : -2.53 (0.49), residues: 110

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.009   0.002   TRP D 357 
 HIS   0.003   0.001   HIS D 109 
 PHE   0.014   0.002   PHE D  89 
 TYR   0.019   0.002   TYR D 385 
 ARG   0.003   0.000   ARG D 240 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.06394 (  625)
  hydrogen bonds       : angle       3.24119 ( 1233)
  covalent geometry    : bond        0.00450 (16462)
  covalent geometry    : angle       0.63828 (24964)
  Misc. bond           : bond        0.00069 (    1)

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

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

  766 Ramachandran restraints generated.
    383 Oldfield, 0 Emsley, 383 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  766 Ramachandran restraints generated.
    383 Oldfield, 0 Emsley, 383 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  52 residues out of total 343 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 21
    poor density    : 31
  time to evaluate  : 1.009 
Fit side-chains
REVERT: D   59 LYS cc_start: 0.7662 (OUTLIER) cc_final: 0.7268 (mtmp)
REVERT: D  247 ARG cc_start: 0.7682 (OUTLIER) cc_final: 0.7098 (ttp80)
REVERT: D  251 GLU cc_start: 0.8278 (OUTLIER) cc_final: 0.7512 (mt-10)
REVERT: D  261 LYS cc_start: 0.8060 (mtmm) cc_final: 0.7511 (mtpp)
REVERT: D  266 ARG cc_start: 0.8443 (OUTLIER) cc_final: 0.7390 (mmm160)
REVERT: D  280 ASP cc_start: 0.7753 (OUTLIER) cc_final: 0.7546 (t0)
REVERT: D  347 ARG cc_start: 0.8037 (mtt-85) cc_final: 0.7466 (mtp180)
REVERT: D  364 GLN cc_start: 0.8340 (OUTLIER) cc_final: 0.7444 (mm-40)
REVERT: D  406 LYS cc_start: 0.8493 (OUTLIER) cc_final: 0.8207 (mppt)
  outliers start: 21
  outliers final: 7
  residues processed: 47
  average time/residue: 2.2490
  time to fit residues: 116.4401
Evaluate side-chains
  42 residues out of total 343 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 28
  time to evaluate  : 0.805 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain D residue   39 GLU
Chi-restraints excluded: chain D residue   59 LYS
Chi-restraints excluded: chain D residue   86 THR
Chi-restraints excluded: chain D residue  101 ILE
Chi-restraints excluded: chain D residue  149 VAL
Chi-restraints excluded: chain D residue  164 ASP
Chi-restraints excluded: chain D residue  166 ASP
Chi-restraints excluded: chain D residue  247 ARG
Chi-restraints excluded: chain D residue  251 GLU
Chi-restraints excluded: chain D residue  255 LEU
Chi-restraints excluded: chain D residue  266 ARG
Chi-restraints excluded: chain D residue  280 ASP
Chi-restraints excluded: chain D residue  364 GLN
Chi-restraints excluded: chain D residue  406 LYS
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 93
   random chunks:
   chunk 50 optimal weight:    3.9990
   chunk 11 optimal weight:    2.9990
   chunk 28 optimal weight:    0.7980
   chunk 47 optimal weight:    2.9990
   chunk 4 optimal weight:    4.9990
   chunk 59 optimal weight:    8.9990
   chunk 24 optimal weight:    2.9990
   chunk 80 optimal weight:   30.0000
   chunk 17 optimal weight:    0.7980
   chunk 0 optimal weight:   10.0000
   chunk 2 optimal weight:    1.9990
   overall best weight:    1.9186

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

Flipped N/Q/H residues before XYZ refinement:
D  96 GLN
D 400 ASN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4029 r_free = 0.4029 target = 0.176754 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 72)----------------|
| r_work = 0.3161 r_free = 0.3161 target = 0.103995 restraints weight = 17869.351|
|-----------------------------------------------------------------------------|
r_work (start): 0.3115 rms_B_bonded: 0.93
r_work: 0.2966 rms_B_bonded: 2.46 restraints_weight: 0.5000
r_work: 0.2845 rms_B_bonded: 3.82 restraints_weight: 0.2500
r_work (final): 0.2845
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8551
moved from start:          0.2153

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.056  16463  Z= 0.268
  Angle     :  0.651   7.538  24964  Z= 0.333
  Chirality :  0.037   0.282   3223
  Planarity :  0.005   0.035   1096
  Dihedral  : 24.491 174.725   8878
  Min Nonbonded Distance : 2.111

Molprobity Statistics.
  All-atom Clashscore : 6.87
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.96 %
    Favored  : 95.04 %
  Rotamer:
    Outliers :  6.71 %
    Allowed  : 20.12 %
    Favored  : 73.18 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -0.59 (0.42), residues: 383
  helix:  0.67 (0.34), residues: 249
  sheet: -1.90 (0.93), residues: 24
  loop : -2.45 (0.51), residues: 110

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.009   0.002   TRP D 357 
 HIS   0.004   0.001   HIS D 109 
 PHE   0.012   0.002   PHE D  89 
 TYR   0.021   0.002   TYR D 385 
 ARG   0.002   0.000   ARG D 240 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.06419 (  625)
  hydrogen bonds       : angle       3.20235 ( 1233)
  covalent geometry    : bond        0.00517 (16462)
  covalent geometry    : angle       0.65121 (24964)
  Misc. bond           : bond        0.00077 (    1)

