Starting phenix.real_space_refine
on Tue Feb  3 14:39:03 2026 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/9v47_64769/02_2026/9v47_64769.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/9v47_64769/02_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 {
    real_map_files = "/net/cci-nas-00/data/ceres_data/9v47_64769/02_2026/9v47_64769.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/9v47_64769/02_2026/9v47_64769.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/9v47_64769/02_2026/9v47_64769.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/9v47_64769/02_2026/9v47_64769.cif"
  }
  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-2.0-5952/lib/python3.9/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: 0.81, per 1000 atoms: 0.21
  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: 0.20
  Conformation dependent library (CDL) restraints added in 86.4 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: 0.27
  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: 0.32

  Time building geometry restraints manager: 0.26 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:                  0.010
  Normalize map: mean=0, sd=1:             3.020
  Set stop_for_unknowns flag:              0.000
  Assert model is a single copy model:     0.000
  Assert all atoms have isotropic ADPs:    0.000
  Construct map_model_manager:             0.000
  Extract box with map and model:          0.070
  Check model and map are aligned:         0.010
  Set scattering table:                    0.010
  Process input model:                     4.150
  Find NCS groups from input model:        0.010
  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:0.870
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:    8.160
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.3604
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= 0.899
  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
  covalent geometry    : bond        0.00840 ( 3880)
  covalent geometry    : angle       1.28844 ( 5263)
  hydrogen bonds       : bond        0.15940 (  161)
  hydrogen bonds       : angle       7.78446 (  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  : 0.150 
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: 0.1125
  time to fit residues: 15.6963
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  : 0.135 
-------------------------------------------------------------------------------
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...

Flipped N/Q/H residues before XYZ refinement:
B 124 ASN
** B 168 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
B 241 GLN
B 334 HIS

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4873 r_free = 0.4873 target = 0.236690 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 46)----------------|
| r_work = 0.4554 r_free = 0.4554 target = 0.205001 restraints weight = 12269.024|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 32)----------------|
| r_work = 0.4573 r_free = 0.4573 target = 0.206768 restraints weight = 11137.063|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 21)----------------|
| r_work = 0.4580 r_free = 0.4580 target = 0.207517 restraints weight = 10171.179|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 39)----------------|
| r_work = 0.4605 r_free = 0.4605 target = 0.209677 restraints weight = 9467.311|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 40)----------------|
| r_work = 0.4617 r_free = 0.4617 target = 0.210831 restraints weight = 8851.431|
|-----------------------------------------------------------------------------|
r_work (final): 0.4582
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.4582
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.4582 r_free = 0.4582    target_work(ls_wunit_k1) = 0.206         |
| occupancies: max = 1.00  min = 0.60   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.4583 r_free = 0.4583    target_work(ls_wunit_k1) = 0.206         |
| occupancies: max = 1.00  min = 0.87   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.4583
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.4250
moved from start:          0.3757

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.034   3880  Z= 0.176
  Angle     :  0.761   7.416   5263  Z= 0.403
  Chirality :  0.045   0.163    573
  Planarity :  0.006   0.069    649
  Dihedral  : 14.465 163.554    625
  Min Nonbonded Distance : 2.520

Molprobity Statistics.
  All-atom Clashscore : 21.68
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  7.57 %
    Favored  : 92.43 %
  Rotamer:
    Outliers :  0.52 %
    Allowed  :  4.18 %
    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: -2.77 (0.34), residues: 449
  helix: -1.26 (0.32), residues: 208
  sheet: -1.24 (1.53), residues: 12
  loop : -2.47 (0.35), residues: 229

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.010   0.001   ARG B 261 
 TYR   0.019   0.002   TYR B  40 
 PHE   0.029   0.003   PHE B  39 
 TRP   0.014   0.002   TRP B 207 
 HIS   0.002   0.001   HIS B 140 

Details of bonding type rmsd
  covalent geometry    : bond        0.00370 ( 3880)
  covalent geometry    : angle       0.76111 ( 5263)
  hydrogen bonds       : bond        0.05377 (  161)
  hydrogen bonds       : angle       5.65967 (  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
  82 residues out of total 383 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 2
    poor density    : 80
  time to evaluate  : 0.141 
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   29 VAL cc_start: 0.5717 (p) cc_final: 0.5473 (p)
REVERT: B   34 ASN cc_start: 0.7103 (t0) cc_final: 0.6661 (t0)
REVERT: B   66 MET cc_start: 0.7430 (mtt) cc_final: 0.7195 (mtt)
REVERT: B  105 MET cc_start: 0.5693 (ptm) cc_final: 0.5074 (pmm)
REVERT: B  192 GLU cc_start: 0.7693 (tm-30) cc_final: 0.7083 (tm-30)
REVERT: B  196 MET cc_start: 0.8315 (mtp) cc_final: 0.7799 (mtp)
REVERT: B  239 MET cc_start: 0.7457 (tpp) cc_final: 0.6647 (tmm)
REVERT: B  240 ASP cc_start: 0.7852 (m-30) cc_final: 0.7619 (m-30)
REVERT: B  440 MET cc_start: 0.7291 (mpp) cc_final: 0.7074 (mpp)
  outliers start: 2
  outliers final: 0
  residues processed: 82
  average time/residue: 0.1110
  time to fit residues: 10.5531
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  : 0.133 
-------------------------------------------------------------------------------
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:    0.6980
   chunk 19 optimal weight:    0.7980
   chunk 5 optimal weight:    0.9980
   chunk 23 optimal weight:    0.9980
   chunk 9 optimal weight:    0.8980
   chunk 28 optimal weight:    0.3980
   chunk 1 optimal weight:    0.9990
   chunk 24 optimal weight:    0.5980
   chunk 3 optimal weight:    0.8980
   chunk 40 optimal weight:    0.6980
   overall best weight:    0.6380

