Starting phenix.real_space_refine
on Tue Aug  4 14:25:14 2026 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/9v47_64769/08_2026/9v47_64769.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/9v47_64769/08_2026/9v47_64769.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=4.52
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    model {
      file = "/net/cci-nas-00/data/ceres_data/9v47_64769/08_2026/9v47_64769.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/9v47_64769/08_2026/9v47_64769.cif"
    real_map_files = "/net/cci-nas-00/data/ceres_data/9v47_64769/08_2026/9v47_64769.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/9v47_64769/08_2026/9v47_64769.map"
  }
  resolution = 4.52
  write_initial_geo_file = False
  refinement {
    macro_cycles = 10
  }


Starting job
===============================================================================
-------------------------------------------------------------------------------
Citation:
*********
Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams
PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography.
Acta Cryst. D74:531-544.

Validating inputs
Origin is already at (0, 0, 0), no shifts will be applied
-------------------------------------------------------------------------------
Processing inputs
*****************
Set random seed
  Set to: 0
Set model cs if undefined
Decide on map wrapping
  Map wrapping is set to: False
Normalize map: mean=0, sd=1
  Input map: mean=   0.000 sd=   0.013
Set stop_for_unknowns flag
  Set to: True
Assert model is a single copy model
Assert all atoms have isotropic ADPs
Construct map_model_manager
Extract box with map and model
Check model and map are aligned
Set scattering table
  Set to: electron
  Number of scattering types: 5
    Type Number    sf(0)   Gaussians
     P      10      5.49       5
     S      29      5.16       5
     C    2312      2.51       5
     N     716      2.21       5
     O     724      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 30 residue(s): 0.00s

  Monomer Library directory:
    "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.2rc3-6140/lib/python3.11/site-packages/chem_data/mon_lib"
  Total number of atoms: 3791
  Number of models: 1
  Model: ""
    Number of chains: 2
    Chain: "B"
      Number of atoms: 3571
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 453, 3571
          Classifications: {'peptide': 453}
          Incomplete info: {'n_c_alpha_c_only': 2}
          Link IDs: {'PTRANS': 17, 'TRANS': 435}
          Chain breaks: 1
          Unresolved chain link angles: 2
          Unresolved non-hydrogen bonds: 2
          Unresolved non-hydrogen angles: 2
    Chain: "C"
      Number of atoms: 220
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 10, 220
          Classifications: {'RNA': 10}
          Modifications used: {'rna2p_pur': 7, 'rna3p_pur': 3}
          Link IDs: {'rna2p': 7, 'rna3p': 2}
  Residues with excluded nonbonded symmetry interactions: 1
    residue:
      pdb=" N   TYR B  78 " occ=0.60
      ... (10 atoms not shown)
      pdb=" OH  TYR B  78 " occ=0.60
  Time building chain proxies: 1.09, per 1000 atoms: 0.29
  Number of scatterers: 3791
  At special positions: 0
  Unit cell: (81.6, 64.32, 83.52, 90, 90, 90)
  Space group: P 1 (No. 1)
  Number of sites at special positions: 0
  Number of scattering types: 5
    Type Number    sf(0)
     S      29     16.00
     P      10     15.00
     O     724      8.00
     N     716      7.00
     C    2312      6.00
    sf(0) = scattering factor at diffraction angle 0.

  Number of disulfides: simple=0, symmetry=0

  Automatic linking
    Parameters for automatic linking
      Linking & cutoffs
        Metal                : Auto  - 3.00
        Amino acid           : True  - 1.90
        Carbohydrate         : True  - 1.99
        Ligands              : True  - 1.99
        Small molecules      : False - 1.98
        Amino acid - RNA/DNA : False
      
  Number of custom bonds: simple=0, symmetry=0
  Time building additional restraints: 0.35
  Conformation dependent library (CDL) restraints added in 131.5 milliseconds
  

  898 Ramachandran restraints generated.
    449 Oldfield, 0 Emsley, 449 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  836

  Finding SS restraints...
    Secondary structure from input PDB file:
      20 helices and 4 sheets defined
      53.0% alpha, 3.5% beta
      0 base pairs and 1 stacking pairs defined.
    Time for finding SS restraints: 0.42
  Creating SS restraints...
    Processing helix  chain 'B' and resid 21 through 48
      removed outlier: 4.311A  pdb=" N   LEU B  47 " --> pdb=" O   MET B  43 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 50 through 55
    Processing helix  chain 'B' and resid 56 through 70
    Processing helix  chain 'B' and resid 113 through 124
    Processing helix  chain 'B' and resid 129 through 148
      removed outlier: 3.635A  pdb=" N   TYR B 148 " --> pdb=" O   ASN B 144 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 151 through 157
    Processing helix  chain 'B' and resid 162 through 166
    Processing helix  chain 'B' and resid 179 through 184
      removed outlier: 3.758A  pdb=" N   VAL B 183 " --> pdb=" O   ALA B 179 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 185 through 202
      removed outlier: 3.615A  pdb=" N   MET B 189 " --> pdb=" O   GLY B 185 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 212 through 229
    Processing helix  chain 'B' and resid 232 through 245
      removed outlier: 3.684A  pdb=" N   SER B 245 " --> pdb=" O   GLN B 241 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 249 through 264
    Processing helix  chain 'B' and resid 277 through 286
      removed outlier: 4.172A  pdb=" N   TYR B 281 " --> pdb=" O   PRO B 277 " (cutoff:3.500A)
      Proline residue:  B 283  - end of helix
    Processing helix  chain 'B' and resid 290 through 295
      removed outlier: 3.651A  pdb=" N   GLU B 294 " --> pdb=" O   ASP B 290 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 301 through 309
      removed outlier: 3.640A  pdb=" N   ASN B 309 " --> pdb=" O   LYS B 305 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 321 through 335
    Processing helix  chain 'B' and resid 340 through 349
    Processing helix  chain 'B' and resid 354 through 358
    Processing helix  chain 'B' and resid 422 through 430
    Processing helix  chain 'B' and resid 438 through 448
      removed outlier: 4.061A  pdb=" N   ALA B 442 " --> pdb=" O   SER B 438 " (cutoff:3.500A)
    Processing sheet with id=AA1, first strand: chain 'B' and resid 91 through 92
    Processing sheet with id=AA2, first strand: chain 'B' and resid 96 through 100
      removed outlier: 3.733A  pdb=" N   ILE B  96 " --> pdb=" O   GLU B 107 " (cutoff:3.500A)
    Processing sheet with id=AA3, first strand: chain 'B' and resid 313 through 314
    Processing sheet with id=AA4, first strand: chain 'B' and resid 385 through 387

    161 hydrogen bonds defined for protein.
    462 hydrogen bond angles defined for protein.
    Restraints generated for nucleic acids:
      0 hydrogen bonds
      0 hydrogen bond angles
      0 basepair planarities
      0 basepair parallelities
      1 stacking parallelities
  Total time for adding SS restraints: 0.52

