# Date 2008-01-16 Time 03:07:44 PST -0800 (1200481664.40 s)
#phil __OFF__

Command line arguments: "../1108.param" "adp.set_b_iso=10" "sites.shake=0.5" "main.number_of_macro_cycles=5" "--overwrite"

HOST = blackbird.lbl.gov
HOSTTYPE = x86_64-linux
USER = phzwart
PID = 5696
JOB_ID = 5158
SGE_ARCH = lx24-amd64
SGE_TASK_FIRST = 1
SGE_TASK_LAST = 1330
SGE_TASK_ID = 1108

-------------------------------------------------------------------------------
  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: (71.655, 45.9914, 87.6859, 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: 2.84, per 1000 atoms: 1.01


================================== 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: (71.655, 45.9914, 87.6859, 90, 90, 90)
Space group: P 21 21 21 (No. 19)
Systematic absences: 0
Centric reflections: 2427
Resolution range: 15.2734 1.96424
Completeness in resolution range: 0.920017
Completeness with d_max=infinity: 0.917432

Number of F-obs in resolution range:                   19589
Number of F-obs <= 0:                                  0
Refinement resolution range: d_max =  15.2734
                             d_min =   1.9642

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: (71.655, 45.9914, 87.6859, 90, 90, 90)
Space group: P 21 21 21 (No. 19)
Systematic absences: 0
Centric reflections: 2427
Resolution range: 15.2734 1.96424
Completeness in resolution range: 0.920017
Completeness with d_max=infinity: 0.917432

Test (R-free flags) flag value: 1

Number of work/free reflections by resolution:
                                         work  free  %free
  bin  1: 15.2739 -  4.2052 [2232/2259]  2009   223  10.0%
  bin  2:  4.2052 -  3.3493 [2155/2175]  1942   213   9.9%
  bin  3:  3.3493 -  2.9293 [2106/2125]  1892   214  10.2%
  bin  4:  2.9293 -  2.6631 [2088/2118]  1874   214  10.2%
  bin  5:  2.6631 -  2.4730 [2109/2128]  1904   205   9.7%
  bin  6:  2.4730 -  2.3278 [2078/2103]  1868   210  10.1%
  bin  7:  2.3278 -  2.2115 [2057/2085]  1846   211  10.3%
  bin  8:  2.2115 -  2.1155 [2065/2101]  1860   205   9.9%
  bin  9:  2.1155 -  2.0343 [2041/2097]  1849   192   9.4%
  bin 10:  2.0343 -  1.9642 [ 658/2101]   586    72  10.9%
                                overall 17630  1959  10.0%
Writing MTZ file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/trial/run_1108/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: 0.12 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:
        1.81 -     2.42: 33
        2.42 -     3.04: 2198
        3.04 -     3.66: 4677
        3.66 -     4.28: 8979
        4.28 -     4.90: 12251
  Nonbonded interactions sorted by model distance:
             atom i - atom j             model   vdw sym.op. j
  " CE BMET A  47 " - " O  BHOH Z  74 "  1.806 3.460
  " OG1 THR A  29 " - " O   HOH Z 245 "  1.883 3.040 x,y+1,z
  " O   HOH Z 201 " - " O   HOH Z 349 "  1.887 3.040 -x+1/2,-y+1,z+1/2
  " O   HOH Z  61 " - " O   HOH Z 246 "  1.941 3.040 x,y+1,z
  " N   ASN A 148 " - " O   HOH Z 138 "  2.019 3.120 x,y-1,z
  ... (remaining 28133 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_1108/model_refine_001.eff

Writing geometry restraints to file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/trial/run_1108/model_refine_001.geo

