# Date 2008-01-16 Time 01:10:19 PST -0800 (1200474619.78 s)
#phil __OFF__

Command line arguments: "../321.param" "adp.set_b_iso=10" "sites.shake=0.5" "main.number_of_macro_cycles=5" "--overwrite"

HOST = sunbird.lbl.gov
HOSTTYPE = x86_64-linux
USER = phzwart
PID = 15786
JOB_ID = 5158
SGE_ARCH = lx24-amd64
SGE_TASK_FIRST = 1
SGE_TASK_LAST = 1330
SGE_TASK_ID = 321

-------------------------------------------------------------------------------
  PHENIX: Python-based Hierarchical ENvironment for Integrated Xtallography
  User: phzwart
-------------------------------------------------------------------------------

              phenix.refine: Macromolecular Structure Refinement

-------------------------------------------------------------------------------
Phenix developers include:
  Paul Adams, Pavel Afonine, Vicent Chen, Ian Davis, Kreshna Gopal,
  Ralf Grosse-Kunstleve, Li-Wei Hung, Robert Immormino, Tom Ioerger,
  Airlie McCoy, Erik McKee, Nigel Moriarty, Reetal Pai, Randy Read,
  Jane Richardson, David Richardson, Tod Romo, Jim Sacchettini,
  Nicholas Sauter, Jacob Smith, Laurent Storoni, Tom Terwilliger,
  Peter Zwart
Phenix home page:
  http://www.phenix-online.org/
-------------------------------------------------------------------------------

-------------------------------------------------------------------------------
Phenix components are copyrighted by:
  - Lawrence Berkeley National Laboratory
  - Los Alamos National Laboratory
  - University of Cambridge
  - Duke University
  - Texas Agricultural Experiment Station &
    Texas Engineering Experiment Station
-------------------------------------------------------------------------------

-------------------------------------------------------------------------------
Major third-party components of Phenix include:
    Python, wxwidgets, wxPython, Boost, SCons, Clipper,
    CCP4 Monomer Library, CCP4 I/O libraries, PyCifRW, FFTPACK, L-BFGS
  Enter phenix.acknowledgments for details.
-------------------------------------------------------------------------------

Processing inputs. This may take a minute or two.

Command line parameter definitions:
  refinement.modify_start_model.adp.set_b_iso = 10

  refinement.modify_start_model.sites.shake = 0.5

  refinement.main.number_of_macro_cycles = 5

Working crystal symmetry after inspecting all inputs:
  Unit cell: (69.1963, 47.3993, 85.0941, 90, 90, 90)
  Space group: P 21 21 21 (No. 19)

/net/cci-filer1/vol1/tmp/phzwart/tassos/trial/model.pdb
  Monomer Library directory:
    "/net/rosie/scratch3/phzwart/CCTBX/Sources/mon_lib"
  Total number of atoms: 2823
  Number of models: 1
  Model: 0
    Number of conformers: 2
    Conformer: "A"
      Number of atoms: 2769
      Number of chains: 2
        Number of residues, atoms: 302, 2333
          Classifications: {'peptide': 302}
          Modifications used: {'COO': 1}
          Link IDs: {'PTRANS': 7, 'CIS': 1, 'TRANS': 293}
        Number of residues, atoms: 436, 436
          Classifications: {'water': 436}
          Link IDs: {None: 435}
    Conformer: "B"
      Number of atoms: 2771
      Common with "A": 2717
      Number of chains: 2
        Number of residues, atoms: 302, 2333
          Classifications: {'peptide': 302}
          Modifications used: {'COO': 1}
          Link IDs: {'PTRANS': 7, 'CIS': 1, 'TRANS': 293}
          bond proxies already assigned to first conformer: 2332
        Number of residues, atoms: 438, 438
          Classifications: {'water': 438}
          Link IDs: {None: 437}
  Time building chain proxies: 3.27, per 1000 atoms: 1.16


================================== X-ray data =================================

F-obs:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/trial/1e0w.cns:FOBS,SIGMA

R-free flags:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/trial/1e0w.cns:TEST

Miller array info: /net/cci-filer1/vol1/tmp/phzwart/tassos/trial/1e0w.cns:FOBS,SIGMA
Observation type: xray.amplitude
Type of data: double, size=19589
Type of sigmas: double, size=19589
Number of Miller indices: 19589
Anomalous flag: False
Unit cell: (69.1963, 47.3993, 85.0941, 90, 90, 90)
Space group: P 21 21 21 (No. 19)
Systematic absences: 0
Centric reflections: 2427
Resolution range: 14.8115 1.9705
Completeness in resolution range: 0.962557
Completeness with d_max=infinity: 0.95954

Number of F-obs in resolution range:                   19589
Number of F-obs <= 0:                                  0
Refinement resolution range: d_max =  14.8115
                             d_min =   1.9705

Miller array info: /net/cci-filer1/vol1/tmp/phzwart/tassos/trial/1e0w.cns:TEST
Observation type: None
Type of data: int, size=19589
Type of sigmas: None
Number of Miller indices: 19589
Anomalous flag: False
Unit cell: (69.1963, 47.3993, 85.0941, 90, 90, 90)
Space group: P 21 21 21 (No. 19)
Systematic absences: 0
Centric reflections: 2427
Resolution range: 14.8115 1.9705
Completeness in resolution range: 0.962557
Completeness with d_max=infinity: 0.95954

Test (R-free flags) flag value: 1

Number of work/free reflections by resolution:
                                         work  free  %free
  bin  1: 14.8119 -  4.2157 [2137/2165]  1923   214  10.0%
  bin  2:  4.2157 -  3.3590 [2042/2065]  1838   204  10.0%
  bin  3:  3.3590 -  2.9382 [2032/2054]  1828   204  10.0%
  bin  4:  2.9382 -  2.6712 [1998/2017]  1802   196   9.8%
  bin  5:  2.6712 -  2.4807 [1999/2028]  1793   206  10.3%
  bin  6:  2.4807 -  2.3351 [1972/2014]  1780   192   9.7%
  bin  7:  2.3351 -  2.2185 [1973/2009]  1778   195   9.9%
  bin  8:  2.2185 -  2.1222 [1977/2014]  1774   203  10.3%
  bin  9:  2.1222 -  2.0408 [1944/1976]  1753   191   9.8%
  bin 10:  2.0408 -  1.9705 [1515/2009]  1361   154  10.2%
                                overall 17630  1959  10.0%
Writing MTZ file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/trial/run_321/model_refine_data.mtz


========================== Anomalous scatterer groups =========================

All atoms refined with f_prime=0 and f_double_prime=0.

========================== Set up restraints manager ==========================

  Number of disulfides: simple=3, symmetry=0
    Simple disulfide: " SG  CYS A 168 " - " SG ACYS A 201 " distance=2.08
    Simple disulfide: " SG  CYS A 168 " - " SG BCYS A 201 " distance=1.98
    Simple disulfide: " SG  CYS A 254 " - " SG  CYS A 260 " distance=2.05
  Time building geometry restraints manager: 0.14 seconds
  Histogram of bond lengths:
        1.21 -     1.38: 943
        1.38 -     1.56: 1465
        1.56 -     1.73: 7
        1.73 -     1.90: 21
        1.90 -     2.08: 3
  Bond restraints sorted by residual:
             atom i - atom j            ideal  model  delta   weight residual
  " SG  CYS A 168 " - " SG BCYS A 201 " 2.031  1.983  0.048 2.50e+03 5.87e+00
  " C   GLN A  88 " - " N   GLN A  89 " 1.329  1.360 -0.031 5.10e+03 4.97e+00
  " SG  CYS A 168 " - " SG ACYS A 201 " 2.031  2.075 -0.044 2.50e+03 4.89e+00
  " CB  CYS A 201 " - " SG ACYS A 201 " 1.808  1.738  0.070 9.18e+02 4.46e+00
  " C   PRO A 198 " - " N   ILE A 199 " 1.329  1.301  0.028 5.10e+03 4.10e+00
  ... (remaining 2434 not shown)
  Histogram of nonbonded interaction distances:
        1.60 -     2.26: 27
        2.26 -     2.92: 1483
        2.92 -     3.58: 4566
        3.58 -     4.24: 9269
        4.24 -     4.90: 13238
  Nonbonded interactions sorted by model distance:
             atom i - atom j             model   vdw sym.op. j
  " O   HOH Z  52 " - " O   HOH Z 183 "  1.595 3.040 -x+1,y+1/2,-z+1/2
  " O   HOH Z  18 " - " O   HOH Z 102 "  1.621 3.040 -x+1,y+1/2,-z+1/2
  " O   HOH Z 178 " - " O   HOH Z 403 "  1.718 3.040 -x+1,y-1/2,-z+1/2
  " CE BMET A  47 " - " O  BHOH Z  74 "  1.806 3.460
  " O   HOH Z  37 " - " O   HOH Z 416 "  1.829 3.040 -x+1,y-1/2,-z+1/2
  ... (remaining 28578 not shown)
  Histogram of dihedral angle deviations from ideal:
        0.01 -    17.19: 754
       17.19 -    34.36: 62
       34.36 -    51.54: 27
       51.54 -    68.71: 23
       68.71 -    85.89: 4
  Dihedral angle restraints sorted by residual:
  " CA  PHE A 192 "
  " CB  PHE A 192 "
  " CG  PHE A 192 "
  " CD1 PHE A 192 "
      ideal   model   delta periodicty    weight residual
      90.00    7.91   82.09     2       2.50e-03 1.68e+01
  " N   PRO A  54 "
  " CG  PRO A  54 "
  " CD  PRO A  54 "
  " CB  PRO A  54 "
      ideal   model   delta periodicty    weight residual
      30.00  -27.17   57.17     3       4.44e-03 1.45e+01
  " N   PRO A 280 "
  " CA  PRO A 280 "
  " CB  PRO A 280 "
  " CG  PRO A 280 "
      ideal   model   delta periodicty    weight residual
     -25.00   38.44   56.56     3       4.44e-03 1.42e+01
  ... (remaining 867 not shown)

==================== Fixing bad ADP in input model (if any) ===================


============================== Scattering factors =============================


                ----------X-ray scattering dictionary----------                

Number of scattering types: 4
  Type Number    sf(0)   Gaussians
   S      13     15.96       2
   O     902      7.97       2
   N     437      6.97       2
   C    1471      5.97       2
  sf(0) = scattering factor at diffraction angle 0.


====================== Modifying start model if requested =====================

Setting all isotropic ADP = 10.000: selected atoms: all (2823)
Shaking sites (RMS = 0.500): selected atoms: all (2823)

==================== Fixing bad ADP in input model (if any) ===================


================== Extract refinement strategy and selections =================

individual_sites       = True
rigid_body             = False
individual_adp         = True
group_adp              = False
tls                    = False
individual_occupancies = True
group_occupancies      = False
group_anomalous        = False
size = 2823

n_use            =  2823
n_use_u_iso      =  2823
n_use_u_aniso    =  0
n_grad_site      =  0
n_grad_u_iso     =  0
n_grad_u_aniso   =  0
n_grad_occupancy =  0
n_grad_fp        =  0
n_grad_fdp       =  0
n_anisotropic_flag =  0
total number of scatterers =  2823

==================== Process input NCS or/and find new NCS ====================

Using existing and finding new NCS is disabled.
Use refinement.main.ncs=true to activate it.
Look at refinement.ncs for more NCS related parameters.

=================== Write initial parameters into .eff file ===================

Writing effective parameters to file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/trial/run_321/model_refine_001.eff

Writing geometry restraints to file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/trial/run_321/model_refine_001.geo

CPU time processing inputs: 9.86


============================ Non-default parameters ===========================

A complete record of all parameters was written to the .eff file above.
Below are only the non-defaults.

