Starting phenix.real_space_refine
on Wed Jun  4 16:10:59 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/8dwj_27756/06_2025/8dwj_27756.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/8dwj_27756/06_2025/8dwj_27756.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=3.9
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/cci-nas-00/data/ceres_data/8dwj_27756/06_2025/8dwj_27756.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/8dwj_27756/06_2025/8dwj_27756.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/8dwj_27756/06_2025/8dwj_27756.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/8dwj_27756/06_2025/8dwj_27756.cif"
  }
  resolution = 3.9
  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=  -0.000 sd=   0.003
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
     Zn      1      6.06       5
     P      14      5.49       5
     S      13      5.16       5
     C    1905      2.51       5
     N     525      2.21       5
     O     585      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 21 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: 3043
  Number of models: 1
  Model: ""
    Number of chains: 4
    Chain: "P"
      Number of atoms: 117
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 5, 117
          Unusual residues: {'GTP': 1}
          Classifications: {'RNA': 4, 'undetermined': 1}
          Modifications used: {'rna3p_pur': 2, 'rna3p_pyr': 2}
          Link IDs: {'rna3p': 3, None: 1}
            Not linked:
              pdbres="GTP P   1 "
              pdbres="  C P   2 "
    Chain: "T"
      Number of atoms: 144
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 7, 144
          Classifications: {'DNA': 7}
          Link IDs: {'rna3p': 6}
    Chain: "A"
      Number of atoms: 2781
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 339, 2781
          Classifications: {'peptide': 339}
          Link IDs: {'PTRANS': 24, 'TRANS': 314}
    Chain: "A"
      Number of atoms: 1
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 1, 1
          Unusual residues: {' ZN': 1}
          Classifications: {'undetermined': 1}

List of CYS excluded from plausible disulfide bonds:
  (reason: may participate in coordination)
  ATOM    556  SG  CYS A  37      35.483  27.676  19.865  1.00234.26           S
  ATOM    576  SG  CYS A  40      35.253  23.162  19.878  1.00251.45           S
  ATOM    775  SG  CYS A  65      36.508  25.850  23.034  1.00220.03           S
  ATOM    801  SG  CYS A  68      38.485  25.430  20.056  1.00211.90           S

  Time building chain proxies: 3.58, per 1000 atoms: 1.18
  Number of scatterers: 3043
  At special positions: 0
  Unit cell: (67.914, 67.914, 82.32, 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)
     Zn      1     29.99
     S      13     16.00
     P      14     15.00
     O     585      8.00
     N     525      7.00
     C    1905      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: 1.62
  Conformation dependent library (CDL) restraints added in 436.0 milliseconds
  
  Dynamic metal coordination
    Zn2+ tetrahedral coordination
      pdb="  ZN A 401 "
        pdb="ZN    ZN A 401 " - pdb=" SG  CYS A  40 "
        pdb="ZN    ZN A 401 " - pdb=" SG  CYS A  37 "
        pdb="ZN    ZN A 401 " - pdb=" SG  CYS A  65 "
        pdb="ZN    ZN A 401 " - pdb=" SG  CYS A  68 "
      Number of angles added : 6


  674 Ramachandran restraints generated.
    337 Oldfield, 0 Emsley, 337 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  642

  Finding SS restraints...
    Secondary structure from input PDB file:
      14 helices and 4 sheets defined
      38.9% alpha, 14.2% beta
      3 base pairs and 7 stacking pairs defined.
    Time for finding SS restraints: 1.17
  Creating SS restraints...
    Processing helix  chain 'A' and resid 4 through 17
    Processing helix  chain 'A' and resid 74 through 82
    Processing helix  chain 'A' and resid 82 through 97
      removed outlier: 3.545A  pdb=" N   ARG A  94 " --> pdb=" O   ILE A  90 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 128 through 130
      No H-bonds generated for 'chain 'A' and resid 128 through 130'
    Processing helix  chain 'A' and resid 134 through 143
    Processing helix  chain 'A' and resid 146 through 152
      removed outlier: 4.212A  pdb=" N   LYS A 151 " --> pdb=" O   ASP A 148 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 158 through 167
    Processing helix  chain 'A' and resid 221 through 225
    Processing helix  chain 'A' and resid 235 through 240
    Processing helix  chain 'A' and resid 274 through 287
      removed outlier: 3.522A  pdb=" N   ALA A 287 " --> pdb=" O   LYS A 283 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 294 through 297
    Processing helix  chain 'A' and resid 303 through 312
    Processing helix  chain 'A' and resid 314 through 324
      removed outlier: 3.512A  pdb=" N   ILE A 318 " --> pdb=" O   THR A 314 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 329 through 341
      removed outlier: 4.306A  pdb=" N   LYS A 341 " --> pdb=" O   SER A 337 " (cutoff:3.500A)
    Processing sheet with id=AA1, first strand: chain 'A' and resid 23 through 27
    Processing sheet with id=AA2, first strand: chain 'A' and resid 124 through 126
    Processing sheet with id=AA3, first strand: chain 'A' and resid 219 through 220
    Processing sheet with id=AA4, first strand: chain 'A' and resid 291 through 292

    116 hydrogen bonds defined for protein.
    306 hydrogen bond angles defined for protein.
    Restraints generated for nucleic acids:
      9 hydrogen bonds
      18 hydrogen bond angles
      0 basepair planarities
      3 basepair parallelities
      7 stacking parallelities
  Total time for adding SS restraints: 0.88