CPU time processing inputs: 8.18


============================ 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 = 71.655 45.9914 87.68585 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: 1.96 - 15.27 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.5098   r_free= 0.4993   ksol= 0.00   Bsol= 0.00   scale= 0.765    |
|                                                                             |
| 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:   0.85 A                  |
| x-ray target function (ml) for work reflections: 6.309642                   |
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
| Bin     Resolution   Compl.  No. Refl.    R-factors          Targets        |
|number     range              work test   work   test        work        test|
|  1: 15.2739 -  4.6912 0.99   1448  161 0.4332 0.4149      6.6596      6.6503|
|  2:  4.6912 -  3.7416 0.99   1398  156 0.4486 0.4354      6.8747       6.864|
|  3:  3.7416 -  3.2739 0.99   1365  151 0.4794 0.4496      6.6975      6.6679|
|  4:  3.2739 -  2.9770 0.99   1361  154 0.5045 0.4982      6.5539      6.5216|
|  5:  2.9770 -  2.7650 0.99   1354  149 0.5397 0.5205       6.388      6.4064|
|  6:  2.7650 -  2.6028 0.99   1343  147 0.5370 0.5269      6.2873      6.2195|
|  7:  2.6028 -  2.4730 0.99   1352  151 0.5542 0.4791      6.2463      6.1806|
|  8:  2.4730 -  2.3658 0.98   1318  148 0.5565 0.5699      6.1848        6.18|
|  9:  2.3658 -  2.2750 0.98   1338  148 0.5450 0.5395      6.1393      6.2045|
| 10:  2.2750 -  2.1967 1.00   1337  153 0.5347 0.5334      6.0692      6.0672|
| 11:  2.1967 -  2.1282 0.98   1316  145 0.5213 0.5641      6.0391      6.0635|
| 12:  2.1282 -  2.0676 0.98   1314  145 0.5559 0.5410      5.9369      5.9322|
| 13:  2.0676 -  2.0133 0.83   1127  122 0.5514 0.5084      5.8844      5.7933|
| 14:  2.0133 -  1.9642 0.19    259   29 0.5653 0.4892      5.8847      5.8911|
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
|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: 15.2739 -  4.6912  1448   161  0.66  38.07   0.77     0.72      88281.53|
|  2:  4.6912 -  3.7416  1398   156  0.66  38.64   0.84     0.74     126738.07|
|  3:  3.7416 -  3.2739  1365   151  0.52  50.48   0.82     0.66     136795.53|
|  4:  3.2739 -  2.9770  1361   154  0.42  58.48   0.74     0.52     124097.25|
|  5:  2.9770 -  2.7650  1354   149  0.32  66.09   0.71     0.41      98863.01|
|  6:  2.7650 -  2.6028  1343   147  0.29  67.92   0.69     0.36      83057.70|
|  7:  2.6028 -  2.4730  1352   151  0.25  71.31   0.71     0.30      73989.18|
|  8:  2.4730 -  2.3658  1318   148  0.20  74.83   0.70     0.25      68850.94|
|  9:  2.3658 -  2.2750  1338   148  0.16  77.97   0.72     0.19      65332.96|
| 10:  2.2750 -  2.1967  1337   153  0.16  78.02   0.72     0.20      58680.14|
| 11:  2.1967 -  2.1282  1316   145  0.18  76.33   0.76     0.23      54901.73|
| 12:  2.1282 -  2.0676  1314   145  0.22  73.96   0.71     0.29      47565.42|
| 13:  2.0676 -  2.0133  1127   122  0.26  70.40   0.69     0.35      39590.00|
| 14:  2.0133 -  1.9642   259    29  0.37  62.12   0.71     0.41      28754.14|
|alpha:            min =        0.19 max =            0.74 mean =         0.41|
|beta:             min =    28754.14 max =       136795.53 mean =     82218.23|
|figures of merit: min =        0.00 max =            1.00 mean =         0.34|
|phase err.(work): min =        0.00 max =           90.00 mean =        64.38|
|phase err.(test): min =        0.00 max =           89.96 mean =        64.48|
|-----------------------------------------------------------------------------|