#phil __ON__
refinement {
  crystal_symmetry {
    unit_cell = 69.19625 47.3993 85.09415 90 90 90
    space_group = "P 21 21 21"
  }
  input {
    pdb {
      file_name = "/net/cci-filer1/vol1/tmp/phzwart/tassos/trial/model.pdb"
    }
    xray_data {
      file_name = "/net/cci-filer1/vol1/tmp/phzwart/tassos/trial/1e0w.cns"
      labels = "FOBS,SIGMA"
      r_free_flags {
        file_name = "/net/cci-filer1/vol1/tmp/phzwart/tassos/trial/1e0w.cns"
        label = "TEST"
        test_flag_value = 1
      }
    }
  }
  output {
    prefix = "model_refine"
    serial = 1
  }
  main {
    number_of_macro_cycles = 5
  }
  modify_start_model {
    adp {
      set_b_iso = 10
    }
    sites {
      shake = 0.5
    }
  }
}
#phil __OFF__


============================= ml refinement start =============================


   ----------structure factors based statistics (before refinement)----------  


                         ----------X-ray data----------                        

|--(resolution: 1.97 - 14.81 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.4724   r_free= 0.4622   ksol= 0.00   Bsol= 0.00   scale= 0.807    |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (0.00,0.00,0.00,0.00,0.00,0.00); trace/3= 0.00                              |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.71 A                  |
| x-ray target function (ml) for work reflections: 6.271091                   |
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
| Bin     Resolution   Compl.  No. Refl.    R-factors          Targets        |
|number     range              work test   work   test        work        test|
|  1: 14.8119 -  4.7017 0.99   1385  155 0.3853 0.3724      6.5634      6.5795|
|  2:  4.7017 -  3.7518 0.99   1339  146 0.3878 0.3846      6.7488       6.771|
|  3:  3.7518 -  3.2835 0.99   1309  152 0.4210 0.3917      6.6488      6.6869|
|  4:  3.2835 -  2.9860 0.99   1301  133 0.4468 0.4316      6.4988      6.4564|
|  5:  2.9860 -  2.7734 0.98   1278  147 0.4932 0.5066      6.3757      6.3968|
|  6:  2.7734 -  2.6109 0.98   1293  142 0.4968 0.5366      6.2724      6.2214|
|  7:  2.6109 -  2.4807 0.99   1279  149 0.5159 0.4658      6.2539      6.1555|
|  8:  2.4807 -  2.3732 0.99   1281  136 0.5160 0.4946       6.183      6.1653|
|  9:  2.3732 -  2.2822 0.98   1286  146 0.5273 0.5470      6.1203      6.1558|
| 10:  2.2822 -  2.2037 0.97   1242  139 0.5242 0.5300      6.1124      6.1018|
| 11:  2.2037 -  2.1350 0.98   1262  144 0.5185 0.5060       6.039      6.0776|
| 12:  2.1350 -  2.0741 0.99   1279  133 0.5344 0.5442      5.9859      6.0189|
| 13:  2.0741 -  2.0197 0.97   1248  134 0.5454 0.5360      5.8996       5.893|
| 14:  2.0197 -  1.9705 0.67    848  103 0.5379 0.4512      5.8901      5.7111|
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
|R-free likelihood based estimates for figures of merit, absolute phase error,|
|and distribution parameters alpha and beta (Acta Cryst. (1995). A51, 880-887)|
|                                                                             |
| Bin     Resolution      No. Refl.   FOM  Phase Scale    Alpha        Beta   |
|  #        range        work  test        error factor                       |
|  1: 14.8119 -  4.7017  1385   155  0.68  35.83   0.81     0.70      74555.56|
|  2:  4.7017 -  3.7518  1339   146  0.70  34.89   0.90     0.77     101586.75|
|  3:  3.7518 -  3.2835  1309   152  0.62  41.98   0.86     0.73     106787.83|
|  4:  3.2835 -  2.9860  1301   133  0.55  47.98   0.82     0.64      91790.30|
|  5:  2.9860 -  2.7734  1278   147  0.45  55.84   0.75     0.54      79684.35|
|  6:  2.7734 -  2.6109  1293   142  0.42  58.08   0.75     0.49      67849.90|
|  7:  2.6109 -  2.4807  1279   149  0.41  59.17   0.73     0.46      62564.00|
|  8:  2.4807 -  2.3732  1281   136  0.41  59.13   0.74     0.47      55025.45|
|  9:  2.3732 -  2.2822  1286   146  0.37  62.28   0.74     0.45      52811.53|
| 10:  2.2822 -  2.2037  1242   139  0.36  63.15   0.76     0.42      49437.77|
| 11:  2.2037 -  2.1350  1262   144  0.31  66.95   0.76     0.37      48434.37|
| 12:  2.1350 -  2.0741  1279   133  0.30  67.32   0.75     0.38      45052.24|
| 13:  2.0741 -  2.0197  1248   134  0.34  64.50   0.74     0.43      36245.43|
| 14:  2.0197 -  1.9705   848   103  0.49  53.49   0.73     0.53      23283.83|
|alpha:            min =        0.37 max =            0.77 mean =         0.53|
|beta:             min =    23283.83 max =       106787.83 mean =     65320.72|
|figures of merit: min =        0.00 max =            1.00 mean =         0.46|
|phase err.(work): min =        0.00 max =           90.00 mean =        54.83|
|phase err.(test): min =        0.00 max =           89.97 mean =        54.81|
|-----------------------------------------------------------------------------|

============================== Outliers rejection =============================

basic_wilson_outliers    = 0
extreme_wilson_outliers  = 0
beamstop_shadow_outliers = 0
total                    = 0

====================== Target weights (before refinement) =====================

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 12.386212             wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 79.555   (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 0.997608              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 82.244   (deg)                 |
|-----------------------------------------------------------------------------|


        ----------Initial model statistics (before refinement)----------       

|-Geometry statistics: start--------------------------------------------------|
|            Histogram of deviations from ideal values for                    |
| Bonds                | Angles                   |  Nonbonded contacts       |
| 0.000 - 0.140:   597 |   0.009 -   7.457:   713 |  1.085 -  1.466:        5 |
| 0.140 - 0.280:   585 |   7.457 -  14.906:   711 |  1.466 -  1.848:        9 |
| 0.280 - 0.420:   441 |  14.906 -  22.354:   630 |  1.848 -  2.229:      125 |
| 0.420 - 0.560:   366 |  22.354 -  29.802:   474 |  2.229 -  2.611:      612 |
| 0.560 - 0.700:   237 |  29.802 -  37.251:   338 |  2.611 -  2.992:     1396 |
| 0.700 - 0.840:   127 |  37.251 -  44.699:   241 |  2.992 -  3.374:     2563 |
| 0.840 - 0.980:    59 |  44.699 -  52.147:   125 |  3.374 -  3.755:     3978 |
| 0.980 - 1.120:    17 |  52.147 -  59.595:    51 |  3.755 -  4.137:     5205 |
| 1.120 - 1.260:     9 |  59.595 -  67.044:    13 |  4.137 -  4.518:     6744 |
| 1.260 - 1.400:     1 |  67.044 -  74.492:     3 |  4.518 -  4.900:     7989 |
|-----------------------------------------------------------------------------|
|-Geometry statistics: start--------------------------------------------------|
|      Type |    Count |    Deviation from ideal |     Targets | Target (sum) |
|           |          |    rmsd      max    min |             |              |
|      bond |     2439 |   0.414    1.400  0.000 |     454.651 |              |
|     angle |     3299 |  24.226   74.492  0.009 |     193.752 |              |
| chirality |      348 |   2.119    6.404  0.009 |     112.240 |       53.299 |
| planarity |      436 |   0.145    0.405  0.000 |     250.485 |              |
|  dihedral |      870 |  33.790  144.062  0.019 |      20.704 |              |
| nonbonded |     2439 |   4.088    4.900  1.085 |       2.199 |              |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 11.637)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      10.00   10.00   10.00    None  None   None       |
|    all(noH): 2823   0      10.00   10.00   10.00    None  None   None       |
|    Sol.    : 438    0      10.00   10.00   10.00    None  None   None       |
|    Mac.    : 2385   0      10.00   10.00   10.00    None  None   None       |
|    Hyd.    : 0      0      None    None    None     None  None   None       |
|    - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -      |
|       Distribution of isotropic (or equivalent) ADP for non-H atoms:        |
|    Bin#      value range     #atoms | Bin#      value range     #atoms      |
|      0:    10.000 -  10.000: 2823   |   5:    10.000 -  10.000:    0        |
|      1:    10.000 -  10.000:    0   |   6:    10.000 -  10.000:    0        |
|      2:    10.000 -  10.000:    0   |   7:    10.000 -  10.000:    0        |
|      3:    10.000 -  10.000:    0   |   8:    10.000 -  10.000:    0        |
|      4:    10.000 -  10.000:    0   |   9:    10.000 -  10.000:    0        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|

|-Occupancies statistics------------------------------------------------------|
| occupancies: max = 1.00   min = 0.30   number of occupancies < 0.1 = 0      |
|-----------------------------------------------------------------------------|

                ----------Modify initial isotropic ADP----------               

Randomizing
|-ADP statistics (Wilson B = 11.637)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.01    19.99   9.86     None  None   None       |
|    all(noH): 2823   0      0.01    19.99   9.86     None  None   None       |
|    Sol.    : 438    0      0.06    19.99   10.10    None  None   None       |
|    Mac.    : 2385   0      0.01    19.98   9.82     None  None   None       |
|    Hyd.    : 0      0      None    None    None     None  None   None       |
|    - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -      |
|       Distribution of isotropic (or equivalent) ADP for non-H atoms:        |
|    Bin#      value range     #atoms | Bin#      value range     #atoms      |
|      0:     0.008 -   2.007:  301   |   5:    10.002 -  12.000:  285        |
|      1:     2.007 -   4.006:  276   |   6:    12.000 -  13.999:  292        |
|      2:     4.006 -   6.004:  309   |   7:    13.999 -  15.998:  289        |
|      3:     6.004 -   8.003:  285   |   8:    15.998 -  17.996:  266        |
|      4:     8.003 -  10.002:  251   |   9:    17.996 -  19.995:  269        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|

*********************** REFINEMENT MACRO_CYCLE 1 OF 5 *************************

|--(resolution: 1.97 - 14.81 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.4780   r_free= 0.4704   ksol= 0.00   Bsol= 0.00   scale= 0.776    |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (0.00,0.00,0.00,0.00,0.00,0.00); trace/3= 0.00                              |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.73 A                  |
| x-ray target function (ml) for work reflections: 6.272243                   |
|-----------------------------------------------------------------------------|

====================== bulk solvent modeling and scaling ======================

|--(resolution: 1.97 - 14.81 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.4635   r_free= 0.4545   ksol= 0.36   Bsol= 15.13   scale= 1.005   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (7.49,9.16,8.36,0.00,0.00,0.00); trace/3= 8.34                              |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.72 A                  |
| x-ray target function (ml) for work reflections: 6.264245                   |
|-----------------------------------------------------------------------------|

========================== Target weights: x-ray data =========================

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 11.536130             wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 81.140   (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 1.089481              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 80.576   (deg)                 |
|-----------------------------------------------------------------------------|


================================ xyz refinement ===============================

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.4635      final r-factor (work) = 0.3722          |
| start r-factor (free) = 0.4545      final r-factor (free) = 0.3946          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 89.4914 = 11.54 * 0.50 * 6.2746 + 1.00 * 53.2991                            |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 35.6971 = 11.54 * 0.50 * 6.1631 + 1.00 * 0.1478                             |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 26     |
|-----------------------------------------------------------------------------|

================================ ADP refinement ===============================


                 ----------Individual ADP refinement----------                 

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.3722      final r-factor (work) = 0.3247          |
| start r-factor (free) = 0.3946      final r-factor (free) = 0.3656          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 6.7289 = 1.09 * 1.00 * 6.1631 + 1.00 * 0.0143                               |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 6.6145 = 1.09 * 1.00 * 6.0568 + 1.00 * 0.0157                               |
|-----------------------------------------------------------------------------|
| number of iterations = 16      |    number of function evaluations = 18     |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 11.637)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.00    64.93   11.93    None  None   None       |
|    all(noH): 2823   0      0.00    64.93   11.93    None  None   None       |
|    Sol.    : 438    0      0.00    64.93   25.79    None  None   None       |
|    Mac.    : 2385   0      0.00    54.04   9.38     None  None   None       |
|    Hyd.    : 0      0      None    None    None     None  None   None       |
|    - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -      |
|       Distribution of isotropic (or equivalent) ADP for non-H atoms:        |
|    Bin#      value range     #atoms | Bin#      value range     #atoms      |
|      0:     0.000 -   6.493: 1111   |   5:    32.465 -  38.959:   97        |
|      1:     6.493 -  12.986:  747   |   6:    38.959 -  45.452:   53        |
|      2:    12.986 -  19.479:  400   |   7:    45.452 -  51.945:   32        |
|      3:    19.479 -  25.972:  223   |   8:    51.945 -  58.438:    8        |
|      4:    25.972 -  32.465:  150   |   9:    58.438 -  64.931:    2        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


======================= Individual occupancy refinement =======================

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.3247 r_free = 0.3656             target_work(ml) = 6.028         |
| occupancies: max = 1.00  min = 0.30   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.3238 r_free = 0.3653             target_work(ml) = 6.027         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        2 |
|-----------------------------------------------------------------------------|

*********************** REFINEMENT MACRO_CYCLE 2 OF 5 *************************

|--(resolution: 1.97 - 14.81 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.3238   r_free= 0.3653   ksol= 0.36   Bsol= 15.13   scale= 1.095   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (7.49,9.16,8.36,0.00,0.00,0.00); trace/3= 8.34                              |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.45 A                  |
| x-ray target function (ml) for work reflections: 6.026557                   |
|-----------------------------------------------------------------------------|

====================== bulk solvent modeling and scaling ======================

|--(resolution: 1.97 - 14.81 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.3207   r_free= 0.3612   ksol= 0.32   Bsol= 31.73   scale= 1.011   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (4.11,5.61,5.54,0.00,0.00,0.00); trace/3= 5.09                              |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.46 A                  |
| x-ray target function (ml) for work reflections: 6.026601                   |
|-----------------------------------------------------------------------------|