  Time building geometry restraints manager: 0.47 seconds

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

  Histogram of bond lengths:
        1.21 -     1.33: 765
        1.33 -     1.45: 950
        1.45 -     1.57: 2094
        1.57 -     1.69: 19
        1.69 -     1.81: 52
  Bond restraints: 3880
  Sorted by residual:
  bond pdb=" CA  ASN B 473 "
       pdb=" C   ASN B 473 "
    ideal  model  delta    sigma   weight residual
    1.522  1.487  0.035 8.40e-03 1.42e+04 1.77e+01
  bond pdb=" N   ARG B 348 "
       pdb=" CA  ARG B 348 "
    ideal  model  delta    sigma   weight residual
    1.457  1.507 -0.050 1.29e-02 6.01e+03 1.52e+01
  bond pdb=" N   ARG B  75 "
       pdb=" CA  ARG B  75 "
    ideal  model  delta    sigma   weight residual
    1.456  1.502 -0.046 1.25e-02 6.40e+03 1.36e+01
  bond pdb=" N   MET B 481 "
       pdb=" CA  MET B 481 "
    ideal  model  delta    sigma   weight residual
    1.457  1.503 -0.046 1.35e-02 5.49e+03 1.17e+01
  bond pdb=" CA  PRO B 173 "
       pdb=" CB  PRO B 173 "
    ideal  model  delta    sigma   weight residual
    1.533  1.498  0.035 1.04e-02 9.25e+03 1.16e+01
  ... (remaining 3875 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     1.59: 4388
        1.59 -     3.18: 707
        3.18 -     4.77: 123
        4.77 -     6.36: 32
        6.36 -     7.95: 13
  Bond angle restraints: 5263
  Sorted by residual:
  angle pdb=" C2'   A C1010 "
        pdb=" C1'   A C1010 "
        pdb=" N9    A C1010 "
      ideal   model   delta    sigma   weight residual
     112.00  119.55   -7.55 1.10e+00 8.26e-01 4.72e+01
  angle pdb=" N   ARG B 162 "
        pdb=" CA  ARG B 162 "
        pdb=" C   ARG B 162 "
      ideal   model   delta    sigma   weight residual
     112.89  105.04    7.85 1.24e+00 6.50e-01 4.01e+01
  angle pdb=" N   GLY B 362 "
        pdb=" CA  GLY B 362 "
        pdb=" C   GLY B 362 "
      ideal   model   delta    sigma   weight residual
     111.93  118.11   -6.18 1.15e+00 7.56e-01 2.89e+01
  angle pdb=" N   PRO B 161 "
        pdb=" CA  PRO B 161 "
        pdb=" C   PRO B 161 "
      ideal   model   delta    sigma   weight residual
     112.48  105.27    7.21 1.35e+00 5.49e-01 2.85e+01
  angle pdb=" N   PHE B 258 "
        pdb=" CA  PHE B 258 "
        pdb=" C   PHE B 258 "
      ideal   model   delta    sigma   weight residual
     110.97  105.30    5.67 1.09e+00 8.42e-01 2.70e+01
  ... (remaining 5258 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    34.98: 2203
       34.98 -    69.96: 142
       69.96 -   104.94: 11
      104.94 -   139.91: 0
      139.91 -   174.89: 1
  Dihedral angle restraints: 2357
    sinusoidal: 1058
      harmonic: 1299
  Sorted by residual:
  dihedral pdb=" CA  LEU B 108 "
           pdb=" C   LEU B 108 "
           pdb=" N   VAL B 109 "
           pdb=" CA  VAL B 109 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  151.98   28.02     0      5.00e+00 4.00e-02 3.14e+01
  dihedral pdb=" O4'   A C1005 "
           pdb=" C1'   A C1005 "
           pdb=" N9    A C1005 "
           pdb=" C4    A C1005 "
      ideal   model   delta sinusoidal    sigma   weight residual
     254.00  172.08   81.92     1      1.70e+01 3.46e-03 2.85e+01
  dihedral pdb=" C4'   A C1009 "
           pdb=" O4'   A C1009 "
           pdb=" C1'   A C1009 "
           pdb=" C2'   A C1009 "
      ideal   model   delta sinusoidal    sigma   weight residual
     -21.00   11.22  -32.22     1      8.00e+00 1.56e-02 2.31e+01
  ... (remaining 2354 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.079: 431
       0.079 -    0.159: 111
       0.159 -    0.238: 28
       0.238 -    0.318: 2
       0.318 -    0.397: 1
  Chirality restraints: 573
  Sorted by residual:
  chirality pdb=" CA  VAL B 312 "
            pdb=" N   VAL B 312 "
            pdb=" C   VAL B 312 "
            pdb=" CB  VAL B 312 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.44    2.84   -0.40 2.00e-01 2.50e+01 3.94e+00
  chirality pdb=" C3'   A C1005 "
            pdb=" C4'   A C1005 "
            pdb=" O3'   A C1005 "
            pdb=" C2'   A C1005 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.74   -2.48   -0.27 2.00e-01 2.50e+01 1.81e+00
  chirality pdb=" CA  TYR B 148 "
            pdb=" N   TYR B 148 "
            pdb=" C   TYR B 148 "
            pdb=" CB  TYR B 148 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.77   -0.26 2.00e-01 2.50e+01 1.64e+00
  ... (remaining 570 not shown)

  Planarity restraints: 649
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  ARG B 156 "    0.014 2.00e-02 2.50e+03   2.77e-02 7.70e+00
        pdb=" C   ARG B 156 "   -0.048 2.00e-02 2.50e+03
        pdb=" O   ARG B 156 "    0.018 2.00e-02 2.50e+03
        pdb=" N   THR B 157 "    0.017 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  GLY B 460 "   -0.012 2.00e-02 2.50e+03   2.48e-02 6.14e+00
        pdb=" C   GLY B 460 "    0.043 2.00e-02 2.50e+03
        pdb=" O   GLY B 460 "   -0.016 2.00e-02 2.50e+03
        pdb=" N   ARG B 461 "   -0.014 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  GLU B  80 "   -0.011 2.00e-02 2.50e+03   2.25e-02 5.05e+00
        pdb=" C   GLU B  80 "    0.039 2.00e-02 2.50e+03
        pdb=" O   GLU B  80 "   -0.015 2.00e-02 2.50e+03
        pdb=" N   GLU B  81 "   -0.013 2.00e-02 2.50e+03
  ... (remaining 646 not shown)

  Histogram of nonbonded interaction distances:
        2.22 -     2.75: 678
        2.75 -     3.29: 4283
        3.29 -     3.83: 6466
        3.83 -     4.36: 7783
        4.36 -     4.90: 11310
  Nonbonded interactions: 30520
  Sorted by model distance:
  nonbonded pdb=" CE1 TYR B 385 "
            pdb=" OE2 GLU B 465 "
     model   vdw
     2.218 3.340
  nonbonded pdb=" N   GLN B  58 "
            pdb=" OE1 GLN B  58 "
     model   vdw
     2.254 3.120
  nonbonded pdb=" O   THR B 433 "
            pdb=" CG  GLU B 434 "
     model   vdw
     2.280 3.440
  nonbonded pdb=" O   GLN B 122 "
            pdb=" ND2 ASN B 125 "
     model   vdw
     2.285 3.120
  nonbonded pdb=" NH2 ARG B 243 "
            pdb=" OE2 GLU B 244 "
     model   vdw
     2.301 3.120
  ... (remaining 30515 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=0.60 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:             3.130
  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:          0.060
  Check model and map are aligned:         0.020
  Set scattering table:                    0.010
  Process input model:                     5.860
  Find NCS groups from input model:        0.020
  Set up NCS constraints:                  0.010
  Set refine NCS operators:                0.000
  Adjust number of macro_cycles:           0.000
  Reset NCS operators:                     0.000
  Extract rigid body selections:           0.000
  Check and reset occupancies:             0.000
  Load rotamer database and sin/cos tables:1.170
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   10.290
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.3500
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   0.050   3880  Z= 0.600
  Angle     :  1.286   7.953   5263  Z= 0.902
  Chirality :  0.076   0.397    573
  Planarity :  0.006   0.048    649
  Dihedral  : 20.271 174.892   1521
  Min Nonbonded Distance : 2.218