============================== 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 = 23.129943             wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 83.633   (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 1.975816              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 78.809   (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 |  1.196 -  1.566:        2 |
| 0.140 - 0.280:   585 |   7.457 -  14.906:   711 |  1.566 -  1.937:       32 |
| 0.280 - 0.420:   441 |  14.906 -  22.354:   630 |  1.937 -  2.307:      170 |
| 0.420 - 0.560:   366 |  22.354 -  29.802:   474 |  2.307 -  2.677:      688 |
| 0.560 - 0.700:   237 |  29.802 -  37.251:   338 |  2.677 -  3.048:     1502 |
| 0.700 - 0.840:   127 |  37.251 -  44.699:   241 |  3.048 -  3.418:     2627 |
| 0.840 - 0.980:    59 |  44.699 -  52.147:   125 |  3.418 -  3.789:     3906 |
| 0.980 - 1.120:    17 |  52.147 -  59.595:    51 |  3.789 -  4.159:     5069 |
| 1.120 - 1.260:     9 |  59.595 -  67.044:    13 |  4.159 -  4.530:     6495 |
| 1.260 - 1.400:     1 |  67.044 -  74.492:     3 |  4.530 -  4.900:     7634 |
|-----------------------------------------------------------------------------|
|-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 |       54.035 |
| 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  1.196 |       1.972 |              |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 12.016)------------------------------------------|
|    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 = 12.016)------------------------------------------|
|    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: 1.96 - 15.27 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.5128   r_free= 0.5024   ksol= 0.00   Bsol= 0.00   scale= 0.738    |
|                                                                             |
| 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:   0.83 A                  |
| x-ray target function (ml) for work reflections: 6.310166                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.96 - 15.27 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.5021   r_free= 0.4890   ksol= 0.30   Bsol= 20.00   scale= 0.938   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (7.25,7.63,8.26,0.00,0.00,0.00); trace/3= 7.71                              |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.85 A                  |
| x-ray target function (ml) for work reflections: 6.305894                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 19.042241             wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 84.467   (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 1.841506              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 76.187   (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.5021      final r-factor (work) = 0.4399          |
| start r-factor (free) = 0.4890      final r-factor (free) = 0.4594          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 114.0370 = 19.04 * 0.50 * 6.3019 + 1.00 * 54.0354                           |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 59.6896 = 19.04 * 0.50 * 6.2525 + 1.00 * 0.1590                             |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 26     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.4399      final r-factor (work) = 0.3988          |
| start r-factor (free) = 0.4594      final r-factor (free) = 0.4622          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 11.5284 = 1.84 * 1.00 * 6.2525 + 1.00 * 0.0145                              |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 11.4420 = 1.84 * 1.00 * 6.2006 + 1.00 * 0.0236                              |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 28     |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 12.016)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.00    93.25   17.49    None  None   None       |
|    all(noH): 2823   0      0.00    93.25   17.49    None  None   None       |
|    Sol.    : 438    0      0.00    93.25   26.60    None  None   None       |
|    Mac.    : 2385   0      0.00    85.98   15.82    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:     0.000 -   9.325:  923   |   5:    46.627 -  55.952:   75        |
|      1:     9.325 -  18.651:  827   |   6:    55.952 -  65.278:   37        |
|      2:    18.651 -  27.976:  523   |   7:    65.278 -  74.603:   10        |
|      3:    27.976 -  37.302:  269   |   8:    74.603 -  83.928:    2        |
|      4:    37.302 -  46.627:  153   |   9:    83.928 -  93.254:    4        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.3988 r_free = 0.4622             target_work(ml) = 6.197         |
| occupancies: max = 1.00  min = 0.30   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.3983 r_free = 0.4623             target_work(ml) = 6.196         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        6 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.96 - 15.27 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.3983   r_free= 0.4623   ksol= 0.30   Bsol= 20.00   scale= 1.110   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (7.25,7.63,8.26,0.00,0.00,0.00); trace/3= 7.71                              |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.73 A                  |
| x-ray target function (ml) for work reflections: 6.195896                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.96 - 15.27 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.3973   r_free= 0.4601   ksol= 0.35   Bsol= 59.33   scale= 1.028   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (4.41,4.19,5.00,0.00,0.00,0.00); trace/3= 4.53                              |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.73 A                  |
| x-ray target function (ml) for work reflections: 6.197617                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 11.026013             wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 101.040  (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 0.695727              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 136.536  (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.3973      final r-factor (work) = 0.3384          |
| start r-factor (free) = 0.4601      final r-factor (free) = 0.4062          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 34.3224 = 11.03 * 0.50 * 6.1969 + 1.00 * 0.1590                             |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 33.9429 = 11.03 * 0.50 * 6.1395 + 1.00 * 0.0959                             |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 27     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.3384      final r-factor (work) = 0.3214          |