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

Flipped N/Q/H residues before XYZ refinement:
B  76 ASN
** B 168 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
B 231 GLN
B 241 GLN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.5063 r_free = 0.5063 target = 0.278883 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 42)----------------|
| r_work = 0.5016 r_free = 0.5016 target = 0.267847 restraints weight = 15185.142|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 33)----------------|
| r_work = 0.5010 r_free = 0.5010 target = 0.268046 restraints weight = 16044.020|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 27)----------------|
| r_work = 0.5017 r_free = 0.5017 target = 0.269022 restraints weight = 13943.487|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 31)----------------|
| r_work = 0.5019 r_free = 0.5019 target = 0.269287 restraints weight = 11164.020|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 26)----------------|
| r_work = 0.5023 r_free = 0.5023 target = 0.269721 restraints weight = 10036.033|
|-----------------------------------------------------------------------------|
r_work (final): 0.4783
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.4781
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.4781 r_free = 0.4781    target_work(ls_wunit_k1) = 0.228         |
| occupancies: max = 1.00  min = 0.87   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.4780 r_free = 0.4780    target_work(ls_wunit_k1) = 0.227         |
| occupancies: max = 1.00  min = 1.00   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.4780
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.4037
moved from start:          0.4963

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.044   3880  Z= 0.177
  Angle     :  0.761   9.698   5263  Z= 0.399
  Chirality :  0.043   0.158    573
  Planarity :  0.006   0.047    649
  Dihedral  : 14.388 165.289    625
  Min Nonbonded Distance : 2.457

Molprobity Statistics.
  All-atom Clashscore : 20.20
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  7.57 %
    Favored  : 92.43 %
  Rotamer:
    Outliers :  0.52 %
    Allowed  :  3.13 %
    Favored  : 96.34 %
  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: -2.12 (0.36), residues: 449
  helix: -0.70 (0.33), residues: 206
  sheet: -1.21 (1.62), residues: 12
  loop : -2.11 (0.37), residues: 231

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.001   ARG B 461 
 TYR   0.011   0.002   TYR B 313 
 PHE   0.028   0.003   PHE B 258 
 TRP   0.012   0.002   TRP B 120 
 HIS   0.004   0.001   HIS B 135 

Details of bonding type rmsd
  covalent geometry    : bond        0.00369 ( 3880)
  covalent geometry    : angle       0.76129 ( 5263)
  hydrogen bonds       : bond        0.05522 (  161)
  hydrogen bonds       : angle       5.57535 (  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
  72 residues out of total 383 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 2
    poor density    : 70
  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: 0.5440 (ptm) cc_final: 0.4843 (pmm)
REVERT: B  167 MET cc_start: 0.1907 (mmp) cc_final: 0.1512 (mmp)
REVERT: B  184 LYS cc_start: 0.7525 (tttp) cc_final: 0.7265 (tttp)
REVERT: B  192 GLU cc_start: 0.7529 (tm-30) cc_final: 0.6833 (tm-30)
REVERT: B  196 MET cc_start: 0.8071 (mtp) cc_final: 0.7642 (mtp)
REVERT: B  227 LYS cc_start: 0.7734 (ttpp) cc_final: 0.6660 (tttp)
REVERT: B  230 PHE cc_start: 0.5834 (p90) cc_final: 0.5535 (p90)
REVERT: B  239 MET cc_start: 0.7518 (tpp) cc_final: 0.6659 (tmm)
REVERT: B  240 ASP cc_start: 0.7940 (m-30) cc_final: 0.7379 (m-30)
REVERT: B  425 ILE cc_start: 0.8215 (mm) cc_final: 0.7968 (mm)
REVERT: B  440 MET cc_start: 0.6987 (mpp) cc_final: 0.6780 (mpp)
REVERT: B  447 MET cc_start: 0.7985 (ppp) cc_final: 0.7635 (ppp)
REVERT: B  486 SER cc_start: 0.6808 (m) cc_final: 0.6426 (m)
  outliers start: 2
  outliers final: 0
  residues processed: 72
  average time/residue: 0.1183
  time to fit residues: 9.8420
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=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 46
   random chunks:
   chunk 32 optimal weight:    2.9990
   chunk 9 optimal weight:    0.6980
   chunk 10 optimal weight:    0.7980
   chunk 37 optimal weight:    0.4980
   chunk 4 optimal weight:    1.9990
   chunk 43 optimal weight:    0.9990
   chunk 15 optimal weight:    1.9990
   chunk 45 optimal weight:    2.9990
   chunk 29 optimal weight:    1.9990
   chunk 2 optimal weight:    0.7980
   chunk 7 optimal weight:    0.3980
   overall best weight:    0.6380

