Starting phenix.real_space_refine
on Wed Jul  1 23:06:53 2026 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/9v47_64769/07_2026/9v47_64769.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/9v47_64769/07_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_64769/07_2026/9v47_64769.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/9v47_64769/07_2026/9v47_64769.cif"
    real_map_files = "/net/cci-nas-00/data/ceres_data/9v47_64769/07_2026/9v47_64769.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/9v47_64769/07_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-dev-6108/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: 1.00, per 1000 atoms: 0.26
  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: 0.33
  Conformation dependent library (CDL) restraints added in 144.7 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: 0.43
  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: 0.54

  Time building geometry restraints manager: 0.44 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: 4384
        1.59 -     3.18: 710
        3.18 -     4.77: 124
        4.77 -     6.36: 32
        6.36 -     7.95: 13
  Bond angle restraints: 5263
  Sorted by residual:
  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
  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 1.50e+00 4.44e-01 2.54e+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: 428
       0.079 -    0.159: 113
       0.159 -    0.238: 29
       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:             4.780
  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:          0.080
  Check model and map are aligned:         0.010
  Set scattering table:                    0.010
  Process input model:                     5.680
  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:1.270
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   11.870
-------------------------------------------------------------------------------
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= 0.598
  Angle     :  1.288   7.953   5263  Z= 0.901
  Chirality :  0.077   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       1.28844 /  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  : 0.127 
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: -0.0431 (tptm)
REVERT: B  105 MET cc_start: 0.5875 (ptm) cc_final: 0.5229 (pmm)
REVERT: B  106 ARG cc_start: 0.5377 (OUTLIER) cc_final: 0.5062 (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: 0.6775 (tm-30)
REVERT: B  196 MET cc_start: 0.8004 (mtp) cc_final: 0.7543 (mtp)
REVERT: B  205 ASN cc_start: 0.7717 (OUTLIER) cc_final: 0.7453 (p0)
REVERT: B  227 LYS cc_start: 0.7384 (OUTLIER) cc_final: 0.6688 (ttpp)
REVERT: B  230 PHE cc_start: 0.6037 (p90) cc_final: 0.5489 (p90)
REVERT: B  239 MET cc_start: 0.7301 (tpp) cc_final: 0.7012 (tmm)
REVERT: B  240 ASP cc_start: 0.7893 (m-30) cc_final: 0.7024 (m-30)
REVERT: B  258 PHE cc_start: 0.7499 (OUTLIER) cc_final: 0.5094 (t80)
REVERT: B  311 GLN cc_start: 0.3471 (OUTLIER) cc_final: 0.3102 (tp40)
REVERT: B  316 ILE cc_start: -0.6506 (OUTLIER) cc_final: -0.6716 (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: 0.1179
  time to fit residues: 16.4970
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  : 0.127 
-------------------------------------------------------------------------------
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 = 0.5055 r_free = 0.5055 target = 0.281314 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 34)----------------|
| r_work = 0.5017 r_free = 0.5017 target = 0.270941 restraints weight = 15471.448|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 26)----------------|
| r_work = 0.5003 r_free = 0.5003 target = 0.270585 restraints weight = 16130.916|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 26)----------------|
| r_work = 0.5009 r_free = 0.5009 target = 0.271324 restraints weight = 13916.554|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 28)----------------|
| r_work = 0.5010 r_free = 0.5010 target = 0.271528 restraints weight = 11851.912|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 23)----------------|
| r_work = 0.5017 r_free = 0.5017 target = 0.272278 restraints weight = 10585.434|
|-----------------------------------------------------------------------------|
r_work (final): 0.4788
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.4783
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.4783 r_free = 0.4783    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 = 0.4778 r_free = 0.4778    target_work(ls_wunit_k1) = 0.230         |
| occupancies: max = 1.00  min = 1.00   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|

Number of minimizer iterations: 4 (9 function evaluations)
r_final: 0.4778
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.3817
moved from start:          0.3203

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.059   3880  Z= 0.219
  Angle     :  0.857   7.537   5263  Z= 0.466
  Chirality :  0.048   0.168    573
  Planarity :  0.009   0.084    649
  Dihedral  : 14.854 164.385    625
  Min Nonbonded Distance : 2.505