========================== Target weights: x-ray data =========================

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 7.444110              wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 97.616   (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 0.485855              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 125.127  (deg)                 |
|-----------------------------------------------------------------------------|


================================ xyz refinement ===============================

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.3207      final r-factor (work) = 0.2150          |
| start r-factor (free) = 0.3612      final r-factor (free) = 0.2578          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 22.6793 = 7.44 * 0.50 * 6.0535 + 1.00 * 0.1478                              |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 21.9321 = 7.44 * 0.50 * 5.8706 + 1.00 * 0.0814                              |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 28     |
|-----------------------------------------------------------------------------|

================================ ADP refinement ===============================


                 ----------Individual ADP refinement----------                 

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.2150      final r-factor (work) = 0.1866          |
| start r-factor (free) = 0.2578      final r-factor (free) = 0.2339          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 2.8697 = 0.49 * 1.00 * 5.8706 + 1.00 * 0.0175                               |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 2.7419 = 0.49 * 1.00 * 5.6202 + 1.00 * 0.0113                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 28     |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 11.637)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.00    70.65   12.30    None  None   None       |
|    all(noH): 2823   0      0.00    70.65   12.30    None  None   None       |
|    Sol.    : 438    0      1.23    70.57   32.69    None  None   None       |
|    Mac.    : 2385   0      0.00    70.65   8.56     None  None   None       |
|    Hyd.    : 0      0      None    None    None     None  None   None       |
|    - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -      |
|       Distribution of isotropic (or equivalent) ADP for non-H atoms:        |
|    Bin#      value range     #atoms | Bin#      value range     #atoms      |
|      0:     0.000 -   7.065: 1363   |   5:    35.323 -  42.387:  102        |
|      1:     7.065 -  14.129:  735   |   6:    42.387 -  49.452:   83        |
|      2:    14.129 -  21.194:  237   |   7:    49.452 -  56.516:   38        |
|      3:    21.194 -  28.258:  128   |   8:    56.516 -  63.581:   21        |
|      4:    28.258 -  35.323:  108   |   9:    63.581 -  70.645:    8        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


======================= Individual occupancy refinement =======================

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.1866 r_free = 0.2339             target_work(ml) = 5.565         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        2 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.1863 r_free = 0.2334             target_work(ml) = 5.565         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        4 |
|-----------------------------------------------------------------------------|

*********************** REFINEMENT MACRO_CYCLE 3 OF 5 *************************

|--(resolution: 1.97 - 14.81 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1863   r_free= 0.2334   ksol= 0.32   Bsol= 31.73   scale= 1.057   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (4.11,5.61,5.54,0.00,0.00,0.00); trace/3= 5.09                              |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.20 A                  |
| x-ray target function (ml) for work reflections: 5.564521                   |
|-----------------------------------------------------------------------------|

====================== bulk solvent modeling and scaling ======================

|--(resolution: 1.97 - 14.81 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1839   r_free= 0.2313   ksol= 0.32   Bsol= 31.73   scale= 1.008   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (2.28,3.69,3.74,0.00,0.00,0.00); trace/3= 3.24                              |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.22 A                  |
| x-ray target function (ml) for work reflections: 5.561991                   |
|-----------------------------------------------------------------------------|

========================== Target weights: x-ray data =========================

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 3.248861              wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 101.122  (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 0.216088              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 131.448  (deg)                 |
|-----------------------------------------------------------------------------|


================================ xyz refinement ===============================

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1839      final r-factor (work) = 0.1370          |
| start r-factor (free) = 0.2313      final r-factor (free) = 0.1804          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 9.2285 = 3.25 * 0.50 * 5.6310 + 1.00 * 0.0813                               |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 8.9061 = 3.25 * 0.50 * 5.4441 + 1.00 * 0.0625                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 28     |
|-----------------------------------------------------------------------------|

================================ ADP refinement ===============================


                 ----------Individual ADP refinement----------                 

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1370      final r-factor (work) = 0.1300          |
| start r-factor (free) = 0.1804      final r-factor (free) = 0.1687          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 1.1876 = 0.22 * 1.00 * 5.4441 + 1.00 * 0.0112                               |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 1.1504 = 0.22 * 1.00 * 5.2815 + 1.00 * 0.0091                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 26     |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 11.637)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.00    72.92   12.20    None  None   None       |
|    all(noH): 2823   0      0.00    72.92   12.20    None  None   None       |
|    Sol.    : 438    0      2.04    65.23   33.61    None  None   None       |
|    Mac.    : 2385   0      0.00    72.92   8.27     None  None   None       |
|    Hyd.    : 0      0      None    None    None     None  None   None       |
|    - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -      |
|       Distribution of isotropic (or equivalent) ADP for non-H atoms:        |
|    Bin#      value range     #atoms | Bin#      value range     #atoms      |
|      0:     0.000 -   7.292: 1458   |   5:    36.458 -  43.749:  103        |
|      1:     7.292 -  14.583:  710   |   6:    43.749 -  51.041:   71        |
|      2:    14.583 -  21.875:  193   |   7:    51.041 -  58.333:   42        |
|      3:    21.875 -  29.166:  104   |   8:    58.333 -  65.624:   17        |
|      4:    29.166 -  36.458:  120   |   9:    65.624 -  72.916:    5        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


======================= Individual occupancy refinement =======================

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.1300 r_free = 0.1687             target_work(ml) = 5.248         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        4 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.1298 r_free = 0.1687             target_work(ml) = 5.247         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        5 |
|-----------------------------------------------------------------------------|

*********************** REFINEMENT MACRO_CYCLE 4 OF 5 *************************

|--(resolution: 1.97 - 14.81 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1298   r_free= 0.1687   ksol= 0.32   Bsol= 31.73   scale= 1.024   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (2.28,3.69,3.74,0.00,0.00,0.00); trace/3= 3.24                              |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.14 A                  |
| x-ray target function (ml) for work reflections: 5.246845                   |
|-----------------------------------------------------------------------------|

====================== bulk solvent modeling and scaling ======================

|--(resolution: 1.97 - 14.81 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1300   r_free= 0.1688   ksol= 0.32   Bsol= 38.85   scale= 1.006   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (1.75,2.90,3.13,0.00,0.00,0.00); trace/3= 2.59                              |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.15 A                  |
| x-ray target function (ml) for work reflections: 5.247541                   |
|-----------------------------------------------------------------------------|

========================== Target weights: x-ray data =========================

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 2.573518              wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 117.077  (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 0.178995              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 144.982  (deg)                 |
|-----------------------------------------------------------------------------|


================================ xyz refinement ===============================

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1300      final r-factor (work) = 0.1165          |
| start r-factor (free) = 0.1688      final r-factor (free) = 0.1584          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 6.8635 = 2.57 * 0.50 * 5.2855 + 1.00 * 0.0623                               |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 6.7584 = 2.57 * 0.50 * 5.1996 + 1.00 * 0.0678                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 27     |
|-----------------------------------------------------------------------------|

================================ ADP refinement ===============================


                 ----------Individual ADP refinement----------                 

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1165      final r-factor (work) = 0.1152          |
| start r-factor (free) = 0.1584      final r-factor (free) = 0.1580          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 0.9398 = 0.18 * 1.00 * 5.1996 + 1.00 * 0.0091                               |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 0.9327 = 0.18 * 1.00 * 5.1611 + 1.00 * 0.0089                               |
|-----------------------------------------------------------------------------|
| number of iterations = 18      |    number of function evaluations = 22     |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 11.637)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.00    73.95   12.03    None  None   None       |
|    all(noH): 2823   0      0.00    73.95   12.03    None  None   None       |
|    Sol.    : 438    0      1.49    66.72   33.10    None  None   None       |
|    Mac.    : 2385   0      0.00    73.95   8.16     None  None   None       |
|    Hyd.    : 0      0      None    None    None     None  None   None       |
|    - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -      |
|       Distribution of isotropic (or equivalent) ADP for non-H atoms:        |
|    Bin#      value range     #atoms | Bin#      value range     #atoms      |
|      0:     0.000 -   7.395: 1493   |   5:    36.977 -  44.372:   89        |
|      1:     7.395 -  14.791:  709   |   6:    44.372 -  51.767:   79        |
|      2:    14.791 -  22.186:  175   |   7:    51.767 -  59.163:   36        |
|      3:    22.186 -  29.581:  119   |   8:    59.163 -  66.558:    7        |
|      4:    29.581 -  36.977:  109   |   9:    66.558 -  73.953:    7        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


======================= Individual occupancy refinement =======================

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.1152 r_free = 0.1580             target_work(ml) = 5.159         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        5 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.1151 r_free = 0.1579             target_work(ml) = 5.158         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        6 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.97 - 14.81 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1151   r_free= 0.1579   ksol= 0.32   Bsol= 38.85   scale= 1.008   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (1.75,2.90,3.13,0.00,0.00,0.00); trace/3= 2.59                              |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.14 A                  |
| x-ray target function (ml) for work reflections: 5.158391                   |
|-----------------------------------------------------------------------------|

====================== bulk solvent modeling and scaling ======================

|--(resolution: 1.97 - 14.81 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1151   r_free= 0.1578   ksol= 0.32   Bsol= 38.52   scale= 1.003   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (1.61,2.67,3.00,0.00,0.00,0.00); trace/3= 2.43                              |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.15 A                  |
| x-ray target function (ml) for work reflections: 5.158601                   |
|-----------------------------------------------------------------------------|

========================== Target weights: x-ray data =========================

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 1.850705              wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 129.424  (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 0.303945              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 103.511  (deg)                 |
|-----------------------------------------------------------------------------|


================================ xyz refinement ===============================

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1151      final r-factor (work) = 0.1142          |
| start r-factor (free) = 0.1578      final r-factor (free) = 0.1566          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 4.8434 = 1.85 * 0.50 * 5.1608 + 1.00 * 0.0678                               |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 4.8305 = 1.85 * 0.50 * 5.1568 + 1.00 * 0.0587                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 27     |
|-----------------------------------------------------------------------------|

================================ ADP refinement ===============================


                 ----------Individual ADP refinement----------                 

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1142      final r-factor (work) = 0.1133          |
| start r-factor (free) = 0.1566      final r-factor (free) = 0.1575          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 1.5779 = 0.30 * 1.00 * 5.1568 + 1.00 * 0.0105                               |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 1.5948 = 0.30 * 1.00 * 5.1474 + 1.00 * 0.0302                               |
|-----------------------------------------------------------------------------|
| number of iterations = 11      |    number of function evaluations = 16     |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 11.637)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.00    74.77   12.07    None  None   None       |
|    all(noH): 2823   0      0.00    74.77   12.07    None  None   None       |
|    Sol.    : 438    0      1.20    67.38   33.35    None  None   None       |
|    Mac.    : 2385   0      0.00    74.77   8.16     None  None   None       |
|    Hyd.    : 0      0      None    None    None     None  None   None       |
|    - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -      |
|       Distribution of isotropic (or equivalent) ADP for non-H atoms:        |
|    Bin#      value range     #atoms | Bin#      value range     #atoms      |
|      0:     0.000 -   7.477: 1507   |   5:    37.386 -  44.863:   91        |
|      1:     7.477 -  14.954:  687   |   6:    44.863 -  52.340:   81        |
|      2:    14.954 -  22.432:  179   |   7:    52.340 -  59.817:   33        |
|      3:    22.432 -  29.909:  124   |   8:    59.817 -  67.295:    7        |
|      4:    29.909 -  37.386:  107   |   9:    67.295 -  74.772:    7        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


======================= Individual occupancy refinement =======================

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.1133 r_free = 0.1575             target_work(ml) = 5.151         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        6 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.1131 r_free = 0.1576             target_work(ml) = 5.151         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        9 |
|-----------------------------------------------------------------------------|