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

Flipped N/Q/H residues before XYZ refinement:
B  76 ASN
B 125 ASN
B 231 GLN
B 241 GLN
** B 415 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.5045 r_free = 0.5045 target = 0.277697 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 43)----------------|
| r_work = 0.4997 r_free = 0.4997 target = 0.265898 restraints weight = 15026.735|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 31)----------------|
| r_work = 0.4986 r_free = 0.4986 target = 0.265898 restraints weight = 14599.949|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 25)----------------|
| r_work = 0.4993 r_free = 0.4993 target = 0.266622 restraints weight = 12147.720|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 28)----------------|
| r_work = 0.4997 r_free = 0.4997 target = 0.267193 restraints weight = 10200.469|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 26)----------------|
| r_work = 0.4999 r_free = 0.4999 target = 0.267341 restraints weight = 9088.005|
|-----------------------------------------------------------------------------|
r_work (final): 0.4748
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.4111
moved from start:          0.5508

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.042   3880  Z= 0.167
  Angle     :  0.738   9.489   5263  Z= 0.384
  Chirality :  0.041   0.159    573
  Planarity :  0.005   0.041    649
  Dihedral  : 14.244 164.430    625
  Min Nonbonded Distance : 2.464

Molprobity Statistics.
  All-atom Clashscore : 19.00
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.68 %
    Favored  : 93.32 %
  Rotamer:
    Outliers :  0.52 %
    Allowed  :  3.13 %
    Favored  : 96.34 %
  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: -1.71 (0.37), residues: 449
  helix: -0.37 (0.34), residues: 208
  sheet: -1.31 (1.60), residues: 12
  loop : -1.87 (0.39), residues: 229

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.001   ARG B 162 
 TYR   0.009   0.001   TYR B 313 
 PHE   0.054   0.003   PHE B  39 
 TRP   0.008   0.001   TRP B 386 
 HIS   0.006   0.002   HIS B 135 

Details of bonding type rmsd
  covalent geometry    : bond        0.00352 ( 3880)
  covalent geometry    : angle       0.73834 ( 5263)
  hydrogen bonds       : bond        0.04924 (  161)
  hydrogen bonds       : angle       5.32700 (  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
  74 residues out of total 383 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 2
    poor density    : 72
  time to evaluate  : 0.136 
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: 0.5283 (ptm) cc_final: 0.4758 (pmm)
REVERT: B  136 MET cc_start: 0.6995 (tpt) cc_final: 0.6659 (tpp)
REVERT: B  167 MET cc_start: 0.1694 (mmp) cc_final: 0.1022 (mmp)
REVERT: B  175 ARG cc_start: 0.6091 (mtp180) cc_final: 0.5864 (mtp180)
REVERT: B  192 GLU cc_start: 0.7535 (tm-30) cc_final: 0.6851 (tm-30)
REVERT: B  196 MET cc_start: 0.8085 (mtp) cc_final: 0.7642 (mtp)
REVERT: B  227 LYS cc_start: 0.7771 (tmmt) cc_final: 0.7383 (tttm)
REVERT: B  239 MET cc_start: 0.7532 (tpp) cc_final: 0.6609 (tmm)
REVERT: B  240 ASP cc_start: 0.8033 (m-30) cc_final: 0.7427 (m-30)
REVERT: B  425 ILE cc_start: 0.8190 (mm) cc_final: 0.7936 (mm)
REVERT: B  447 MET cc_start: 0.7988 (ppp) cc_final: 0.7647 (ppp)
REVERT: B  486 SER cc_start: 0.7091 (m) cc_final: 0.6113 (m)
  outliers start: 2
  outliers final: 0
  residues processed: 74
  average time/residue: 0.0893
  time to fit residues: 7.7220
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  : 0.086 
-------------------------------------------------------------------------------
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:    3.9990
   chunk 7 optimal weight:    0.5980
   chunk 6 optimal weight:    4.9990
   chunk 19 optimal weight:    0.5980
   chunk 28 optimal weight:    0.9990
   chunk 16 optimal weight:    0.5980
   chunk 10 optimal weight:    4.9990
   chunk 25 optimal weight:    0.6980
   chunk 38 optimal weight:    0.7980
   chunk 8 optimal weight:    0.5980
   overall best weight:    0.5580

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

Flipped N/Q/H residues before XYZ refinement:
B  76 ASN
B 168 GLN
B 231 GLN
B 241 GLN

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.5040 r_free = 0.5040 target = 0.277938 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 46)----------------|
| r_work = 0.4991 r_free = 0.4991 target = 0.266727 restraints weight = 15031.480|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 29)----------------|
| r_work = 0.4980 r_free = 0.4980 target = 0.266102 restraints weight = 16538.900|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 30)----------------|
| r_work = 0.4987 r_free = 0.4987 target = 0.266933 restraints weight = 13846.674|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 26)----------------|
| r_work = 0.4991 r_free = 0.4991 target = 0.267402 restraints weight = 11311.637|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 24)----------------|
| r_work = 0.4992 r_free = 0.4992 target = 0.267491 restraints weight = 10310.409|
|-----------------------------------------------------------------------------|
r_work (final): 0.4750
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.4113
moved from start:          0.6118