Molprobity Statistics.
  All-atom Clashscore : 23.68
  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: -3.33 (0.33), residues: 449
  helix: -1.77 (0.31), residues: 208
  sheet: -1.59 (1.44), residues: 12
  loop : -2.71 (0.35), 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   0.038   0.004   PHE B 258 
 TRP   0.013   0.003   TRP B 207 
 HIS   0.006   0.002   HIS B 140 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00459 /  0.22 ( 3880)
  covalent geometry    : angle       0.85687 /  0.47 ( 5263)
  hydrogen bonds       : bond        0.06227 /  4.41 (  161)
  hydrogen bonds       : angle       6.35918 /  4.48 (  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: B   34 ASN cc_start: 0.7086 (t0) cc_final: 0.6559 (t0)
REVERT: B   66 MET cc_start: 0.7355 (mtt) cc_final: 0.7097 (mtt)
REVERT: B  105 MET cc_start: 0.5294 (ptm) cc_final: 0.4801 (pmm)
REVERT: B  136 MET cc_start: 0.7116 (mtp) cc_final: 0.6775 (mtp)
REVERT: B  192 GLU cc_start: 0.7516 (tm-30) cc_final: 0.6802 (tm-30)
REVERT: B  196 MET cc_start: 0.8085 (mtp) cc_final: 0.7625 (mtp)
REVERT: B  227 LYS cc_start: 0.7201 (ttpt) cc_final: 0.6819 (ttpp)
REVERT: B  230 PHE cc_start: 0.5634 (p90) cc_final: 0.5172 (p90)
REVERT: B  239 MET cc_start: 0.7570 (tpp) cc_final: 0.6756 (tmm)
REVERT: B  240 ASP cc_start: 0.7941 (m-30) cc_final: 0.7564 (m-30)
REVERT: B  416 ARG cc_start: 0.7555 (mpt90) cc_final: 0.7354 (mpt90)
REVERT: B  440 MET cc_start: 0.6913 (mpp) cc_final: 0.6607 (mpp)
  outliers start: 4
  outliers final: 0
  residues processed: 81
  average time/residue: 0.1059
  time to fit residues: 10.0004
Evaluate side-chains
  72 residues out of total 383 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 72
  time to evaluate  : 0.131 
-------------------------------------------------------------------------------
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:    0.9990
   chunk 19 optimal weight:    0.5980
   chunk 5 optimal weight:    0.5980
   chunk 23 optimal weight:    2.9990
   chunk 9 optimal weight:    0.8980
   chunk 28 optimal weight:    0.9980
   chunk 1 optimal weight:    0.5980
   chunk 24 optimal weight:    0.9990
   chunk 3 optimal weight:    0.5980
   chunk 40 optimal weight:    5.9990
   overall best weight:    0.6580

-------------------------------------------------------------------------------
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 = 0.5054 r_free = 0.5054 target = 0.280168 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 40)----------------|
| r_work = 0.5019 r_free = 0.5019 target = 0.269469 restraints weight = 15354.760|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 29)----------------|
| r_work = 0.5000 r_free = 0.5000 target = 0.268749 restraints weight = 15798.879|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 28)----------------|
| r_work = 0.5006 r_free = 0.5006 target = 0.269418 restraints weight = 14167.325|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 28)----------------|
| r_work = 0.5010 r_free = 0.5010 target = 0.269978 restraints weight = 11690.338|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 28)----------------|
| r_work = 0.5013 r_free = 0.5013 target = 0.270229 restraints weight = 10593.592|
|-----------------------------------------------------------------------------|
r_work (final): 0.4765
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.3896
moved from start:          0.3937

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.085   3880  Z= 0.211
  Angle     :  0.826  14.164   5263  Z= 0.438
  Chirality :  0.045   0.163    573
  Planarity :  0.006   0.054    649
  Dihedral  : 14.764 165.826    625
  Min Nonbonded Distance : 2.469

Molprobity Statistics.
  All-atom Clashscore : 24.22
  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: -2.80 (0.35), residues: 449
  helix: -1.49 (0.32), residues: 210
  sheet: -1.01 (1.56), residues: 12
  loop : -2.27 (0.37), residues: 227

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.009   0.001   ARG B 117 
 TYR   0.016   0.002   TYR B  40 
 PHE   0.027   0.003   PHE B 338 
 TRP   0.021   0.003   TRP B 120 
 HIS   0.005   0.001   HIS B 140 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00453 /  0.21 ( 3880)
  covalent geometry    : angle       0.82563 /  0.44 ( 5263)
  hydrogen bonds       : bond        0.05760 /  4.06 (  161)
  hydrogen bonds       : angle       6.19339 /  4.33 (  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
  74 residues out of total 383 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 2
    poor density    : 72
  time to evaluate  : 0.127 
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   34 ASN cc_start: 0.7284 (t0) cc_final: 0.6717 (t0)
REVERT: B   66 MET cc_start: 0.7530 (mtt) cc_final: 0.7259 (mtt)
REVERT: B  105 MET cc_start: 0.5447 (ptm) cc_final: 0.4832 (pmm)
REVERT: B  136 MET cc_start: 0.7123 (mtp) cc_final: 0.6674 (mtp)
REVERT: B  137 MET cc_start: 0.5452 (ptm) cc_final: 0.4863 (ptm)
REVERT: B  167 MET cc_start: 0.1999 (mmp) cc_final: 0.1691 (mmp)
REVERT: B  192 GLU cc_start: 0.7487 (tm-30) cc_final: 0.6784 (tm-30)
REVERT: B  196 MET cc_start: 0.8087 (mtp) cc_final: 0.7611 (mtp)
REVERT: B  230 PHE cc_start: 0.6016 (p90) cc_final: 0.5415 (p90)
REVERT: B  239 MET cc_start: 0.7591 (tpp) cc_final: 0.6679 (tmm)
REVERT: B  240 ASP cc_start: 0.7929 (m-30) cc_final: 0.7526 (m-30)
  outliers start: 2
  outliers final: 1
  residues processed: 74
  average time/residue: 0.1032
  time to fit residues: 8.9375
Evaluate side-chains
  69 residues out of total 383 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 68
  time to evaluate  : 0.081 
-------------------------------------------------------------------------------
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:    0.7980
   chunk 10 optimal weight:    0.0970
   chunk 37 optimal weight:    0.9980
   chunk 4 optimal weight:    0.1980
   chunk 43 optimal weight:    0.0870
   chunk 15 optimal weight:    3.9990
   chunk 45 optimal weight:    5.9990
   chunk 29 optimal weight:    0.3980
   chunk 2 optimal weight:    0.6980
   chunk 7 optimal weight:    0.5980
   overall best weight:    0.2756