                         ----------X-ray data----------                        

|--(resolution: 1.97 - 14.81 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1131   r_free= 0.1576   ksol= 0.32   Bsol= 38.52   scale= 1.003   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (1.61,2.67,3.00,0.00,0.00,0.00); trace/3= 2.43                              |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.15 A                  |
| x-ray target function (ml) for work reflections: 5.150706                   |
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
| Bin     Resolution   Compl.  No. Refl.    R-factors          Targets        |
|number     range              work test   work   test        work        test|
|  1: 14.8119 -  4.7017 0.99   1385  155 0.1030 0.1290      5.3957      5.5205|
|  2:  4.7017 -  3.7518 0.99   1339  146 0.0892 0.1120       5.459      5.6462|
|  3:  3.7518 -  3.2835 0.99   1309  152 0.1056 0.1535      5.4752      5.8538|
|  4:  3.2835 -  2.9860 0.99   1301  133 0.1230 0.1534      5.4574      5.6257|
|  5:  2.9860 -  2.7734 0.98   1278  147 0.1303 0.1603      5.3277      5.4759|
|  6:  2.7734 -  2.6109 0.98   1293  142 0.1295 0.1982      5.2443      5.5065|
|  7:  2.6109 -  2.4807 0.99   1279  149 0.1200 0.1574      5.1562      5.3759|
|  8:  2.4807 -  2.3732 0.99   1281  136 0.1183 0.1813       5.095      5.3636|
|  9:  2.3732 -  2.2822 0.98   1286  146 0.1189 0.1825       5.038      5.3188|
| 10:  2.2822 -  2.2037 0.97   1242  139 0.1133 0.1758      4.9683       5.189|
| 11:  2.2037 -  2.1350 0.98   1262  144 0.1137 0.1631      4.9145      5.2405|
| 12:  2.1350 -  2.0741 0.99   1279  133 0.1089 0.1749      4.8487      5.1393|
| 13:  2.0741 -  2.0197 0.97   1248  134 0.1144 0.1681      4.7999      5.0362|
| 14:  2.0197 -  1.9705 0.67    848  103 0.1103 0.1757        4.72      4.9445|
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
|R-free likelihood based estimates for figures of merit, absolute phase error,|
|and distribution parameters alpha and beta (Acta Cryst. (1995). A51, 880-887)|
|                                                                             |
| Bin     Resolution      No. Refl.   FOM  Phase Scale    Alpha        Beta   |
|  #        range        work  test        error factor                       |
|  1: 14.8119 -  4.7017  1385   155  0.94   8.77   0.98     0.97       6970.41|
|  2:  4.7017 -  3.7518  1339   146  0.95   8.12   1.02     1.00       9081.71|
|  3:  3.7518 -  3.2835  1309   152  0.94  11.17   1.03     1.01      10424.87|
|  4:  3.2835 -  2.9860  1301   133  0.92  13.51   1.01     1.00      10176.48|
|  5:  2.9860 -  2.7734  1278   147  0.90  15.63   0.99     0.96       8194.41|
|  6:  2.7734 -  2.6109  1293   142  0.90  16.27   0.98     0.95       7313.21|
|  7:  2.6109 -  2.4807  1279   149  0.91  15.57   0.98     0.96       6196.50|
|  8:  2.4807 -  2.3732  1281   136  0.91  15.25   1.00     0.97       5614.67|
|  9:  2.3732 -  2.2822  1286   146  0.90  15.82   1.01     0.99       5052.12|
| 10:  2.2822 -  2.2037  1242   139  0.90  15.59   1.00     0.97       4475.06|
| 11:  2.2037 -  2.1350  1262   144  0.91  15.15   1.00     0.96       4000.49|
| 12:  2.1350 -  2.0741  1279   133  0.92  14.47   1.01     1.00       3651.80|
| 13:  2.0741 -  2.0197  1248   134  0.91  15.69   1.00     1.00       3359.83|
| 14:  2.0197 -  1.9705   848   103  0.90  15.81   0.99     0.95       2837.26|
|alpha:            min =        0.95 max =            1.01 mean =         0.98|
|beta:             min =     2837.26 max =        10424.87 mean =      6359.60|
|figures of merit: min =        0.00 max =            1.00 mean =         0.92|
|phase err.(work): min =        0.00 max =           89.98 mean =        13.95|
|phase err.(test): min =        0.00 max =           88.49 mean =        13.44|
|-----------------------------------------------------------------------------|

====================== bulk solvent modeling and scaling ======================

|--(resolution: 1.97 - 14.81 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1131   r_free= 0.1576   ksol= 0.32   Bsol= 41.78   scale= 1.005   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-0.80,0.25,0.55,0.00,0.00,0.00); trace/3= -0.00                            |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.14 A                  |
| x-ray target function (ml) for work reflections: 5.150638                   |
|-----------------------------------------------------------------------------|

                         ----------X-ray data----------                        

|--(resolution: 1.97 - 14.81 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1131   r_free= 0.1576   ksol= 0.32   Bsol= 41.78   scale= 1.005   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-0.80,0.25,0.55,0.00,0.00,0.00); trace/3= -0.00                            |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.14 A                  |
| x-ray target function (ml) for work reflections: 5.150638                   |
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
| Bin     Resolution   Compl.  No. Refl.    R-factors          Targets        |
|number     range              work test   work   test        work        test|
|  1: 14.8119 -  4.7017 0.99   1385  155 0.1031 0.1292      5.3959      5.5211|
|  2:  4.7017 -  3.7518 0.99   1339  146 0.0894 0.1121        5.46      5.6473|
|  3:  3.7518 -  3.2835 0.99   1309  152 0.1057 0.1536      5.4758      5.8542|
|  4:  3.2835 -  2.9860 0.99   1301  133 0.1230 0.1534      5.4574      5.6257|
|  5:  2.9860 -  2.7734 0.98   1278  147 0.1303 0.1602      5.3274      5.4756|
|  6:  2.7734 -  2.6109 0.98   1293  142 0.1294 0.1982      5.2439      5.5063|
|  7:  2.6109 -  2.4807 0.99   1279  149 0.1200 0.1575       5.156       5.376|
|  8:  2.4807 -  2.3732 0.99   1281  136 0.1183 0.1812      5.0949      5.3632|
|  9:  2.3732 -  2.2822 0.98   1286  146 0.1189 0.1825      5.0379      5.3187|
| 10:  2.2822 -  2.2037 0.97   1242  139 0.1133 0.1758       4.968      5.1886|
| 11:  2.2037 -  2.1350 0.98   1262  144 0.1136 0.1630      4.9142      5.2402|
| 12:  2.1350 -  2.0741 0.99   1279  133 0.1089 0.1750      4.8484       5.139|
| 13:  2.0741 -  2.0197 0.97   1248  134 0.1143 0.1680      4.7996      5.0357|
| 14:  2.0197 -  1.9705 0.67    848  103 0.1102 0.1756      4.7197      4.9442|
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
|R-free likelihood based estimates for figures of merit, absolute phase error,|
|and distribution parameters alpha and beta (Acta Cryst. (1995). A51, 880-887)|
|                                                                             |
| Bin     Resolution      No. Refl.   FOM  Phase Scale    Alpha        Beta   |
|  #        range        work  test        error factor                       |
|  1: 14.8119 -  4.7017  1385   155  0.94   8.77   0.98     0.97       6975.52|
|  2:  4.7017 -  3.7518  1339   146  0.95   8.13   1.02     1.01       9096.35|
|  3:  3.7518 -  3.2835  1309   152  0.93  11.19   1.03     1.02      10442.23|
|  4:  3.2835 -  2.9860  1301   133  0.92  13.51   1.01     1.00      10176.59|
|  5:  2.9860 -  2.7734  1278   147  0.90  15.62   0.99     0.96       8191.95|
|  6:  2.7734 -  2.6109  1293   142  0.90  16.27   0.98     0.95       7308.45|
|  7:  2.6109 -  2.4807  1279   149  0.91  15.57   0.99     0.96       6194.73|
|  8:  2.4807 -  2.3732  1281   136  0.91  15.25   1.00     0.97       5612.00|
|  9:  2.3732 -  2.2822  1286   146  0.90  15.81   1.01     0.99       5049.83|
| 10:  2.2822 -  2.2037  1242   139  0.90  15.58   1.01     0.98       4471.99|
| 11:  2.2037 -  2.1350  1262   144  0.91  15.14   1.01     0.97       3997.68|
| 12:  2.1350 -  2.0741  1279   133  0.92  14.46   1.01     1.00       3648.35|
| 13:  2.0741 -  2.0197  1248   134  0.91  15.69   1.01     1.01       3356.69|
| 14:  2.0197 -  1.9705   848   103  0.90  15.81   1.00     0.95       2834.84|
|alpha:            min =        0.95 max =            1.02 mean =         0.98|
|beta:             min =     2834.84 max =        10442.23 mean =      6360.38|
|figures of merit: min =        0.00 max =            1.00 mean =         0.92|
|phase err.(work): min =        0.00 max =           89.98 mean =        13.95|
|phase err.(test): min =        0.00 max =           88.25 mean =        13.44|
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 11.637)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      2.51    77.28   14.58    None  None   None       |
|    all(noH): 2823   0      2.51    77.28   14.58    None  None   None       |
|    Sol.    : 438    0      3.71    69.89   35.86    None  None   None       |
|    Mac.    : 2385   0      2.51    77.28   10.67    None  None   None       |
|    Hyd.    : 0      0      None    None    None     None  None   None       |
|    - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -      |
|       Distribution of isotropic (or equivalent) ADP for non-H atoms:        |
|    Bin#      value range     #atoms | Bin#      value range     #atoms      |
|      0:     2.512 -   9.989: 1507   |   5:    39.898 -  47.375:   91        |
|      1:     9.989 -  17.466:  687   |   6:    47.375 -  54.852:   81        |
|      2:    17.466 -  24.943:  179   |   7:    54.852 -  62.329:   33        |
|      3:    24.943 -  32.421:  124   |   8:    62.329 -  69.806:    7        |
|      4:    32.421 -  39.898:  107   |   9:    69.806 -  77.284:    7        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


========== residual map mFobs-DFmodel: highest peaks and deepst holes =========


                           ----------peaks----------                           

Number of peaks found at mFobs-DFmodel map (map cutoff=3.00 sigma)= 310         
Filter by distance & map next to the model:
   mapped sites are within: 0.340 - 4.326
   number of sites selected in [dist_min= 0.70, dist_max= 6.00]: 306 from: 310
   mapped sites are within: 0.741 - 4.326