Molprobity Statistics.
  All-atom Clashscore : 47.77
  Ramachandran Plot:
    Outliers :  0.22 %
    Allowed  : 10.91 %
    Favored  : 88.86 %
  Rotamer:
    Outliers : 13.84 %
    Allowed  : 12.53 %
    Favored  : 73.63 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -4.59 (0.30), residues: 449
  helix: -2.73 (0.29), residues: 204
  sheet:  None (None), residues: 0
  loop : -3.45 (0.30), residues: 245

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.001   ARG B 441 
 TYR   0.023   0.002   TYR B  40 
 PHE   0.017   0.002   PHE B 464 
 TRP   0.010   0.002   TRP B 330 
 HIS   0.003   0.001   HIS B 334 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00840 /  0.60 ( 3880)
  covalent geometry    : angle       1.28590 /  0.90 ( 5263)
  hydrogen bonds       : bond        0.15940 / 11.34 (  161)
  hydrogen bonds       : angle       7.78446 /  5.50 (  462)

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

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

  898 Ramachandran restraints generated.
    449 Oldfield, 0 Emsley, 449 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  898 Ramachandran restraints generated.
    449 Oldfield, 0 Emsley, 449 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  134 residues out of total 383 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 53
    poor density    : 81
  time to evaluate  : 0.126 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: B   90 LYS cc_start: 0.0683 (OUTLIER) cc_final: -0.0444 (tptm)
REVERT: B  105 MET cc_start: 0.5875 (ptm) cc_final: 0.5228 (pmm)
REVERT: B  106 ARG cc_start: 0.5377 (OUTLIER) cc_final: 0.5064 (ttt90)
REVERT: B  184 LYS cc_start: 0.5266 (tttt) cc_final: 0.5036 (tttt)
REVERT: B  192 GLU cc_start: 0.7317 (tm-30) cc_final: 0.6758 (tm-30)
REVERT: B  196 MET cc_start: 0.8004 (mtp) cc_final: 0.7533 (mtp)
REVERT: B  205 ASN cc_start: 0.7717 (OUTLIER) cc_final: 0.7457 (p0)
REVERT: B  227 LYS cc_start: 0.7384 (OUTLIER) cc_final: 0.6690 (ttpp)
REVERT: B  230 PHE cc_start: 0.6037 (p90) cc_final: 0.5486 (p90)
REVERT: B  239 MET cc_start: 0.7301 (tpp) cc_final: 0.7008 (tmm)
REVERT: B  240 ASP cc_start: 0.7893 (m-30) cc_final: 0.7017 (m-30)
REVERT: B  258 PHE cc_start: 0.7499 (OUTLIER) cc_final: 0.5102 (t80)
REVERT: B  311 GLN cc_start: 0.3471 (OUTLIER) cc_final: 0.3101 (tp40)
REVERT: B  316 ILE cc_start: -0.6506 (OUTLIER) cc_final: -0.6712 (tp)
REVERT: B  364 GLN cc_start: -0.3695 (OUTLIER) cc_final: -0.4119 (tp40)
  outliers start: 53
  outliers final: 25
  residues processed: 123
  average time/residue: 0.1102
  time to fit residues: 15.4732
Evaluate side-chains
  104 residues out of total 383 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 33
    poor density    : 71
  time to evaluate  : 0.117 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 46
   random chunks:
   chunk 24 optimal weight:    1.9990
   chunk 26 optimal weight:    0.6980
   chunk 2 optimal weight:    0.6980
   chunk 16 optimal weight:    0.0970
   chunk 32 optimal weight:    0.5980
   chunk 31 optimal weight:    0.8980
   chunk 25 optimal weight:    0.8980
   chunk 19 optimal weight:    2.9990
   chunk 30 optimal weight:    0.4980
   chunk 22 optimal weight:    0.8980
   chunk 37 optimal weight:    0.0470
   overall best weight:    0.3876

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
B 124 ASN
B 149 GLN
** B 168 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
B 211 ASN
B 241 GLN
B 334 HIS

Total number of N/Q/H flips: 5

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.5054 r_free = 0.5054 target = 0.281066 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 35)----------------|
| r_work = 0.5012 r_free = 0.5012 target = 0.270270 restraints weight = 15508.463|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 27)----------------|
| r_work = 0.5005 r_free = 0.5005 target = 0.270367 restraints weight = 15478.449|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 24)----------------|
| r_work = 0.5014 r_free = 0.5014 target = 0.271663 restraints weight = 13098.342|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 26)----------------|
| r_work = 0.5018 r_free = 0.5018 target = 0.271890 restraints weight = 9496.195|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 28)----------------|
| r_work = 0.5023 r_free = 0.5023 target = 0.272491 restraints weight = 8639.206|
|-----------------------------------------------------------------------------|
r_work (final): 0.4789
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.4789
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.4789 r_free = 0.4789    target_work(ls_wunit_k1) = 0.231         |
| occupancies: max = 1.00  min = 0.60   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.4783 r_free = 0.4783    target_work(ls_wunit_k1) = 0.230         |
| occupancies: max = 1.00  min = 1.00   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|

Number of minimizer iterations: 5 (10 function evaluations)
r_final: 0.4783
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.3795
moved from start:          0.3194

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.058   3880  Z= 0.217
  Angle     :  0.868   7.719   5263  Z= 0.465
  Chirality :  0.051   0.303    573
  Planarity :  0.009   0.080    649
  Dihedral  : 14.739 166.201    625
  Min Nonbonded Distance : 2.431

Molprobity Statistics.
  All-atom Clashscore : 23.28
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  7.13 %
    Favored  : 92.87 %
  Rotamer:
    Outliers :  1.04 %
    Allowed  :  3.13 %
    Favored  : 95.82 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -3.34 (0.33), residues: 449
  helix: -1.77 (0.31), residues: 208
  sheet: -1.62 (1.43), residues: 12
  loop : -2.73 (0.34), residues: 229

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.012   0.001   ARG B 317 
 TYR   0.031   0.003   TYR B  40 
 PHE   0.039   0.004   PHE B 258 
 TRP   0.013   0.003   TRP B 207 
 HIS   0.005   0.002   HIS B 140 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00460 /  0.22 ( 3880)
  covalent geometry    : angle       0.86837 /  0.46 ( 5263)
  hydrogen bonds       : bond        0.06178 /  4.36 (  161)
  hydrogen bonds       : angle       6.37591 /  4.49 (  462)