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.043   3880  Z= 0.158
  Angle     :  0.715   7.560   5263  Z= 0.372
  Chirality :  0.041   0.156    573
  Planarity :  0.005   0.041    649
  Dihedral  : 14.026 165.059    625
  Min Nonbonded Distance : 2.485

Molprobity Statistics.
  All-atom Clashscore : 17.39
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  7.35 %
    Favored  : 92.65 %
  Rotamer:
    Outliers :  0.52 %
    Allowed  :  2.35 %
    Favored  : 97.13 %
  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: -1.30 (0.38), residues: 449
  helix:  0.09 (0.34), residues: 208
  sheet: -1.89 (1.60), residues: 12
  loop : -1.73 (0.40), residues: 229

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.006   0.001   ARG B 162 
 TYR   0.009   0.001   TYR B 313 
 PHE   0.044   0.003   PHE B  39 
 TRP   0.009   0.002   TRP B 104 
 HIS   0.006   0.002   HIS B 135 

Details of bonding type rmsd
  covalent geometry    : bond        0.00337 ( 3880)
  covalent geometry    : angle       0.71515 ( 5263)
  hydrogen bonds       : bond        0.04659 (  161)
  hydrogen bonds       : angle       5.10451 (  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
  72 residues out of total 383 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 2
    poor density    : 70
  time to evaluate  : 0.136 
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: symmetry clash
   revert: symmetry clash
REVERT: B  105 MET cc_start: 0.5398 (ptm) cc_final: 0.4855 (pmm)
REVERT: B  167 MET cc_start: 0.2161 (mmp) cc_final: 0.1578 (mmp)
REVERT: B  189 MET cc_start: 0.7403 (tpt) cc_final: 0.6416 (tpt)
REVERT: B  192 GLU cc_start: 0.7457 (tm-30) cc_final: 0.6918 (tm-30)
REVERT: B  196 MET cc_start: 0.8091 (mtp) cc_final: 0.7666 (mtp)
REVERT: B  221 ARG cc_start: 0.7610 (ptt-90) cc_final: 0.7383 (ptt-90)
REVERT: B  222 MET cc_start: 0.7858 (mtm) cc_final: 0.6955 (tmm)
REVERT: B  239 MET cc_start: 0.7611 (tpp) cc_final: 0.6850 (tmm)
REVERT: B  240 ASP cc_start: 0.7999 (m-30) cc_final: 0.7457 (m-30)
REVERT: B  425 ILE cc_start: 0.8173 (mm) cc_final: 0.7903 (mm)
REVERT: B  440 MET cc_start: 0.6921 (mpp) cc_final: 0.6373 (mpp)
REVERT: B  447 MET cc_start: 0.7941 (ppp) cc_final: 0.7492 (ppp)
  outliers start: 2
  outliers final: 0
  residues processed: 71
  average time/residue: 0.1193
  time to fit residues: 9.7596
Evaluate side-chains
  62 residues out of total 383 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 62
  time to evaluate  : 0.132 
-------------------------------------------------------------------------------
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:    2.9990
   chunk 19 optimal weight:    0.4980
   chunk 40 optimal weight:    2.9990
   chunk 27 optimal weight:    4.9990
   chunk 36 optimal weight:    2.9990
   chunk 16 optimal weight:    0.4980
   chunk 0 optimal weight:    2.9990
   chunk 18 optimal weight:    2.9990
   chunk 14 optimal weight:    0.0870
   chunk 29 optimal weight:    0.5980
   chunk 10 optimal weight:    3.9990
   overall best weight:    0.9360

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

Flipped N/Q/H residues before XYZ refinement:
B 125 ASN
B 168 GLN
B 231 GLN
B 241 GLN

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4778 r_free = 0.4778 target = 0.230263 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 50)----------------|
| r_work = 0.4488 r_free = 0.4488 target = 0.199682 restraints weight = 12399.249|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 26)----------------|
| r_work = 0.4507 r_free = 0.4507 target = 0.201506 restraints weight = 11169.581|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 25)----------------|
| r_work = 0.4516 r_free = 0.4516 target = 0.202413 restraints weight = 10235.254|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 22)----------------|
| r_work = 0.4516 r_free = 0.4516 target = 0.202413 restraints weight = 9557.632|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 22)----------------|
| r_work = 0.4516 r_free = 0.4516 target = 0.202413 restraints weight = 9557.219|
|-----------------------------------------------------------------------------|
r_work (final): 0.4474
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.4668
moved from start:          0.6618

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.043   3880  Z= 0.203
  Angle     :  0.803   9.849   5263  Z= 0.423
  Chirality :  0.044   0.162    573
  Planarity :  0.005   0.032    649
  Dihedral  : 14.070 164.569    625
  Min Nonbonded Distance : 2.458

Molprobity Statistics.
  All-atom Clashscore : 20.60
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  7.57 %
    Favored  : 92.43 %
  Rotamer:
    Outliers :  0.26 %
    Allowed  :  3.66 %
    Favored  : 96.08 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z 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: -1.47 (0.38), residues: 449
  helix: -0.13 (0.34), residues: 208
  sheet: -2.64 (1.35), residues: 12
  loop : -1.70 (0.40), residues: 229