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
B  76 ASN
B 168 GLN
** B 241 GLN ** 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 = 0.5079 r_free = 0.5079 target = 0.281646 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 28)----------------|
| r_work = 0.5019 r_free = 0.5019 target = 0.270344 restraints weight = 15328.135|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 24)----------------|
| r_work = 0.5022 r_free = 0.5022 target = 0.271117 restraints weight = 16856.649|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 26)----------------|
| r_work = 0.5028 r_free = 0.5028 target = 0.271464 restraints weight = 15638.969|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 23)----------------|
| r_work = 0.5033 r_free = 0.5033 target = 0.271861 restraints weight = 12520.057|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 26)----------------|
| r_work = 0.5035 r_free = 0.5035 target = 0.272096 restraints weight = 11299.429|
|-----------------------------------------------------------------------------|
r_work (final): 0.4791
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.3864
moved from start:          0.4320

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.053   3880  Z= 0.162
  Angle     :  0.742  11.723   5263  Z= 0.394
  Chirality :  0.042   0.165    573
  Planarity :  0.006   0.057    649
  Dihedral  : 14.590 166.576    625
  Min Nonbonded Distance : 2.489

Molprobity Statistics.
  All-atom Clashscore : 19.53
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.46 %
    Favored  : 93.54 %
  Rotamer:
    Outliers :  0.26 %
    Allowed  :  4.44 %
    Favored  : 95.30 %
  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: -2.14 (0.37), residues: 449
  helix: -0.91 (0.34), residues: 210
  sheet: -0.74 (1.51), residues: 12
  loop : -1.96 (0.40), residues: 227

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.010   0.001   ARG B 174 
 TYR   0.011   0.002   TYR B  40 
 PHE   0.039   0.003   PHE B  39 
 TRP   0.014   0.002   TRP B 330 
 HIS   0.012   0.003   HIS B 135 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00342 /  0.16 ( 3880)
  covalent geometry    : angle       0.74209 /  0.39 ( 5263)
  hydrogen bonds       : bond        0.05400 /  3.79 (  161)
  hydrogen bonds       : angle       5.79197 /  4.04 (  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
  71 residues out of total 383 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 70
  time to evaluate  : 0.142 
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: 0.5282 (ptm) cc_final: 0.4907 (pmm)
REVERT: B  137 MET cc_start: 0.5317 (ptm) cc_final: 0.5091 (ptm)
REVERT: B  167 MET cc_start: 0.1895 (mmp) cc_final: 0.1501 (mmp)
REVERT: B  175 ARG cc_start: 0.5760 (ptm160) cc_final: 0.5500 (ptm160)
REVERT: B  184 LYS cc_start: 0.7314 (tttp) cc_final: 0.7074 (tttp)
REVERT: B  192 GLU cc_start: 0.7424 (tm-30) cc_final: 0.6755 (tm-30)
REVERT: B  196 MET cc_start: 0.8122 (mtp) cc_final: 0.7647 (mtp)
REVERT: B  221 ARG cc_start: 0.7597 (ptt-90) cc_final: 0.7295 (ptt-90)
REVERT: B  230 PHE cc_start: 0.5917 (p90) cc_final: 0.5267 (p90)
REVERT: B  239 MET cc_start: 0.7569 (tpp) cc_final: 0.6736 (tmm)
REVERT: B  240 ASP cc_start: 0.7982 (m-30) cc_final: 0.7617 (m-30)
REVERT: B  425 ILE cc_start: 0.8132 (mm) cc_final: 0.7893 (mm)
REVERT: B  486 SER cc_start: 0.7018 (m) cc_final: 0.6559 (m)
  outliers start: 1
  outliers final: 0
  residues processed: 71
  average time/residue: 0.1089
  time to fit residues: 8.9901
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  : 0.132 
-------------------------------------------------------------------------------
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:    0.6980
   chunk 27 optimal weight:    0.8980
   chunk 7 optimal weight:    0.2980
   chunk 6 optimal weight:    5.9990
   chunk 19 optimal weight:    0.9990
   chunk 28 optimal weight:    0.1980
   chunk 16 optimal weight:    0.9980
   chunk 10 optimal weight:    0.1980
   chunk 25 optimal weight:    0.5980
   chunk 38 optimal weight:    0.0980
   chunk 8 optimal weight:    2.9990
   overall best weight:    0.2780