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

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

  898 Ramachandran restraints generated.
    449 Oldfield, 0 Emsley, 449 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  898 Ramachandran restraints generated.
    449 Oldfield, 0 Emsley, 449 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  81 residues out of total 383 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 4
    poor density    : 77
  time to evaluate  : 0.128 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: B   34 ASN cc_start: 0.7039 (t0) cc_final: 0.6487 (t0)
REVERT: B   66 MET cc_start: 0.7384 (mtt) cc_final: 0.7129 (mtt)
REVERT: B  105 MET cc_start: 0.5252 (ptm) cc_final: 0.4646 (pmm)
REVERT: B  136 MET cc_start: 0.7095 (mtp) cc_final: 0.6743 (mtp)
REVERT: B  192 GLU cc_start: 0.7464 (tm-30) cc_final: 0.6763 (tm-30)
REVERT: B  196 MET cc_start: 0.8039 (mtp) cc_final: 0.7583 (mtp)
REVERT: B  227 LYS cc_start: 0.7198 (ttpt) cc_final: 0.6819 (ttpp)
REVERT: B  230 PHE cc_start: 0.5578 (p90) cc_final: 0.5056 (p90)
REVERT: B  239 MET cc_start: 0.7537 (tpp) cc_final: 0.6735 (tmm)
REVERT: B  240 ASP cc_start: 0.7936 (m-30) cc_final: 0.7552 (m-30)
REVERT: B  440 MET cc_start: 0.6815 (mpp) cc_final: 0.6524 (mpp)
  outliers start: 4
  outliers final: 0
  residues processed: 81
  average time/residue: 0.1037
  time to fit residues: 9.8093
Evaluate side-chains
  71 residues out of total 383 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 71
  time to evaluate  : 0.127 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 46
   random chunks:
   chunk 41 optimal weight:    1.9990
   chunk 16 optimal weight:    0.9980
   chunk 19 optimal weight:    0.6980
   chunk 5 optimal weight:    0.9980
   chunk 23 optimal weight:    2.9990
   chunk 9 optimal weight:    0.9980
   chunk 28 optimal weight:    0.7980
   chunk 1 optimal weight:    0.7980
   chunk 24 optimal weight:    0.9990
   chunk 3 optimal weight:    0.0980
   chunk 40 optimal weight:    3.9990
   overall best weight:    0.6780

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
B  76 ASN
** B 168 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
B 241 GLN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4848 r_free = 0.4848 target = 0.236259 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 47)----------------|
| r_work = 0.4545 r_free = 0.4545 target = 0.205205 restraints weight = 11668.757|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 20)----------------|
| r_work = 0.4557 r_free = 0.4557 target = 0.206552 restraints weight = 10409.969|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 44)----------------|
| r_work = 0.4575 r_free = 0.4575 target = 0.208087 restraints weight = 9876.029|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 29)----------------|
| r_work = 0.4585 r_free = 0.4585 target = 0.209102 restraints weight = 9254.973|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 25)----------------|
| r_work = 0.4589 r_free = 0.4589 target = 0.209592 restraints weight = 8743.329|
|-----------------------------------------------------------------------------|
r_work (final): 0.4554
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.4272
moved from start:          0.3910

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.096   3880  Z= 0.208
  Angle     :  0.815  14.105   5263  Z= 0.433
  Chirality :  0.047   0.327    573
  Planarity :  0.006   0.052    649
  Dihedral  : 14.659 168.190    625
  Min Nonbonded Distance : 2.457

Molprobity Statistics.
  All-atom Clashscore : 23.15
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  7.13 %
    Favored  : 92.87 %
  Rotamer:
    Outliers :  0.52 %
    Allowed  :  3.66 %
    Favored  : 95.82 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -2.83 (0.35), residues: 449
  helix: -1.50 (0.32), residues: 210
  sheet: -1.46 (1.44), residues: 12
  loop : -2.26 (0.37), residues: 227

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.010   0.001   ARG B 261 
 TYR   0.017   0.002   TYR B  40 
 PHE   0.031   0.004   PHE B 338 
 TRP   0.024   0.003   TRP B 120 
 HIS   0.005   0.001   HIS B 140 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00451 /  0.21 ( 3880)
  covalent geometry    : angle       0.81549 /  0.43 ( 5263)
  hydrogen bonds       : bond        0.05803 /  4.11 (  161)
  hydrogen bonds       : angle       6.19218 /  4.32 (  462)

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

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

  898 Ramachandran restraints generated.
    449 Oldfield, 0 Emsley, 449 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  898 Ramachandran restraints generated.
    449 Oldfield, 0 Emsley, 449 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  75 residues out of total 383 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 2
    poor density    : 73
  time to evaluate  : 0.128 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: B   46 GLU cc_start: 0.7583 (mp0) cc_final: 0.7346 (mp0)
REVERT: B   66 MET cc_start: 0.7542 (mtt) cc_final: 0.7267 (mtt)
REVERT: B  105 MET cc_start: 0.5731 (ptm) cc_final: 0.4930 (pmm)
REVERT: B  136 MET cc_start: 0.7271 (mtp) cc_final: 0.6902 (mtp)
REVERT: B  137 MET cc_start: 0.5614 (ptm) cc_final: 0.5254 (ptm)
REVERT: B  192 GLU cc_start: 0.7732 (tm-30) cc_final: 0.7071 (tm-30)
REVERT: B  196 MET cc_start: 0.8285 (mtp) cc_final: 0.7786 (mtp)
REVERT: B  230 PHE cc_start: 0.6367 (p90) cc_final: 0.5628 (p90)
REVERT: B  239 MET cc_start: 0.7686 (tpp) cc_final: 0.6732 (tmm)
REVERT: B  240 ASP cc_start: 0.7900 (m-30) cc_final: 0.7567 (m-30)
  outliers start: 2
  outliers final: 1
  residues processed: 75
  average time/residue: 0.1114
  time to fit residues: 9.7230
Evaluate side-chains
  71 residues out of total 383 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 70
  time to evaluate  : 0.128 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 46
   random chunks:
   chunk 32 optimal weight:    2.9990
   chunk 9 optimal weight:    0.5980
   chunk 10 optimal weight:    0.7980
   chunk 37 optimal weight:    0.9990
   chunk 4 optimal weight:    0.0870
   chunk 43 optimal weight:    0.1980
   chunk 15 optimal weight:    3.9990
   chunk 45 optimal weight:    6.9990
   chunk 29 optimal weight:    1.9990
   chunk 2 optimal weight:    0.1980
   chunk 7 optimal weight:    0.8980
   overall best weight:    0.3758

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
B  76 ASN
B 168 GLN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.5072 r_free = 0.5072 target = 0.281048 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 41)----------------|
| r_work = 0.5029 r_free = 0.5029 target = 0.270185 restraints weight = 15274.391|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 27)----------------|
| r_work = 0.5022 r_free = 0.5022 target = 0.270409 restraints weight = 14951.368|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 27)----------------|
| r_work = 0.5032 r_free = 0.5032 target = 0.271652 restraints weight = 12507.938|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 26)----------------|
| r_work = 0.5035 r_free = 0.5035 target = 0.271912 restraints weight = 9286.594|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 26)----------------|
| r_work = 0.5040 r_free = 0.5040 target = 0.272462 restraints weight = 8729.648|
|-----------------------------------------------------------------------------|
r_work (final): 0.4795
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.3852
moved from start:          0.4354

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.051   3880  Z= 0.170
  Angle     :  0.765  12.642   5263  Z= 0.402
  Chirality :  0.045   0.323    573
  Planarity :  0.006   0.077    649
  Dihedral  : 14.535 169.875    625
  Min Nonbonded Distance : 2.467

Molprobity Statistics.
  All-atom Clashscore : 20.20
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  7.35 %
    Favored  : 92.65 %
  Rotamer:
    Outliers :  0.26 %
    Allowed  :  4.18 %
    Favored  : 95.56 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -2.23 (0.37), residues: 449
  helix: -1.00 (0.33), residues: 212
  sheet: -1.45 (1.70), residues: 12
  loop : -1.95 (0.40), residues: 225

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.015   0.001   ARG B 174 
 TYR   0.008   0.002   TYR B  97 
 PHE   0.040   0.003   PHE B  39 
 TRP   0.020   0.003   TRP B 104 
 HIS   0.010   0.002   HIS B 135 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00363 /  0.17 ( 3880)
  covalent geometry    : angle       0.76514 /  0.40 ( 5263)
  hydrogen bonds       : bond        0.05438 /  3.78 (  161)
  hydrogen bonds       : angle       5.80490 /  4.05 (  462)