  Time building geometry restraints manager: 1.28 seconds

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

  Histogram of bond lengths:
        1.22 -     1.34: 801
        1.34 -     1.45: 621
        1.45 -     1.57: 1675
        1.57 -     1.69: 25
        1.69 -     1.81: 20
  Bond restraints: 3142
  Sorted by residual:
  bond pdb=" N   VAL A 232 "
       pdb=" CA  VAL A 232 "
    ideal  model  delta    sigma   weight residual
    1.458  1.493 -0.035 1.21e-02 6.83e+03 8.34e+00
  bond pdb=" N   ILE A 308 "
       pdb=" CA  ILE A 308 "
    ideal  model  delta    sigma   weight residual
    1.459  1.494 -0.034 1.21e-02 6.83e+03 8.01e+00
  bond pdb=" N   LYS A 300 "
       pdb=" CA  LYS A 300 "
    ideal  model  delta    sigma   weight residual
    1.458  1.490 -0.032 1.14e-02 7.69e+03 7.83e+00
  bond pdb=" N   ILE A 103 "
       pdb=" CA  ILE A 103 "
    ideal  model  delta    sigma   weight residual
    1.460  1.495 -0.035 1.26e-02 6.30e+03 7.56e+00
  bond pdb=" N   SER A 100 "
       pdb=" CA  SER A 100 "
    ideal  model  delta    sigma   weight residual
    1.454  1.487 -0.033 1.21e-02 6.83e+03 7.40e+00
  ... (remaining 3137 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     2.27: 4121
        2.27 -     4.54: 141
        4.54 -     6.80: 20
        6.80 -     9.07: 9
        9.07 -    11.34: 6
  Bond angle restraints: 4297
  Sorted by residual:
  angle pdb=" N   ARG A  87 "
        pdb=" CA  ARG A  87 "
        pdb=" C   ARG A  87 "
      ideal   model   delta    sigma   weight residual
     110.97  105.46    5.51 1.09e+00 8.42e-01 2.55e+01
  angle pdb=" CA  LYS A 161 "
        pdb=" CB  LYS A 161 "
        pdb=" CG  LYS A 161 "
      ideal   model   delta    sigma   weight residual
     114.10  122.41   -8.31 2.00e+00 2.50e-01 1.73e+01
  angle pdb=" PB  GTP P   1 "
        pdb=" O3B GTP P   1 "
        pdb=" PG  GTP P   1 "
      ideal   model   delta    sigma   weight residual
     120.50  131.84  -11.34 3.00e+00 1.11e-01 1.43e+01
  angle pdb=" CB  MET A 292 "
        pdb=" CG  MET A 292 "
        pdb=" SD  MET A 292 "
      ideal   model   delta    sigma   weight residual
     112.70  123.89  -11.19 3.00e+00 1.11e-01 1.39e+01
  angle pdb=" C   TYR A  86 "
        pdb=" N   ARG A  87 "
        pdb=" CA  ARG A  87 "
      ideal   model   delta    sigma   weight residual
     120.65  115.88    4.77 1.32e+00 5.74e-01 1.30e+01
  ... (remaining 4292 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    17.58: 1660
       17.58 -    35.16: 166
       35.16 -    52.73: 44
       52.73 -    70.31: 16
       70.31 -    87.88: 7
  Dihedral angle restraints: 1893
    sinusoidal: 895
      harmonic: 998
  Sorted by residual:
  dihedral pdb=" C5' GTP P   1 "
           pdb=" O5' GTP P   1 "
           pdb=" PA  GTP P   1 "
           pdb=" O3A GTP P   1 "
      ideal   model   delta sinusoidal    sigma   weight residual
      69.27  143.55  -74.28     1      2.00e+01 2.50e-03 1.75e+01
  dihedral pdb=" C8  GTP P   1 "
           pdb=" C1' GTP P   1 "
           pdb=" N9  GTP P   1 "
           pdb=" O4' GTP P   1 "
      ideal   model   delta sinusoidal    sigma   weight residual
     104.59   42.71   61.88     1      2.00e+01 2.50e-03 1.27e+01
  dihedral pdb=" CA  GLU A 114 "
           pdb=" C   GLU A 114 "
           pdb=" N   LYS A 115 "
           pdb=" CA  LYS A 115 "
      ideal   model   delta  harmonic     sigma   weight residual
    -180.00 -162.47  -17.53     0      5.00e+00 4.00e-02 1.23e+01
  ... (remaining 1890 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.040: 274
       0.040 -    0.079: 101
       0.079 -    0.118: 44
       0.118 -    0.158: 22
       0.158 -    0.197: 10
  Chirality restraints: 451
  Sorted by residual:
  chirality pdb=" CA  MET A 281 "
            pdb=" N   MET A 281 "
            pdb=" C   MET A 281 "
            pdb=" CB  MET A 281 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.71   -0.20 2.00e-01 2.50e+01 9.74e-01
  chirality pdb=" CA  LEU A 336 "
            pdb=" N   LEU A 336 "
            pdb=" C   LEU A 336 "
            pdb=" CB  LEU A 336 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.71   -0.20 2.00e-01 2.50e+01 9.67e-01
  chirality pdb=" CA  MET A 307 "
            pdb=" N   MET A 307 "
            pdb=" C   MET A 307 "
            pdb=" CB  MET A 307 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.70   -0.19 2.00e-01 2.50e+01 8.82e-01
  ... (remaining 448 not shown)

  Planarity restraints: 506
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   ILE A 145 "   -0.042 5.00e-02 4.00e+02   6.43e-02 6.61e+00
        pdb=" N   PRO A 146 "    0.111 5.00e-02 4.00e+02
        pdb=" CA  PRO A 146 "   -0.034 5.00e-02 4.00e+02
        pdb=" CD  PRO A 146 "   -0.035 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   ALA A 203 "   -0.042 5.00e-02 4.00e+02   6.42e-02 6.58e+00
        pdb=" N   PRO A 204 "    0.111 5.00e-02 4.00e+02
        pdb=" CA  PRO A 204 "   -0.033 5.00e-02 4.00e+02
        pdb=" CD  PRO A 204 "   -0.036 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   THR A 314 "   -0.038 5.00e-02 4.00e+02   5.81e-02 5.40e+00
        pdb=" N   PRO A 315 "    0.100 5.00e-02 4.00e+02
        pdb=" CA  PRO A 315 "   -0.030 5.00e-02 4.00e+02
        pdb=" CD  PRO A 315 "   -0.032 5.00e-02 4.00e+02
  ... (remaining 503 not shown)

  Histogram of nonbonded interaction distances:
        2.22 -     2.75: 364
        2.75 -     3.29: 2886
        3.29 -     3.83: 5595
        3.83 -     4.36: 6432
        4.36 -     4.90: 10310
  Nonbonded interactions: 25587
  Sorted by model distance:
  nonbonded pdb=" OD1 ASP A   8 "
            pdb=" OH  TYR A  89 "
     model   vdw
     2.218 3.040
  nonbonded pdb=" OH  TYR A  55 "
            pdb=" OH  TYR A  66 "
     model   vdw
     2.305 3.040
  nonbonded pdb=" O   LEU A 268 "
            pdb=" NE1 TRP A 294 "
     model   vdw
     2.370 3.120
  nonbonded pdb=" NE2 GLN A 195 "
            pdb=" OG1 THR A 209 "
     model   vdw
     2.380 3.120
  nonbonded pdb=" N   ASP A  84 "
            pdb=" OD1 ASP A  84 "
     model   vdw
     2.384 3.120
  ... (remaining 25582 not shown)

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

  No NCS relation were found !!!