| start r-factor (free) = 0.4062      final r-factor (free) = 0.3893          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 4.2952 = 0.70 * 1.00 * 6.1395 + 1.00 * 0.0238                               |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 4.2316 = 0.70 * 1.00 * 6.0636 + 1.00 * 0.0129                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 28     |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 12.016)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.00    77.78   16.29    None  None   None       |
|    all(noH): 2823   0      0.00    77.78   16.29    None  None   None       |
|    Sol.    : 438    0      0.00    77.78   30.87    None  None   None       |
|    Mac.    : 2385   0      0.00    69.79   13.61    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 -   7.778:  816   |   5:    38.889 -  46.666:   98        |
|      1:     7.778 -  15.555:  818   |   6:    46.666 -  54.444:   52        |
|      2:    15.555 -  23.333:  536   |   7:    54.444 -  62.222:   22        |
|      3:    23.333 -  31.111:  305   |   8:    62.222 -  69.999:   11        |
|      4:    31.111 -  38.889:  160   |   9:    69.999 -  77.777:    5        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.3214 r_free = 0.3893             target_work(ml) = 6.047         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        6 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.3213 r_free = 0.3882             target_work(ml) = 6.046         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        7 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.96 - 15.27 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.3213   r_free= 0.3882   ksol= 0.35   Bsol= 59.33   scale= 1.070   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (4.41,4.19,5.00,0.00,0.00,0.00); trace/3= 4.53                              |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.53 A                  |
| x-ray target function (ml) for work reflections: 6.045630                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.96 - 15.27 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.3202   r_free= 0.3857   ksol= 0.35   Bsol= 67.52   scale= 1.009   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (1.95,1.67,2.91,0.00,0.00,0.00); trace/3= 2.18                              |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.53 A                  |
| x-ray target function (ml) for work reflections: 6.045893                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 5.628261              wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 101.720  (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 0.429345              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 118.977  (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.3202      final r-factor (work) = 0.2556          |
| start r-factor (free) = 0.3857      final r-factor (free) = 0.3187          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 17.1597 = 5.63 * 0.50 * 6.0636 + 1.00 * 0.0959                              |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 16.8763 = 5.63 * 0.50 * 5.9643 + 1.00 * 0.0919                              |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 28     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.2556      final r-factor (work) = 0.2383          |
| start r-factor (free) = 0.3187      final r-factor (free) = 0.3058          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 2.5742 = 0.43 * 1.00 * 5.9643 + 1.00 * 0.0135                               |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 2.5302 = 0.43 * 1.00 * 5.8330 + 1.00 * 0.0258                               |
|-----------------------------------------------------------------------------|
| number of iterations = 12      |    number of function evaluations = 14     |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 12.016)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.00    217.17  16.09    None  None   None       |
|    all(noH): 2823   0      0.00    217.17  16.09    None  None   None       |
|    Sol.    : 438    0      0.00    76.95   33.78    None  None   None       |
|    Mac.    : 2385   0      0.00    217.17  12.84    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 -  21.717: 2099   |   5:   108.583 - 130.299:    0        |
|      1:    21.717 -  43.433:  600   |   6:   130.299 - 152.016:    0        |
|      2:    43.433 -  65.150:  113   |   7:   152.016 - 173.732:    0        |
|      3:    65.150 -  86.866:   10   |   8:   173.732 - 195.449:    0        |
|      4:    86.866 - 108.583:    0   |   9:   195.449 - 217.166:    1        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.2383 r_free = 0.3058             target_work(ml) = 5.813         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        7 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.2379 r_free = 0.3054             target_work(ml) = 5.812         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        5 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.96 - 15.27 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.2379   r_free= 0.3054   ksol= 0.35   Bsol= 67.52   scale= 1.038   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (1.95,1.67,2.91,0.00,0.00,0.00); trace/3= 2.18                              |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.35 A                  |
| x-ray target function (ml) for work reflections: 5.812122                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.96 - 15.27 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.2374   r_free= 0.3055   ksol= 0.34   Bsol= 60.85   scale= 1.007   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (0.71,0.45,1.85,0.00,0.00,0.00); trace/3= 1.01                              |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.35 A                  |
| x-ray target function (ml) for work reflections: 5.812526                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 5.626670              wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 93.631   (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 0.639776              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 104.055  (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.2374      final r-factor (work) = 0.1845          |
| start r-factor (free) = 0.3055      final r-factor (free) = 0.2443          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 16.5048 = 5.63 * 0.50 * 5.8340 + 1.00 * 0.0919                              |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 16.1448 = 5.63 * 0.50 * 5.7118 + 1.00 * 0.0756                              |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 28     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1845      final r-factor (work) = 0.1631          |