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

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

  766 Ramachandran restraints generated.
    383 Oldfield, 0 Emsley, 383 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  766 Ramachandran restraints generated.
    383 Oldfield, 0 Emsley, 383 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  51 residues out of total 343 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 23
    poor density    : 28
  time to evaluate  : 0.694 
Fit side-chains
REVERT: D   59 LYS cc_start: 0.7626 (OUTLIER) cc_final: 0.7255 (mtmp)
REVERT: D  247 ARG cc_start: 0.7754 (OUTLIER) cc_final: 0.7121 (ttp80)
REVERT: D  251 GLU cc_start: 0.8287 (OUTLIER) cc_final: 0.7519 (mt-10)
REVERT: D  261 LYS cc_start: 0.8004 (OUTLIER) cc_final: 0.7452 (mtpp)
REVERT: D  266 ARG cc_start: 0.8438 (OUTLIER) cc_final: 0.7298 (mmm160)
REVERT: D  280 ASP cc_start: 0.7745 (OUTLIER) cc_final: 0.7538 (t0)
REVERT: D  347 ARG cc_start: 0.8128 (mtt-85) cc_final: 0.7537 (mtp180)
REVERT: D  364 GLN cc_start: 0.8339 (OUTLIER) cc_final: 0.7455 (mm-40)
REVERT: D  406 LYS cc_start: 0.8480 (OUTLIER) cc_final: 0.8121 (tttt)
  outliers start: 23
  outliers final: 8
  residues processed: 45
  average time/residue: 1.7189
  time to fit residues: 83.6738
Evaluate side-chains
  45 residues out of total 343 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 29
  time to evaluate  : 0.711 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain D residue   39 GLU
Chi-restraints excluded: chain D residue   59 LYS
Chi-restraints excluded: chain D residue   82 VAL
Chi-restraints excluded: chain D residue   86 THR
Chi-restraints excluded: chain D residue  101 ILE
Chi-restraints excluded: chain D residue  149 VAL
Chi-restraints excluded: chain D residue  164 ASP
Chi-restraints excluded: chain D residue  166 ASP
Chi-restraints excluded: chain D residue  247 ARG
Chi-restraints excluded: chain D residue  251 GLU
Chi-restraints excluded: chain D residue  255 LEU
Chi-restraints excluded: chain D residue  261 LYS
Chi-restraints excluded: chain D residue  266 ARG
Chi-restraints excluded: chain D residue  280 ASP
Chi-restraints excluded: chain D residue  364 GLN
Chi-restraints excluded: chain D residue  406 LYS
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 93
   random chunks:
   chunk 72 optimal weight:    8.9990
   chunk 64 optimal weight:    3.9990
   chunk 21 optimal weight:    0.7980
   chunk 36 optimal weight:    0.8980
   chunk 75 optimal weight:    4.9990
   chunk 12 optimal weight:    1.9990
   chunk 1 optimal weight:   10.0000
   chunk 63 optimal weight:    5.9990
   chunk 67 optimal weight:   30.0000
   chunk 55 optimal weight:    3.9990
   chunk 74 optimal weight:    2.9990
   overall best weight:    2.1386

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

Flipped N/Q/H residues before XYZ refinement:
D  96 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4034 r_free = 0.4034 target = 0.176665 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 69)----------------|
| r_work = 0.3154 r_free = 0.3154 target = 0.103270 restraints weight = 18201.310|
|-----------------------------------------------------------------------------|
r_work (start): 0.3105 rms_B_bonded: 0.95
r_work: 0.2955 rms_B_bonded: 2.51 restraints_weight: 0.5000
r_work: 0.2832 rms_B_bonded: 3.90 restraints_weight: 0.2500
r_work (final): 0.2832
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8576
moved from start:          0.2437

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.006   0.059  16463  Z= 0.293
  Angle     :  0.668   7.303  24964  Z= 0.340
  Chirality :  0.038   0.284   3223
  Planarity :  0.005   0.035   1096
  Dihedral  : 24.485 174.117   8878
  Min Nonbonded Distance : 2.090

Molprobity Statistics.
  All-atom Clashscore : 6.78
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.48 %
    Favored  : 94.52 %
  Rotamer:
    Outliers :  7.87 %
    Allowed  : 20.99 %
    Favored  : 71.14 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -0.54 (0.43), residues: 383
  helix:  0.73 (0.34), residues: 249
  sheet: -1.97 (0.93), residues: 24
  loop : -2.47 (0.51), residues: 110

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.010   0.002   TRP D 357 
 HIS   0.004   0.001   HIS D 109 
 PHE   0.012   0.002   PHE D  89 
 TYR   0.021   0.002   TYR D 385 
 ARG   0.002   0.000   ARG D 407 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.06515 (  625)
  hydrogen bonds       : angle       3.19422 ( 1233)
  covalent geometry    : bond        0.00566 (16462)
  covalent geometry    : angle       0.66753 (24964)
  Misc. bond           : bond        0.00085 (    1)