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

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

  898 Ramachandran restraints generated.
    449 Oldfield, 0 Emsley, 449 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  898 Ramachandran restraints generated.
    449 Oldfield, 0 Emsley, 449 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  72 residues out of total 383 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 71
  time to evaluate  : 0.129 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: B  105 MET cc_start: 0.4943 (ptm) cc_final: 0.4354 (pmm)
REVERT: B  137 MET cc_start: 0.5212 (ptm) cc_final: 0.4979 (ptm)
REVERT: B  167 MET cc_start: 0.2111 (mmp) cc_final: 0.1492 (mmp)
REVERT: B  175 ARG cc_start: 0.5787 (ptm160) cc_final: 0.5526 (ptm160)
REVERT: B  184 LYS cc_start: 0.7236 (tttp) cc_final: 0.7013 (tttp)
REVERT: B  192 GLU cc_start: 0.7352 (tm-30) cc_final: 0.6685 (tm-30)
REVERT: B  196 MET cc_start: 0.8064 (mtp) cc_final: 0.7594 (mtp)
REVERT: B  221 ARG cc_start: 0.7432 (ptt-90) cc_final: 0.7108 (ptt-90)
REVERT: B  239 MET cc_start: 0.7418 (tpp) cc_final: 0.6661 (tmm)
REVERT: B  240 ASP cc_start: 0.7977 (m-30) cc_final: 0.7597 (m-30)
REVERT: B  425 ILE cc_start: 0.8133 (mm) cc_final: 0.7884 (mm)
REVERT: B  440 MET cc_start: 0.6782 (mpp) cc_final: 0.6338 (mpp)
  outliers start: 1
  outliers final: 0
  residues processed: 72
  average time/residue: 0.1109
  time to fit residues: 9.2540
Evaluate side-chains
  68 residues out of total 383 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 68
  time to evaluate  : 0.128 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 46
   random chunks:
   chunk 44 optimal weight:    0.3980
   chunk 27 optimal weight:    7.9990
   chunk 7 optimal weight:    0.6980
   chunk 6 optimal weight:    6.9990
   chunk 19 optimal weight:    0.8980
   chunk 28 optimal weight:    0.6980
   chunk 16 optimal weight:    0.9990
   chunk 10 optimal weight:    0.0870
   chunk 25 optimal weight:    0.5980
   chunk 38 optimal weight:    0.0670
   chunk 8 optimal weight:    0.6980
   overall best weight:    0.3696

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
B  76 ASN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4851 r_free = 0.4851 target = 0.235782 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 44)----------------|
| r_work = 0.4549 r_free = 0.4549 target = 0.205042 restraints weight = 11750.731|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 37)----------------|
| r_work = 0.4568 r_free = 0.4568 target = 0.206659 restraints weight = 10542.443|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 24)----------------|
| r_work = 0.4575 r_free = 0.4575 target = 0.207313 restraints weight = 9852.126|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 18)----------------|
| r_work = 0.4575 r_free = 0.4575 target = 0.207318 restraints weight = 9214.465|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 22)----------------|
| r_work = 0.4575 r_free = 0.4575 target = 0.207318 restraints weight = 9217.429|
|-----------------------------------------------------------------------------|
r_work (final): 0.4541
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.4290
moved from start:          0.4654

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.061   3880  Z= 0.167
  Angle     :  0.755  10.847   5263  Z= 0.397
  Chirality :  0.045   0.322    573
  Planarity :  0.006   0.066    649
  Dihedral  : 14.503 169.718    625
  Min Nonbonded Distance : 2.473

Molprobity Statistics.
  All-atom Clashscore : 19.80
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.68 %
    Favored  : 93.32 %
  Rotamer:
    Outliers :  0.26 %
    Allowed  :  1.57 %
    Favored  : 98.17 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -1.90 (0.37), residues: 449
  helix: -0.67 (0.34), residues: 209
  sheet: -1.70 (1.55), residues: 12
  loop : -1.79 (0.40), residues: 228

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.006   0.001   ARG B 416 
 TYR   0.006   0.001   TYR B 296 
 PHE   0.044   0.003   PHE B  39 
 TRP   0.013   0.002   TRP B 330 
 HIS   0.005   0.002   HIS B 135 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00351 /  0.17 ( 3880)
  covalent geometry    : angle       0.75455 /  0.40 ( 5263)
  hydrogen bonds       : bond        0.05310 /  3.74 (  161)
  hydrogen bonds       : angle       5.62371 /  3.92 (  462)

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

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

  898 Ramachandran restraints generated.
    449 Oldfield, 0 Emsley, 449 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  898 Ramachandran restraints generated.
    449 Oldfield, 0 Emsley, 449 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  71 residues out of total 383 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 70
  time to evaluate  : 0.132 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: B  105 MET cc_start: 0.5448 (ptm) cc_final: 0.4834 (pmm)
REVERT: B  167 MET cc_start: 0.2429 (mmp) cc_final: 0.2033 (mmp)
REVERT: B  184 LYS cc_start: 0.7968 (tttp) cc_final: 0.7651 (tttp)
REVERT: B  192 GLU cc_start: 0.7666 (tm-30) cc_final: 0.7045 (tm-30)
REVERT: B  196 MET cc_start: 0.8352 (mtp) cc_final: 0.7882 (mtp)
REVERT: B  230 PHE cc_start: 0.6132 (p90) cc_final: 0.5494 (p90)
REVERT: B  239 MET cc_start: 0.7561 (tpp) cc_final: 0.6758 (tmm)
REVERT: B  240 ASP cc_start: 0.7872 (m-30) cc_final: 0.7613 (m-30)
REVERT: B  341 LEU cc_start: 0.1800 (mp) cc_final: 0.1332 (tt)
REVERT: B  486 SER cc_start: 0.7266 (m) cc_final: 0.6290 (m)
  outliers start: 1
  outliers final: 0
  residues processed: 71
  average time/residue: 0.1096
  time to fit residues: 9.0744
Evaluate side-chains
  67 residues out of total 383 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 67
  time to evaluate  : 0.130 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 46
   random chunks:
   chunk 45 optimal weight:    7.9990
   chunk 19 optimal weight:    0.9990
   chunk 40 optimal weight:    0.9990
   chunk 27 optimal weight:    0.9990
   chunk 36 optimal weight:    2.9990
   chunk 16 optimal weight:    1.9990
   chunk 0 optimal weight:    0.5980
   chunk 18 optimal weight:    0.2980
   chunk 14 optimal weight:    0.9980
   chunk 29 optimal weight:    2.9990
   chunk 10 optimal weight:    0.7980
   overall best weight:    0.7382

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
B  76 ASN
B 125 ASN
B 327 GLN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.5053 r_free = 0.5053 target = 0.279158 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 37)----------------|
| r_work = 0.5005 r_free = 0.5005 target = 0.267892 restraints weight = 15293.059|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 27)----------------|
| r_work = 0.4998 r_free = 0.4998 target = 0.268330 restraints weight = 15583.829|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 27)----------------|
| r_work = 0.5008 r_free = 0.5008 target = 0.269457 restraints weight = 13325.586|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 26)----------------|
| r_work = 0.5013 r_free = 0.5013 target = 0.269949 restraints weight = 10012.702|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 31)----------------|
| r_work = 0.5022 r_free = 0.5022 target = 0.270785 restraints weight = 8880.011|
|-----------------------------------------------------------------------------|
r_work (final): 0.4779
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.3944
moved from start:          0.4858

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.057   3880  Z= 0.186
  Angle     :  0.783  10.862   5263  Z= 0.413
  Chirality :  0.046   0.313    573
  Planarity :  0.006   0.057    649
  Dihedral  : 14.464 168.893    625
  Min Nonbonded Distance : 2.480