peak=   10.849 closest distance to " CB  VAL A 230 " =    1.446
peak=    7.361 closest distance to " CG2 VAL A 296 " =    1.107
peak=    6.053 closest distance to " CG  LEU A   5 " =    1.253
peak=    5.715 closest distance to " NH2 ARG A  56 " =    2.164
peak=    5.624 closest distance to " CB  VAL A 296 " =    1.067
peak=    5.343 closest distance to " CD2 LEU A   5 " =    1.179
peak=    5.282 closest distance to " O   HOH Z 193 " =    1.814
peak=    5.226 closest distance to " CB  ARG A 275 " =    0.940
peak=    5.215 closest distance to " CG  LEU A 228 " =    1.201
peak=    5.177 closest distance to " CG  PRO A  54 " =    1.308
peak=    5.169 closest distance to " O   HOH Z 402 " =    1.510
peak=    5.023 closest distance to " CB  SER A  63 " =    1.165
peak=    5.005 closest distance to " CB  GLN A 223 " =    1.388
peak=    5.000 closest distance to " CG  PRO A 213 " =    1.274
peak=    4.852 closest distance to " O   HOH Z 126 " =    1.906
peak=    4.790 closest distance to " O   HOH Z 124 " =    1.540
peak=    4.777 closest distance to " O   HOH Z 142 " =    1.685
peak=    4.638 closest distance to " C   PRO A 198 " =    1.511
peak=    4.616 closest distance to " O   HOH Z 128 " =    2.181
peak=    4.610 closest distance to " CB  GLN A 183 " =    1.290
peak=    4.555 closest distance to " O   HOH Z 234 " =    3.625
peak=    4.554 closest distance to " O   SER A  87 " =    2.176
peak=    4.548 closest distance to " CB  GLU A 152 " =    1.141
peak=    4.522 closest distance to " O   HOH Z  85 " =    1.573
peak=    4.509 closest distance to " CB  VAL A 230 " =    1.186
peak=    4.492 closest distance to " O   HOH Z  48 " =    1.811
peak=    4.491 closest distance to " O   HOH Z 278 " =    1.230
peak=    4.487 closest distance to " CB  SER A   3 " =    1.265
peak=    4.483 closest distance to " O   HOH Z 232 " =    2.287
peak=    4.434 closest distance to " CB  PRO A  54 " =    0.915
peak=    4.433 closest distance to " O   HOH Z  59 " =    2.275
peak=    4.430 closest distance to " NE2 GLN A  11 " =    1.093
peak=    4.429 closest distance to " O   HOH Z 236 " =    1.867
peak=    4.403 closest distance to " O   HOH Z 272 " =    1.922
peak=    4.388 closest distance to " O   HOH Z 368 " =    2.183
peak=    4.377 closest distance to " CG  PRO A 198 " =    1.195
peak=    4.341 closest distance to " O   HOH Z  97 " =    1.924
peak=    4.292 closest distance to " O   HOH Z 316 " =    2.819
peak=    4.262 closest distance to " CA  VAL A  41 " =    0.816
peak=    4.254 closest distance to " O   HOH Z 403 " =    1.804
peak=    4.237 closest distance to " O   HOH Z 298 " =    1.837
peak=    4.231 closest distance to " O   HOH Z  80 " =    1.704
peak=    4.231 closest distance to " O   HOH Z  97 " =    2.500
peak=    4.230 closest distance to " CD2 LEU A 228 " =    1.201
peak=    4.228 closest distance to " O   HOH Z 423 " =    1.842
peak=    4.221 closest distance to " O   HOH Z  54 " =    1.562
peak=    4.195 closest distance to " CG  PRO A 243 " =    1.155
peak=    4.176 closest distance to " CG1BVAL A  72 " =    1.657
peak=    4.161 closest distance to " O   HOH Z 227 " =    1.611
peak=    4.150 closest distance to " O   HOH Z 209 " =    2.346
peak=    4.145 closest distance to " O   HOH Z 346 " =    1.475
peak=    4.111 closest distance to " O   TRP A 274 " =    1.936
peak=    4.086 closest distance to " O   HOH Z 414 " =    1.615
peak=    4.085 closest distance to " CA  TYR A  30 " =    0.950
peak=    4.084 closest distance to " CA  ALA A  21 " =    1.202
peak=    4.065 closest distance to " O   HOH Z 327 " =    1.681
peak=    4.057 closest distance to " CB  TRP A 179 " =    1.233
peak=    4.048 closest distance to " OD1 ASN A  69 " =    2.616
peak=    4.044 closest distance to " CB  GLU A 128 " =    1.073
peak=    4.030 closest distance to " O   HOH Z 357 " =    1.906
peak=    4.030 closest distance to " O   HOH Z 411 " =    3.557
peak=    4.020 closest distance to " O   HOH Z 303 " =    2.037
peak=    4.012 closest distance to " O   HOH Z 345 " =    2.832
peak=    4.012 closest distance to " O   HOH Z 197 " =    2.648
peak=    4.006 closest distance to " CB  SER A  26 " =    1.690
peak=    4.003 closest distance to " N   ASN A  39 " =    1.153
peak=    3.999 closest distance to " ND2 ASN A 187 " =    1.587
peak=    3.992 closest distance to " CB  ASN A 148 " =    1.372
peak=    3.992 closest distance to " CD  ARG A 269 " =    1.077
peak=    3.992 closest distance to " O   HOH Z 371 " =    3.186
peak=    3.968 closest distance to " CB  TYR A 169 " =    0.761
peak=    3.965 closest distance to " CB  ASN A  39 " =    0.836
peak=    3.955 closest distance to " O   HOH Z 369 " =    2.298
peak=    3.949 closest distance to " CB  GLU A 277 " =    3.510
peak=    3.946 closest distance to " O   HOH Z 344 " =    2.683
peak=    3.926 closest distance to " CA  ASP A 140 " =    1.165
peak=    3.919 closest distance to " O   HOH Z 130 " =    2.383
peak=    3.917 closest distance to " O   HOH Z 416 " =    2.684
peak=    3.913 closest distance to " O   HOH Z 189 " =    2.439
peak=    3.904 closest distance to " CG2 ILE A  20 " =    1.453
peak=    3.895 closest distance to " CB  ALA A   9 " =    1.585
peak=    3.891 closest distance to " CG  ARG A  66 " =    1.032
peak=    3.883 closest distance to " O   HOH Z 389 " =    1.876
peak=    3.881 closest distance to " CB  ARG A  79 " =    1.348
peak=    3.865 closest distance to " CB  ARG A 139 " =    0.955
peak=    3.861 closest distance to " CB  VAL A 265 " =    1.248
peak=    3.829 closest distance to " O   HOH Z 102 " =    1.264
peak=    3.825 closest distance to " O   HOH Z 245 " =    1.408
peak=    3.823 closest distance to " O   HOH Z  61 " =    1.623
peak=    3.821 closest distance to " O   HOH Z 137 " =    1.650
peak=    3.815 closest distance to " O   HOH Z 417 " =    3.373
peak=    3.813 closest distance to " NZ  LYS A 117 " =    3.010
peak=    3.800 closest distance to " CB  ALA A 248 " =    1.345
peak=    3.799 closest distance to " O   HOH Z  78 " =    1.604
peak=    3.796 closest distance to " O   HOH Z 130 " =    2.882
peak=    3.792 closest distance to " O   HOH Z  40 " =    1.700
peak=    3.790 closest distance to " O   HOH Z 419 " =    1.625
peak=    3.784 closest distance to " CG2 ILE A 120 " =    1.326
peak=    3.781 closest distance to " CB  PRO A 198 " =    1.063
peak=    3.768 closest distance to " OD2 ASP A 286 " =    2.701
peak=    3.766 closest distance to " CG  GLN A  77 " =    2.258
peak=    3.765 closest distance to " O   HOH Z 203 " =    1.670
peak=    3.764 closest distance to " O   HOH Z 250 " =    1.495
peak=    3.761 closest distance to " O   HOH Z 426 " =    1.435
peak=    3.761 closest distance to " CA  LYS A 117 " =    1.329
peak=    3.751 closest distance to " O   HOH Z 280 " =    2.895
peak=    3.742 closest distance to " O   HOH Z 134 " =    1.531
peak=    3.728 closest distance to " O   HOH Z 128 " =    1.896
peak=    3.710 closest distance to " CB  ALA A   1 " =    1.207
peak=    3.705 closest distance to " O   HOH Z  47 " =    1.629
peak=    3.700 closest distance to " O   HOH Z 273 " =    2.761
peak=    3.700 closest distance to " CD2 TRP A 179 " =    1.402
peak=    3.700 closest distance to " O   HOH Z  54 " =    2.394
peak=    3.691 closest distance to " CA  ARG A  36 " =    1.028
peak=    3.688 closest distance to " CB  TRP A 266 " =    1.018
peak=    3.687 closest distance to " CE1 TYR A 186 " =    1.273
peak=    3.679 closest distance to " O   ASP A 124 " =    1.232
peak=    3.671 closest distance to " O   HOH Z 366 " =    2.903
peak=    3.667 closest distance to " O   HOH Z 263 " =    1.563
peak=    3.664 closest distance to " CB  ALA A 295 " =    1.091
peak=    3.664 closest distance to " N   SER A 288 " =    1.796
peak=    3.663 closest distance to " CA  ALA A  51 " =    1.014
peak=    3.661 closest distance to " O   HOH Z  63 " =    2.422
peak=    3.660 closest distance to " O   HOH Z  43 " =    2.245
peak=    3.656 closest distance to " O   HOH Z 367 " =    3.347
peak=    3.651 closest distance to " O   HOH Z 261 " =    2.089
peak=    3.649 closest distance to " O   HOH Z 406 " =    1.536
peak=    3.643 closest distance to " O   HOH Z 154 " =    1.439
peak=    3.631 closest distance to " O   HOH Z  44 " =    1.941
peak=    3.629 closest distance to " O   HOH Z 411 " =    1.783
peak=    3.606 closest distance to " O   HOH Z  49 " =    2.410
peak=    3.600 closest distance to " CG1 ILE A  33 " =    1.306
peak=    3.590 closest distance to " O   HOH Z 247 " =    1.300
peak=    3.586 closest distance to " CB  ARG A 190 " =    1.717
peak=    3.582 closest distance to " O   HOH Z  15 " =    2.092
peak=    3.579 closest distance to " O   HOH Z 322 " =    2.144
peak=    3.573 closest distance to " CD  LYS A 166 " =    1.315
peak=    3.556 closest distance to " O   HOH Z 209 " =    2.320
peak=    3.544 closest distance to " O   HOH Z 193 " =    2.043
peak=    3.542 closest distance to " CD  ARG A 159 " =    0.744
peak=    3.539 closest distance to " OG1 THR A 294 " =    2.325
peak=    3.533 closest distance to " NH2 ARG A 156 " =    1.091
peak=    3.533 closest distance to " CG1 VAL A 296 " =    1.141
peak=    3.531 closest distance to " CG2AVAL A 121 " =    2.170
peak=    3.531 closest distance to " CA  ASP A 191 " =    1.135
peak=    3.530 closest distance to " CA  ASN A 215 " =    1.213
peak=    3.529 closest distance to " CG2 THR A 221 " =    1.226
peak=    3.526 closest distance to " O   HOH Z 108 " =    2.432
peak=    3.524 closest distance to " O   HOH Z 214 " =    2.615
peak=    3.523 closest distance to " O   HOH Z  66 " =    2.015
peak=    3.520 closest distance to " OD2 ASP A 298 " =    3.952
peak=    3.519 closest distance to " OG BSER A 164 " =    2.216
peak=    3.517 closest distance to " O   HOH Z 148 " =    3.163