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

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

  766 Ramachandran restraints generated.
    383 Oldfield, 0 Emsley, 383 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  766 Ramachandran restraints generated.
    383 Oldfield, 0 Emsley, 383 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  58 residues out of total 343 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 27
    poor density    : 31
  time to evaluate  : 0.740 
Fit side-chains
REVERT: D   59 LYS cc_start: 0.7627 (OUTLIER) cc_final: 0.7267 (mtmp)
REVERT: D  105 GLN cc_start: 0.8228 (mt0) cc_final: 0.7825 (mt0)
REVERT: D  247 ARG cc_start: 0.7792 (OUTLIER) cc_final: 0.7145 (ttp80)
REVERT: D  251 GLU cc_start: 0.8311 (OUTLIER) cc_final: 0.7499 (mt-10)
REVERT: D  253 LEU cc_start: 0.8549 (OUTLIER) cc_final: 0.7962 (mp)
REVERT: D  261 LYS cc_start: 0.7993 (OUTLIER) cc_final: 0.7437 (mtpp)
REVERT: D  280 ASP cc_start: 0.7811 (OUTLIER) cc_final: 0.7598 (t0)
REVERT: D  347 ARG cc_start: 0.8140 (mtt-85) cc_final: 0.7560 (mtp180)
REVERT: D  364 GLN cc_start: 0.8374 (OUTLIER) cc_final: 0.7534 (mm-40)
REVERT: D  388 LYS cc_start: 0.7961 (OUTLIER) cc_final: 0.7378 (ptmm)
REVERT: D  406 LYS cc_start: 0.8470 (OUTLIER) cc_final: 0.8008 (ttpp)
  outliers start: 27
  outliers final: 7
  residues processed: 48
  average time/residue: 1.5433
  time to fit residues: 80.8801
Evaluate side-chains
  43 residues out of total 343 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 27
  time to evaluate  : 0.670 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain D residue   39 GLU
Chi-restraints excluded: chain D residue   59 LYS
Chi-restraints excluded: chain D residue   82 VAL
Chi-restraints excluded: chain D residue   86 THR
Chi-restraints excluded: chain D residue  101 ILE
Chi-restraints excluded: chain D residue  149 VAL
Chi-restraints excluded: chain D residue  161 THR
Chi-restraints excluded: chain D residue  247 ARG
Chi-restraints excluded: chain D residue  251 GLU
Chi-restraints excluded: chain D residue  253 LEU
Chi-restraints excluded: chain D residue  255 LEU
Chi-restraints excluded: chain D residue  261 LYS
Chi-restraints excluded: chain D residue  280 ASP
Chi-restraints excluded: chain D residue  364 GLN
Chi-restraints excluded: chain D residue  388 LYS
Chi-restraints excluded: chain D residue  406 LYS
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 93
   random chunks:
   chunk 1 optimal weight:    6.9990
   chunk 50 optimal weight:    2.9990
   chunk 66 optimal weight:   10.9990
   chunk 42 optimal weight:   10.0000
   chunk 27 optimal weight:    0.5980
   chunk 0 optimal weight:    7.9990
   chunk 51 optimal weight:    3.9990
   chunk 30 optimal weight:    0.6980
   chunk 47 optimal weight:    2.9990
   chunk 29 optimal weight:    0.0770
   chunk 5 optimal weight:    9.9990
   overall best weight:    1.4742

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

Flipped N/Q/H residues before XYZ refinement:
D  96 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4042 r_free = 0.4042 target = 0.177219 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 76)----------------|
| r_work = 0.3190 r_free = 0.3190 target = 0.105385 restraints weight = 17905.175|
|-----------------------------------------------------------------------------|
r_work (start): 0.3134 rms_B_bonded: 0.86
r_work: 0.2988 rms_B_bonded: 2.42 restraints_weight: 0.5000
r_work: 0.2866 rms_B_bonded: 3.76 restraints_weight: 0.2500
r_work (final): 0.2866
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8540
moved from start:          0.2431

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.046  16463  Z= 0.223
  Angle     :  0.639  11.354  24964  Z= 0.326
  Chirality :  0.036   0.285   3223
  Planarity :  0.004   0.038   1096
  Dihedral  : 24.509 173.955   8876
  Min Nonbonded Distance : 2.097

Molprobity Statistics.
  All-atom Clashscore : 7.20
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.48 %
    Favored  : 94.52 %
  Rotamer:
    Outliers :  6.12 %
    Allowed  : 23.62 %
    Favored  : 70.26 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -0.40 (0.43), residues: 383
  helix:  0.84 (0.34), residues: 249
  sheet: -1.98 (0.93), residues: 24
  loop : -2.41 (0.52), residues: 110

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.009   0.002   TRP D 357 
 HIS   0.003   0.001   HIS D 109 
 PHE   0.012   0.002   PHE D  89 
 TYR   0.021   0.002   TYR D 385 
 ARG   0.002   0.000   ARG D 240 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.06391 (  625)
  hydrogen bonds       : angle       3.16310 ( 1233)
  covalent geometry    : bond        0.00428 (16462)
  covalent geometry    : angle       0.63939 (24964)
  Misc. bond           : bond        0.00069 (    1)