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

Found NCS groups:
  found none.
Set up NCS constraints
  No NCS constraints will be used in refinement.
Set refine NCS operators
Adjust number of macro_cycles
  Number of macro_cycles: 10
Reset NCS operators
Extract rigid body selections
Check and reset occupancies
  Occupancies: min=1.00 max=1.00 mean=1.00
Load rotamer database and sin/cos tables
Set ADP refinement strategy
  ADPs will be refined as group one per residue
Make a string to write initial .geo file
Internal consistency checks
Time:
  Set random seed:                         0.000
  Set model cs if undefined:               0.000
  Decide on map wrapping:                  0.000
  Normalize map: mean=0, sd=1:             1.350
  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:             0.010
  Extract box with map and model:          0.120
  Check model and map are aligned:         0.020
  Set scattering table:                    0.030
  Process input model:                     16.270
  Find NCS groups from input model:        0.030
  Set up NCS constraints:                  0.020
  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:3.010
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   20.860
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.5760
moved from start:          0.0000

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.008   0.182   3147  Z= 0.392
  Angle     :  1.176  22.256   4303  Z= 0.591
  Chirality :  0.059   0.197    451
  Planarity :  0.008   0.064    506
  Dihedral  : 16.243  87.883   1251
  Min Nonbonded Distance : 2.218

Molprobity Statistics.
  All-atom Clashscore : 13.71
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.93 %
    Favored  : 94.07 %
  Rotamer:
    Outliers :  0.33 %
    Allowed  : 14.29 %
    Favored  : 85.38 %
  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: -2.71 (0.41), residues: 337
  helix: -2.26 (0.37), residues: 116
  sheet: -1.88 (0.68), residues: 51
  loop : -1.29 (0.46), residues: 170

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.031   0.003   TRP A 266 
 HIS   0.002   0.001   HIS A  71 
 PHE   0.010   0.002   PHE A 293 
 TYR   0.015   0.002   TYR A 321 
 ARG   0.003   0.000   ARG A 264 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.18315 (  125)
  hydrogen bonds       : angle       9.02912 (  324)
  metal coordination   : bond        0.16030 (    4)
  metal coordination   : angle      14.13845 (    6)
  covalent geometry    : bond        0.00536 ( 3142)
  covalent geometry    : angle       1.05129 ( 4297)
  Misc. bond           : bond        0.05167 (    1)

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

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

  674 Ramachandran restraints generated.
    337 Oldfield, 0 Emsley, 337 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  674 Ramachandran restraints generated.
    337 Oldfield, 0 Emsley, 337 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  98 residues out of total 301 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 97
  time to evaluate  : 0.343 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   53 TRP cc_start: 0.4145 (m100) cc_final: 0.3613 (m100)
REVERT: A   87 ARG cc_start: 0.6932 (OUTLIER) cc_final: 0.5065 (mtt180)
REVERT: A   91 PHE cc_start: 0.6079 (t80) cc_final: 0.5870 (t80)
REVERT: A   95 LYS cc_start: 0.7872 (tttt) cc_final: 0.6654 (mmmt)
REVERT: A  137 ILE cc_start: 0.6298 (mm) cc_final: 0.5943 (tp)
REVERT: A  147 LYS cc_start: 0.5333 (mmtt) cc_final: 0.5107 (tptt)
REVERT: A  158 GLU cc_start: 0.7217 (mt-10) cc_final: 0.6955 (mm-30)
REVERT: A  176 SER cc_start: 0.4986 (m) cc_final: 0.4551 (p)
REVERT: A  177 GLU cc_start: 0.6151 (tt0) cc_final: 0.5704 (mp0)
REVERT: A  183 PRO cc_start: 0.5777 (Cg_exo) cc_final: 0.5370 (Cg_endo)
REVERT: A  197 ARG cc_start: 0.5058 (tpt170) cc_final: 0.4838 (tpt170)
REVERT: A  238 ASP cc_start: 0.6641 (m-30) cc_final: 0.6287 (t0)
REVERT: A  258 VAL cc_start: 0.7790 (t) cc_final: 0.7587 (t)
REVERT: A  264 ARG cc_start: 0.6642 (ptt180) cc_final: 0.6262 (ptt180)
REVERT: A  266 TRP cc_start: 0.7664 (m100) cc_final: 0.7348 (m100)
REVERT: A  267 VAL cc_start: 0.7865 (t) cc_final: 0.7545 (t)
REVERT: A  279 LYS cc_start: 0.8305 (tttt) cc_final: 0.7956 (mtpp)
REVERT: A  292 MET cc_start: 0.8457 (tmm) cc_final: 0.8071 (tpt)
REVERT: A  322 MET cc_start: 0.7559 (mmt) cc_final: 0.7007 (ptp)
REVERT: A  334 MET cc_start: 0.1537 (mmt) cc_final: 0.0137 (ttp)
  outliers start: 1
  outliers final: 0
  residues processed: 97
  average time/residue: 0.2064
  time to fit residues: 23.1367
Evaluate side-chains
  51 residues out of total 301 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 50
  time to evaluate  : 0.357 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   87 ARG
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 34
   random chunks:
   chunk 28 optimal weight:    3.9990
   chunk 25 optimal weight:    9.9990
   chunk 14 optimal weight:    1.9990
   chunk 8 optimal weight:    4.9990
   chunk 17 optimal weight:    5.9990
   chunk 13 optimal weight:    5.9990
   chunk 26 optimal weight:    0.5980
   chunk 10 optimal weight:    6.9990
   chunk 16 optimal weight:    5.9990
   chunk 19 optimal weight:    7.9990
   chunk 30 optimal weight:    9.9990
   overall best weight:    3.5188

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

Flipped N/Q/H residues before XYZ refinement:
** A  24 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
A  48 ASN
** A  67 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 134 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 274 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
A 305 ASN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4387 r_free = 0.4387 target = 0.130523 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 53)----------------|
| r_work = 0.4089 r_free = 0.4089 target = 0.113253 restraints weight = 11641.172|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 37)----------------|
| r_work = 0.4114 r_free = 0.4114 target = 0.114593 restraints weight = 7540.218|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 42)----------------|
| r_work = 0.4131 r_free = 0.4131 target = 0.115453 restraints weight = 5624.887|
|-----------------------------------------------------------------------------|
r_work (final): 0.4116
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.5794
moved from start:          0.3435

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.027   3147  Z= 0.178
  Angle     :  0.736   8.865   4303  Z= 0.371
  Chirality :  0.048   0.179    451
  Planarity :  0.007   0.056    506
  Dihedral  : 15.154  79.437    519
  Min Nonbonded Distance : 2.575

Molprobity Statistics.
  All-atom Clashscore : 15.38
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.34 %
    Favored  : 94.66 %
  Rotamer:
    Outliers :  1.99 %
    Allowed  : 16.61 %
    Favored  : 81.40 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -1.37 (0.43), residues: 337
  helix: -0.33 (0.47), residues: 109
  sheet: -1.93 (0.70), residues: 52
  loop : -0.86 (0.43), residues: 176

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.020   0.002   TRP A 294 
 HIS   0.005   0.001   HIS A  64 
 PHE   0.015   0.003   PHE A 241 
 TYR   0.011   0.002   TYR A  54 
 ARG   0.003   0.001   ARG A 263 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04224 (  125)
  hydrogen bonds       : angle       7.11599 (  324)
  metal coordination   : bond        0.01443 (    4)
  metal coordination   : angle       3.82547 (    6)
  covalent geometry    : bond        0.00393 ( 3142)
  covalent geometry    : angle       0.72203 ( 4297)
  Misc. bond           : bond        0.00098 (    1)