Molprobity Statistics.
  All-atom Clashscore : 19.13
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  7.13 %
    Favored  : 92.87 %
  Rotamer:
    Outliers :  0.26 %
    Allowed  :  1.57 %
    Favored  : 98.17 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -1.72 (0.37), residues: 449
  helix: -0.49 (0.34), residues: 206
  sheet: -1.55 (1.57), residues: 12
  loop : -1.73 (0.40), residues: 231

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.009   0.001   ARG B 174 
 TYR   0.012   0.002   TYR B 313 
 PHE   0.038   0.003   PHE B  39 
 TRP   0.013   0.002   TRP B 330 
 HIS   0.006   0.002   HIS B 135 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00389 /  0.19 ( 3880)
  covalent geometry    : angle       0.78320 /  0.41 ( 5263)
  hydrogen bonds       : bond        0.05586 /  3.94 (  161)
  hydrogen bonds       : angle       5.63637 /  3.97 (  462)

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

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

  898 Ramachandran restraints generated.
    449 Oldfield, 0 Emsley, 449 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  898 Ramachandran restraints generated.
    449 Oldfield, 0 Emsley, 449 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  73 residues out of total 383 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 72
  time to evaluate  : 0.130 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: B  167 MET cc_start: 0.1960 (mmp) cc_final: 0.1577 (mmp)
REVERT: B  184 LYS cc_start: 0.7347 (tttp) cc_final: 0.7141 (tttp)
REVERT: B  192 GLU cc_start: 0.7404 (tm-30) cc_final: 0.6743 (tm-30)
REVERT: B  196 MET cc_start: 0.8084 (mtp) cc_final: 0.7590 (mtp)
REVERT: B  221 ARG cc_start: 0.7331 (ptt-90) cc_final: 0.6985 (ptt-90)
REVERT: B  239 MET cc_start: 0.7482 (tpp) cc_final: 0.6768 (tmm)
REVERT: B  240 ASP cc_start: 0.8025 (m-30) cc_final: 0.7679 (m-30)
REVERT: B  341 LEU cc_start: 0.1786 (mp) cc_final: 0.1351 (tt)
REVERT: B  425 ILE cc_start: 0.8142 (mm) cc_final: 0.7917 (mm)
REVERT: B  486 SER cc_start: 0.7091 (m) cc_final: 0.5853 (m)
  outliers start: 1
  outliers final: 0
  residues processed: 73
  average time/residue: 0.1072
  time to fit residues: 9.0755
Evaluate side-chains
  68 residues out of total 383 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 68
  time to evaluate  : 0.127 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 46
   random chunks:
   chunk 1 optimal weight:    2.9990
   chunk 7 optimal weight:    0.0470
   chunk 3 optimal weight:    0.9980
   chunk 16 optimal weight:    2.9990
   chunk 22 optimal weight:    0.0570
   chunk 33 optimal weight:    0.5980
   chunk 38 optimal weight:    0.1980
   chunk 42 optimal weight:    2.9990
   chunk 23 optimal weight:    0.8980
   chunk 6 optimal weight:    4.9990
   chunk 4 optimal weight:    1.9990
   overall best weight:    0.3596

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

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.5065 r_free = 0.5065 target = 0.279566 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 37)----------------|
| r_work = 0.5021 r_free = 0.5021 target = 0.268564 restraints weight = 15542.529|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 24)----------------|
| r_work = 0.5020 r_free = 0.5020 target = 0.269483 restraints weight = 13959.345|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 26)----------------|
| r_work = 0.5021 r_free = 0.5021 target = 0.269973 restraints weight = 12214.209|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 26)----------------|
| r_work = 0.5030 r_free = 0.5030 target = 0.270737 restraints weight = 9573.732|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 27)----------------|
| r_work = 0.5034 r_free = 0.5034 target = 0.271082 restraints weight = 8003.851|
|-----------------------------------------------------------------------------|
r_work (final): 0.4792
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.3887
moved from start:          0.5151

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.052   3880  Z= 0.157
  Angle     :  0.741  10.098   5263  Z= 0.384
  Chirality :  0.044   0.307    573
  Planarity :  0.005   0.042    649
  Dihedral  : 14.226 167.413    625
  Min Nonbonded Distance : 2.472

Molprobity Statistics.
  All-atom Clashscore : 16.72
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  7.35 %
    Favored  : 92.65 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  1.04 %
    Favored  : 98.96 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -1.46 (0.38), residues: 449
  helix: -0.14 (0.35), residues: 206
  sheet: -1.89 (1.44), residues: 12
  loop : -1.70 (0.39), residues: 231

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.007   0.001   ARG B 416 
 TYR   0.008   0.001   TYR B 313 
 PHE   0.032   0.003   PHE B  39 
 TRP   0.010   0.002   TRP B 330 
 HIS   0.007   0.002   HIS B 135 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00337 /  0.16 ( 3880)
  covalent geometry    : angle       0.74128 /  0.38 ( 5263)
  hydrogen bonds       : bond        0.05150 /  3.63 (  161)
  hydrogen bonds       : angle       5.45368 /  3.81 (  462)

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

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

  898 Ramachandran restraints generated.
    449 Oldfield, 0 Emsley, 449 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  898 Ramachandran restraints generated.
    449 Oldfield, 0 Emsley, 449 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  71 residues out of total 383 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 71
  time to evaluate  : 0.134 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: B  105 MET cc_start: 0.4739 (ptm) cc_final: 0.4384 (pmm)
REVERT: B  137 MET cc_start: 0.5443 (ptm) cc_final: 0.4948 (ptm)
REVERT: B  167 MET cc_start: 0.1691 (mmp) cc_final: 0.1345 (mmp)
REVERT: B  192 GLU cc_start: 0.7340 (tm-30) cc_final: 0.6648 (tm-30)
REVERT: B  196 MET cc_start: 0.8041 (mtp) cc_final: 0.7593 (mtp)
REVERT: B  227 LYS cc_start: 0.7487 (ttpt) cc_final: 0.6893 (tttp)
REVERT: B  230 PHE cc_start: 0.5940 (p90) cc_final: 0.5028 (p90)
REVERT: B  239 MET cc_start: 0.7437 (tpp) cc_final: 0.6747 (tmm)
REVERT: B  240 ASP cc_start: 0.8041 (m-30) cc_final: 0.7547 (m-30)
REVERT: B  341 LEU cc_start: 0.1612 (mp) cc_final: 0.1280 (tt)
REVERT: B  425 ILE cc_start: 0.8145 (mm) cc_final: 0.7892 (mm)
REVERT: B  486 SER cc_start: 0.6843 (m) cc_final: 0.5723 (m)
  outliers start: 0
  outliers final: 0
  residues processed: 71
  average time/residue: 0.0806
  time to fit residues: 6.7839
Evaluate side-chains
  68 residues out of total 383 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 68
  time to evaluate  : 0.077 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 46
   random chunks:
   chunk 16 optimal weight:    0.7980
   chunk 35 optimal weight:    1.9990
   chunk 19 optimal weight:    1.9990
   chunk 14 optimal weight:    0.7980
   chunk 5 optimal weight:    0.5980
   chunk 36 optimal weight:    2.9990
   chunk 45 optimal weight:    6.9990
   chunk 34 optimal weight:    0.5980
   chunk 9 optimal weight:    0.3980
   chunk 10 optimal weight:    0.8980
   chunk 29 optimal weight:    0.8980
   overall best weight:    0.6380