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

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

  766 Ramachandran restraints generated.
    383 Oldfield, 0 Emsley, 383 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  766 Ramachandran restraints generated.
    383 Oldfield, 0 Emsley, 383 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  50 residues out of total 343 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 21
    poor density    : 29
  time to evaluate  : 0.718 
Fit side-chains
REVERT: D   59 LYS cc_start: 0.7623 (OUTLIER) cc_final: 0.7262 (mtmp)
REVERT: D  105 GLN cc_start: 0.8224 (mt0) cc_final: 0.7815 (mt0)
REVERT: D  247 ARG cc_start: 0.7783 (OUTLIER) cc_final: 0.7138 (ttp80)
REVERT: D  251 GLU cc_start: 0.8284 (OUTLIER) cc_final: 0.7493 (mt-10)
REVERT: D  253 LEU cc_start: 0.8532 (OUTLIER) cc_final: 0.7955 (mp)
REVERT: D  261 LYS cc_start: 0.7973 (OUTLIER) cc_final: 0.7419 (mtpp)
REVERT: D  266 ARG cc_start: 0.8425 (OUTLIER) cc_final: 0.8038 (mmm-85)
REVERT: D  280 ASP cc_start: 0.7749 (OUTLIER) cc_final: 0.7528 (t0)
REVERT: D  347 ARG cc_start: 0.8108 (mtt-85) cc_final: 0.7532 (mtp180)
REVERT: D  364 GLN cc_start: 0.8307 (OUTLIER) cc_final: 0.7460 (mm-40)
REVERT: D  388 LYS cc_start: 0.7933 (OUTLIER) cc_final: 0.7344 (ptmm)
REVERT: D  406 LYS cc_start: 0.8460 (OUTLIER) cc_final: 0.7971 (ttpp)
  outliers start: 21
  outliers final: 7
  residues processed: 42
  average time/residue: 1.7038
  time to fit residues: 77.4765
Evaluate side-chains
  43 residues out of total 343 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 17
    poor density    : 26
  time to evaluate  : 0.637 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain D residue   39 GLU
Chi-restraints excluded: chain D residue   59 LYS
Chi-restraints excluded: chain D residue   82 VAL
Chi-restraints excluded: chain D residue   86 THR
Chi-restraints excluded: chain D residue  101 ILE
Chi-restraints excluded: chain D residue  149 VAL
Chi-restraints excluded: chain D residue  247 ARG
Chi-restraints excluded: chain D residue  251 GLU
Chi-restraints excluded: chain D residue  253 LEU
Chi-restraints excluded: chain D residue  255 LEU
Chi-restraints excluded: chain D residue  261 LYS
Chi-restraints excluded: chain D residue  266 ARG
Chi-restraints excluded: chain D residue  280 ASP
Chi-restraints excluded: chain D residue  302 MET
Chi-restraints excluded: chain D residue  364 GLN
Chi-restraints excluded: chain D residue  388 LYS
Chi-restraints excluded: chain D residue  406 LYS
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 93
   random chunks:
   chunk 32 optimal weight:    0.9990
   chunk 14 optimal weight:    0.0670
   chunk 64 optimal weight:    4.9990
   chunk 53 optimal weight:    2.9990
   chunk 36 optimal weight:    0.7980
   chunk 80 optimal weight:   30.0000
   chunk 17 optimal weight:    3.9990
   chunk 87 optimal weight:    2.9990
   chunk 82 optimal weight:   20.0000
   chunk 24 optimal weight:    0.0000
   chunk 43 optimal weight:    7.9990
   overall best weight:    0.9726

-------------------------------------------------------------------------------
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 = 0.4065 r_free = 0.4065 target = 0.179585 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 69)----------------|
| r_work = 0.3203 r_free = 0.3203 target = 0.106701 restraints weight = 18166.419|
|-----------------------------------------------------------------------------|
r_work (start): 0.3152 rms_B_bonded: 0.86
r_work: 0.3000 rms_B_bonded: 2.51 restraints_weight: 0.5000
r_work: 0.2883 rms_B_bonded: 3.86 restraints_weight: 0.2500
r_work (final): 0.2883
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8516
moved from start:          0.2411

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.042  16463  Z= 0.164
  Angle     :  0.615  11.186  24964  Z= 0.314
  Chirality :  0.034   0.276   3223
  Planarity :  0.004   0.037   1096
  Dihedral  : 24.518 173.602   8876
  Min Nonbonded Distance : 2.101

Molprobity Statistics.
  All-atom Clashscore : 7.69
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.22 %
    Favored  : 94.78 %
  Rotamer:
    Outliers :  4.37 %
    Allowed  : 25.07 %
    Favored  : 70.55 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -0.23 (0.43), residues: 383
  helix:  0.98 (0.34), residues: 249
  sheet: -1.95 (0.94), residues: 24
  loop : -2.34 (0.53), residues: 110

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.009   0.001   TRP D 357 
 HIS   0.002   0.001   HIS D 109 
 PHE   0.013   0.002   PHE D  89 
 TYR   0.019   0.001   TYR D 385 
 ARG   0.001   0.000   ARG D 117 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.06213 (  625)
  hydrogen bonds       : angle       3.12736 ( 1233)
  covalent geometry    : bond        0.00312 (16462)
  covalent geometry    : angle       0.61493 (24964)
  Misc. bond           : bond        0.00053 (    1)