peak=    3.516 closest distance to " CB  VAL A 202 " =    1.484
peak=    3.512 closest distance to " O   HOH Z 280 " =    2.448
peak=    3.509 closest distance to " CG  GLN A  58 " =    2.624
peak=    3.507 closest distance to " O   HOH Z  21 " =    1.840
peak=    3.506 closest distance to " O   HOH Z 380 " =    1.935
peak=    3.506 closest distance to " O   HOH Z 250 " =    1.368
peak=    3.500 closest distance to " OE1 GLU A   2 " =    2.077
peak=    3.498 closest distance to " O   HOH Z 251 " =    1.749
peak=    3.494 closest distance to " O   HOH Z 427 " =    2.757
peak=    3.491 closest distance to " O   HOH Z 261 " =    2.106
peak=    3.488 closest distance to " CA  ASP A 162 " =    1.041
peak=    3.486 closest distance to " C   ALA A   1 " =    1.783
peak=    3.476 closest distance to " O   HOH Z 421 " =    1.755
peak=    3.474 closest distance to " CZ  PHE A 218 " =    1.058
peak=    3.473 closest distance to " CE1 HIS A 108 " =    1.158
peak=    3.467 closest distance to " O   HOH Z 408 " =    1.596
peak=    3.465 closest distance to " O   HOH Z 118 " =    1.220
peak=    3.462 closest distance to " CD1 LEU A  96 " =    0.741
peak=    3.460 closest distance to " CB  THR A  31 " =    1.595
peak=    3.457 closest distance to " O   GLY A  91 " =    1.405
peak=    3.456 closest distance to " NZ  LYS A  76 " =    1.540
peak=    3.454 closest distance to " OE1 GLN A  11 " =    1.739
peak=    3.453 closest distance to " CD BLYS A 290 " =    1.123
peak=    3.453 closest distance to " O   HOH Z 383 " =    1.864
peak=    3.452 closest distance to " O   HOH Z 420 " =    1.956
peak=    3.450 closest distance to " CD  GLN A 194 " =    1.524
peak=    3.447 closest distance to " CB AVAL A  41 " =    1.197
peak=    3.447 closest distance to " O   HOH Z  71 " =    1.887
peak=    3.447 closest distance to " O   HOH Z 344 " =    1.897
peak=    3.446 closest distance to " CA  GLN A 194 " =    1.099
peak=    3.435 closest distance to " CB  GLN A 205 " =    1.191
peak=    3.432 closest distance to " CB  TYR A 169 " =    0.851
peak=    3.431 closest distance to " CB  GLN A 278 " =    0.811
peak=    3.430 closest distance to " CD2 HIS A  81 " =    1.074
peak=    3.423 closest distance to " O   HOH Z 329 " =    3.738
peak=    3.423 closest distance to " O   HOH Z 422 " =    2.612
peak=    3.417 closest distance to " N   ARG A 190 " =    1.033
peak=    3.414 closest distance to " O   HOH Z 374 " =    2.499
peak=    3.407 closest distance to " O   HOH Z 345 " =    1.613
peak=    3.405 closest distance to " O   HOH Z 248 " =    1.677
peak=    3.401 closest distance to " O   HOH Z  67 " =    1.728
peak=    3.390 closest distance to " O   HOH Z 147 " =    1.760
peak=    3.389 closest distance to " O   HOH Z 404 " =    2.166
peak=    3.381 closest distance to " OH  TYR A 116 " =    1.099
peak=    3.379 closest distance to " O   HOH Z 109 " =    2.368
peak=    3.375 closest distance to " C   ALA A 299 " =    0.898
peak=    3.368 closest distance to " O   MET A 105 " =    1.838
peak=    3.366 closest distance to " CA  ASN A 176 " =    1.026
peak=    3.361 closest distance to " O   HOH Z 423 " =    3.267
peak=    3.360 closest distance to " CZ2 TRP A 179 " =    1.843
peak=    3.359 closest distance to " O   HOH Z 435 " =    1.902
peak=    3.358 closest distance to " O   HOH Z 132 " =    2.709
peak=    3.353 closest distance to " N   SER A 135 " =    1.255
peak=    3.352 closest distance to " CG AARG A 275 " =    1.149
peak=    3.351 closest distance to " O   HOH Z 313 " =    1.741
peak=    3.343 closest distance to " OG BSER A 212 " =    2.719
peak=    3.342 closest distance to " CG1 VAL A 153 " =    1.027
peak=    3.341 closest distance to " CB  ALA A  71 " =    1.209
peak=    3.337 closest distance to " CG2 ILE A 106 " =    0.808
peak=    3.334 closest distance to " CB  GLN A  88 " =    1.157
peak=    3.331 closest distance to " CZ AARG A 102 " =    1.790
peak=    3.330 closest distance to " O   HOH Z 155 " =    2.909
peak=    3.330 closest distance to " O   HOH Z 291 " =    1.616
peak=    3.330 closest distance to " O   HOH Z 332 " =    1.442
peak=    3.311 closest distance to " O   HOH Z 438 " =    2.078
peak=    3.307 closest distance to " NH2BARG A 145 " =    2.128
peak=    3.306 closest distance to " O   HOH Z 158 " =    3.051
peak=    3.299 closest distance to " CG  MET A 185 " =    1.157
peak=    3.298 closest distance to " O   HOH Z 244 " =    1.597
peak=    3.291 closest distance to " O   HOH Z 227 " =    1.570
peak=    3.290 closest distance to " O   HOH Z 303 " =    1.581
peak=    3.288 closest distance to " CE  LYS A 119 " =    0.989
peak=    3.287 closest distance to " CA  ALA A 158 " =    1.275
peak=    3.286 closest distance to " O   HOH Z 425 " =    2.002
peak=    3.285 closest distance to " OG  SER A 276 " =    1.364
peak=    3.285 closest distance to " CZ2 TRP A 274 " =    1.630
peak=    3.285 closest distance to " CG2 ILE A 234 " =    2.045
peak=    3.281 closest distance to " CD1 ILE A 106 " =    1.102
peak=    3.276 closest distance to " O   HOH Z 118 " =    1.338
peak=    3.276 closest distance to " NH1 ARG A 138 " =    1.334
peak=    3.273 closest distance to " O   HOH Z 286 " =    2.304
peak=    3.270 closest distance to " CB  THR A 279 " =    1.577
peak=    3.266 closest distance to " O   HOH Z 299 " =    4.326
peak=    3.265 closest distance to " CA  GLY A  80 " =    0.816
peak=    3.254 closest distance to " O   HOH Z 155 " =    1.543
peak=    3.248 closest distance to " NH2 ARG A  79 " =    1.282
peak=    3.247 closest distance to " CG1 ILE A  49 " =    1.423
peak=    3.247 closest distance to " O   HOH Z 227 " =    2.197
peak=    3.246 closest distance to " CB  ALA A 291 " =    1.257
peak=    3.245 closest distance to " O   HOH Z 334 " =    1.359
peak=    3.244 closest distance to " O   HOH Z 215 " =    1.466
peak=    3.241 closest distance to " O   HOH Z 164 " =    2.070
peak=    3.239 closest distance to " O   HOH Z 359 " =    1.525
peak=    3.238 closest distance to " CD2 TYR A  30 " =    0.906
peak=    3.238 closest distance to " CG2 THR A 294 " =    1.599
peak=    3.231 closest distance to " O   PHE A  38 " =    1.880
peak=    3.227 closest distance to " NH1AARG A 145 " =    1.092
peak=    3.217 closest distance to " CE BMET A  47 " =    0.921
peak=    3.217 closest distance to " CB  GLU A  46 " =    1.041
peak=    3.209 closest distance to " CA  ALA A 295 " =    1.076
peak=    3.209 closest distance to " O   HOH Z 261 " =    1.685
peak=    3.204 closest distance to " O   HOH Z 188 " =    1.957
peak=    3.200 closest distance to " O   HOH Z 192 " =    1.905
peak=    3.199 closest distance to " OD1 ASP A 231 " =    1.910
peak=    3.198 closest distance to " CA  ARG A 195 " =    1.145
peak=    3.193 closest distance to " CA  PHE A  59 " =    0.914
peak=    3.191 closest distance to " O   HOH Z  83 " =    1.526
peak=    3.186 closest distance to " O   HOH Z 394 " =    1.468
peak=    3.185 closest distance to " CB  PRO A 243 " =    1.184
peak=    3.184 closest distance to " ND2 ASN A 110 " =    1.627
peak=    3.184 closest distance to " O   HOH Z 406 " =    1.103
peak=    3.181 closest distance to " CB  ALA A 100 " =    1.140
peak=    3.177 closest distance to " CH2 TRP A 274 " =    2.033
peak=    3.174 closest distance to " CB  SER A 273 " =    0.811
peak=    3.173 closest distance to " O   HOH Z 180 " =    2.160
peak=    3.170 closest distance to " O   HOH Z  50 " =    2.053
peak=    3.164 closest distance to " O   SER A 164 " =    1.278
peak=    3.164 closest distance to " CG  GLN A  89 " =    1.589
peak=    3.164 closest distance to " O   HOH Z 112 " =    1.598
peak=    3.157 closest distance to " CA  LYS A 290 " =    1.215
peak=    3.156 closest distance to " CB  ILE A 120 " =    1.518
peak=    3.151 closest distance to " CA  GLU A  37 " =    0.846
peak=    3.149 closest distance to " O   HOH Z 213 " =    1.630
peak=    3.146 closest distance to " O   HOH Z 185 " =    1.649
peak=    3.144 closest distance to " CD  LYS A 119 " =    1.955
peak=    3.143 closest distance to " O   HOH Z 279 " =    2.093
peak=    3.142 closest distance to " O   HOH Z 197 " =    1.909
peak=    3.139 closest distance to " O   HOH Z   9 " =    2.152
peak=    3.138 closest distance to " CA  ASN A 217 " =    1.356
peak=    3.136 closest distance to " O   HOH Z 409 " =    3.733
peak=    3.128 closest distance to " N   ARG A 156 " =    1.341
peak=    3.125 closest distance to " O   HOH Z 388 " =    1.981
peak=    3.122 closest distance to " O   HOH Z  39 " =    2.781
peak=    3.118 closest distance to " CG2 THR A  42 " =    0.818
peak=    3.118 closest distance to " O   HOH Z  59 " =    2.353
peak=    3.111 closest distance to " O   HOH Z  11 " =    2.291
peak=    3.109 closest distance to " O   HOH Z  46 " =    1.478
peak=    3.107 closest distance to " O   HOH Z  66 " =    1.722
peak=    3.107 closest distance to " CD1 ILE A  33 " =    1.635
peak=    3.103 closest distance to " CB  ASN A 215 " =    1.090
peak=    3.098 closest distance to " CG  LEU A 281 " =    1.070
peak=    3.096 closest distance to " CA  ARG A  66 " =    0.922
peak=    3.088 closest distance to " O   HOH Z 266 " =    1.454
peak=    3.088 closest distance to " O   HOH Z  78 " =    2.065
peak=    3.084 closest distance to " CB  TYR A 247 " =    0.963
peak=    3.077 closest distance to " OG  SER A  97 " =    2.547
peak=    3.076 closest distance to " OD1 ASN A  45 " =    1.278
peak=    3.073 closest distance to " O   ILE A  33 " =    1.251
peak=    3.068 closest distance to " CB  GLN A 103 " =    0.879
peak=    3.068 closest distance to " OG BSER A 258 " =    3.290
peak=    3.061 closest distance to " NH1 ARG A 269 " =    0.854
peak=    3.045 closest distance to " O   HOH Z 362 " =    3.436
peak=    3.037 closest distance to " CG1 ILE A 120 " =    1.179