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
B 415 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4841 r_free = 0.4841 target = 0.233968 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 60)----------------|
| r_work = 0.4557 r_free = 0.4557 target = 0.205297 restraints weight = 12380.199|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 42)----------------|
| r_work = 0.4572 r_free = 0.4572 target = 0.206655 restraints weight = 11388.111|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 18)----------------|
| r_work = 0.4574 r_free = 0.4574 target = 0.206920 restraints weight = 10889.492|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 17)----------------|
| r_work = 0.4574 r_free = 0.4574 target = 0.206924 restraints weight = 10357.735|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 22)----------------|
| r_work = 0.4574 r_free = 0.4574 target = 0.206924 restraints weight = 10360.416|
|-----------------------------------------------------------------------------|
r_work (final): 0.4537
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.4409
moved from start:          0.5330

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.053   3880  Z= 0.175
  Angle     :  0.758   9.599   5263  Z= 0.399
  Chirality :  0.045   0.317    573
  Planarity :  0.005   0.047    649
  Dihedral  : 14.143 168.032    625
  Min Nonbonded Distance : 2.433

Molprobity Statistics.
  All-atom Clashscore : 18.06
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  7.57 %
    Favored  : 92.43 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  0.26 %
    Favored  : 99.74 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -1.36 (0.38), residues: 449
  helix: -0.07 (0.35), residues: 207
  sheet: -2.06 (1.41), residues: 12
  loop : -1.63 (0.40), residues: 230

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.013   0.001   ARG B 174 
 TYR   0.009   0.002   TYR B 313 
 PHE   0.033   0.003   PHE B  39 
 TRP   0.009   0.002   TRP B 330 
 HIS   0.005   0.002   HIS B 135 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00370 /  0.17 ( 3880)
  covalent geometry    : angle       0.75822 /  0.40 ( 5263)
  hydrogen bonds       : bond        0.05264 /  3.74 (  161)
  hydrogen bonds       : angle       5.44247 /  3.80 (  462)

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

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

  898 Ramachandran restraints generated.
    449 Oldfield, 0 Emsley, 449 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  898 Ramachandran restraints generated.
    449 Oldfield, 0 Emsley, 449 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  71 residues out of total 383 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 71
  time to evaluate  : 0.132 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: B  105 MET cc_start: 0.5470 (ptm) cc_final: 0.4772 (pmm)
REVERT: B  167 MET cc_start: 0.2228 (mmp) cc_final: 0.1785 (mmp)
REVERT: B  184 LYS cc_start: 0.7567 (tttp) cc_final: 0.7246 (tttp)
REVERT: B  192 GLU cc_start: 0.7606 (tm-30) cc_final: 0.6982 (tm-30)
REVERT: B  196 MET cc_start: 0.8381 (mtp) cc_final: 0.7855 (mtp)
REVERT: B  227 LYS cc_start: 0.7589 (ttpt) cc_final: 0.6966 (tttm)
REVERT: B  230 PHE cc_start: 0.6434 (p90) cc_final: 0.5480 (p90)
REVERT: B  239 MET cc_start: 0.7628 (tpp) cc_final: 0.6785 (tmm)
REVERT: B  240 ASP cc_start: 0.7908 (m-30) cc_final: 0.7638 (m-30)
REVERT: B  341 LEU cc_start: 0.1992 (mp) cc_final: 0.1685 (tt)
REVERT: B  425 ILE cc_start: 0.8176 (mm) cc_final: 0.7970 (mm)
REVERT: B  446 ARG cc_start: 0.7072 (ttp80) cc_final: 0.6747 (ttp80)
REVERT: B  486 SER cc_start: 0.6997 (m) cc_final: 0.6146 (m)
  outliers start: 0
  outliers final: 0
  residues processed: 71
  average time/residue: 0.1018
  time to fit residues: 8.4755
Evaluate side-chains
  69 residues out of total 383 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 69
  time to evaluate  : 0.130 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 46
   random chunks:
   chunk 12 optimal weight:    0.0770
   chunk 40 optimal weight:    0.4980
   chunk 8 optimal weight:    0.8980
   chunk 41 optimal weight:    0.9990
   chunk 28 optimal weight:    7.9990
   chunk 26 optimal weight:    1.9990
   chunk 13 optimal weight:   10.0000
   chunk 2 optimal weight:    0.6980
   chunk 29 optimal weight:    0.0670
   chunk 21 optimal weight:    0.8980
   chunk 42 optimal weight:    4.9990
   overall best weight:    0.4476

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
B 415 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.5053 r_free = 0.5053 target = 0.278730 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 41)----------------|
| r_work = 0.5012 r_free = 0.5012 target = 0.267605 restraints weight = 15206.206|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 24)----------------|
| r_work = 0.4998 r_free = 0.4998 target = 0.267539 restraints weight = 17118.921|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 27)----------------|
| r_work = 0.5010 r_free = 0.5010 target = 0.268950 restraints weight = 14003.238|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 26)----------------|
| r_work = 0.5013 r_free = 0.5013 target = 0.269193 restraints weight = 10501.851|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 26)----------------|
| r_work = 0.5019 r_free = 0.5019 target = 0.269838 restraints weight = 9390.310|
|-----------------------------------------------------------------------------|
r_work (final): 0.4782
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.3943
moved from start:          0.5594

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.047   3880  Z= 0.147
  Angle     :  0.714   8.143   5263  Z= 0.378
  Chirality :  0.045   0.323    573
  Planarity :  0.005   0.043    649
  Dihedral  : 13.969 167.307    625
  Min Nonbonded Distance : 2.429

Molprobity Statistics.
  All-atom Clashscore : 15.65
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  7.13 %
    Favored  : 92.87 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  0.26 %
    Favored  : 99.74 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -1.23 (0.39), residues: 449
  helix:  0.06 (0.35), residues: 208
  sheet: -1.87 (1.58), residues: 12
  loop : -1.61 (0.40), residues: 229

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.007   0.001   ARG B 416 
 TYR   0.010   0.002   TYR B 313 
 PHE   0.030   0.003   PHE B  39 
 TRP   0.010   0.002   TRP B 120 
 HIS   0.005   0.002   HIS B 135 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00310 /  0.15 ( 3880)
  covalent geometry    : angle       0.71439 /  0.38 ( 5263)
  hydrogen bonds       : bond        0.04910 /  3.47 (  161)
  hydrogen bonds       : angle       5.35916 /  3.73 (  462)

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

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

  898 Ramachandran restraints generated.
    449 Oldfield, 0 Emsley, 449 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  898 Ramachandran restraints generated.
    449 Oldfield, 0 Emsley, 449 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  68 residues out of total 383 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 68
  time to evaluate  : 0.131 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: B  105 MET cc_start: 0.4783 (ptm) cc_final: 0.4329 (pmm)
REVERT: B  167 MET cc_start: 0.1647 (mmp) cc_final: 0.1167 (mmp)
REVERT: B  184 LYS cc_start: 0.6980 (tttp) cc_final: 0.6644 (tttp)
REVERT: B  192 GLU cc_start: 0.7307 (tm-30) cc_final: 0.6635 (tm-30)
REVERT: B  196 MET cc_start: 0.8015 (mtp) cc_final: 0.7600 (mtp)
REVERT: B  227 LYS cc_start: 0.7628 (ttpt) cc_final: 0.6594 (ptmm)
REVERT: B  230 PHE cc_start: 0.6010 (p90) cc_final: 0.5227 (p90)
REVERT: B  239 MET cc_start: 0.7506 (tpp) cc_final: 0.6853 (tmm)
REVERT: B  240 ASP cc_start: 0.7974 (m-30) cc_final: 0.7590 (m-30)
REVERT: B  425 ILE cc_start: 0.8118 (mm) cc_final: 0.7876 (mm)
REVERT: B  447 MET cc_start: 0.7599 (ppp) cc_final: 0.7365 (ppp)
REVERT: B  486 SER cc_start: 0.6921 (m) cc_final: 0.5646 (m)
  outliers start: 0
  outliers final: 0
  residues processed: 68
  average time/residue: 0.1052
  time to fit residues: 8.3298
Evaluate side-chains
  65 residues out of total 383 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 65
  time to evaluate  : 0.164 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 46
   random chunks:
   chunk 2 optimal weight:    0.5980
   chunk 13 optimal weight:    1.9990
   chunk 40 optimal weight:    0.0670
   chunk 41 optimal weight:    0.9990
   chunk 17 optimal weight:    1.9990
   chunk 20 optimal weight:    0.7980
   chunk 19 optimal weight:    0.2980
   chunk 14 optimal weight:    0.0980
   chunk 45 optimal weight:    6.9990
   chunk 44 optimal weight:    0.9990
   chunk 26 optimal weight:    0.8980
   overall best weight:    0.3718