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

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

  674 Ramachandran restraints generated.
    337 Oldfield, 0 Emsley, 337 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  674 Ramachandran restraints generated.
    337 Oldfield, 0 Emsley, 337 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  57 residues out of total 301 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 6
    poor density    : 51
  time to evaluate  : 0.377 
Fit side-chains
   revert: symmetry clash
REVERT: A   87 ARG cc_start: 0.7238 (tmt-80) cc_final: 0.4737 (mtt180)
REVERT: A   95 LYS cc_start: 0.7300 (tttt) cc_final: 0.6725 (tppt)
REVERT: A  176 SER cc_start: 0.4816 (m) cc_final: 0.4493 (p)
REVERT: A  177 GLU cc_start: 0.6255 (tt0) cc_final: 0.4956 (mp0)
REVERT: A  273 ARG cc_start: 0.3852 (mtt180) cc_final: 0.2243 (ttt180)
  outliers start: 6
  outliers final: 2
  residues processed: 54
  average time/residue: 0.2258
  time to fit residues: 14.1310
Evaluate side-chains
  39 residues out of total 301 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 2
    poor density    : 37
  time to evaluate  : 0.351 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue    7 ILE
Chi-restraints excluded: chain A residue  334 MET
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 34
   random chunks:
   chunk 22 optimal weight:    0.5980
   chunk 30 optimal weight:    9.9990
   chunk 4 optimal weight:    0.2980
   chunk 27 optimal weight:    7.9990
   chunk 25 optimal weight:    0.9990
   chunk 21 optimal weight:    0.6980
   chunk 6 optimal weight:    2.9990
   chunk 2 optimal weight:    5.9990
   chunk 10 optimal weight:    0.7980
   chunk 9 optimal weight:    0.9990
   chunk 11 optimal weight:    5.9990
   overall best weight:    0.6782

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

Flipped N/Q/H residues before XYZ refinement:
A  24 GLN
A  48 ASN
** A  67 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 134 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 305 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4399 r_free = 0.4399 target = 0.131634 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 38)----------------|
| r_work = 0.4160 r_free = 0.4160 target = 0.116922 restraints weight = 12497.335|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 29)----------------|
| r_work = 0.4147 r_free = 0.4147 target = 0.116430 restraints weight = 10487.546|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 28)----------------|
| r_work = 0.4152 r_free = 0.4152 target = 0.116793 restraints weight = 8195.719|
|-----------------------------------------------------------------------------|
r_work (final): 0.4118
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.5762
moved from start:          0.4056

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.026   3147  Z= 0.116
  Angle     :  0.637   8.751   4303  Z= 0.320
  Chirality :  0.045   0.142    451
  Planarity :  0.006   0.051    506
  Dihedral  : 14.602  80.507    515
  Min Nonbonded Distance : 2.560

Molprobity Statistics.
  All-atom Clashscore : 14.21
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.45 %
    Favored  : 95.55 %
  Rotamer:
    Outliers :  2.66 %
    Allowed  : 17.28 %
    Favored  : 80.07 %
  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: -0.84 (0.45), residues: 337
  helix:  0.49 (0.50), residues: 109
  sheet: -1.63 (0.65), residues: 63
  loop : -0.73 (0.46), residues: 165

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.023   0.002   TRP A 266 
 HIS   0.006   0.001   HIS A 134 
 PHE   0.012   0.002   PHE A 194 
 TYR   0.009   0.001   TYR A 213 
 ARG   0.001   0.000   ARG A 263 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03752 (  125)
  hydrogen bonds       : angle       6.59153 (  324)
  metal coordination   : bond        0.00349 (    4)
  metal coordination   : angle       1.87327 (    6)
  covalent geometry    : bond        0.00256 ( 3142)
  covalent geometry    : angle       0.63394 ( 4297)
  Misc. bond           : bond        0.00051 (    1)

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

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

  674 Ramachandran restraints generated.
    337 Oldfield, 0 Emsley, 337 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  674 Ramachandran restraints generated.
    337 Oldfield, 0 Emsley, 337 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  49 residues out of total 301 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 8
    poor density    : 41
  time to evaluate  : 0.346 
Fit side-chains
REVERT: A   87 ARG cc_start: 0.7194 (tmt-80) cc_final: 0.4790 (mtt180)
REVERT: A   95 LYS cc_start: 0.6799 (tttt) cc_final: 0.6365 (mmmt)
REVERT: A  177 GLU cc_start: 0.5805 (tt0) cc_final: 0.4685 (mp0)
REVERT: A  319 MET cc_start: 0.6211 (mpp) cc_final: 0.6007 (mpp)
REVERT: A  334 MET cc_start: 0.2242 (mmt) cc_final: 0.0729 (ttp)
  outliers start: 8
  outliers final: 3
  residues processed: 49
  average time/residue: 0.2167
  time to fit residues: 12.4522
Evaluate side-chains
  37 residues out of total 301 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 3
    poor density    : 34
  time to evaluate  : 0.363 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   23 THR
Chi-restraints excluded: chain A residue  118 ILE
Chi-restraints excluded: chain A residue  145 ILE
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 34
   random chunks:
   chunk 33 optimal weight:    5.9990
   chunk 19 optimal weight:   10.0000
   chunk 10 optimal weight:    6.9990
   chunk 9 optimal weight:    2.9990
   chunk 22 optimal weight:    0.6980
   chunk 14 optimal weight:    8.9990
   chunk 4 optimal weight:    9.9990
   chunk 8 optimal weight:    0.3980
   chunk 23 optimal weight:    8.9990
   chunk 7 optimal weight:   20.0000
   chunk 6 optimal weight:    5.9990
   overall best weight:    3.2186

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

Flipped N/Q/H residues before XYZ refinement:
A  48 ASN
** A  67 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 134 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4361 r_free = 0.4361 target = 0.129528 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 66)----------------|
| r_work = 0.4091 r_free = 0.4091 target = 0.113351 restraints weight = 12415.269|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 49)----------------|
| r_work = 0.4112 r_free = 0.4112 target = 0.114485 restraints weight = 8449.539|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 38)----------------|
| r_work = 0.4125 r_free = 0.4125 target = 0.115235 restraints weight = 6686.159|
|-----------------------------------------------------------------------------|
r_work (final): 0.4097
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.5858
moved from start:          0.4996

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.031   3147  Z= 0.157
  Angle     :  0.691   7.386   4303  Z= 0.349
  Chirality :  0.046   0.154    451
  Planarity :  0.006   0.051    506
  Dihedral  : 15.006  81.664    515
  Min Nonbonded Distance : 2.513

Molprobity Statistics.
  All-atom Clashscore : 18.39
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.93 %
    Favored  : 94.07 %
  Rotamer:
    Outliers :  1.99 %
    Allowed  : 18.94 %
    Favored  : 79.07 %
  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: -0.86 (0.44), residues: 337
  helix:  0.57 (0.49), residues: 110
  sheet: -1.55 (0.66), residues: 63
  loop : -0.86 (0.45), residues: 164

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.041   0.003   TRP A 266 
 HIS   0.005   0.002   HIS A  64 
 PHE   0.013   0.002   PHE A 241 
 TYR   0.011   0.002   TYR A  54 
 ARG   0.004   0.001   ARG A 280 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04156 (  125)
  hydrogen bonds       : angle       6.63701 (  324)
  metal coordination   : bond        0.01098 (    4)
  metal coordination   : angle       2.93438 (    6)
  covalent geometry    : bond        0.00355 ( 3142)
  covalent geometry    : angle       0.68225 ( 4297)
  Misc. bond           : bond        0.00098 (    1)