                           ----------holes----------                           

Number of peaks found at mFobs-DFmodel map (map cutoff=3.00 sigma)= 202         
Filter by distance & map next to the model:
   mapped sites are within: 0.603 - 5.342
   number of sites selected in [dist_min= 0.70, dist_max= 6.00]: 197 from: 202
   mapped sites are within: 0.818 - 5.342

peak=   -4.686 closest distance to " CD  ARG A 156 " =    2.061
peak=   -4.529 closest distance to " O   HOH Z 290 " =    0.949
peak=   -4.432 closest distance to " CG2BVAL A  41 " =    2.663
peak=   -4.373 closest distance to " SG  CYS A 254 " =    3.168
peak=   -4.352 closest distance to " O   HOH Z 266 " =    4.530
peak=   -4.308 closest distance to " O   PRO A 163 " =    2.031
peak=   -4.291 closest distance to " CD1 LEU A 101 " =    2.513
peak=   -4.236 closest distance to " O   HOH Z 166 " =    1.812
peak=   -4.221 closest distance to " C   HIS A 108 " =    1.204
peak=   -4.099 closest distance to " CB  ALA A 161 " =    2.486
peak=   -4.090 closest distance to " OXT GLY A 302 " =    2.737
peak=   -4.069 closest distance to " O   HOH Z  13 " =    1.479
peak=   -4.015 closest distance to " CE2 TYR A  30 " =    2.792
peak=   -4.012 closest distance to " CG  ASP A 231 " =    0.875
peak=   -3.992 closest distance to " O   HOH Z 351 " =    1.475
peak=   -3.978 closest distance to " C   THR A 279 " =    1.194
peak=   -3.886 closest distance to " N   ALA A 248 " =    1.777
peak=   -3.868 closest distance to " ND2 ASN A  45 " =    1.002
peak=   -3.846 closest distance to " O   VAL A  67 " =    2.524
peak=   -3.812 closest distance to " O   HOH Z  11 " =    1.844
peak=   -3.773 closest distance to " N   GLN A  58 " =    1.974
peak=   -3.770 closest distance to " OG BSER A 134 " =    1.303
peak=   -3.755 closest distance to " CB  ALA A 248 " =    1.929
peak=   -3.740 closest distance to " O   HOH Z 196 " =    2.109
peak=   -3.740 closest distance to " C   MET A 188 " =    1.566
peak=   -3.735 closest distance to " O   HOH Z 407 " =    2.883
peak=   -3.711 closest distance to " OG ASER A 134 " =    1.219
peak=   -3.711 closest distance to " O   PRO A 198 " =    1.227
peak=   -3.707 closest distance to " O   HOH Z 231 " =    2.099
peak=   -3.704 closest distance to " CD2 LEU A 300 " =    2.779
peak=   -3.703 closest distance to " CB  ALA A 291 " =    2.337
peak=   -3.697 closest distance to " CD  GLN A  58 " =    1.238
peak=   -3.690 closest distance to " O   HOH Z 166 " =    1.802
peak=   -3.684 closest distance to " O   HOH Z  71 " =    1.115
peak=   -3.679 closest distance to " O   MET A  40 " =    2.707
peak=   -3.674 closest distance to " O   HOH Z  17 " =    1.159
peak=   -3.668 closest distance to " ND2 ASN A 187 " =    1.514
peak=   -3.665 closest distance to " O   HOH Z 174 " =    4.305
peak=   -3.649 closest distance to " O   HOH Z 118 " =    3.104
peak=   -3.645 closest distance to " CD  ARG A 139 " =    1.605
peak=   -3.641 closest distance to " O   HOH Z  37 " =    1.914
peak=   -3.640 closest distance to " N   THR A 157 " =    1.570
peak=   -3.636 closest distance to " OG  SER A  97 " =    2.286
peak=   -3.633 closest distance to " OD1 ASN A  39 " =    2.197
peak=   -3.631 closest distance to " N   ALA A 226 " =    1.922
peak=   -3.627 closest distance to " O   HOH Z 426 " =    1.743
peak=   -3.621 closest distance to " CG  GLN A 223 " =    2.143
peak=   -3.616 closest distance to " CB  PHE A 192 " =    1.904
peak=   -3.614 closest distance to " O   ASN A  45 " =    1.820
peak=   -3.611 closest distance to " CB  GLN A  11 " =    1.855
peak=   -3.595 closest distance to " CD  GLN A  88 " =    1.080
peak=   -3.595 closest distance to " NH2 ARG A  66 " =    1.541
peak=   -3.589 closest distance to " O   HOH Z 250 " =    1.392
peak=   -3.581 closest distance to " NH2AARG A 275 " =    4.853
peak=   -3.580 closest distance to " CD1 PHE A  59 " =    2.297
peak=   -3.576 closest distance to " CB  ASN A  39 " =    2.168
peak=   -3.573 closest distance to " CD1 LEU A 255 " =    2.720
peak=   -3.567 closest distance to " O   GLY A  80 " =    2.406
peak=   -3.563 closest distance to " O   HOH Z 423 " =    2.275
peak=   -3.557 closest distance to " O   HOH Z  92 " =    1.689
peak=   -3.551 closest distance to " O   SER A 210 " =    1.940
peak=   -3.551 closest distance to " O   ALA A 256 " =    1.467
peak=   -3.544 closest distance to " NE2 GLN A  88 " =    1.930
peak=   -3.544 closest distance to " CH2 TRP A 179 " =    1.301
peak=   -3.542 closest distance to " CD  LYS A 289 " =    2.491
peak=   -3.532 closest distance to " CZ  TYR A 169 " =    1.789
peak=   -3.527 closest distance to " O   HOH Z 165 " =    1.912
peak=   -3.523 closest distance to " CD1 PHE A  59 " =    1.889
peak=   -3.520 closest distance to " O   ALA A 161 " =    1.674
peak=   -3.517 closest distance to " O   HOH Z 193 " =    1.531
peak=   -3.511 closest distance to " NH2 ARG A  79 " =    1.940
peak=   -3.506 closest distance to " CB  PRO A 163 " =    2.635
peak=   -3.500 closest distance to " CG2 VAL A 296 " =    1.094
peak=   -3.496 closest distance to " C   ASP A 231 " =    2.437
peak=   -3.492 closest distance to " OG  SER A   3 " =    1.519
peak=   -3.484 closest distance to " CE  LYS A 166 " =    3.034
peak=   -3.484 closest distance to " CG  ASP A  50 " =    2.450
peak=   -3.473 closest distance to " O   HOH Z  43 " =    1.900
peak=   -3.471 closest distance to " CG  GLU A 277 " =    1.140
peak=   -3.467 closest distance to " O   HOH Z  63 " =    1.060
peak=   -3.465 closest distance to " CG  LYS A 193 " =    2.249
peak=   -3.465 closest distance to " CG1 VAL A 112 " =    2.552
peak=   -3.461 closest distance to " CB  PRO A 243 " =    2.628
peak=   -3.460 closest distance to " O   GLY A 196 " =    1.026
peak=   -3.459 closest distance to " O   ALA A  51 " =    1.452
peak=   -3.457 closest distance to " CE2 PHE A 218 " =    2.688
peak=   -3.455 closest distance to " O   HOH Z 353 " =    2.078
peak=   -3.443 closest distance to " CD1 LEU A  25 " =    2.476
peak=   -3.439 closest distance to " OG BSER A 134 " =    1.670
peak=   -3.432 closest distance to " N   GLY A 133 " =    1.938
peak=   -3.422 closest distance to " C   ALA A 158 " =    1.242
peak=   -3.418 closest distance to " O   GLY A  75 " =    1.779
peak=   -3.415 closest distance to " CG  GLU A  53 " =    1.507
peak=   -3.412 closest distance to " O   HOH Z 234 " =    4.070
peak=   -3.411 closest distance to " N   SER A 276 " =    1.280
peak=   -3.411 closest distance to " O   HOH Z 123 " =    2.333
peak=   -3.408 closest distance to " O   HOH Z 431 " =    1.891
peak=   -3.407 closest distance to " CB  ASP A 162 " =    2.561
peak=   -3.402 closest distance to " O   VAL A 125 " =    2.282
peak=   -3.400 closest distance to " N   THR A 235 " =    1.316
peak=   -3.400 closest distance to " CB  ALA A 248 " =    2.260
peak=   -3.397 closest distance to " O   HOH Z  44 " =    2.147
peak=   -3.375 closest distance to " CE  MET A 105 " =    2.120
peak=   -3.366 closest distance to " O   HOH Z 411 " =    1.490
peak=   -3.363 closest distance to " N   HIS A 115 " =    2.010
peak=   -3.357 closest distance to " O   HOH Z 191 " =    5.342
peak=   -3.348 closest distance to " CD  GLN A  11 " =    0.818
peak=   -3.344 closest distance to " OG  SER A 206 " =    1.561
peak=   -3.340 closest distance to " N   SER A 206 " =    1.857
peak=   -3.337 closest distance to " CB  PRO A 280 " =    2.072
peak=   -3.335 closest distance to " O   HOH Z  52 " =    1.658
peak=   -3.334 closest distance to " O   SER A 146 " =    0.968
peak=   -3.333 closest distance to " O   VAL A 197 " =    1.307
peak=   -3.329 closest distance to " ND2 ASN A  39 " =    1.144
peak=   -3.324 closest distance to " O   HOH Z  11 " =    1.757
peak=   -3.323 closest distance to " O   PHE A 218 " =    1.684
peak=   -3.321 closest distance to " O   HOH Z 151 " =    1.449
peak=   -3.320 closest distance to " O   HOH Z 377 " =    1.290
peak=   -3.319 closest distance to " OXT GLY A 302 " =    3.434
peak=   -3.309 closest distance to " CE3 TRP A 150 " =    2.067
peak=   -3.306 closest distance to " CD2 TYR A 293 " =    2.070
peak=   -3.304 closest distance to " CG1 VAL A  78 " =    2.463
peak=   -3.297 closest distance to " OG  SER A  62 " =    1.290
peak=   -3.296 closest distance to " O   HOH Z 222 " =    1.502
peak=   -3.295 closest distance to " CA  ASP A 298 " =    1.049
peak=   -3.294 closest distance to " CD2 LEU A 237 " =    2.612
peak=   -3.293 closest distance to " NZ  LYS A 119 " =    3.373
peak=   -3.292 closest distance to " O   HOH Z 427 " =    1.464
peak=   -3.290 closest distance to " N   ALA A 248 " =    2.241
peak=   -3.289 closest distance to " CG1 VAL A 112 " =    2.616
peak=   -3.283 closest distance to " CG1 VAL A 296 " =    1.185
peak=   -3.281 closest distance to " CE BMET A  47 " =    1.634
peak=   -3.281 closest distance to " O   TRP A  92 " =    1.856
peak=   -3.280 closest distance to " OG1 THR A  82 " =    1.298
peak=   -3.277 closest distance to " CB  ASP A 132 " =    2.321
peak=   -3.275 closest distance to " O   SER A  95 " =    1.606
peak=   -3.275 closest distance to " O   HOH Z 136 " =    2.054
peak=   -3.274 closest distance to " O   HOH Z 283 " =    1.779
peak=   -3.267 closest distance to " O   ALA A   1 " =    1.771
peak=   -3.256 closest distance to " NE2 GLN A 194 " =    1.717
peak=   -3.252 closest distance to " OG  SER A  26 " =    1.251
peak=   -3.245 closest distance to " O   HOH Z  97 " =    1.343
peak=   -3.245 closest distance to " CG  GLU A   2 " =    1.796
peak=   -3.243 closest distance to " O   ALA A 160 " =    1.434
peak=   -3.242 closest distance to " O   HOH Z 422 " =    1.530
peak=   -3.239 closest distance to " ND2 ASN A  69 " =    1.550
peak=   -3.236 closest distance to " CD1 TYR A 247 " =    2.356
peak=   -3.235 closest distance to " O   LEU A 167 " =    1.602
peak=   -3.235 closest distance to " O   HOH Z 211 " =    1.561
peak=   -3.233 closest distance to " OD1 ASN A 249 " =    1.607
peak=   -3.233 closest distance to " CD1 LEU A 228 " =    2.132
peak=   -3.229 closest distance to " N   GLN A  77 " =    1.350
peak=   -3.229 closest distance to " O   HOH Z 389 " =    1.656
peak=   -3.226 closest distance to " CG2 ILE A 263 " =    2.254
peak=   -3.224 closest distance to " CG  PHE A 283 " =    2.732
peak=   -3.219 closest distance to " O   HOH Z 429 " =    2.127
peak=   -3.209 closest distance to " CE1 TYR A 169 " =    2.301
peak=   -3.200 closest distance to " O   HOH Z  47 " =    1.566
peak=   -3.199 closest distance to " O   HOH Z 265 " =    2.061
peak=   -3.199 closest distance to " OD2 ASP A 171 " =    2.427
peak=   -3.198 closest distance to " O   VAL A 174 " =    1.886
peak=   -3.197 closest distance to " O   HOH Z 185 " =    2.313
peak=   -3.195 closest distance to " CB  PHE A 208 " =    2.265
peak=   -3.183 closest distance to " NH2 ARG A  66 " =    4.757
peak=   -3.181 closest distance to " O   HOH Z 166 " =    1.938
peak=   -3.181 closest distance to " O   ASN A 187 " =    1.505
peak=   -3.172 closest distance to " N   GLY A  23 " =    2.108
peak=   -3.163 closest distance to " CG  ARG A 219 " =    2.703
peak=   -3.161 closest distance to " CG  LEU A 228 " =    1.027
peak=   -3.161 closest distance to " O   HOH Z 397 " =    1.218
peak=   -3.156 closest distance to " CG  ASP A 132 " =    2.207
peak=   -3.154 closest distance to " N   VAL A 230 " =    1.048
peak=   -3.136 closest distance to " CA  VAL A 296 " =    0.956
peak=   -3.132 closest distance to " CA  GLY A 241 " =    2.313
peak=   -3.130 closest distance to " CG  ARG A 269 " =    2.201
peak=   -3.130 closest distance to " O   HOH Z 414 " =    2.313
peak=   -3.130 closest distance to " O   PRO A 198 " =    1.252
peak=   -3.129 closest distance to " N   SER A 271 " =    1.475
peak=   -3.122 closest distance to " O   HOH Z 292 " =    2.764
peak=   -3.121 closest distance to " O   HOH Z 407 " =    3.442
peak=   -3.121 closest distance to " CG  GLU A 152 " =    2.197
peak=   -3.106 closest distance to " CD2 LEU A 167 " =    1.691
peak=   -3.106 closest distance to " O   HOH Z 262 " =    2.492
peak=   -3.104 closest distance to " O   HOH Z 339 " =    1.763
peak=   -3.079 closest distance to " NH1 ARG A  66 " =    5.057
peak=   -3.076 closest distance to " O   ASP A 107 " =    1.481
peak=   -3.073 closest distance to " CD  ARG A 195 " =    5.141
peak=   -3.072 closest distance to " O   HOH Z  61 " =    1.529
peak=   -3.065 closest distance to " CB  CYS A 254 " =    2.574
peak=   -3.059 closest distance to " OD1 ASP A 200 " =    1.237
peak=   -3.055 closest distance to " OD1 ASN A 148 " =    1.534
peak=   -3.051 closest distance to " O   ALA A 100 " =    2.345
peak=   -3.051 closest distance to " O   HOH Z 110 " =    1.519
peak=   -3.042 closest distance to " N   THR A  52 " =    1.687
peak=   -3.042 closest distance to " CG  GLN A  11 " =    1.264
peak=   -3.041 closest distance to " O   SER A   3 " =    1.100
peak=   -3.006 closest distance to " O   HOH Z 377 " =    1.400