-------------------------------------------------------------------------------
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 = 0.4860 r_free = 0.4860 target = 0.236634 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 51)----------------|
| r_work = 0.4550 r_free = 0.4550 target = 0.205126 restraints weight = 11645.063|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 31)----------------|
| r_work = 0.4567 r_free = 0.4567 target = 0.206697 restraints weight = 10586.913|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 22)----------------|
| r_work = 0.4576 r_free = 0.4576 target = 0.207616 restraints weight = 9712.941|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 48)----------------|
| r_work = 0.4598 r_free = 0.4598 target = 0.209662 restraints weight = 9111.822|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 24)----------------|
| r_work = 0.4604 r_free = 0.4604 target = 0.210221 restraints weight = 8557.979|
|-----------------------------------------------------------------------------|
r_work (final): 0.4572
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.4230
moved from start:          0.4655

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.063   3880  Z= 0.162
  Angle     :  0.722  10.661   5263  Z= 0.384
  Chirality :  0.042   0.175    573
  Planarity :  0.005   0.040    649
  Dihedral  : 14.550 166.386    625
  Min Nonbonded Distance : 2.473

Molprobity Statistics.
  All-atom Clashscore : 18.46
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.46 %
    Favored  : 93.54 %
  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: -1.79 (0.37), residues: 449
  helix: -0.55 (0.34), residues: 209
  sheet: -1.14 (1.39), residues: 12
  loop : -1.80 (0.40), residues: 228

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.006   0.001   ARG B 261 
 TYR   0.006   0.001   TYR B 281 
 PHE   0.039   0.003   PHE B  39 
 TRP   0.012   0.002   TRP B 330 
 HIS   0.006   0.002   HIS B 135 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00350 /  0.16 ( 3880)
  covalent geometry    : angle       0.72238 /  0.38 ( 5263)
  hydrogen bonds       : bond        0.05103 /  3.57 (  161)
  hydrogen bonds       : angle       5.55176 /  3.87 (  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
  70 residues out of total 383 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 69
  time to evaluate  : 0.137 
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: 0.5449 (ptm) cc_final: 0.4940 (pmm)
REVERT: B  167 MET cc_start: 0.2155 (mmp) cc_final: 0.1859 (mmp)
REVERT: B  184 LYS cc_start: 0.7954 (tttp) cc_final: 0.7647 (tttp)
REVERT: B  192 GLU cc_start: 0.7685 (tm-30) cc_final: 0.7042 (tm-30)
REVERT: B  196 MET cc_start: 0.8350 (mtp) cc_final: 0.7880 (mtp)
REVERT: B  221 ARG cc_start: 0.7676 (ptt-90) cc_final: 0.7472 (ptt-90)
REVERT: B  230 PHE cc_start: 0.6214 (p90) cc_final: 0.5625 (p90)
REVERT: B  239 MET cc_start: 0.7581 (tpp) cc_final: 0.6757 (tmm)
REVERT: B  240 ASP cc_start: 0.7873 (m-30) cc_final: 0.7604 (m-30)
  outliers start: 1
  outliers final: 0
  residues processed: 70
  average time/residue: 0.1106
  time to fit residues: 8.9880
Evaluate side-chains
  66 residues out of total 383 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 66
  time to evaluate  : 0.129 
-------------------------------------------------------------------------------
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:    4.9990
   chunk 19 optimal weight:    0.9990
   chunk 40 optimal weight:    0.9990
   chunk 27 optimal weight:    2.9990
   chunk 36 optimal weight:    2.9990
   chunk 16 optimal weight:    1.9990
   chunk 0 optimal weight:    0.5980
   chunk 18 optimal weight:    1.9990
   chunk 14 optimal weight:    0.8980
   chunk 29 optimal weight:    0.0060
   chunk 10 optimal weight:    0.0670
   overall best weight:    0.5136

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
B  76 ASN
B 327 GLN
B 415 GLN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.5069 r_free = 0.5069 target = 0.280620 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 33)----------------|
| r_work = 0.5009 r_free = 0.5009 target = 0.269624 restraints weight = 15365.263|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 24)----------------|
| r_work = 0.5010 r_free = 0.5010 target = 0.270051 restraints weight = 16077.640|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 27)----------------|
| r_work = 0.5020 r_free = 0.5020 target = 0.271033 restraints weight = 13048.687|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 26)----------------|
| r_work = 0.5025 r_free = 0.5025 target = 0.271362 restraints weight = 9682.570|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 26)----------------|
| r_work = 0.5037 r_free = 0.5037 target = 0.272174 restraints weight = 8622.193|
|-----------------------------------------------------------------------------|
r_work (final): 0.4797
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.3874
moved from start:          0.4869

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.056   3880  Z= 0.170
  Angle     :  0.749  10.404   5263  Z= 0.399
  Chirality :  0.043   0.160    573
  Planarity :  0.005   0.041    649
  Dihedral  : 14.460 165.600    625
  Min Nonbonded Distance : 2.488