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

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

  674 Ramachandran restraints generated.
    337 Oldfield, 0 Emsley, 337 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  674 Ramachandran restraints generated.
    337 Oldfield, 0 Emsley, 337 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  40 residues out of total 301 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 6
    poor density    : 34
  time to evaluate  : 0.344 
Fit side-chains
REVERT: A   87 ARG cc_start: 0.7324 (tmt-80) cc_final: 0.4791 (mtt180)
REVERT: A   95 LYS cc_start: 0.7188 (tttt) cc_final: 0.6704 (tppt)
REVERT: A  177 GLU cc_start: 0.5796 (tt0) cc_final: 0.4619 (mp0)
REVERT: A  292 MET cc_start: 0.7676 (tmm) cc_final: 0.7462 (tmm)
  outliers start: 6
  outliers final: 4
  residues processed: 39
  average time/residue: 0.2037
  time to fit residues: 9.4629
Evaluate side-chains
  34 residues out of total 301 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 4
    poor density    : 30
  time to evaluate  : 0.313 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   23 THR
Chi-restraints excluded: chain A residue  118 ILE
Chi-restraints excluded: chain A residue  230 VAL
Chi-restraints excluded: chain A residue  334 MET
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 34
   random chunks:
   chunk 17 optimal weight:   20.0000
   chunk 33 optimal weight:    9.9990
   chunk 6 optimal weight:   20.0000
   chunk 21 optimal weight:    0.0470
   chunk 23 optimal weight:    7.9990
   chunk 22 optimal weight:    1.9990
   chunk 11 optimal weight:    1.9990
   chunk 12 optimal weight:    7.9990
   chunk 7 optimal weight:    5.9990
   chunk 5 optimal weight:    0.8980
   chunk 30 optimal weight:   10.0000
   overall best weight:    2.1884

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

Flipped N/Q/H residues before XYZ refinement:
A  48 ASN
** A  67 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 134 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 305 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4362 r_free = 0.4362 target = 0.129779 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 72)----------------|
| r_work = 0.4094 r_free = 0.4094 target = 0.113760 restraints weight = 12488.522|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 49)----------------|
| r_work = 0.4113 r_free = 0.4113 target = 0.114935 restraints weight = 8642.846|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 42)----------------|
| r_work = 0.4127 r_free = 0.4127 target = 0.115681 restraints weight = 6783.817|
|-----------------------------------------------------------------------------|
r_work (final): 0.4095
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.5862
moved from start:          0.5348

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.024   3147  Z= 0.131
  Angle     :  0.660  10.430   4303  Z= 0.331
  Chirality :  0.045   0.176    451
  Planarity :  0.006   0.050    506
  Dihedral  : 14.863  84.758    515
  Min Nonbonded Distance : 2.437

Molprobity Statistics.
  All-atom Clashscore : 15.05
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.04 %
    Favored  : 94.96 %
  Rotamer:
    Outliers :  3.99 %
    Allowed  : 18.60 %
    Favored  : 77.41 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -0.99 (0.43), residues: 337
  helix:  0.55 (0.49), residues: 110
  sheet: -1.64 (0.64), residues: 63
  loop : -1.01 (0.44), residues: 164

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.034   0.003   TRP A 266 
 HIS   0.003   0.001   HIS A  64 
 PHE   0.012   0.002   PHE A  11 
 TYR   0.009   0.001   TYR A  54 
 ARG   0.002   0.000   ARG A  14 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03767 (  125)
  hydrogen bonds       : angle       6.52983 (  324)
  metal coordination   : bond        0.00721 (    4)
  metal coordination   : angle       2.14744 (    6)
  covalent geometry    : bond        0.00290 ( 3142)
  covalent geometry    : angle       0.65535 ( 4297)
  Misc. bond           : bond        0.00077 (    1)

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

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

  674 Ramachandran restraints generated.
    337 Oldfield, 0 Emsley, 337 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  674 Ramachandran restraints generated.
    337 Oldfield, 0 Emsley, 337 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  47 residues out of total 301 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 35
  time to evaluate  : 0.319 
Fit side-chains
   revert: symmetry clash
REVERT: A   87 ARG cc_start: 0.7340 (OUTLIER) cc_final: 0.4785 (mtt180)
REVERT: A   95 LYS cc_start: 0.7164 (tttt) cc_final: 0.6639 (tppt)
REVERT: A  118 ILE cc_start: -0.1287 (OUTLIER) cc_final: -0.1511 (mt)
REVERT: A  177 GLU cc_start: 0.5803 (tt0) cc_final: 0.4737 (mp0)
REVERT: A  292 MET cc_start: 0.7917 (tmm) cc_final: 0.7690 (tmm)
REVERT: A  319 MET cc_start: 0.6267 (mpp) cc_final: 0.5685 (mpp)
REVERT: A  331 MET cc_start: 0.2907 (mmt) cc_final: 0.2681 (mmt)
REVERT: A  334 MET cc_start: 0.2798 (OUTLIER) cc_final: 0.0971 (ttp)
  outliers start: 12
  outliers final: 3
  residues processed: 45
  average time/residue: 0.1865
  time to fit residues: 10.0846
Evaluate side-chains
  37 residues out of total 301 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 6
    poor density    : 31
  time to evaluate  : 0.322 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue    7 ILE
Chi-restraints excluded: chain A residue   23 THR
Chi-restraints excluded: chain A residue   87 ARG
Chi-restraints excluded: chain A residue  118 ILE
Chi-restraints excluded: chain A residue  257 VAL
Chi-restraints excluded: chain A residue  334 MET
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 34
   random chunks:
   chunk 24 optimal weight:    6.9990
   chunk 20 optimal weight:   10.0000
   chunk 29 optimal weight:    8.9990
   chunk 26 optimal weight:   20.0000
   chunk 23 optimal weight:    4.9990
   chunk 6 optimal weight:    0.7980
   chunk 16 optimal weight:   10.0000
   chunk 28 optimal weight:    0.8980
   chunk 13 optimal weight:    5.9990
   chunk 2 optimal weight:    0.3980
   chunk 3 optimal weight:    7.9990
   overall best weight:    2.6184

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

Flipped N/Q/H residues before XYZ refinement:
A  48 ASN
** A  67 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 112 GLN
** A 134 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4357 r_free = 0.4357 target = 0.129631 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 34)----------------|
| r_work = 0.4092 r_free = 0.4092 target = 0.113718 restraints weight = 11855.826|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 25)----------------|
| r_work = 0.4092 r_free = 0.4092 target = 0.113612 restraints weight = 9118.155|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 25)----------------|
| r_work = 0.4095 r_free = 0.4095 target = 0.113757 restraints weight = 7645.205|
|-----------------------------------------------------------------------------|
r_work (final): 0.4081
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.5867
moved from start:          0.5695