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
B 168 GLN
B 415 GLN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.5050 r_free = 0.5050 target = 0.278813 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 35)----------------|
| r_work = 0.5007 r_free = 0.5007 target = 0.267712 restraints weight = 15317.746|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 26)----------------|
| r_work = 0.4994 r_free = 0.4994 target = 0.267518 restraints weight = 16621.272|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 24)----------------|
| r_work = 0.5006 r_free = 0.5006 target = 0.268928 restraints weight = 13943.999|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 26)----------------|
| r_work = 0.5006 r_free = 0.5006 target = 0.268906 restraints weight = 11216.247|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 26)----------------|
| r_work = 0.5015 r_free = 0.5015 target = 0.269749 restraints weight = 9738.040|
|-----------------------------------------------------------------------------|
r_work (final): 0.4773
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.3949
moved from start:          0.5761

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.048   3880  Z= 0.145
  Angle     :  0.720   8.350   5263  Z= 0.377
  Chirality :  0.045   0.319    573
  Planarity :  0.005   0.055    649
  Dihedral  : 13.933 166.959    625
  Min Nonbonded Distance : 2.389

Molprobity Statistics.
  All-atom Clashscore : 16.19
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  8.02 %
    Favored  : 91.98 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  0.52 %
    Favored  : 99.48 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -1.14 (0.39), residues: 449
  helix:  0.16 (0.36), residues: 208
  sheet: -1.77 (1.63), residues: 12
  loop : -1.57 (0.41), residues: 229

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.006   0.001   ARG B 261 
 TYR   0.008   0.001   TYR B 313 
 PHE   0.028   0.002   PHE B  39 
 TRP   0.011   0.002   TRP B 120 
 HIS   0.006   0.002   HIS B 135 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00311 /  0.15 ( 3880)
  covalent geometry    : angle       0.71986 /  0.38 ( 5263)
  hydrogen bonds       : bond        0.04777 /  3.39 (  161)
  hydrogen bonds       : angle       5.29317 /  3.67 (  462)

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

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

  898 Ramachandran restraints generated.
    449 Oldfield, 0 Emsley, 449 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  898 Ramachandran restraints generated.
    449 Oldfield, 0 Emsley, 449 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  67 residues out of total 383 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 67
  time to evaluate  : 0.135 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: B  105 MET cc_start: 0.4720 (ptm) cc_final: 0.4292 (pmm)
REVERT: B  167 MET cc_start: 0.1560 (mmp) cc_final: 0.1032 (mmp)
REVERT: B  184 LYS cc_start: 0.6991 (tttp) cc_final: 0.6643 (tttp)
REVERT: B  192 GLU cc_start: 0.7323 (tm-30) cc_final: 0.6647 (tm-30)
REVERT: B  196 MET cc_start: 0.8026 (mtp) cc_final: 0.7641 (mtp)
REVERT: B  227 LYS cc_start: 0.7666 (ttpt) cc_final: 0.7404 (ptmm)
REVERT: B  230 PHE cc_start: 0.5968 (p90) cc_final: 0.5725 (p90)
REVERT: B  239 MET cc_start: 0.7570 (tpp) cc_final: 0.6947 (tmm)
REVERT: B  240 ASP cc_start: 0.7992 (m-30) cc_final: 0.7594 (m-30)
REVERT: B  425 ILE cc_start: 0.8117 (mm) cc_final: 0.7857 (mm)
REVERT: B  446 ARG cc_start: 0.6688 (ttp80) cc_final: 0.6413 (ttp80)
REVERT: B  486 SER cc_start: 0.6717 (m) cc_final: 0.6062 (m)
  outliers start: 0
  outliers final: 0
  residues processed: 67
  average time/residue: 0.1057
  time to fit residues: 8.3221
Evaluate side-chains
  63 residues out of total 383 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 63
  time to evaluate  : 0.131 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 46
   random chunks:
   chunk 44 optimal weight:    0.9980
   chunk 27 optimal weight:    0.9980
   chunk 26 optimal weight:    5.9990
   chunk 35 optimal weight:    0.5980
   chunk 13 optimal weight:    1.9990
   chunk 22 optimal weight:    1.9990
   chunk 2 optimal weight:    0.7980
   chunk 4 optimal weight:    0.9980
   chunk 24 optimal weight:    0.9990
   chunk 6 optimal weight:    0.0470
   chunk 28 optimal weight:    0.1980
   overall best weight:    0.5278

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
B 124 ASN
** B 168 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
B 415 GLN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4832 r_free = 0.4832 target = 0.233921 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 47)----------------|
| r_work = 0.4532 r_free = 0.4532 target = 0.203202 restraints weight = 12438.472|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 31)----------------|
| r_work = 0.4540 r_free = 0.4540 target = 0.203956 restraints weight = 11929.793|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 21)----------------|
| r_work = 0.4540 r_free = 0.4540 target = 0.203956 restraints weight = 11419.878|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 29)----------------|
| r_work = 0.4544 r_free = 0.4544 target = 0.204361 restraints weight = 11419.793|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 26)----------------|
| r_work = 0.4551 r_free = 0.4551 target = 0.204994 restraints weight = 11037.001|
|-----------------------------------------------------------------------------|
r_work (final): 0.4515
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.4462
moved from start:          0.5882

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.048   3880  Z= 0.153
  Angle     :  0.714   8.171   5263  Z= 0.380
  Chirality :  0.044   0.317    573
  Planarity :  0.006   0.082    649
  Dihedral  : 13.885 166.901    625
  Min Nonbonded Distance : 2.396

Molprobity Statistics.
  All-atom Clashscore : 16.46
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  7.57 %
    Favored  : 92.43 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  0.26 %
    Favored  : 99.74 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -1.12 (0.39), residues: 449
  helix:  0.18 (0.36), residues: 208
  sheet: -1.64 (1.67), residues: 12
  loop : -1.59 (0.41), residues: 229

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.006   0.001   ARG B 221 
 TYR   0.008   0.001   TYR B  97 
 PHE   0.028   0.002   PHE B  39 
 TRP   0.010   0.002   TRP B 120 
 HIS   0.009   0.002   HIS B 135 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00329 /  0.15 ( 3880)
  covalent geometry    : angle       0.71368 /  0.38 ( 5263)
  hydrogen bonds       : bond        0.04871 /  3.47 (  161)
  hydrogen bonds       : angle       5.22162 /  3.63 (  462)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 989.99 seconds
wall clock time: 17 minutes 45.88 seconds (1065.88 seconds total)