Molprobity Statistics.
  All-atom Clashscore : 18.33
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.46 %
    Favored  : 93.54 %
  Rotamer:
    Outliers :  0.26 %
    Allowed  :  1.04 %
    Favored  : 98.69 %
  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: -1.62 (0.38), residues: 449
  helix: -0.42 (0.34), residues: 209
  sheet: -1.06 (1.45), residues: 12
  loop : -1.70 (0.40), residues: 228

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.009   0.001   ARG B 174 
 TYR   0.007   0.001   TYR B  97 
 PHE   0.037   0.003   PHE B  39 
 TRP   0.012   0.002   TRP B 330 
 HIS   0.006   0.002   HIS B 135 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00353 /  0.17 ( 3880)
  covalent geometry    : angle       0.74918 /  0.40 ( 5263)
  hydrogen bonds       : bond        0.05309 /  3.76 (  161)
  hydrogen bonds       : angle       5.53267 /  3.89 (  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  : 0.116 
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: 0.5197 (ptm) cc_final: 0.4754 (pmm)
REVERT: B  167 MET cc_start: 0.1740 (mmp) cc_final: 0.1429 (mmp)
REVERT: B  184 LYS cc_start: 0.7427 (tttp) cc_final: 0.7202 (tttp)
REVERT: B  192 GLU cc_start: 0.7382 (tm-30) cc_final: 0.6714 (tm-30)
REVERT: B  196 MET cc_start: 0.8051 (mtp) cc_final: 0.7570 (mtp)
REVERT: B  221 ARG cc_start: 0.7522 (ptt-90) cc_final: 0.7204 (ptt-90)
REVERT: B  239 MET cc_start: 0.7495 (tpp) cc_final: 0.6793 (tmm)
REVERT: B  240 ASP cc_start: 0.8000 (m-30) cc_final: 0.7644 (m-30)
REVERT: B  341 LEU cc_start: 0.1572 (mp) cc_final: 0.1106 (tt)
REVERT: B  425 ILE cc_start: 0.8095 (mm) cc_final: 0.7870 (mm)
REVERT: B  486 SER cc_start: 0.7022 (m) cc_final: 0.5480 (m)
  outliers start: 1
  outliers final: 0
  residues processed: 73
  average time/residue: 0.1056
  time to fit residues: 8.9503
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=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 46
   random chunks:
   chunk 1 optimal weight:    2.9990
   chunk 7 optimal weight:    0.1980
   chunk 3 optimal weight:    0.7980
   chunk 16 optimal weight:    0.9990
   chunk 22 optimal weight:    4.9990
   chunk 33 optimal weight:    0.4980
   chunk 38 optimal weight:    0.0020
   chunk 42 optimal weight:    0.4980
   chunk 23 optimal weight:    0.8980
   chunk 6 optimal weight:    2.9990
   chunk 4 optimal weight:    0.8980
   overall best weight:    0.3988

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
B  76 ASN
B 415 GLN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.5079 r_free = 0.5079 target = 0.280877 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 33)----------------|
| r_work = 0.5029 r_free = 0.5029 target = 0.269265 restraints weight = 15633.014|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 29)----------------|
| r_work = 0.5023 r_free = 0.5023 target = 0.269657 restraints weight = 16894.537|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 25)----------------|
| r_work = 0.5030 r_free = 0.5030 target = 0.270477 restraints weight = 13835.612|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 27)----------------|
| r_work = 0.5032 r_free = 0.5032 target = 0.270763 restraints weight = 11337.996|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 26)----------------|
| r_work = 0.5043 r_free = 0.5043 target = 0.271721 restraints weight = 10319.450|
|-----------------------------------------------------------------------------|
r_work (final): 0.4799
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.3873
moved from start:          0.5136

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.053   3880  Z= 0.158
  Angle     :  0.732  10.680   5263  Z= 0.382
  Chirality :  0.042   0.179    573
  Planarity :  0.005   0.040    649
  Dihedral  : 14.383 166.009    625
  Min Nonbonded Distance : 2.490

Molprobity Statistics.
  All-atom Clashscore : 16.06
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.90 %
    Favored  : 93.10 %
  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: -1.32 (0.38), residues: 449
  helix: -0.00 (0.35), residues: 206
  sheet: -1.12 (1.47), residues: 12
  loop : -1.70 (0.39), residues: 231