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.007   0.001   ARG B  77 
 TYR   0.014   0.002   TYR B 313 
 PHE   0.052   0.003   PHE B  39 
 TRP   0.007   0.002   TRP B 104 
 HIS   0.006   0.002   HIS B 135 

Details of bonding type rmsd
  covalent geometry    : bond        0.00431 ( 3880)
  covalent geometry    : angle       0.80266 ( 5263)
  hydrogen bonds       : bond        0.05442 (  161)
  hydrogen bonds       : angle       5.49044 (  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
  76 residues out of total 383 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 75
  time to evaluate  : 0.144 
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   66 MET cc_start: 0.7590 (mtt) cc_final: 0.6797 (ppp)
REVERT: B  110 LEU cc_start: 0.5490 (mp) cc_final: 0.5262 (mp)
REVERT: B  167 MET cc_start: 0.2632 (mmp) cc_final: 0.1906 (mmp)
REVERT: B  189 MET cc_start: 0.7655 (tpt) cc_final: 0.7266 (tpt)
REVERT: B  192 GLU cc_start: 0.7581 (tm-30) cc_final: 0.6971 (tm-30)
REVERT: B  196 MET cc_start: 0.8423 (mtp) cc_final: 0.7863 (mtp)
REVERT: B  222 MET cc_start: 0.8082 (mtm) cc_final: 0.7174 (tmm)
REVERT: B  239 MET cc_start: 0.7738 (tpp) cc_final: 0.7025 (tmm)
REVERT: B  240 ASP cc_start: 0.7755 (m-30) cc_final: 0.7524 (m-30)
REVERT: B  412 PHE cc_start: 0.8016 (p90) cc_final: 0.7754 (p90)
  outliers start: 1
  outliers final: 0
  residues processed: 76
  average time/residue: 0.1135
  time to fit residues: 10.0583
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  : 0.112 
-------------------------------------------------------------------------------
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:    0.9980
   chunk 7 optimal weight:    0.4980
   chunk 3 optimal weight:    0.9980
   chunk 16 optimal weight:    0.8980
   chunk 22 optimal weight:    0.6980
   chunk 33 optimal weight:    0.2980
   chunk 38 optimal weight:    3.9990
   chunk 42 optimal weight:    4.9990
   chunk 23 optimal weight:    2.9990
   chunk 6 optimal weight:    0.0050
   chunk 4 optimal weight:    0.9980
   overall best weight:    0.4794

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

Flipped N/Q/H residues before XYZ refinement:
B 231 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.5016 r_free = 0.5016 target = 0.275717 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 41)----------------|
| r_work = 0.4969 r_free = 0.4969 target = 0.263372 restraints weight = 15524.412|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 27)----------------|
| r_work = 0.4969 r_free = 0.4969 target = 0.264378 restraints weight = 14661.884|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 30)----------------|
| r_work = 0.4974 r_free = 0.4974 target = 0.265050 restraints weight = 11048.501|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 27)----------------|
| r_work = 0.4977 r_free = 0.4977 target = 0.265332 restraints weight = 9687.240|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 28)----------------|
| r_work = 0.4979 r_free = 0.4979 target = 0.265589 restraints weight = 9018.183|
|-----------------------------------------------------------------------------|
r_work (final): 0.4734
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.4175
moved from start:          0.7020

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.038   3880  Z= 0.151
  Angle     :  0.733   9.420   5263  Z= 0.382
  Chirality :  0.042   0.195    573
  Planarity :  0.006   0.092    649
  Dihedral  : 13.835 164.863    625
  Min Nonbonded Distance : 2.447

Molprobity Statistics.
  All-atom Clashscore : 15.52
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  7.35 %
    Favored  : 92.65 %
  Rotamer:
    Outliers :  0.26 %
    Allowed  :  2.09 %
    Favored  : 97.65 %
  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: -1.40 (0.38), residues: 449
  helix: -0.05 (0.35), residues: 208
  sheet: -2.89 (1.35), residues: 12
  loop : -1.66 (0.40), residues: 229

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.009   0.001   ARG B 236 
 TYR   0.011   0.001   TYR B 313 
 PHE   0.035   0.003   PHE B  39 
 TRP   0.007   0.001   TRP B 386 
 HIS   0.005   0.001   HIS B 135 