| start r-factor (free) = 0.2443      final r-factor (free) = 0.2217          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 3.6929 = 0.64 * 1.00 * 5.7118 + 1.00 * 0.0386                               |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 3.5520 = 0.64 * 1.00 * 5.5321 + 1.00 * 0.0127                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 26     |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 12.016)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.00    135.98  16.19    None  None   None       |
|    all(noH): 2823   0      0.00    135.98  16.19    None  None   None       |
|    Sol.    : 438    0      3.20    78.35   40.60    None  None   None       |
|    Mac.    : 2385   0      0.00    135.98  11.71    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 -  13.598: 1774   |   5:    67.990 -  81.588:   16        |
|      1:    13.598 -  27.196:  572   |   6:    81.588 -  95.186:    0        |
|      2:    27.196 -  40.794:  188   |   7:    95.186 - 108.785:    0        |
|      3:    40.794 -  54.392:  183   |   8:   108.785 - 122.383:    0        |
|      4:    54.392 -  67.990:   88   |   9:   122.383 - 135.981:    2        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.1631 r_free = 0.2217             target_work(ml) = 5.484         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        5 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.1630 r_free = 0.2218             target_work(ml) = 5.483         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        7 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.96 - 15.27 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1630   r_free= 0.2218   ksol= 0.34   Bsol= 60.85   scale= 1.022   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (0.71,0.45,1.85,0.00,0.00,0.00); trace/3= 1.01                              |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.22 A                  |
| x-ray target function (ml) for work reflections: 5.483345                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.96 - 15.27 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1631   r_free= 0.2212   ksol= 0.32   Bsol= 60.85   scale= 1.003   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (0.16,-0.55,1.35,-0.00,0.00,0.00); trace/3= 0.32                            |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.22 A                  |
| x-ray target function (ml) for work reflections: 5.481343                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 3.614019              wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 109.527  (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 0.958896              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 135.592  (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1631      final r-factor (work) = 0.1387          |
| start r-factor (free) = 0.2212      final r-factor (free) = 0.1913          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 10.0758 = 3.61 * 0.50 * 5.5341 + 1.00 * 0.0756                              |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 9.8648 = 3.61 * 0.50 * 5.4204 + 1.00 * 0.0700                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 27     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1387      final r-factor (work) = 0.1316          |
| start r-factor (free) = 0.1913      final r-factor (free) = 0.1842          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 5.2102 = 0.96 * 1.00 * 5.4204 + 1.00 * 0.0126                               |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 5.1142 = 0.96 * 1.00 * 5.3195 + 1.00 * 0.0134                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 27     |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 12.016)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.00    101.78  16.42    None  None   None       |
|    all(noH): 2823   0      0.00    101.78  16.42    None  None   None       |
|    Sol.    : 438    0      3.91    92.82   43.81    None  None   None       |
|    Mac.    : 2385   0      0.00    101.78  11.39    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 -  10.178: 1421   |   5:    50.891 -  61.070:  101        |
|      1:    10.178 -  20.357:  794   |   6:    61.070 -  71.248:   58        |
|      2:    20.357 -  30.535:  199   |   7:    71.248 -  81.426:   34        |
|      3:    30.535 -  40.713:  112   |   8:    81.426 -  91.604:    9        |
|      4:    40.713 -  50.891:   91   |   9:    91.604 - 101.783:    4        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.1316 r_free = 0.1842             target_work(ml) = 5.300         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        7 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.1315 r_free = 0.1840             target_work(ml) = 5.299         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        7 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.96 - 15.27 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1315   r_free= 0.1840   ksol= 0.32   Bsol= 60.85   scale= 1.005   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (0.16,-0.55,1.35,-0.00,0.00,0.00); trace/3= 0.32                            |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.18 A                  |
| x-ray target function (ml) for work reflections: 5.298951                   |
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
| Bin     Resolution   Compl.  No. Refl.    R-factors          Targets        |
|number     range              work test   work   test        work        test|
|  1: 15.2739 -  4.6912 0.99   1448  161 0.0965 0.1402      5.3953      5.6266|
|  2:  4.6912 -  3.7416 0.99   1398  156 0.0904 0.1182      5.4996      5.7131|
|  3:  3.7416 -  3.2739 0.99   1365  151 0.1204 0.1654      5.5703      5.8712|
|  4:  3.2739 -  2.9770 0.99   1361  154 0.1477 0.1943      5.5893      5.7531|
|  5:  2.9770 -  2.7650 0.99   1354  149 0.1571 0.2144      5.4781      5.7402|
|  6:  2.7650 -  2.6028 0.99   1343  147 0.1527 0.2276      5.3715      5.6176|
|  7:  2.6028 -  2.4730 0.99   1352  151 0.1511 0.1923      5.3166      5.4535|
|  8:  2.4730 -  2.3658 0.98   1318  148 0.1473 0.2056      5.2413      5.4758|
|  9:  2.3658 -  2.2750 0.98   1338  148 0.1477 0.2196      5.2088      5.4704|
| 10:  2.2750 -  2.1967 1.00   1337  153 0.1389 0.2040      5.1146      5.3468|
| 11:  2.1967 -  2.1282 0.98   1316  145 0.1369 0.2099      5.0968       5.456|