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.001   ARG B 261 
 TYR   0.006   0.001   TYR B 296 
 PHE   0.036   0.003   PHE B  39 
 TRP   0.010   0.002   TRP B 330 
 HIS   0.009   0.002   HIS B 135 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00339 /  0.16 ( 3880)
  covalent geometry    : angle       0.73159 /  0.38 ( 5263)
  hydrogen bonds       : bond        0.05046 /  3.57 (  161)
  hydrogen bonds       : angle       5.35854 /  3.72 (  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
  72 residues out of total 383 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 71
  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: B  105 MET cc_start: 0.5172 (ptm) cc_final: 0.4727 (pmm)
REVERT: B  137 MET cc_start: 0.5439 (ptm) cc_final: 0.4296 (ptm)
REVERT: B  167 MET cc_start: 0.1724 (mmp) cc_final: 0.1377 (mmp)
REVERT: B  192 GLU cc_start: 0.7413 (tm-30) cc_final: 0.6699 (tm-30)
REVERT: B  196 MET cc_start: 0.8074 (mtp) cc_final: 0.7624 (mtp)
REVERT: B  221 ARG cc_start: 0.7542 (ptt-90) cc_final: 0.7244 (ptt-90)
REVERT: B  239 MET cc_start: 0.7496 (tpp) cc_final: 0.6857 (tmm)
REVERT: B  240 ASP cc_start: 0.7996 (m-30) cc_final: 0.7597 (m-30)
REVERT: B  341 LEU cc_start: 0.1657 (mp) cc_final: 0.1276 (tt)
REVERT: B  425 ILE cc_start: 0.8128 (mm) cc_final: 0.7881 (mm)
REVERT: B  486 SER cc_start: 0.7088 (m) cc_final: 0.5544 (m)
  outliers start: 1
  outliers final: 0
  residues processed: 72
  average time/residue: 0.1016
  time to fit residues: 8.4905
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  : 0.133 
-------------------------------------------------------------------------------
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:    0.0980
   chunk 19 optimal weight:    0.7980
   chunk 14 optimal weight:    0.9980
   chunk 5 optimal weight:    0.3980
   chunk 36 optimal weight:    0.8980
   chunk 45 optimal weight:    4.9990
   chunk 34 optimal weight:    0.9980
   chunk 9 optimal weight:    0.8980
   chunk 10 optimal weight:    1.9990
   chunk 29 optimal weight:    1.9990
   overall best weight:    0.5980

-------------------------------------------------------------------------------
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 = 0.5063 r_free = 0.5063 target = 0.279982 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 31)----------------|
| r_work = 0.5014 r_free = 0.5014 target = 0.268144 restraints weight = 15335.768|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 24)----------------|
| r_work = 0.5009 r_free = 0.5009 target = 0.268483 restraints weight = 15654.975|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 24)----------------|
| r_work = 0.5015 r_free = 0.5015 target = 0.269480 restraints weight = 13309.584|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 26)----------------|
| r_work = 0.5020 r_free = 0.5020 target = 0.269850 restraints weight = 10319.836|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 28)----------------|
| r_work = 0.5028 r_free = 0.5028 target = 0.270610 restraints weight = 9105.877|
|-----------------------------------------------------------------------------|
r_work (final): 0.4781
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.3921
moved from start:          0.5299

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.056   3880  Z= 0.172
  Angle     :  0.741   9.307   5263  Z= 0.393
  Chirality :  0.044   0.199    573
  Planarity :  0.006   0.078    649
  Dihedral  : 14.217 162.835    625
  Min Nonbonded Distance : 2.423

Molprobity Statistics.
  All-atom Clashscore : 16.72
  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: -1.32 (0.38), residues: 449
  helix: -0.04 (0.35), residues: 207
  sheet: -0.93 (1.53), residues: 12
  loop : -1.67 (0.40), residues: 230

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.006   0.001   ARG B  74 
 TYR   0.006   0.001   TYR B 313 
 PHE   0.030   0.003   PHE B  39 
 TRP   0.010   0.002   TRP B 120 
 HIS   0.006   0.001   HIS B 135 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00370 /  0.17 ( 3880)
  covalent geometry    : angle       0.74142 /  0.39 ( 5263)
  hydrogen bonds       : bond        0.05121 /  3.62 (  161)
  hydrogen bonds       : angle       5.43507 /  3.79 (  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  : 0.106 
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: 0.5301 (ptm) cc_final: 0.4591 (pmm)
REVERT: B  167 MET cc_start: 0.1658 (mmp) cc_final: 0.1219 (mmp)
REVERT: B  184 LYS cc_start: 0.7146 (tttp) cc_final: 0.6832 (tttp)
REVERT: B  192 GLU cc_start: 0.7397 (tm-30) cc_final: 0.6698 (tm-30)
REVERT: B  196 MET cc_start: 0.8053 (mtp) cc_final: 0.7614 (mtp)
REVERT: B  221 ARG cc_start: 0.7517 (ptt-90) cc_final: 0.7228 (ptt-90)
REVERT: B  230 PHE cc_start: 0.5983 (p90) cc_final: 0.5697 (p90)
REVERT: B  239 MET cc_start: 0.7637 (tpp) cc_final: 0.7204 (tmm)
REVERT: B  240 ASP cc_start: 0.7921 (m-30) cc_final: 0.7463 (m-30)
REVERT: B  341 LEU cc_start: 0.1807 (mp) cc_final: 0.1349 (tt)
REVERT: B  425 ILE cc_start: 0.8127 (mm) cc_final: 0.7868 (mm)
REVERT: B  446 ARG cc_start: 0.6697 (ttp80) cc_final: 0.6392 (ttp80)
REVERT: B  486 SER cc_start: 0.7081 (m) cc_final: 0.5485 (m)
  outliers start: 0
  outliers final: 0
  residues processed: 71
  average time/residue: 0.1064
  time to fit residues: 8.7843
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  : 0.129 
-------------------------------------------------------------------------------
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:    0.6980
   chunk 40 optimal weight:    0.0670
   chunk 8 optimal weight:    0.9990
   chunk 41 optimal weight:    0.8980
   chunk 28 optimal weight:    6.9990
   chunk 26 optimal weight:    0.8980
   chunk 13 optimal weight:    0.9990
   chunk 2 optimal weight:    0.5980
   chunk 29 optimal weight:    2.9990
   chunk 21 optimal weight:    0.6980
   chunk 42 optimal weight:    0.4980
   overall best weight:    0.5118