Details of bonding type rmsd
  covalent geometry    : bond        0.00325 ( 3880)
  covalent geometry    : angle       0.73291 ( 5263)
  hydrogen bonds       : bond        0.04841 (  161)
  hydrogen bonds       : angle       5.21239 (  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
  75 residues out of total 383 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 74
  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: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: B   66 MET cc_start: 0.7625 (mtt) cc_final: 0.6694 (ppp)
REVERT: B  105 MET cc_start: 0.4679 (ptm) cc_final: 0.4417 (pmm)
REVERT: B  110 LEU cc_start: 0.5026 (mp) cc_final: 0.4802 (mp)
REVERT: B  175 ARG cc_start: 0.6310 (mtp180) cc_final: 0.5930 (mtp180)
REVERT: B  189 MET cc_start: 0.7373 (tpt) cc_final: 0.6382 (tpt)
REVERT: B  192 GLU cc_start: 0.7486 (tm-30) cc_final: 0.7066 (tm-30)
REVERT: B  196 MET cc_start: 0.8099 (mtp) cc_final: 0.7713 (mtp)
REVERT: B  222 MET cc_start: 0.7862 (mtm) cc_final: 0.6921 (tmm)
REVERT: B  239 MET cc_start: 0.7790 (tpp) cc_final: 0.7187 (tmm)
REVERT: B  443 GLU cc_start: 0.7380 (tp30) cc_final: 0.6998 (mm-30)
  outliers start: 1
  outliers final: 0
  residues processed: 75
  average time/residue: 0.1082
  time to fit residues: 9.4695
Evaluate side-chains
  73 residues out of total 383 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 73
  time to evaluate  : 0.129 
-------------------------------------------------------------------------------
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:    3.9990
   chunk 35 optimal weight:    1.9990
   chunk 19 optimal weight:    0.7980
   chunk 14 optimal weight:    0.9990
   chunk 5 optimal weight:    0.8980
   chunk 36 optimal weight:    3.9990
   chunk 45 optimal weight:    1.9990
   chunk 34 optimal weight:    7.9990
   chunk 9 optimal weight:    0.0670
   chunk 10 optimal weight:    0.9990
   chunk 29 optimal weight:    0.5980
   overall best weight:    0.6720

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

Flipped N/Q/H residues before XYZ refinement:
B 231 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4793 r_free = 0.4793 target = 0.229403 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 40)----------------|
| r_work = 0.4471 r_free = 0.4471 target = 0.196072 restraints weight = 11715.185|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 36)----------------|
| r_work = 0.4493 r_free = 0.4493 target = 0.198233 restraints weight = 10516.589|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 34)----------------|
| r_work = 0.4509 r_free = 0.4509 target = 0.199886 restraints weight = 9597.948|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 25)----------------|
| r_work = 0.4518 r_free = 0.4518 target = 0.200754 restraints weight = 8907.894|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 38)----------------|
| r_work = 0.4533 r_free = 0.4533 target = 0.202144 restraints weight = 8486.441|
|-----------------------------------------------------------------------------|
r_work (final): 0.4501
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.4635
moved from start:          0.7383

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.042   3880  Z= 0.168
  Angle     :  0.754   8.923   5263  Z= 0.394
  Chirality :  0.043   0.174    573
  Planarity :  0.006   0.082    649
  Dihedral  : 13.675 163.863    625
  Min Nonbonded Distance : 2.415

Molprobity Statistics.
  All-atom Clashscore : 19.53
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  8.02 %
    Favored  : 91.98 %
  Rotamer:
    Outliers :  0.26 %
    Allowed  :  0.52 %
    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: -1.51 (0.38), residues: 449
  helix: -0.13 (0.35), residues: 207
  sheet: -3.57 (1.15), residues: 12
  loop : -1.68 (0.40), residues: 230

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.006   0.001   ARG B 174 
 TYR   0.016   0.002   TYR B 313 
 PHE   0.027   0.003   PHE B 230 
 TRP   0.006   0.001   TRP B 386 
 HIS   0.003   0.001   HIS B 135 

Details of bonding type rmsd
  covalent geometry    : bond        0.00356 ( 3880)
  covalent geometry    : angle       0.75373 ( 5263)
  hydrogen bonds       : bond        0.04888 (  161)
  hydrogen bonds       : angle       5.30414 (  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
  76 residues out of total 383 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 75
  time to evaluate  : 0.139 
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   48 LYS cc_start: 0.6523 (mtpt) cc_final: 0.6320 (mtpt)
REVERT: B   66 MET cc_start: 0.7744 (mtt) cc_final: 0.6787 (ppp)
REVERT: B  105 MET cc_start: 0.5281 (ptm) cc_final: 0.4803 (pmm)
REVERT: B  110 LEU cc_start: 0.5483 (mp) cc_final: 0.5282 (mp)
REVERT: B  189 MET cc_start: 0.7648 (tpt) cc_final: 0.7167 (tpt)
REVERT: B  192 GLU cc_start: 0.7605 (tm-30) cc_final: 0.7136 (tm-30)
REVERT: B  196 MET cc_start: 0.8343 (mtp) cc_final: 0.7871 (mtp)
REVERT: B  222 MET cc_start: 0.8129 (mtm) cc_final: 0.7135 (tmm)
REVERT: B  238 MET cc_start: 0.7661 (mtm) cc_final: 0.7449 (mtm)
REVERT: B  239 MET cc_start: 0.7863 (tpp) cc_final: 0.6878 (tpp)
REVERT: B  412 PHE cc_start: 0.8077 (p90) cc_final: 0.7864 (p90)
  outliers start: 1
  outliers final: 0
  residues processed: 76
  average time/residue: 0.1048
  time to fit residues: 9.3913
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  : 0.146 
-------------------------------------------------------------------------------
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:    0.0370
   chunk 8 optimal weight:    0.4980
   chunk 41 optimal weight:    0.6980
   chunk 28 optimal weight:    0.9980
   chunk 26 optimal weight:    3.9990
   chunk 13 optimal weight:    4.9990
   chunk 2 optimal weight:    0.5980
   chunk 29 optimal weight:    0.6980
   chunk 21 optimal weight:    0.0470
   chunk 42 optimal weight:    0.0770
   overall best weight:    0.2514