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

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

  766 Ramachandran restraints generated.
    383 Oldfield, 0 Emsley, 383 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  766 Ramachandran restraints generated.
    383 Oldfield, 0 Emsley, 383 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  44 residues out of total 343 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 15
    poor density    : 29
  time to evaluate  : 0.816 
Fit side-chains
REVERT: D   59 LYS cc_start: 0.7623 (OUTLIER) cc_final: 0.7265 (mtmp)
REVERT: D  251 GLU cc_start: 0.8311 (OUTLIER) cc_final: 0.7829 (mt-10)
REVERT: D  253 LEU cc_start: 0.8556 (OUTLIER) cc_final: 0.7969 (mp)
REVERT: D  261 LYS cc_start: 0.7995 (OUTLIER) cc_final: 0.7439 (mtpp)
REVERT: D  266 ARG cc_start: 0.8421 (OUTLIER) cc_final: 0.8039 (mmm-85)
REVERT: D  280 ASP cc_start: 0.7756 (OUTLIER) cc_final: 0.7546 (t0)
REVERT: D  347 ARG cc_start: 0.8107 (mtt-85) cc_final: 0.7537 (mtp180)
REVERT: D  364 GLN cc_start: 0.8279 (OUTLIER) cc_final: 0.7452 (mm-40)
REVERT: D  406 LYS cc_start: 0.8482 (OUTLIER) cc_final: 0.7975 (ttpp)
  outliers start: 15
  outliers final: 5
  residues processed: 38
  average time/residue: 1.5892
  time to fit residues: 65.8312
Evaluate side-chains
  39 residues out of total 343 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 26
  time to evaluate  : 0.694 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain D residue   39 GLU
Chi-restraints excluded: chain D residue   59 LYS
Chi-restraints excluded: chain D residue   82 VAL
Chi-restraints excluded: chain D residue  101 ILE
Chi-restraints excluded: chain D residue  149 VAL
Chi-restraints excluded: chain D residue  251 GLU
Chi-restraints excluded: chain D residue  253 LEU
Chi-restraints excluded: chain D residue  255 LEU
Chi-restraints excluded: chain D residue  261 LYS
Chi-restraints excluded: chain D residue  266 ARG
Chi-restraints excluded: chain D residue  280 ASP
Chi-restraints excluded: chain D residue  364 GLN
Chi-restraints excluded: chain D residue  406 LYS
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 93
   random chunks:
   chunk 39 optimal weight:    3.9990
   chunk 60 optimal weight:    3.9990
   chunk 4 optimal weight:    5.9990
   chunk 22 optimal weight:    4.9990
   chunk 12 optimal weight:    1.9990
   chunk 29 optimal weight:    0.0670
   chunk 38 optimal weight:    7.9990
   chunk 73 optimal weight:    4.9990
   chunk 42 optimal weight:   10.0000
   chunk 21 optimal weight:    0.3980
   chunk 55 optimal weight:    2.9990
   overall best weight:    1.8924

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

Flipped N/Q/H residues before XYZ refinement:
D  96 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4041 r_free = 0.4041 target = 0.177001 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 73)----------------|
| r_work = 0.3192 r_free = 0.3192 target = 0.105591 restraints weight = 17944.488|
|-----------------------------------------------------------------------------|
r_work (start): 0.3131 rms_B_bonded: 0.88
r_work: 0.2979 rms_B_bonded: 2.41 restraints_weight: 0.5000
r_work: 0.2862 rms_B_bonded: 3.75 restraints_weight: 0.2500
r_work (final): 0.2862
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8550
moved from start:          0.2518

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.055  16463  Z= 0.265
  Angle     :  0.653   9.325  24964  Z= 0.331
  Chirality :  0.037   0.279   3223
  Planarity :  0.004   0.037   1096
  Dihedral  : 24.449 173.776   8876
  Min Nonbonded Distance : 2.094

Molprobity Statistics.
  All-atom Clashscore : 6.99
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.74 %
    Favored  : 94.26 %
  Rotamer:
    Outliers :  5.83 %
    Allowed  : 24.20 %
    Favored  : 69.97 %
  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: -0.26 (0.43), residues: 383
  helix:  0.94 (0.34), residues: 249
  sheet: -1.81 (0.99), residues: 24
  loop : -2.36 (0.52), residues: 110

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.010   0.002   TRP D 357 
 HIS   0.003   0.001   HIS D 109 
 PHE   0.010   0.002   PHE D  89 
 TYR   0.021   0.002   TYR D 385 
 ARG   0.002   0.000   ARG D 351 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.06362 (  625)
  hydrogen bonds       : angle       3.15744 ( 1233)
  covalent geometry    : bond        0.00512 (16462)
  covalent geometry    : angle       0.65272 (24964)
  Misc. bond           : bond        0.00080 (    1)