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.030   3147  Z= 0.139
  Angle     :  0.664   7.123   4303  Z= 0.334
  Chirality :  0.045   0.149    451
  Planarity :  0.006   0.050    506
  Dihedral  : 15.050  85.864    515
  Min Nonbonded Distance : 2.447

Molprobity Statistics.
  All-atom Clashscore : 15.55
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.04 %
    Favored  : 94.96 %
  Rotamer:
    Outliers :  3.32 %
    Allowed  : 19.93 %
    Favored  : 76.74 %
  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: -1.04 (0.43), residues: 337
  helix:  0.65 (0.48), residues: 111
  sheet: -1.66 (0.62), residues: 63
  loop : -1.18 (0.44), residues: 163

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.035   0.003   TRP A 150 
 HIS   0.003   0.001   HIS A  64 
 PHE   0.007   0.001   PHE A 241 
 TYR   0.011   0.001   TYR A 231 
 ARG   0.003   0.000   ARG A 280 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03858 (  125)
  hydrogen bonds       : angle       6.54426 (  324)
  metal coordination   : bond        0.00920 (    4)
  metal coordination   : angle       2.40684 (    6)
  covalent geometry    : bond        0.00310 ( 3142)
  covalent geometry    : angle       0.65819 ( 4297)
  Misc. bond           : bond        0.00102 (    1)

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

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

  674 Ramachandran restraints generated.
    337 Oldfield, 0 Emsley, 337 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  674 Ramachandran restraints generated.
    337 Oldfield, 0 Emsley, 337 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  43 residues out of total 301 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 33
  time to evaluate  : 0.317 
Fit side-chains
   revert: symmetry clash
REVERT: A   87 ARG cc_start: 0.7741 (OUTLIER) cc_final: 0.5129 (mtt180)
REVERT: A   95 LYS cc_start: 0.7157 (tttt) cc_final: 0.6694 (tppt)
REVERT: A  118 ILE cc_start: -0.1433 (OUTLIER) cc_final: -0.1645 (mt)
REVERT: A  177 GLU cc_start: 0.5604 (tt0) cc_final: 0.4669 (mp0)
REVERT: A  292 MET cc_start: 0.8065 (tmm) cc_final: 0.7747 (tmm)
REVERT: A  319 MET cc_start: 0.6129 (mpp) cc_final: 0.5890 (mpp)
REVERT: A  334 MET cc_start: 0.2755 (OUTLIER) cc_final: 0.1070 (ttp)
  outliers start: 10
  outliers final: 3
  residues processed: 41
  average time/residue: 0.1957
  time to fit residues: 9.5882
Evaluate side-chains
  36 residues out of total 301 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 6
    poor density    : 30
  time to evaluate  : 0.350 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue    7 ILE
Chi-restraints excluded: chain A residue   23 THR
Chi-restraints excluded: chain A residue   87 ARG
Chi-restraints excluded: chain A residue  118 ILE
Chi-restraints excluded: chain A residue  257 VAL
Chi-restraints excluded: chain A residue  334 MET
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 34
   random chunks:
   chunk 33 optimal weight:    5.9990
   chunk 21 optimal weight:   20.0000
   chunk 16 optimal weight:   20.0000
   chunk 27 optimal weight:    6.9990
   chunk 20 optimal weight:    9.9990
   chunk 19 optimal weight:    9.9990
   chunk 10 optimal weight:    4.9990
   chunk 32 optimal weight:    0.8980
   chunk 26 optimal weight:    5.9990
   chunk 18 optimal weight:    5.9990
   chunk 13 optimal weight:    0.5980
   overall best weight:    3.6986

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

Flipped N/Q/H residues before XYZ refinement:
A  48 ASN
** A  67 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 134 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4348 r_free = 0.4348 target = 0.129668 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 36)----------------|
| r_work = 0.4115 r_free = 0.4115 target = 0.114669 restraints weight = 12066.703|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 29)----------------|
| r_work = 0.4109 r_free = 0.4109 target = 0.114471 restraints weight = 9115.546|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 32)----------------|
| r_work = 0.4115 r_free = 0.4115 target = 0.114817 restraints weight = 7806.460|
|-----------------------------------------------------------------------------|
r_work (final): 0.4090
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.5947
moved from start:          0.6315

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.027   3147  Z= 0.169
  Angle     :  0.714   7.013   4303  Z= 0.361
  Chirality :  0.047   0.208    451
  Planarity :  0.007   0.077    506
  Dihedral  : 15.388  88.239    515
  Min Nonbonded Distance : 2.441

Molprobity Statistics.
  All-atom Clashscore : 19.90
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.04 %
    Favored  : 94.96 %
  Rotamer:
    Outliers :  3.99 %
    Allowed  : 18.94 %
    Favored  : 77.08 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -1.32 (0.43), residues: 337
  helix:  0.25 (0.47), residues: 118
  sheet: -1.65 (0.62), residues: 63
  loop : -1.34 (0.44), residues: 156

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.046   0.003   TRP A 150 
 HIS   0.004   0.002   HIS A  71 
 PHE   0.008   0.002   PHE A  11 
 TYR   0.012   0.002   TYR A  54 
 ARG   0.005   0.001   ARG A 280 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04195 (  125)
  hydrogen bonds       : angle       6.74508 (  324)
  metal coordination   : bond        0.01251 (    4)
  metal coordination   : angle       3.20506 (    6)
  covalent geometry    : bond        0.00375 ( 3142)
  covalent geometry    : angle       0.70424 ( 4297)
  Misc. bond           : bond        0.00144 (    1)

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

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

  674 Ramachandran restraints generated.
    337 Oldfield, 0 Emsley, 337 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  674 Ramachandran restraints generated.
    337 Oldfield, 0 Emsley, 337 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  45 residues out of total 301 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 33
  time to evaluate  : 0.266 
Fit side-chains
REVERT: A   87 ARG cc_start: 0.7866 (OUTLIER) cc_final: 0.5294 (mtt180)
REVERT: A   95 LYS cc_start: 0.7290 (tttt) cc_final: 0.6759 (tppt)
REVERT: A  118 ILE cc_start: -0.1425 (OUTLIER) cc_final: -0.1713 (mt)
REVERT: A  243 GLU cc_start: 0.6531 (pm20) cc_final: 0.6082 (pm20)
REVERT: A  292 MET cc_start: 0.8233 (tmm) cc_final: 0.7853 (tmm)
REVERT: A  319 MET cc_start: 0.6213 (mpp) cc_final: 0.5967 (mpp)
  outliers start: 12
  outliers final: 7
  residues processed: 41
  average time/residue: 0.1830
  time to fit residues: 8.9472
Evaluate side-chains
  36 residues out of total 301 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 9
    poor density    : 27
  time to evaluate  : 0.348 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue    7 ILE
Chi-restraints excluded: chain A residue   23 THR
Chi-restraints excluded: chain A residue   87 ARG
Chi-restraints excluded: chain A residue   90 ILE
Chi-restraints excluded: chain A residue  118 ILE
Chi-restraints excluded: chain A residue  148 ASP
Chi-restraints excluded: chain A residue  175 ILE
Chi-restraints excluded: chain A residue  182 ILE
Chi-restraints excluded: chain A residue  334 MET
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 34
   random chunks:
   chunk 12 optimal weight:    2.9990
   chunk 27 optimal weight:    9.9990
   chunk 9 optimal weight:    4.9990
   chunk 7 optimal weight:    6.9990
   chunk 15 optimal weight:    3.9990
   chunk 20 optimal weight:   10.0000
   chunk 1 optimal weight:    0.0270
   chunk 3 optimal weight:    8.9990
   chunk 23 optimal weight:    3.9990
   chunk 4 optimal weight:    6.9990
   chunk 11 optimal weight:    0.0040
   overall best weight:    2.2056