| 12:  2.1282 -  2.0676 0.98   1314  145 0.1413 0.2235      5.0444      5.2929|
| 13:  2.0676 -  2.0133 0.83   1127  122 0.1405 0.1956       4.963      5.1583|
| 14:  2.0133 -  1.9642 0.19    259   29 0.1179 0.1743       4.808      5.0666|
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
|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: 15.2739 -  4.6912  1448   161  0.93   9.84   0.97     0.95       8166.25|
|  2:  4.6912 -  3.7416  1398   156  0.94   9.12   1.02     1.00      10597.89|
|  3:  3.7416 -  3.2739  1365   151  0.92  13.47   1.04     1.04      12863.95|
|  4:  3.2739 -  2.9770  1361   154  0.89  17.22   1.02     1.00      13796.24|
|  5:  2.9770 -  2.7650  1354   149  0.87  19.13   1.01     0.98      11560.97|
|  6:  2.7650 -  2.6028  1343   147  0.86  20.37   0.99     0.94       9931.49|
|  7:  2.6028 -  2.4730  1352   151  0.88  18.84   1.00     0.97       8651.53|
|  8:  2.4730 -  2.3658  1318   148  0.87  19.75   1.00     0.95       7647.89|
|  9:  2.3658 -  2.2750  1338   148  0.87  19.85   1.00     0.94       7137.02|
| 10:  2.2750 -  2.1967  1337   153  0.87  19.56   1.00     0.96       6244.63|
| 11:  2.1967 -  2.1282  1316   145  0.86  20.14   1.00     0.94       6157.09|
| 12:  2.1282 -  2.0676  1314   145  0.86  20.58   1.00     0.99       5835.46|
| 13:  2.0676 -  2.0133  1127   122  0.86  21.16   0.99     0.96       5018.23|
| 14:  2.0133 -  1.9642   259    29  0.90  17.09   0.98     0.96       3662.87|
|alpha:            min =        0.94 max =            1.04 mean =         0.97|
|beta:             min =     3662.87 max =        13796.24 mean =      8736.13|
|figures of merit: min =        0.00 max =            1.00 mean =         0.88|
|phase err.(work): min =        0.00 max =           89.97 mean =        17.48|
|phase err.(test): min =        0.00 max =           89.10 mean =        16.80|
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.96 - 15.27 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1320   r_free= 0.1836   ksol= 0.32   Bsol= 64.82   scale= 1.000   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-0.18,-0.86,1.04,-0.00,0.00,0.00); trace/3= 0.00                           |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.18 A                  |
| x-ray target function (ml) for work reflections: 5.298930                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.96 - 15.27 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1320   r_free= 0.1836   ksol= 0.32   Bsol= 64.82   scale= 1.000   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-0.18,-0.86,1.04,-0.00,0.00,0.00); trace/3= 0.00                           |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.18 A                  |
| x-ray target function (ml) for work reflections: 5.298930                   |
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
| Bin     Resolution   Compl.  No. Refl.    R-factors          Targets        |
|number     range              work test   work   test        work        test|
|  1: 15.2739 -  4.6912 0.99   1448  161 0.0982 0.1364       5.393      5.6109|
|  2:  4.6912 -  3.7416 0.99   1398  156 0.0917 0.1183      5.5021      5.7137|
|  3:  3.7416 -  3.2739 0.99   1365  151 0.1209 0.1659      5.5722      5.8779|
|  4:  3.2739 -  2.9770 0.99   1361  154 0.1477 0.1937      5.5899      5.7521|
|  5:  2.9770 -  2.7650 0.99   1354  149 0.1573 0.2147      5.4784      5.7411|
|  6:  2.7650 -  2.6028 0.99   1343  147 0.1526 0.2274      5.3705      5.6157|
|  7:  2.6028 -  2.4730 0.99   1352  151 0.1510 0.1924      5.3161      5.4539|
|  8:  2.4730 -  2.3658 0.98   1318  148 0.1472 0.2054      5.2403      5.4756|
|  9:  2.3658 -  2.2750 0.98   1338  148 0.1477 0.2196      5.2084      5.4703|
| 10:  2.2750 -  2.1967 1.00   1337  153 0.1388 0.2039      5.1142      5.3471|
| 11:  2.1967 -  2.1282 0.98   1316  145 0.1368 0.2099      5.0967      5.4557|
| 12:  2.1282 -  2.0676 0.98   1314  145 0.1414 0.2234      5.0445       5.293|
| 13:  2.0676 -  2.0133 0.83   1127  122 0.1405 0.1956       4.963      5.1585|
| 14:  2.0133 -  1.9642 0.19    259   29 0.1181 0.1743      4.8083      5.0676|
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
|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: 15.2739 -  4.6912  1448   161  0.94   9.56   0.96     0.94       7848.34|
|  2:  4.6912 -  3.7416  1398   156  0.95   9.00   1.02     1.00      10429.82|
|  3:  3.7416 -  3.2739  1365   151  0.92  13.46   1.04     1.04      12851.15|
|  4:  3.2739 -  2.9770  1361   154  0.89  17.26   1.02     1.00      13850.63|
|  5:  2.9770 -  2.7650  1354   149  0.87  19.13   1.00     0.98      11562.87|
|  6:  2.7650 -  2.6028  1343   147  0.86  20.35   0.98     0.94       9913.62|
|  7:  2.6028 -  2.4730  1352   151  0.88  18.84   0.99     0.96       8647.38|
|  8:  2.4730 -  2.3658  1318   148  0.87  19.73   0.99     0.95       7633.95|
|  9:  2.3658 -  2.2750  1338   148  0.87  19.84   0.99     0.94       7132.71|
| 10:  2.2750 -  2.1967  1337   153  0.87  19.55   1.00     0.96       6242.45|
| 11:  2.1967 -  2.1282  1316   145  0.86  20.13   0.99     0.93       6158.07|
| 12:  2.1282 -  2.0676  1314   145  0.86  20.58   0.99     0.98       5836.09|
| 13:  2.0676 -  2.0133  1127   122  0.86  21.17   0.99     0.95       5020.15|
| 14:  2.0133 -  1.9642   259    29  0.90  17.09   0.98     0.95       3664.99|
|alpha:            min =        0.93 max =            1.04 mean =         0.97|
|beta:             min =     3664.99 max =        13850.63 mean =      8697.11|
|figures of merit: min =        0.00 max =            1.00 mean =         0.88|
|phase err.(work): min =        0.00 max =           89.97 mean =        17.44|
|phase err.(test): min =        0.00 max =           89.08 mean =        16.76|
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 12.016)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.18    101.96  16.60    None  None   None       |
|    all(noH): 2823   0      0.18    101.96  16.60    None  None   None       |
|    Sol.    : 438    0      4.09    93.00   43.99    None  None   None       |
|    Mac.    : 2385   0      0.18    101.96  11.56    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:     0.179 -  10.357: 1421   |   5:    51.070 -  61.249:  101        |
|      1:    10.357 -  20.535:  794   |   6:    61.249 -  71.427:   58        |
|      2:    20.535 -  30.714:  199   |   7:    71.427 -  81.605:   34        |
|      3:    30.714 -  40.892:  112   |   8:    81.605 -  91.783:    9        |
|      4:    40.892 -  51.070:   91   |   9:    91.783 - 101.962:    4        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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