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.5027 r_free = 0.5027 target = 0.277059 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 43)----------------|
| r_work = 0.4983 r_free = 0.4983 target = 0.264770 restraints weight = 15279.688|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 29)----------------|
| r_work = 0.4976 r_free = 0.4976 target = 0.265042 restraints weight = 13968.458|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 25)----------------|
| r_work = 0.4981 r_free = 0.4981 target = 0.265731 restraints weight = 11744.307|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 27)----------------|
| r_work = 0.4982 r_free = 0.4982 target = 0.265986 restraints weight = 10394.032|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 30)----------------|
| r_work = 0.4986 r_free = 0.4986 target = 0.266571 restraints weight = 9596.645|
|-----------------------------------------------------------------------------|
r_work (final): 0.4738
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.4138
moved from start:          0.7699

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.035   3880  Z= 0.133
  Angle     :  0.685   8.388   5263  Z= 0.355
  Chirality :  0.041   0.170    573
  Planarity :  0.005   0.073    649
  Dihedral  : 13.450 164.542    625
  Min Nonbonded Distance : 2.407

Molprobity Statistics.
  All-atom Clashscore : 14.85
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.68 %
    Favored  : 93.32 %
  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: -1.32 (0.39), residues: 449
  helix:  0.05 (0.36), residues: 209
  sheet: -3.40 (1.20), residues: 12
  loop : -1.63 (0.40), residues: 228

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.006   0.001   ARG B 174 
 TYR   0.007   0.001   TYR B  40 
 PHE   0.026   0.002   PHE B  39 
 TRP   0.009   0.001   TRP B 386 
 HIS   0.004   0.001   HIS B 135 

Details of bonding type rmsd
  covalent geometry    : bond        0.00286 ( 3880)
  covalent geometry    : angle       0.68458 ( 5263)
  hydrogen bonds       : bond        0.04418 (  161)
  hydrogen bonds       : angle       4.99807 (  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
  74 residues out of total 383 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 74
  time to evaluate  : 0.143 
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   48 LYS cc_start: 0.6384 (mtpt) cc_final: 0.6157 (mtpt)
REVERT: B   52 TYR cc_start: 0.0285 (t80) cc_final: -0.1322 (t80)
REVERT: B   66 MET cc_start: 0.7769 (mtt) cc_final: 0.6786 (ppp)
REVERT: B  167 MET cc_start: 0.3057 (mmp) cc_final: 0.2685 (mmp)
REVERT: B  175 ARG cc_start: 0.6365 (mtp180) cc_final: 0.5988 (mtp180)
REVERT: B  189 MET cc_start: 0.7282 (tpt) cc_final: 0.6274 (tpt)
REVERT: B  192 GLU cc_start: 0.7503 (tm-30) cc_final: 0.7103 (tm-30)
REVERT: B  196 MET cc_start: 0.8002 (mtp) cc_final: 0.7669 (mtp)
REVERT: B  219 TYR cc_start: 0.7782 (t80) cc_final: 0.7433 (t80)
REVERT: B  222 MET cc_start: 0.8087 (mtm) cc_final: 0.7162 (tmm)
REVERT: B  238 MET cc_start: 0.7273 (mtm) cc_final: 0.6767 (mtm)
REVERT: B  239 MET cc_start: 0.7517 (tpp) cc_final: 0.6940 (tmm)
  outliers start: 0
  outliers final: 0
  residues processed: 74
  average time/residue: 0.1046
  time to fit residues: 9.1279
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  : 0.135 
-------------------------------------------------------------------------------
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:    0.4980
   chunk 13 optimal weight:    0.9980
   chunk 40 optimal weight:    0.4980
   chunk 41 optimal weight:    0.7980
   chunk 17 optimal weight:    0.9980
   chunk 20 optimal weight:    0.9980
   chunk 19 optimal weight:    0.9980
   chunk 14 optimal weight:    0.7980
   chunk 45 optimal weight:    2.9990
   chunk 44 optimal weight:    0.0870
   chunk 26 optimal weight:    0.8980
   overall best weight:    0.5358

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4803 r_free = 0.4803 target = 0.232022 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 50)----------------|
| r_work = 0.4524 r_free = 0.4524 target = 0.201734 restraints weight = 12967.144|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 23)----------------|
| r_work = 0.4535 r_free = 0.4535 target = 0.202938 restraints weight = 12071.077|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 41)----------------|
| r_work = 0.4546 r_free = 0.4546 target = 0.203993 restraints weight = 11352.546|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 22)----------------|
| r_work = 0.4546 r_free = 0.4546 target = 0.203994 restraints weight = 10746.622|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 15)----------------|
| r_work = 0.4546 r_free = 0.4546 target = 0.203994 restraints weight = 10746.293|
|-----------------------------------------------------------------------------|
r_work (final): 0.4493
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.4618
moved from start:          0.7937