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

Flipped N/Q/H residues before XYZ refinement:
A  48 ASN
** A 134 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4349 r_free = 0.4349 target = 0.129749 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 63)----------------|
| r_work = 0.4094 r_free = 0.4094 target = 0.114025 restraints weight = 11719.821|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 53)----------------|
| r_work = 0.4115 r_free = 0.4115 target = 0.115150 restraints weight = 8245.236|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 35)----------------|
| r_work = 0.4124 r_free = 0.4124 target = 0.115692 restraints weight = 6586.366|
|-----------------------------------------------------------------------------|
r_work (final): 0.4103
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.5828
moved from start:          0.6477

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.044   3147  Z= 0.142
  Angle     :  0.687   7.421   4303  Z= 0.345
  Chirality :  0.046   0.172    451
  Planarity :  0.007   0.070    506
  Dihedral  : 14.994  89.733    515
  Min Nonbonded Distance : 2.463

Molprobity Statistics.
  All-atom Clashscore : 17.06
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.75 %
    Favored  : 95.25 %
  Rotamer:
    Outliers :  2.99 %
    Allowed  : 19.93 %
    Favored  : 77.08 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -1.18 (0.44), residues: 337
  helix:  0.51 (0.49), residues: 117
  sheet: -1.51 (0.63), residues: 61
  loop : -1.43 (0.44), residues: 159

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.054   0.003   TRP A 150 
 HIS   0.002   0.001   HIS A  64 
 PHE   0.008   0.002   PHE A  11 
 TYR   0.008   0.001   TYR A  54 
 ARG   0.008   0.001   ARG A  36 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03848 (  125)
  hydrogen bonds       : angle       6.58882 (  324)
  metal coordination   : bond        0.00598 (    4)
  metal coordination   : angle       3.44852 (    6)
  covalent geometry    : bond        0.00316 ( 3142)
  covalent geometry    : angle       0.67533 ( 4297)
  Misc. bond           : bond        0.00108 (    1)

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

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

  674 Ramachandran restraints generated.
    337 Oldfield, 0 Emsley, 337 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  674 Ramachandran restraints generated.
    337 Oldfield, 0 Emsley, 337 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  41 residues out of total 301 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 9
    poor density    : 32
  time to evaluate  : 0.344 
Fit side-chains
REVERT: A   87 ARG cc_start: 0.7763 (OUTLIER) cc_final: 0.5235 (mtt180)
REVERT: A   95 LYS cc_start: 0.7023 (tttt) cc_final: 0.6662 (tppt)
REVERT: A  118 ILE cc_start: -0.1026 (OUTLIER) cc_final: -0.1267 (mp)
REVERT: A  334 MET cc_start: 0.2903 (OUTLIER) cc_final: 0.1361 (ttp)
  outliers start: 9
  outliers final: 1
  residues processed: 37
  average time/residue: 0.1681
  time to fit residues: 7.7199
Evaluate side-chains
  33 residues out of total 301 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 4
    poor density    : 29
  time to evaluate  : 0.340 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   23 THR
Chi-restraints excluded: chain A residue   87 ARG
Chi-restraints excluded: chain A residue  118 ILE
Chi-restraints excluded: chain A residue  334 MET
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 34
   random chunks:
   chunk 9 optimal weight:    3.9990
   chunk 7 optimal weight:   10.0000
   chunk 6 optimal weight:    3.9990
   chunk 25 optimal weight:   10.0000
   chunk 23 optimal weight:    8.9990
   chunk 13 optimal weight:    0.0870
   chunk 10 optimal weight:    0.9980
   chunk 3 optimal weight:   10.0000
   chunk 20 optimal weight:   20.0000
   chunk 11 optimal weight:   10.0000
   chunk 30 optimal weight:   10.0000
   overall best weight:    3.6164

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

Flipped N/Q/H residues before XYZ refinement:
A  48 ASN
** A  67 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 134 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4341 r_free = 0.4341 target = 0.129298 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 71)----------------|
| r_work = 0.4098 r_free = 0.4098 target = 0.113831 restraints weight = 12021.947|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 35)----------------|
| r_work = 0.4112 r_free = 0.4112 target = 0.114630 restraints weight = 9007.025|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 47)----------------|
| r_work = 0.4121 r_free = 0.4121 target = 0.115130 restraints weight = 7635.802|
|-----------------------------------------------------------------------------|
r_work (final): 0.4095
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.5903
moved from start:          0.6793

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.047   3147  Z= 0.172
  Angle     :  0.782  13.954   4303  Z= 0.386
  Chirality :  0.049   0.269    451
  Planarity :  0.007   0.072    506
  Dihedral  : 15.147  89.856    515
  Min Nonbonded Distance : 2.457

Molprobity Statistics.
  All-atom Clashscore : 21.24
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.23 %
    Favored  : 93.77 %
  Rotamer:
    Outliers :  2.99 %
    Allowed  : 21.59 %
    Favored  : 75.42 %
  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: -1.57 (0.43), residues: 337
  helix:  0.07 (0.48), residues: 118
  sheet: -1.70 (0.62), residues: 63
  loop : -1.57 (0.44), residues: 156

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.065   0.004   TRP A 150 
 HIS   0.004   0.002   HIS A  64 
 PHE   0.008   0.001   PHE A  81 
 TYR   0.011   0.001   TYR A  54 
 ARG   0.007   0.001   ARG A  36 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04301 (  125)
  hydrogen bonds       : angle       6.88620 (  324)
  metal coordination   : bond        0.01099 (    4)
  metal coordination   : angle       4.30781 (    6)
  covalent geometry    : bond        0.00389 ( 3142)
  covalent geometry    : angle       0.76604 ( 4297)
  Misc. bond           : bond        0.00151 (    1)