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

Number of peaks found at mFobs-DFmodel map (map cutoff=3.00 sigma)= 351         
Filter by distance & map next to the model:
   mapped sites are within: 0.146 - 5.786
   number of sites selected in [dist_min= 0.70, dist_max= 6.00]: 348 from: 351
   mapped sites are within: 0.728 - 5.786

peak=    9.081 closest distance to " CB  VAL A 230 " =    1.467
peak=    7.285 closest distance to " O   HOH Z 130 " =    1.503
peak=    6.712 closest distance to " CG2 VAL A 296 " =    1.203
peak=    6.647 closest distance to " CG  ARG A 138 " =    1.273
peak=    6.555 closest distance to " CD2 LEU A   5 " =    1.354
peak=    6.176 closest distance to " O   HOH Z 268 " =    1.122
peak=    5.961 closest distance to " O   HOH Z  65 " =    1.456
peak=    5.551 closest distance to " O   HOH Z 222 " =    1.666
peak=    5.414 closest distance to " O   HOH Z  63 " =    1.637
peak=    5.385 closest distance to " CD1AILE A 234 " =    1.073
peak=    5.328 closest distance to " NE2 GLN A  11 " =    1.150
peak=    5.040 closest distance to " O   HOH Z   7 " =    2.007
peak=    5.021 closest distance to " CG  PRO A  54 " =    1.517
peak=    4.893 closest distance to " CB  PRO A  54 " =    1.148
peak=    4.855 closest distance to " CG  LEU A   5 " =    1.143
peak=    4.811 closest distance to " O   HOH Z 232 " =    2.160
peak=    4.801 closest distance to " NH1 ARG A 138 " =    1.067
peak=    4.757 closest distance to " CB  VAL A 230 " =    1.277
peak=    4.744 closest distance to " O   HOH Z 427 " =    2.552
peak=    4.699 closest distance to " O   HOH Z 417 " =    1.608
peak=    4.668 closest distance to " CG  LEU A 228 " =    1.140
peak=    4.656 closest distance to " CB  GLN A 223 " =    1.554
peak=    4.611 closest distance to " O   HOH Z 245 " =    1.316
peak=    4.606 closest distance to " O   HOH Z  97 " =    1.460
peak=    4.604 closest distance to " O   HOH Z 287 " =    1.933
peak=    4.550 closest distance to " CD  ARG A 138 " =    0.971
peak=    4.452 closest distance to " O   HOH Z 410 " =    1.683
peak=    4.433 closest distance to " CD2 LEU A 228 " =    1.385
peak=    4.416 closest distance to " CG2 THR A 221 " =    1.267
peak=    4.407 closest distance to " C   ASN A 209 " =    1.588
peak=    4.398 closest distance to " O   HOH Z 425 " =    1.779
peak=    4.382 closest distance to " CB  ASN A 148 " =    1.441
peak=    4.350 closest distance to " NZ BLYS A 290 " =    1.001
peak=    4.325 closest distance to " CB  SER A 216 " =    1.129
peak=    4.311 closest distance to " O   HOH Z 103 " =    0.874
peak=    4.307 closest distance to " O   HOH Z 350 " =    1.514
peak=    4.300 closest distance to " O   HOH Z 183 " =    1.369
peak=    4.276 closest distance to " OE1 GLN A  73 " =    2.204
peak=    4.275 closest distance to " O   HOH Z  69 " =    2.141
peak=    4.249 closest distance to " O   HOH Z 186 " =    1.305
peak=    4.228 closest distance to " O   HOH Z 255 " =    1.083
peak=    4.206 closest distance to " O   PRO A 198 " =    1.336
peak=    4.205 closest distance to " CE3 TRP A 274 " =    1.377
peak=    4.200 closest distance to " CB  SER A  63 " =    1.377
peak=    4.191 closest distance to " O   HOH Z 148 " =    1.547
peak=    4.188 closest distance to " O   HOH Z 401 " =    1.098
peak=    4.164 closest distance to " O   HOH Z 139 " =    1.230
peak=    4.159 closest distance to " O   HOH Z 369 " =    2.158
peak=    4.147 closest distance to " O   HOH Z 403 " =    1.260
peak=    4.146 closest distance to " O   HOH Z  39 " =    1.265
peak=    4.123 closest distance to " O   HOH Z 385 " =    0.993
peak=    4.118 closest distance to " CD2 TRP A 179 " =    2.240
peak=    4.108 closest distance to " O   HOH Z 126 " =    2.179
peak=    4.090 closest distance to " O   HOH Z 117 " =    1.114
peak=    4.087 closest distance to " O   HOH Z 373 " =    1.624
peak=    4.086 closest distance to " CA  VAL A 296 " =    1.138
peak=    4.083 closest distance to " CA  ILE A 234 " =    1.108
peak=    4.070 closest distance to " NH1AARG A 145 " =    1.187
peak=    4.066 closest distance to " O   HOH Z 414 " =    1.484
peak=    4.063 closest distance to " O   HOH Z 411 " =    2.976
peak=    4.052 closest distance to " CD1 ILE A  33 " =    1.828
peak=    4.045 closest distance to " O   HOH Z  56 " =    2.003
peak=    4.030 closest distance to " CG  PRO A 243 " =    1.036
peak=    4.026 closest distance to " O   HOH Z 193 " =    1.727
peak=    4.024 closest distance to " CA  ALA A  51 " =    1.054
peak=    3.997 closest distance to " O   HOH Z 423 " =    1.792
peak=    3.981 closest distance to " CZ3 TRP A 266 " =    1.212
peak=    3.980 closest distance to " O   HOH Z  68 " =    1.954
peak=    3.959 closest distance to " O   HOH Z   9 " =    2.077
peak=    3.948 closest distance to " CB  TRP A 266 " =    0.984
peak=    3.945 closest distance to " CB  SER A   3 " =    1.633
peak=    3.943 closest distance to " CE  MET A  93 " =    1.535
peak=    3.938 closest distance to " O   HOH Z 133 " =    2.866
peak=    3.937 closest distance to " CG  LEU A 167 " =    1.287
peak=    3.934 closest distance to " N   CYS A 260 " =    0.961
peak=    3.931 closest distance to " CB  MET A  40 " =    0.871
peak=    3.920 closest distance to " O   HOH Z  30 " =    2.239
peak=    3.917 closest distance to " O   HOH Z 298 " =    1.989
peak=    3.915 closest distance to " CG  PRO A 280 " =    1.150
peak=    3.903 closest distance to " O   HOH Z  59 " =    1.960
peak=    3.903 closest distance to " O   HOH Z 427 " =    1.139
peak=    3.900 closest distance to " O   HOH Z 218 " =    1.922
peak=    3.898 closest distance to " O   HOH Z 389 " =    1.453
peak=    3.881 closest distance to " O   HOH Z  61 " =    1.827
peak=    3.880 closest distance to " O   HOH Z 425 " =    2.081
peak=    3.878 closest distance to " O   HOH Z 360 " =    1.226
peak=    3.874 closest distance to " O   HOH Z 225 " =    1.561