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

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

  766 Ramachandran restraints generated.
    383 Oldfield, 0 Emsley, 383 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  766 Ramachandran restraints generated.
    383 Oldfield, 0 Emsley, 383 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  49 residues out of total 343 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 20
    poor density    : 29
  time to evaluate  : 0.728 
Fit side-chains
REVERT: D   39 GLU cc_start: 0.7148 (OUTLIER) cc_final: 0.6666 (pt0)
REVERT: D   59 LYS cc_start: 0.7623 (OUTLIER) cc_final: 0.7266 (mtmp)
REVERT: D  105 GLN cc_start: 0.8227 (mt0) cc_final: 0.7827 (mt0)
REVERT: D  247 ARG cc_start: 0.7823 (OUTLIER) cc_final: 0.7163 (ttp80)
REVERT: D  251 GLU cc_start: 0.8233 (OUTLIER) cc_final: 0.7436 (mt-10)
REVERT: D  261 LYS cc_start: 0.7967 (OUTLIER) cc_final: 0.7412 (mtpp)
REVERT: D  266 ARG cc_start: 0.8431 (OUTLIER) cc_final: 0.8048 (mmm-85)
REVERT: D  280 ASP cc_start: 0.7822 (OUTLIER) cc_final: 0.7602 (t0)
REVERT: D  347 ARG cc_start: 0.8137 (mtt-85) cc_final: 0.7552 (mtp180)
REVERT: D  364 GLN cc_start: 0.8340 (OUTLIER) cc_final: 0.7475 (mm-40)
REVERT: D  388 LYS cc_start: 0.7942 (OUTLIER) cc_final: 0.7351 (ptmm)
REVERT: D  406 LYS cc_start: 0.8437 (OUTLIER) cc_final: 0.7973 (ttpp)
  outliers start: 20
  outliers final: 6
  residues processed: 44
  average time/residue: 1.6605
  time to fit residues: 79.5582
Evaluate side-chains
  42 residues out of total 343 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 26
  time to evaluate  : 0.762 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain D residue   39 GLU
Chi-restraints excluded: chain D residue   59 LYS
Chi-restraints excluded: chain D residue   82 VAL
Chi-restraints excluded: chain D residue   86 THR
Chi-restraints excluded: chain D residue  101 ILE
Chi-restraints excluded: chain D residue  149 VAL
Chi-restraints excluded: chain D residue  161 THR
Chi-restraints excluded: chain D residue  247 ARG
Chi-restraints excluded: chain D residue  251 GLU
Chi-restraints excluded: chain D residue  255 LEU
Chi-restraints excluded: chain D residue  261 LYS
Chi-restraints excluded: chain D residue  266 ARG
Chi-restraints excluded: chain D residue  280 ASP
Chi-restraints excluded: chain D residue  364 GLN
Chi-restraints excluded: chain D residue  388 LYS
Chi-restraints excluded: chain D residue  406 LYS
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 93
   random chunks:
   chunk 28 optimal weight:    0.5980
   chunk 56 optimal weight:    4.9990
   chunk 76 optimal weight:   10.0000
   chunk 61 optimal weight:    3.9990
   chunk 75 optimal weight:    4.9990
   chunk 9 optimal weight:    1.9990
   chunk 40 optimal weight:    3.9990
   chunk 62 optimal weight:    3.9990
   chunk 50 optimal weight:    2.9990
   chunk 14 optimal weight:    6.9990
   chunk 30 optimal weight:    0.7980
   overall best weight:    2.0786

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

Flipped N/Q/H residues before XYZ refinement:
D  96 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4039 r_free = 0.4039 target = 0.177074 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 75)----------------|
| r_work = 0.3161 r_free = 0.3161 target = 0.103802 restraints weight = 17979.611|
|-----------------------------------------------------------------------------|
r_work (start): 0.3111 rms_B_bonded: 0.95
r_work: 0.2961 rms_B_bonded: 2.51 restraints_weight: 0.5000
r_work: 0.2839 rms_B_bonded: 3.90 restraints_weight: 0.2500
r_work (final): 0.2839
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8570
moved from start:          0.2560

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.006   0.058  16463  Z= 0.287
  Angle     :  0.667   9.793  24964  Z= 0.339
  Chirality :  0.038   0.281   3223
  Planarity :  0.005   0.041   1096
  Dihedral  : 24.429 173.847   8876
  Min Nonbonded Distance : 2.092

Molprobity Statistics.
  All-atom Clashscore : 6.99
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.01 %
    Favored  : 93.99 %
  Rotamer:
    Outliers :  5.83 %
    Allowed  : 24.49 %
    Favored  : 69.68 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -0.34 (0.43), residues: 383
  helix:  0.86 (0.34), residues: 249
  sheet: -1.70 (1.01), residues: 24
  loop : -2.38 (0.52), residues: 110

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.011   0.002   TRP D 357 
 HIS   0.004   0.001   HIS D 109 
 PHE   0.018   0.002   PHE D  89 
 TYR   0.022   0.002   TYR D 385 
 ARG   0.002   0.000   ARG D 407 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.06453 (  625)
  hydrogen bonds       : angle       3.23341 ( 1233)
  covalent geometry    : bond        0.00556 (16462)
  covalent geometry    : angle       0.66669 (24964)
  Misc. bond           : bond        0.00082 (    1)