================= overall refinement statistics: step by step =================

****************** REFINEMENT STATISTICS STEP BY STEP ******************
leading digit, like 1_, means number of macro-cycle                     
0    : statistics at the very beginning when nothing is done yet        
1_bss: bulk solvent correction and/or (anisotropic) scaling             
1_xyz: refinement of coordinates                                        
1_adp: refinement of ADPs (Atomic Displacement Parameters)              
1_occ: refinement of individual occupancies                             
------------------------------------------------------------------------
 R-factors, x-ray target values and norm of gradient of x-ray target
 stage     r-work r-free  xray_target_w  xray_target_t
   0    :  0.4724 0.4622   6.271091e+00   6.260046e+00
   1_bss:  0.4635 0.4545   6.264245e+00   6.250287e+00
   1_xyz:  0.3722 0.3946   6.126480e+00   6.166126e+00
   1_adp:  0.3247 0.3656   6.027790e+00   6.117372e+00
   1_occ:  0.3238 0.3653   6.026557e+00   6.117161e+00
   2_bss:  0.3207 0.3612   6.026601e+00   6.115000e+00
   2_xyz:  0.2150 0.2578   5.689803e+00   5.853552e+00
   2_adp:  0.1866 0.2339   5.565461e+00   5.752838e+00
   2_occ:  0.1863 0.2334   5.564521e+00   5.752064e+00
   3_bss:  0.1839 0.2313   5.561991e+00   5.747170e+00
   3_xyz:  0.1370 0.1804   5.306131e+00   5.519463e+00
   3_adp:  0.1300 0.1687   5.247798e+00   5.454266e+00
   3_occ:  0.1298 0.1687   5.246845e+00   5.453801e+00
   4_bss:  0.1300 0.1688   5.247541e+00   5.452804e+00
   4_xyz:  0.1165 0.1584   5.166722e+00   5.394125e+00
   4_adp:  0.1152 0.1580   5.158895e+00   5.390137e+00
   4_occ:  0.1151 0.1579   5.158391e+00   5.389885e+00
   5_bss:  0.1151 0.1578   5.158601e+00   5.390110e+00
   5_xyz:  0.1142 0.1566   5.152044e+00   5.382164e+00
   5_adp:  0.1133 0.1575   5.151262e+00   5.388126e+00
   5_occ:  0.1131 0.1576   5.150706e+00   5.388197e+00
   5_bss:  0.1131 0.1576   5.150638e+00   5.388172e+00
------------------------------------------------------------------------
 stage     k_sol   b_sol     b11     b22     b33     b12     b13     b23
   0    :  0.000   0.000   0.000   0.000   0.000   0.000   0.000   0.000
   1_bss:  0.360  15.125   7.494   9.161   8.360   0.000   0.000   0.000
   1_xyz:  0.360  15.125   7.494   9.161   8.360   0.000   0.000   0.000
   1_adp:  0.360  15.125   7.494   9.161   8.360   0.000   0.000   0.000
   1_occ:  0.360  15.125   7.494   9.161   8.360   0.000   0.000   0.000
   2_bss:  0.323  31.726   4.106   5.614   5.538   0.000   0.000   0.000
   2_xyz:  0.323  31.726   4.106   5.614   5.538   0.000   0.000   0.000
   2_adp:  0.323  31.726   4.106   5.614   5.538   0.000   0.000   0.000
   2_occ:  0.323  31.726   4.106   5.614   5.538   0.000   0.000   0.000
   3_bss:  0.324  31.726   2.284   3.685   3.740   0.000   0.000   0.000
   3_xyz:  0.324  31.726   2.284   3.685   3.740   0.000   0.000   0.000
   3_adp:  0.324  31.726   2.284   3.685   3.740   0.000   0.000   0.000
   3_occ:  0.324  31.726   2.284   3.685   3.740   0.000   0.000   0.000
   4_bss:  0.317  38.855   1.751   2.904   3.125   0.000   0.000   0.000
   4_xyz:  0.317  38.855   1.751   2.904   3.125   0.000   0.000   0.000
   4_adp:  0.317  38.855   1.751   2.904   3.125   0.000   0.000   0.000
   4_occ:  0.317  38.855   1.751   2.904   3.125   0.000   0.000   0.000
   5_bss:  0.325  38.517   1.613   2.673   2.999   0.000   0.000   0.000
   5_xyz:  0.325  38.517   1.613   2.673   2.999   0.000   0.000   0.000
   5_adp:  0.325  38.517   1.613   2.673   2.999   0.000   0.000   0.000
   5_occ:  0.325  38.517   1.613   2.673   2.999   0.000   0.000   0.000
   5_bss:  0.324  41.785  -0.798   0.246   0.551   0.000   0.000   0.000
------------------------------------------------------------------------
 stage     <pher>    fom   alpha         beta
   0    :  54.825 0.4608  0.5309    65311.641
   1_bss:  55.115 0.4546  0.6675    62819.782
   1_xyz:  45.526 0.5738  0.8292    44897.656
   1_adp:  40.191 0.6397  0.9449    37558.329
   1_occ:  40.141 0.6403  0.9439    37451.991
   2_bss:  39.868 0.6435  0.8455    37060.309
   2_xyz:  26.786 0.7914  1.0029    17761.229
   2_adp:  22.934 0.8326  1.0353    14016.498
   2_occ:  22.903 0.8329  1.0354    13985.570
   3_bss:  22.755 0.8342  0.9679    13799.649
   3_xyz:  16.982 0.8892  1.0005     8283.348
   3_adp:  15.409 0.9034  1.0084     7302.485
   3_occ:  15.390 0.9036  1.0085     7296.277
   4_bss:  15.375 0.9037  0.9850     7296.970
   4_xyz:  14.123 0.9142  0.9874     6459.687
   4_adp:  13.994 0.9154  0.9870     6425.262
   4_occ:  13.984 0.9155  0.9869     6422.746
   5_bss:  13.986 0.9155  0.9811     6427.956
   5_xyz:  13.787 0.9171  0.9814     6286.085
   5_adp:  13.903 0.9162  0.9785     6349.113
   5_occ:  13.903 0.9162  0.9782     6358.562
   5_bss:  13.902 0.9162  0.9813     6359.354
------------------------------------------------------------------------
 stage       angl   bond   chir   dihe   plan   repu  geom_target
   0    :  24.226  0.414  2.119 33.790  0.145  4.088   5.3299e+01
   1_bss:  24.226  0.414  2.119 33.790  0.145  4.088   5.3299e+01
   1_xyz:   1.738  0.014  0.112 18.158  0.007  4.109   1.4777e-01
   1_adp:   1.738  0.014  0.112 18.158  0.007  4.109   1.4777e-01
   1_occ:   1.738  0.014  0.112 18.158  0.007  4.109   1.4777e-01
   2_bss:   1.738  0.014  0.112 18.158  0.007  4.109   1.4777e-01
   2_xyz:   1.156  0.009  0.082 16.419  0.005  4.123   8.1449e-02
   2_adp:   1.156  0.009  0.082 16.419  0.005  4.123   8.1449e-02
   2_occ:   1.156  0.009  0.082 16.419  0.005  4.123   8.1449e-02
   3_bss:   1.156  0.009  0.082 16.419  0.005  4.123   8.1449e-02
   3_xyz:   1.027  0.006  0.077 15.606  0.004  4.118   6.2471e-02
   3_adp:   1.027  0.006  0.077 15.606  0.004  4.118   6.2471e-02
   3_occ:   1.027  0.006  0.077 15.606  0.004  4.118   6.2471e-02
   4_bss:   1.027  0.006  0.077 15.606  0.004  4.118   6.2471e-02
   4_xyz:   1.076  0.007  0.084 15.709  0.004  4.117   6.7830e-02
   4_adp:   1.076  0.007  0.084 15.709  0.004  4.117   6.7830e-02
   4_occ:   1.076  0.007  0.084 15.709  0.004  4.117   6.7830e-02
   5_bss:   1.076  0.007  0.084 15.709  0.004  4.117   6.7830e-02
   5_xyz:   0.982  0.006  0.077 15.281  0.004  4.116   5.8668e-02
   5_adp:   0.982  0.006  0.077 15.281  0.004  4.116   5.8668e-02
   5_occ:   0.982  0.006  0.077 15.281  0.004  4.116   5.8668e-02
   5_bss:   0.982  0.006  0.077 15.281  0.004  4.116   5.8668e-02
------------------------------------------------------------------------
                      Maximal deviations:
 stage       angl   bond   chir   dihe   plan   repu       |grad|
   0    :  74.492  1.400  6.404144.062  0.405  1.085   6.9068e+00
   1_bss:  74.492  1.400  6.404144.062  0.405  1.085   6.9068e+00
   1_xyz:  15.885  0.169  0.565 85.402  0.049  2.216   1.0705e-01
   1_adp:  15.885  0.169  0.565 85.402  0.049  2.216   1.0705e-01
   1_occ:  15.885  0.169  0.565 85.402  0.049  2.216   1.0705e-01
   2_bss:  15.885  0.169  0.565 85.402  0.049  2.216   1.0705e-01
   2_xyz:   7.346  0.134  0.290 83.754  0.044  2.232   7.6546e-02
   2_adp:   7.346  0.134  0.290 83.754  0.044  2.232   7.6546e-02
   2_occ:   7.346  0.134  0.290 83.754  0.044  2.232   7.6546e-02
   3_bss:   7.346  0.134  0.290 83.754  0.044  2.232   7.6546e-02
   3_xyz:   6.645  0.045  0.518 81.711  0.035  2.291   4.9504e-02
   3_adp:   6.645  0.045  0.518 81.711  0.035  2.291   4.9504e-02
   3_occ:   6.645  0.045  0.518 81.711  0.035  2.291   4.9504e-02
   4_bss:   6.645  0.045  0.518 81.711  0.035  2.291   4.9504e-02
   4_xyz:   7.245  0.039  0.638 82.537  0.037  2.272   6.5250e-02
   4_adp:   7.245  0.039  0.638 82.537  0.037  2.272   6.5250e-02
   4_occ:   7.245  0.039  0.638 82.537  0.037  2.272   6.5250e-02
   5_bss:   7.245  0.039  0.638 82.537  0.037  2.272   6.5250e-02
   5_xyz:   6.781  0.045  0.520 82.138  0.032  2.332   3.8879e-02
   5_adp:   6.781  0.045  0.520 82.138  0.032  2.332   3.8879e-02
   5_occ:   6.781  0.045  0.520 82.138  0.032  2.332   3.8879e-02
   5_bss:   6.781  0.045  0.520 82.138  0.032  2.332   3.8879e-02
------------------------------------------------------------------------
           |-----overall-----|---macromolecule----|------solvent-------|
  stage    b_max  b_min  b_ave  b_max  b_min  b_ave  b_max  b_min  b_ave
   0    :  10.00  10.00  10.00  10.00  10.00  10.00  10.00  10.00  10.00
   1_bss:  19.99   0.01   9.86  19.98   0.01   9.82  19.99   0.06  10.10
   1_xyz:  19.99   0.01   9.86  19.98   0.01   9.82  19.99   0.06  10.10
   1_adp:  64.93   0.00  11.93  54.04   0.00   9.38  64.93   0.00  25.79
   1_occ:  64.93   0.00  11.93  54.04   0.00   9.38  64.93   0.00  25.79
   2_bss:  64.93   0.00  11.93  54.04   0.00   9.38  64.93   0.00  25.79
   2_xyz:  64.93   0.00  11.93  54.04   0.00   9.38  64.93   0.00  25.79
   2_adp:  70.65   0.00  12.30  70.65   0.00   8.56  70.57   1.23  32.69
   2_occ:  70.65   0.00  12.30  70.65   0.00   8.56  70.57   1.23  32.69
   3_bss:  70.65   0.00  12.30  70.65   0.00   8.56  70.57   1.23  32.69
   3_xyz:  70.65   0.00  12.30  70.65   0.00   8.56  70.57   1.23  32.69
   3_adp:  72.92   0.00  12.20  72.92   0.00   8.27  65.23   2.04  33.61
   3_occ:  72.92   0.00  12.20  72.92   0.00   8.27  65.23   2.04  33.61
   4_bss:  72.92   0.00  12.20  72.92   0.00   8.27  65.23   2.04  33.61
   4_xyz:  72.92   0.00  12.20  72.92   0.00   8.27  65.23   2.04  33.61
   4_adp:  73.95   0.00  12.03  73.95   0.00   8.16  66.72   1.49  33.10
   4_occ:  73.95   0.00  12.03  73.95   0.00   8.16  66.72   1.49  33.10
   5_bss:  73.95   0.00  12.03  73.95   0.00   8.16  66.72   1.49  33.10
   5_xyz:  73.95   0.00  12.03  73.95   0.00   8.16  66.72   1.49  33.10
   5_adp:  74.77   0.00  12.07  74.77   0.00   8.16  67.38   1.20  33.35
   5_occ:  74.77   0.00  12.07  74.77   0.00   8.16  67.38   1.20  33.35
   5_bss:  77.28   2.51  14.58  77.28   2.51  10.67  69.89   3.71  35.86
------------------------------------------------------------------------
 stage        Deviation of refined
              model from start model
               max      min     mean
   0    :    0.000    0.000    0.000
   1_bss:    0.000    0.000    0.000
   1_xyz:    1.209    0.020    0.419
   1_adp:    1.209    0.020    0.419
   1_occ:    1.209    0.020    0.419
   2_bss:    1.209    0.020    0.419
   2_xyz:    1.571    0.042    0.598
   2_adp:    1.571    0.042    0.598
   2_occ:    1.571    0.042    0.598
   3_bss:    1.571    0.042    0.598
   3_xyz:    1.589    0.051    0.650
   3_adp:    1.589    0.051    0.650
   3_occ:    1.589    0.051    0.650
   4_bss:    1.589    0.051    0.650
   4_xyz:    1.698    0.034    0.682
   4_adp:    1.698    0.034    0.682
   4_occ:    1.698    0.034    0.682
   5_bss:    1.698    0.034    0.682
   5_xyz:    1.751    0.069    0.689
   5_adp:    1.751    0.069    0.689
   5_occ:    1.751    0.069    0.689
   5_bss:    1.751    0.069    0.689
------------------------------------------------------------------------

CPU time actual refinement: 343.12


============================== Exporting results ==============================

Writing refined structure to PDB file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/trial/run_321/model_refine_001.pdb
n_use            =  2823
n_use_u_iso      =  2823
n_use_u_aniso    =  0
n_grad_site      =  0
n_grad_u_iso     =  0
n_grad_u_aniso   =  0
n_grad_occupancy =  106
n_grad_fp        =  0
n_grad_fdp       =  0
n_anisotropic_flag =  0
total number of scatterers =  2823

Writing 2mFobs-DFmodel XPLOR map to file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/trial/run_321/model_refine_001_2mFobs-DFmodel.map
Writing mFobs-DFmodel XPLOR map to file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/trial/run_321/model_refine_001_mFobs-DFmodel.map
Writing map coefficients to MTZ file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/trial/run_321/model_refine_001_map_coeffs.mtz

Writing default parameters for subsequent refinement:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/trial/run_321/model_refine_002.def


=============================== Detailed timings ==============================

Pure refinement (no I/O, processing, etc)= 342.97 
  Macro-tasks:
    bulk solvent and scale       = 39.59  
    individual site refinement   = 140.49 
    weights calculation          = 32.95  
    collect and process          = 6.44   
    model show statistics        = 0.12   
    TOTAL for macro-tasks        = 219.59 
  Micro-tasks:
    mask                            = 1.90   
    f_calc                          = 108.07 
    alpha_beta                      = 8.23   
    target                          = 1.18   
    gradients_wrt_atomic_parameters = 118.59 
    fmodel                         = 7.25   
    r_factors                      = 0.19   
    phase_errors                   = 10.37  
    foms                           = 0.29   
    TOTAL for micro-tasks          = 256.07 
NUMBER OF MASK CALCS=  4
Time per interpreted Python bytecode instruction: 4.802 micro seconds
Total CPU time: 5.95 minutes
from_scatterers_fft:    673 calls, 107.75 s
gradients_fft:          617 calls, 105.09 s

=========================== phenix.refine: finished ===========================

# Date 2008-01-16 Time 01:16:15 PST -0800 (1200474975.01 s)
Start R-work = 0.4724, R-free = 0.4622 (no bulk solvent and anisotropic scale)
Final R-work = 0.1309, R-free = 0.1739 (no bulk solvent and anisotropic scale)

Start R-work = 0.4635, R-free = 0.4545
Final R-work = 0.1131, R-free = 0.1576