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
B  76 ASN
B 415 GLN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4844 r_free = 0.4844 target = 0.235294 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 43)----------------|
| r_work = 0.4536 r_free = 0.4536 target = 0.204327 restraints weight = 12185.072|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 37)----------------|
| r_work = 0.4549 r_free = 0.4549 target = 0.205824 restraints weight = 11221.226|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 28)----------------|
| r_work = 0.4559 r_free = 0.4559 target = 0.206925 restraints weight = 10325.404|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 36)----------------|
| r_work = 0.4568 r_free = 0.4568 target = 0.207785 restraints weight = 9787.544|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 25)----------------|
| r_work = 0.4572 r_free = 0.4572 target = 0.208177 restraints weight = 9404.696|
|-----------------------------------------------------------------------------|
r_work (final): 0.4534
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.4376
moved from start:          0.5492

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.051   3880  Z= 0.159
  Angle     :  0.727   9.136   5263  Z= 0.388
  Chirality :  0.044   0.188    573
  Planarity :  0.006   0.090    649
  Dihedral  : 14.036 162.829    625
  Min Nonbonded Distance : 2.444

Molprobity Statistics.
  All-atom Clashscore : 17.66
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  7.13 %
    Favored  : 92.87 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  0.78 %
    Favored  : 99.22 %
  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: -1.17 (0.39), residues: 449
  helix:  0.16 (0.36), residues: 206
  sheet: -1.04 (1.58), residues: 12
  loop : -1.66 (0.40), residues: 231

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.015   0.001   ARG B 175 
 TYR   0.007   0.001   TYR B 313 
 PHE   0.032   0.003   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        0.00337 /  0.16 ( 3880)
  covalent geometry    : angle       0.72739 /  0.39 ( 5263)
  hydrogen bonds       : bond        0.05098 /  3.63 (  161)
  hydrogen bonds       : angle       5.31816 /  3.70 (  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  : 0.129 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: B  105 MET cc_start: 0.5645 (ptm) cc_final: 0.4984 (pmm)
REVERT: B  167 MET cc_start: 0.2217 (mmp) cc_final: 0.1703 (mmp)
REVERT: B  184 LYS cc_start: 0.7607 (tttp) cc_final: 0.7257 (tttp)
REVERT: B  192 GLU cc_start: 0.7657 (tm-30) cc_final: 0.7014 (tm-30)
REVERT: B  196 MET cc_start: 0.8386 (mtp) cc_final: 0.7883 (mtp)
REVERT: B  230 PHE cc_start: 0.6455 (p90) cc_final: 0.6014 (p90)
REVERT: B  239 MET cc_start: 0.7838 (tpp) cc_final: 0.7186 (tmm)
REVERT: B  240 ASP cc_start: 0.7826 (m-30) cc_final: 0.7437 (m-30)
REVERT: B  341 LEU cc_start: 0.2042 (mp) cc_final: 0.1776 (tt)
REVERT: B  425 ILE cc_start: 0.8136 (mm) cc_final: 0.7933 (mm)
REVERT: B  446 ARG cc_start: 0.7053 (ttp80) cc_final: 0.6740 (ttp80)
REVERT: B  486 SER cc_start: 0.7243 (m) cc_final: 0.6109 (m)
  outliers start: 0
  outliers final: 0
  residues processed: 68
  average time/residue: 0.1080
  time to fit residues: 8.5921
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  : 0.124 
-------------------------------------------------------------------------------
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:    0.3980
   chunk 13 optimal weight:    1.9990
   chunk 40 optimal weight:    0.0270
   chunk 41 optimal weight:    0.9990
   chunk 17 optimal weight:    3.9990
   chunk 20 optimal weight:    0.9990
   chunk 19 optimal weight:    0.9990
   chunk 14 optimal weight:    0.4980
   chunk 45 optimal weight:    4.9990
   chunk 44 optimal weight:    0.1980
   chunk 26 optimal weight:    1.9990
   overall best weight:    0.4240

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
B 124 ASN
B 415 GLN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4849 r_free = 0.4849 target = 0.235591 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 59)----------------|
| r_work = 0.4534 r_free = 0.4534 target = 0.204099 restraints weight = 12434.963|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 24)----------------|
| r_work = 0.4540 r_free = 0.4540 target = 0.204746 restraints weight = 11473.597|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 22)----------------|
| r_work = 0.4540 r_free = 0.4540 target = 0.204750 restraints weight = 10612.859|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 22)----------------|
| r_work = 0.4540 r_free = 0.4540 target = 0.204750 restraints weight = 10615.884|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 22)----------------|
| r_work = 0.4540 r_free = 0.4540 target = 0.204750 restraints weight = 10615.891|
|-----------------------------------------------------------------------------|
r_work (final): 0.4500
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.4442
moved from start:          0.5828