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.036   3880  Z= 0.151
  Angle     :  0.710   8.744   5263  Z= 0.370
  Chirality :  0.042   0.165    573
  Planarity :  0.005   0.055    649
  Dihedral  : 13.386 161.829    625
  Min Nonbonded Distance : 2.383

Molprobity Statistics.
  All-atom Clashscore : 17.80
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  7.35 %
    Favored  : 92.65 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  0.00 %
    Favored  : 100.00 %
  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: -1.41 (0.39), residues: 449
  helix: -0.07 (0.35), residues: 209
  sheet: -3.61 (1.14), residues: 12
  loop : -1.62 (0.41), residues: 228

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.007   0.001   ARG B 174 
 TYR   0.009   0.001   TYR B  97 
 PHE   0.025   0.003   PHE B  39 
 TRP   0.004   0.001   TRP B 386 
 HIS   0.003   0.001   HIS B 324 

Details of bonding type rmsd
  covalent geometry    : bond        0.00322 ( 3880)
  covalent geometry    : angle       0.70990 ( 5263)
  hydrogen bonds       : bond        0.04546 (  161)
  hydrogen bonds       : angle       5.11597 (  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
  76 residues out of total 383 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 76
  time to evaluate  : 0.147 
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   48 LYS cc_start: 0.6370 (mtpt) cc_final: 0.6156 (mtpt)
REVERT: B   66 MET cc_start: 0.7728 (mtt) cc_final: 0.6799 (ppp)
REVERT: B  127 ASP cc_start: 0.6404 (m-30) cc_final: 0.5533 (p0)
REVERT: B  159 MET cc_start: 0.6803 (mtm) cc_final: 0.6564 (mtm)
REVERT: B  167 MET cc_start: 0.3355 (mmp) cc_final: 0.2852 (mmp)
REVERT: B  192 GLU cc_start: 0.7616 (tm-30) cc_final: 0.7044 (tm-30)
REVERT: B  196 MET cc_start: 0.8353 (mtp) cc_final: 0.7904 (mtp)
REVERT: B  219 TYR cc_start: 0.8356 (t80) cc_final: 0.7792 (t80)
REVERT: B  239 MET cc_start: 0.7609 (tpp) cc_final: 0.7184 (ttm)
REVERT: B  446 ARG cc_start: 0.7426 (ttp80) cc_final: 0.6989 (ttp80)
  outliers start: 0
  outliers final: 0
  residues processed: 76
  average time/residue: 0.0904
  time to fit residues: 8.2239
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  : 0.136 
-------------------------------------------------------------------------------
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:    0.0670
   chunk 27 optimal weight:    5.9990
   chunk 26 optimal weight:    3.9990
   chunk 35 optimal weight:    0.5980
   chunk 13 optimal weight:    0.9980
   chunk 22 optimal weight:    0.0070
   chunk 2 optimal weight:    0.6980
   chunk 4 optimal weight:    0.6980
   chunk 24 optimal weight:    0.7980
   chunk 6 optimal weight:    0.0870
   chunk 28 optimal weight:    2.9990
   overall best weight:    0.2914

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4822 r_free = 0.4822 target = 0.233748 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 48)----------------|
| r_work = 0.4540 r_free = 0.4540 target = 0.203742 restraints weight = 13057.709|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 35)----------------|
| r_work = 0.4555 r_free = 0.4555 target = 0.205350 restraints weight = 12133.518|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 25)----------------|
| r_work = 0.4561 r_free = 0.4561 target = 0.206018 restraints weight = 11219.109|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 48)----------------|
| r_work = 0.4576 r_free = 0.4576 target = 0.207499 restraints weight = 10646.548|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 19)----------------|
| r_work = 0.4581 r_free = 0.4581 target = 0.208049 restraints weight = 10082.939|
|-----------------------------------------------------------------------------|
r_work (final): 0.4532
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.4504
moved from start:          0.8189

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.034   3880  Z= 0.131
  Angle     :  0.685   8.533   5263  Z= 0.350
  Chirality :  0.040   0.160    573
  Planarity :  0.005   0.078    649
  Dihedral  : 13.075 160.210    625
  Min Nonbonded Distance : 2.392

Molprobity Statistics.
  All-atom Clashscore : 15.25
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.46 %
    Favored  : 93.54 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  0.00 %
    Favored  : 100.00 %
  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: -1.26 (0.39), residues: 449
  helix:  0.09 (0.36), residues: 209
  sheet: -1.92 (0.91), residues: 22
  loop : -1.64 (0.42), residues: 218

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.007   0.001   ARG B 174 
 TYR   0.007   0.001   TYR B  40 
 PHE   0.024   0.002   PHE B  39 
 TRP   0.010   0.001   TRP B 386 
 HIS   0.003   0.001   HIS B 135 

Details of bonding type rmsd
  covalent geometry    : bond        0.00284 ( 3880)
  covalent geometry    : angle       0.68511 ( 5263)
  hydrogen bonds       : bond        0.04362 (  161)
  hydrogen bonds       : angle       4.95526 (  462)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 1004.40 seconds
wall clock time: 18 minutes 0.66 seconds (1080.66 seconds total)