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

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

  766 Ramachandran restraints generated.
    383 Oldfield, 0 Emsley, 383 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  766 Ramachandran restraints generated.
    383 Oldfield, 0 Emsley, 383 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  48 residues out of total 343 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 20
    poor density    : 28
  time to evaluate  : 0.709 
Fit side-chains
REVERT: D   59 LYS cc_start: 0.7628 (OUTLIER) cc_final: 0.7264 (mtmp)
REVERT: D  105 GLN cc_start: 0.8240 (mt0) cc_final: 0.7809 (mt0)
REVERT: D  247 ARG cc_start: 0.7773 (OUTLIER) cc_final: 0.7127 (ttp80)
REVERT: D  251 GLU cc_start: 0.8296 (OUTLIER) cc_final: 0.7516 (mt-10)
REVERT: D  253 LEU cc_start: 0.8578 (OUTLIER) cc_final: 0.7958 (mp)
REVERT: D  261 LYS cc_start: 0.7970 (OUTLIER) cc_final: 0.7410 (mtpp)
REVERT: D  266 ARG cc_start: 0.8431 (OUTLIER) cc_final: 0.8047 (mmm-85)
REVERT: D  280 ASP cc_start: 0.7829 (OUTLIER) cc_final: 0.7613 (t0)
REVERT: D  347 ARG cc_start: 0.8153 (mtt-85) cc_final: 0.7562 (mtp180)
REVERT: D  364 GLN cc_start: 0.8359 (OUTLIER) cc_final: 0.7493 (mm-40)
REVERT: D  388 LYS cc_start: 0.7939 (OUTLIER) cc_final: 0.7355 (ptmm)
REVERT: D  406 LYS cc_start: 0.8447 (OUTLIER) cc_final: 0.7974 (ttpp)
  outliers start: 20
  outliers final: 7
  residues processed: 43
  average time/residue: 1.6114
  time to fit residues: 75.1495
Evaluate side-chains
  44 residues out of total 343 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 17
    poor density    : 27
  time to evaluate  : 0.681 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain D residue   39 GLU
Chi-restraints excluded: chain D residue   59 LYS
Chi-restraints excluded: chain D residue   82 VAL
Chi-restraints excluded: chain D residue   86 THR
Chi-restraints excluded: chain D residue  101 ILE
Chi-restraints excluded: chain D residue  149 VAL
Chi-restraints excluded: chain D residue  161 THR
Chi-restraints excluded: chain D residue  247 ARG
Chi-restraints excluded: chain D residue  251 GLU
Chi-restraints excluded: chain D residue  253 LEU
Chi-restraints excluded: chain D residue  255 LEU
Chi-restraints excluded: chain D residue  261 LYS
Chi-restraints excluded: chain D residue  266 ARG
Chi-restraints excluded: chain D residue  280 ASP
Chi-restraints excluded: chain D residue  364 GLN
Chi-restraints excluded: chain D residue  388 LYS
Chi-restraints excluded: chain D residue  406 LYS
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 93
   random chunks:
   chunk 68 optimal weight:   30.0000
   chunk 9 optimal weight:    1.9990
   chunk 23 optimal weight:    0.0070
   chunk 66 optimal weight:   10.0000
   chunk 60 optimal weight:    3.9990
   chunk 21 optimal weight:    0.0970
   chunk 57 optimal weight:    1.9990
   chunk 28 optimal weight:    0.7980
   chunk 47 optimal weight:    3.9990
   chunk 70 optimal weight:    3.9990
   chunk 64 optimal weight:    3.9990
   overall best weight:    0.9800

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

Flipped N/Q/H residues before XYZ refinement:
D  96 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4063 r_free = 0.4063 target = 0.179129 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 71)----------------|
| r_work = 0.3224 r_free = 0.3224 target = 0.107985 restraints weight = 18092.464|
|-----------------------------------------------------------------------------|
r_work (start): 0.3159 rms_B_bonded: 0.83
r_work: 0.3011 rms_B_bonded: 2.39 restraints_weight: 0.5000
r_work: 0.2888 rms_B_bonded: 3.72 restraints_weight: 0.2500
r_work (final): 0.2888
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8512
moved from start:          0.2542

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.070  16463  Z= 0.172
  Angle     :  0.624  11.086  24964  Z= 0.317
  Chirality :  0.034   0.285   3223
  Planarity :  0.004   0.041   1096
  Dihedral  : 24.486 173.490   8876
  Min Nonbonded Distance : 2.098

Molprobity Statistics.
  All-atom Clashscore : 7.69
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.74 %
    Favored  : 94.26 %
  Rotamer:
    Outliers :  4.96 %
    Allowed  : 25.66 %
    Favored  : 69.39 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -0.18 (0.44), residues: 383
  helix:  1.00 (0.34), residues: 249
  sheet: -1.63 (1.03), residues: 24
  loop : -2.37 (0.52), residues: 110

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.009   0.002   TRP D 357 
 HIS   0.002   0.001   HIS D 291 
 PHE   0.020   0.002   PHE D  89 
 TYR   0.020   0.002   TYR D 385 
 ARG   0.002   0.000   ARG D 240 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.06281 (  625)
  hydrogen bonds       : angle       3.18076 ( 1233)
  covalent geometry    : bond        0.00333 (16462)
  covalent geometry    : angle       0.62442 (24964)
  Misc. bond           : bond        0.00055 (    1)