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.044   3880  Z= 0.149
  Angle     :  0.708   8.907   5263  Z= 0.377
  Chirality :  0.043   0.193    573
  Planarity :  0.005   0.059    649
  Dihedral  : 13.921 162.158    625
  Min Nonbonded Distance : 2.416

Molprobity Statistics.
  All-atom Clashscore : 15.79
  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: -1.12 (0.39), residues: 449
  helix:  0.24 (0.36), residues: 206
  sheet: -0.91 (1.00), residues: 22
  loop : -1.70 (0.41), residues: 221

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.011   0.001   ARG B 174 
 TYR   0.006   0.001   TYR B 385 
 PHE   0.030   0.003   PHE B  39 
 TRP   0.012   0.002   TRP B 120 
 HIS   0.007   0.002   HIS B 135 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00315 /  0.15 ( 3880)
  covalent geometry    : angle       0.70773 /  0.38 ( 5263)
  hydrogen bonds       : bond        0.04988 /  3.57 (  161)
  hydrogen bonds       : angle       5.22991 /  3.63 (  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
  69 residues out of total 383 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 69
  time to evaluate  : 0.138 
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: 0.5635 (ptm) cc_final: 0.4986 (pmm)
REVERT: B  167 MET cc_start: 0.2520 (mmp) cc_final: 0.1588 (mmp)
REVERT: B  184 LYS cc_start: 0.7571 (tttp) cc_final: 0.7231 (tttp)
REVERT: B  192 GLU cc_start: 0.7616 (tm-30) cc_final: 0.6973 (tm-30)
REVERT: B  196 MET cc_start: 0.8408 (mtp) cc_final: 0.7928 (mtp)
REVERT: B  239 MET cc_start: 0.7839 (tpp) cc_final: 0.7217 (tmm)
REVERT: B  240 ASP cc_start: 0.7799 (m-30) cc_final: 0.7368 (m-30)
REVERT: B  446 ARG cc_start: 0.7125 (ttp80) cc_final: 0.6827 (ttp80)
REVERT: B  486 SER cc_start: 0.7281 (m) cc_final: 0.6878 (m)
  outliers start: 0
  outliers final: 0
  residues processed: 69
  average time/residue: 0.1017
  time to fit residues: 8.2459
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  : 0.138 
-------------------------------------------------------------------------------
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:    0.7980
   chunk 27 optimal weight:    6.9990
   chunk 26 optimal weight:    0.5980
   chunk 35 optimal weight:    0.9980
   chunk 13 optimal weight:    0.8980
   chunk 22 optimal weight:    3.9990
   chunk 2 optimal weight:    0.6980
   chunk 4 optimal weight:    1.9990
   chunk 24 optimal weight:    0.3980
   chunk 6 optimal weight:    0.9990
   chunk 28 optimal weight:    0.7980
   overall best weight:    0.6580

-------------------------------------------------------------------------------
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 = 0.4837 r_free = 0.4837 target = 0.234566 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 48)----------------|
| r_work = 0.4516 r_free = 0.4516 target = 0.202639 restraints weight = 12147.882|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 39)----------------|
| r_work = 0.4530 r_free = 0.4530 target = 0.204197 restraints weight = 11036.218|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 34)----------------|
| r_work = 0.4542 r_free = 0.4542 target = 0.205351 restraints weight = 10304.106|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 26)----------------|
| r_work = 0.4548 r_free = 0.4548 target = 0.206009 restraints weight = 9745.213|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 24)----------------|
| r_work = 0.4551 r_free = 0.4551 target = 0.206325 restraints weight = 9349.109|
|-----------------------------------------------------------------------------|
r_work (final): 0.4521
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.4451
moved from start:          0.5981

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.049   3880  Z= 0.168
  Angle     :  0.748   9.088   5263  Z= 0.396
  Chirality :  0.043   0.182    573
  Planarity :  0.006   0.057    649
  Dihedral  : 13.848 161.629    625
  Min Nonbonded Distance : 2.404

Molprobity Statistics.
  All-atom Clashscore : 18.20
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  7.57 %
    Favored  : 92.43 %
  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: -1.13 (0.39), residues: 449
  helix:  0.21 (0.35), residues: 206
  sheet: -1.03 (1.02), residues: 22
  loop : -1.67 (0.42), residues: 221

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.008   0.001   ARG B 174 
 TYR   0.008   0.001   TYR B  97 
 PHE   0.034   0.003   PHE B 230 
 TRP   0.009   0.002   TRP B 330 
 HIS   0.004   0.002   HIS B 135 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00362 /  0.17 ( 3880)
  covalent geometry    : angle       0.74758 /  0.40 ( 5263)
  hydrogen bonds       : bond        0.05059 /  3.60 (  161)
  hydrogen bonds       : angle       5.25580 /  3.64 (  462)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 999.00 seconds
wall clock time: 17 minutes 57.66 seconds (1077.66 seconds total)