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

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

  674 Ramachandran restraints generated.
    337 Oldfield, 0 Emsley, 337 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  674 Ramachandran restraints generated.
    337 Oldfield, 0 Emsley, 337 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  41 residues out of total 301 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 9
    poor density    : 32
  time to evaluate  : 0.309 
Fit side-chains
REVERT: A   18 HIS cc_start: 0.6734 (m-70) cc_final: 0.6182 (p-80)
REVERT: A   87 ARG cc_start: 0.7826 (OUTLIER) cc_final: 0.5274 (mtt180)
REVERT: A   95 LYS cc_start: 0.7054 (tttt) cc_final: 0.6643 (tppt)
REVERT: A  118 ILE cc_start: -0.1417 (OUTLIER) cc_final: -0.1633 (mp)
  outliers start: 9
  outliers final: 5
  residues processed: 38
  average time/residue: 0.1965
  time to fit residues: 8.9523
Evaluate side-chains
  36 residues out of total 301 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 7
    poor density    : 29
  time to evaluate  : 0.315 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue    7 ILE
Chi-restraints excluded: chain A residue   23 THR
Chi-restraints excluded: chain A residue   87 ARG
Chi-restraints excluded: chain A residue   90 ILE
Chi-restraints excluded: chain A residue  118 ILE
Chi-restraints excluded: chain A residue  182 ILE
Chi-restraints excluded: chain A residue  334 MET
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 34
   random chunks:
   chunk 33 optimal weight:    0.9990
   chunk 30 optimal weight:    2.9990
   chunk 28 optimal weight:    0.9980
   chunk 18 optimal weight:    0.7980
   chunk 4 optimal weight:    0.7980
   chunk 8 optimal weight:    0.6980
   chunk 13 optimal weight:    0.0060
   chunk 1 optimal weight:    0.8980
   chunk 31 optimal weight:    0.9990
   chunk 32 optimal weight:    7.9990
   chunk 10 optimal weight:    2.9990
   overall best weight:    0.6396

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

Flipped N/Q/H residues before XYZ refinement:
A  48 ASN
** A 134 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4368 r_free = 0.4368 target = 0.130298 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 54)----------------|
| r_work = 0.4089 r_free = 0.4089 target = 0.113282 restraints weight = 11877.799|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 54)----------------|
| r_work = 0.4112 r_free = 0.4112 target = 0.114744 restraints weight = 7664.267|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 56)----------------|
| r_work = 0.4129 r_free = 0.4129 target = 0.115689 restraints weight = 5801.215|
|-----------------------------------------------------------------------------|
r_work (final): 0.4100
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.5828
moved from start:          0.6834

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.048   3147  Z= 0.132
  Angle     :  0.718  11.194   4303  Z= 0.354
  Chirality :  0.047   0.205    451
  Planarity :  0.006   0.054    506
  Dihedral  : 14.532  88.892    515
  Min Nonbonded Distance : 2.473

Molprobity Statistics.
  All-atom Clashscore : 14.21
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.86 %
    Favored  : 96.14 %
  Rotamer:
    Outliers :  1.33 %
    Allowed  : 22.92 %
    Favored  : 75.75 %
  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: -1.46 (0.43), residues: 337
  helix:  0.43 (0.49), residues: 116
  sheet: -1.74 (0.60), residues: 65
  loop : -1.66 (0.44), residues: 156

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.060   0.003   TRP A 150 
 HIS   0.002   0.001   HIS A 134 
 PHE   0.010   0.001   PHE A 194 
 TYR   0.007   0.001   TYR A 213 
 ARG   0.008   0.000   ARG A  36 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03824 (  125)
  hydrogen bonds       : angle       6.54333 (  324)
  metal coordination   : bond        0.00464 (    4)
  metal coordination   : angle       3.50877 (    6)
  covalent geometry    : bond        0.00300 ( 3142)
  covalent geometry    : angle       0.70635 ( 4297)
  Misc. bond           : bond        0.00052 (    1)

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

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

  674 Ramachandran restraints generated.
    337 Oldfield, 0 Emsley, 337 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  674 Ramachandran restraints generated.
    337 Oldfield, 0 Emsley, 337 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  44 residues out of total 301 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 4
    poor density    : 40
  time to evaluate  : 0.351 
Fit side-chains
REVERT: A   18 HIS cc_start: 0.6794 (m-70) cc_final: 0.6336 (p-80)
REVERT: A   87 ARG cc_start: 0.7815 (OUTLIER) cc_final: 0.5274 (mtt180)
REVERT: A   95 LYS cc_start: 0.7180 (tttt) cc_final: 0.6634 (tppt)
REVERT: A  334 MET cc_start: 0.2456 (OUTLIER) cc_final: 0.0806 (ttp)
  outliers start: 4
  outliers final: 0
  residues processed: 43
  average time/residue: 0.1734
  time to fit residues: 9.0770
Evaluate side-chains
  36 residues out of total 301 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 2
    poor density    : 34
  time to evaluate  : 0.336 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   87 ARG
Chi-restraints excluded: chain A residue  334 MET
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 34
   random chunks:
   chunk 25 optimal weight:    8.9990
   chunk 31 optimal weight:    7.9990
   chunk 28 optimal weight:    0.6980
   chunk 15 optimal weight:    0.8980
   chunk 4 optimal weight:   10.0000
   chunk 30 optimal weight:    2.9990
   chunk 1 optimal weight:    0.9990
   chunk 17 optimal weight:    4.9990
   chunk 11 optimal weight:    5.9990
   chunk 8 optimal weight:    2.9990
   chunk 18 optimal weight:   20.0000
   overall best weight:    1.7186

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

Flipped N/Q/H residues before XYZ refinement:
** A  48 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
A  67 ASN
** A 134 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4352 r_free = 0.4352 target = 0.129726 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 66)----------------|
| r_work = 0.4069 r_free = 0.4069 target = 0.112427 restraints weight = 12031.282|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 46)----------------|
| r_work = 0.4094 r_free = 0.4094 target = 0.113933 restraints weight = 7636.790|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 56)----------------|
| r_work = 0.4110 r_free = 0.4110 target = 0.114872 restraints weight = 5787.578|
|-----------------------------------------------------------------------------|
r_work (final): 0.4086
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.5853
moved from start:          0.7047

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.042   3147  Z= 0.141
  Angle     :  0.751  10.889   4303  Z= 0.374
  Chirality :  0.048   0.188    451
  Planarity :  0.006   0.058    506
  Dihedral  : 14.426  88.592    515
  Min Nonbonded Distance : 2.473

Molprobity Statistics.
  All-atom Clashscore : 15.38
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.23 %
    Favored  : 93.77 %
  Rotamer:
    Outliers :  1.00 %
    Allowed  : 24.92 %
    Favored  : 74.09 %
  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: -1.55 (0.43), residues: 337
  helix:  0.25 (0.49), residues: 115
  sheet: -1.66 (0.60), residues: 65
  loop : -1.68 (0.44), residues: 157

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.038   0.003   TRP A 150 
 HIS   0.003   0.001   HIS A  64 
 PHE   0.012   0.001   PHE A  31 
 TYR   0.008   0.001   TYR A  54 
 ARG   0.007   0.000   ARG A  36 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04122 (  125)
  hydrogen bonds       : angle       6.58209 (  324)
  metal coordination   : bond        0.00583 (    4)
  metal coordination   : angle       3.83530 (    6)
  covalent geometry    : bond        0.00322 ( 3142)
  covalent geometry    : angle       0.73800 ( 4297)
  Misc. bond           : bond        0.00065 (    1)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 1571.58 seconds
wall clock time: 27 minutes 56.28 seconds (1676.28 seconds total)