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

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

  766 Ramachandran restraints generated.
    383 Oldfield, 0 Emsley, 383 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  766 Ramachandran restraints generated.
    383 Oldfield, 0 Emsley, 383 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  44 residues out of total 343 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 17
    poor density    : 27
  time to evaluate  : 0.764 
Fit side-chains
REVERT: D   39 GLU cc_start: 0.7274 (OUTLIER) cc_final: 0.6913 (pt0)
REVERT: D   59 LYS cc_start: 0.7614 (OUTLIER) cc_final: 0.7252 (mtmp)
REVERT: D  105 GLN cc_start: 0.8215 (mt0) cc_final: 0.7809 (mt0)
REVERT: D  247 ARG cc_start: 0.7745 (OUTLIER) cc_final: 0.7119 (ttp80)
REVERT: D  251 GLU cc_start: 0.8265 (OUTLIER) cc_final: 0.7475 (mt-10)
REVERT: D  253 LEU cc_start: 0.8540 (OUTLIER) cc_final: 0.7924 (mp)
REVERT: D  261 LYS cc_start: 0.7952 (OUTLIER) cc_final: 0.7388 (mtpp)
REVERT: D  266 ARG cc_start: 0.8403 (OUTLIER) cc_final: 0.8033 (mmm-85)
REVERT: D  280 ASP cc_start: 0.7815 (OUTLIER) cc_final: 0.7594 (t0)
REVERT: D  347 ARG cc_start: 0.8097 (mtt-85) cc_final: 0.7515 (mtp180)
REVERT: D  364 GLN cc_start: 0.8272 (OUTLIER) cc_final: 0.7408 (mm-40)
REVERT: D  388 LYS cc_start: 0.7867 (OUTLIER) cc_final: 0.7301 (ptmm)
REVERT: D  406 LYS cc_start: 0.8450 (OUTLIER) cc_final: 0.7934 (ttpp)
  outliers start: 17
  outliers final: 5
  residues processed: 39
  average time/residue: 1.7897
  time to fit residues: 75.2851
Evaluate side-chains
  43 residues out of total 343 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 27
  time to evaluate  : 0.733 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain D residue   39 GLU
Chi-restraints excluded: chain D residue   59 LYS
Chi-restraints excluded: chain D residue   82 VAL
Chi-restraints excluded: chain D residue  101 ILE
Chi-restraints excluded: chain D residue  149 VAL
Chi-restraints excluded: chain D residue  161 THR
Chi-restraints excluded: chain D residue  247 ARG
Chi-restraints excluded: chain D residue  251 GLU
Chi-restraints excluded: chain D residue  253 LEU
Chi-restraints excluded: chain D residue  255 LEU
Chi-restraints excluded: chain D residue  261 LYS
Chi-restraints excluded: chain D residue  266 ARG
Chi-restraints excluded: chain D residue  280 ASP
Chi-restraints excluded: chain D residue  364 GLN
Chi-restraints excluded: chain D residue  388 LYS
Chi-restraints excluded: chain D residue  406 LYS
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 93
   random chunks:
   chunk 14 optimal weight:    7.9990
   chunk 42 optimal weight:   10.0000
   chunk 82 optimal weight:   20.0000
   chunk 61 optimal weight:    3.9990
   chunk 76 optimal weight:   10.0000
   chunk 84 optimal weight:   10.0000
   chunk 34 optimal weight:    0.6980
   chunk 59 optimal weight:    8.9990
   chunk 26 optimal weight:    0.5980
   chunk 31 optimal weight:    0.5980
   chunk 62 optimal weight:    3.9990
   overall best weight:    1.9784

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

Flipped N/Q/H residues before XYZ refinement:
D  96 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4039 r_free = 0.4039 target = 0.176845 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 57)----------------|
| r_work = 0.3191 r_free = 0.3191 target = 0.105495 restraints weight = 18005.358|
|-----------------------------------------------------------------------------|
r_work (start): 0.3130 rms_B_bonded: 0.89
r_work: 0.2979 rms_B_bonded: 2.40 restraints_weight: 0.5000
r_work: 0.2863 rms_B_bonded: 3.73 restraints_weight: 0.2500
r_work (final): 0.2863
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8550
moved from start:          0.2613

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.068  16463  Z= 0.276
  Angle     :  0.656  10.703  24964  Z= 0.334
  Chirality :  0.037   0.280   3223
  Planarity :  0.005   0.041   1096
  Dihedral  : 24.415 173.769   8876
  Min Nonbonded Distance : 2.093

Molprobity Statistics.
  All-atom Clashscore : 6.99
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.01 %
    Favored  : 93.99 %
  Rotamer:
    Outliers :  4.96 %
    Allowed  : 25.66 %
    Favored  : 69.39 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -0.25 (0.44), residues: 383
  helix:  0.94 (0.34), residues: 249
  sheet: -1.58 (1.07), residues: 24
  loop : -2.39 (0.52), residues: 110

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.011   0.002   TRP D 357 
 HIS   0.003   0.001   HIS D 109 
 PHE   0.016   0.002   PHE D  89 
 TYR   0.022   0.002   TYR D 385 
 ARG   0.002   0.000   ARG D 243 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.06385 (  625)
  hydrogen bonds       : angle       3.19710 ( 1233)
  covalent geometry    : bond        0.00537 (16462)
  covalent geometry    : angle       0.65572 (24964)
  Misc. bond           : bond        0.00080 (    1)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 10656.30 seconds
wall clock time: 185 minutes 56.61 seconds (11156.61 seconds total)