peak=    3.868 closest distance to " O   HOH Z 154 " =    1.991
peak=    3.865 closest distance to " CG  PRO A 198 " =    1.299
peak=    3.856 closest distance to " CB  ASP A 124 " =    0.838
peak=    3.851 closest distance to " CB  ARG A 138 " =    1.177
peak=    3.848 closest distance to " O   HOH Z  41 " =    0.990
peak=    3.847 closest distance to " O   HOH Z 238 " =    1.379
peak=    3.845 closest distance to " O   HOH Z 424 " =    1.226
peak=    3.832 closest distance to " O   HOH Z 316 " =    3.007
peak=    3.826 closest distance to " O   HOH Z 143 " =    1.446
peak=    3.819 closest distance to " CB  MET A  47 " =    1.213
peak=    3.805 closest distance to " O   HOH Z 392 " =    1.169
peak=    3.802 closest distance to " O   HOH Z  57 " =    1.466
peak=    3.796 closest distance to " O   HOH Z 172 " =    2.135
peak=    3.790 closest distance to " CG  LYS A  76 " =    1.683
peak=    3.789 closest distance to " O   HOH Z 361 " =    1.349
peak=    3.787 closest distance to " O   HOH Z 368 " =    3.479
peak=    3.781 closest distance to " NH1 ARG A  56 " =    1.221
peak=    3.770 closest distance to " O   HOH Z 127 " =    1.151
peak=    3.760 closest distance to " CG2 ILE A 234 " =    0.981
peak=    3.759 closest distance to " CG  PRO A 213 " =    1.339
peak=    3.751 closest distance to " CD  ARG A 159 " =    0.794
peak=    3.750 closest distance to " O   HOH Z 132 " =    1.218
peak=    3.747 closest distance to " CZ  PHE A 218 " =    1.185
peak=    3.747 closest distance to " CB  LEU A 237 " =    0.887
peak=    3.746 closest distance to " O   HOH Z  30 " =    1.380
peak=    3.736 closest distance to " N   TYR A  15 " =    1.051
peak=    3.735 closest distance to " O   HOH Z 359 " =    1.382
peak=    3.733 closest distance to " O   HOH Z 167 " =    1.810
peak=    3.718 closest distance to " CB  VAL A 265 " =    1.374
peak=    3.711 closest distance to " CA  ASN A 127 " =    1.213
peak=    3.708 closest distance to " O   HOH Z  91 " =    2.439
peak=    3.701 closest distance to " O   HOH Z 258 " =    2.114
peak=    3.694 closest distance to " CB  GLN A 183 " =    1.250
peak=    3.685 closest distance to " O   HOH Z  26 " =    1.492
peak=    3.684 closest distance to " O   HOH Z  52 " =    1.057
peak=    3.679 closest distance to " CD  ARG A 269 " =    0.966
peak=    3.678 closest distance to " O   HOH Z 353 " =    2.394
peak=    3.677 closest distance to " O   HOH Z  80 " =    1.576
peak=    3.674 closest distance to " OE2 GLU A   2 " =    2.026
peak=    3.671 closest distance to " NH2AARG A 190 " =    1.639
peak=    3.667 closest distance to " O   HOH Z 217 " =    2.892
peak=    3.666 closest distance to " CB  GLU A 277 " =    3.721
peak=    3.659 closest distance to " NH2AARG A 145 " =    1.123
peak=    3.654 closest distance to " CA  GLY A 136 " =    1.160
peak=    3.652 closest distance to " O   HOH Z 422 " =    2.697
peak=    3.651 closest distance to " CD  ARG A  66 " =    2.294
peak=    3.651 closest distance to " CA  ALA A 160 " =    1.094
peak=    3.650 closest distance to " CZ  PHE A 192 " =    0.989
peak=    3.647 closest distance to " CG1 VAL A 296 " =    1.228
peak=    3.637 closest distance to " O   HOH Z  78 " =    1.701
peak=    3.637 closest distance to " O   HOH Z 158 " =    2.895
peak=    3.634 closest distance to " CB  ASN A  60 " =    1.015
peak=    3.630 closest distance to " CA  ALA A 295 " =    0.989
peak=    3.624 closest distance to " O   HOH Z   2 " =    1.755
peak=    3.623 closest distance to " CE  LYS A  76 " =    0.878
peak=    3.621 closest distance to " CB  VAL A 250 " =    1.128
peak=    3.620 closest distance to " CE3 TRP A  85 " =    1.117
peak=    3.620 closest distance to " O   HOH Z 272 " =    1.932
peak=    3.619 closest distance to " O   HOH Z 273 " =    1.473
peak=    3.618 closest distance to " ND1 HIS A  81 " =    1.755
peak=    3.610 closest distance to " CG2 VAL A 268 " =    1.050
peak=    3.607 closest distance to " CB  ASP A  50 " =    1.266
peak=    3.605 closest distance to " N   GLN A 278 " =    1.263
peak=    3.605 closest distance to " CB  LYS A 290 " =    0.937
peak=    3.604 closest distance to " CB  GLU A 128 " =    1.097
peak=    3.597 closest distance to " OG  SER A  62 " =    2.801
peak=    3.595 closest distance to " O   HOH Z 233 " =    1.270
peak=    3.591 closest distance to " NE2 GLN A  58 " =    4.220
peak=    3.588 closest distance to " O   HOH Z 373 " =    2.204
peak=    3.587 closest distance to " CB  VAL A 202 " =    1.577
peak=    3.585 closest distance to " CD  ARG A 195 " =    3.602
peak=    3.575 closest distance to " N   SER A  97 " =    0.775
peak=    3.566 closest distance to " CB  ASN A  39 " =    0.968
peak=    3.553 closest distance to " NH2BARG A 190 " =    1.409
peak=    3.552 closest distance to " O   HOH Z 145 " =    2.182
peak=    3.552 closest distance to " ND2BASN A 224 " =    0.938
peak=    3.552 closest distance to " N   TRP A 177 " =    1.657
peak=    3.551 closest distance to " CG  ASN A  60 " =    1.068
peak=    3.549 closest distance to " O   HOH Z 170 " =    1.148
peak=    3.543 closest distance to " O   HOH Z 109 " =    2.482
peak=    3.542 closest distance to " OG ASER A 212 " =    1.637
peak=    3.540 closest distance to " CD BLYS A 290 " =    1.066
peak=    3.537 closest distance to " CB  ALA A  43 " =    0.974
peak=    3.529 closest distance to " CA  ILE A 106 " =    0.839
peak=    3.528 closest distance to " O   HOH Z  88 " =    3.223
peak=    3.519 closest distance to " CA  THR A 221 " =    0.960
peak=    3.519 closest distance to " O   THR A 182 " =    1.624
peak=    3.518 closest distance to " O   HOH Z 290 " =    1.208
peak=    3.512 closest distance to " CZ3 TRP A 123 " =    1.434
peak=    3.507 closest distance to " O   HOH Z  59 " =    2.462
peak=    3.505 closest distance to " O   ALA A 180 " =    1.294
peak=    3.495 closest distance to " CD  GLN A 240 " =    1.773
peak=    3.495 closest distance to " O   HOH Z 181 " =    2.430
peak=    3.490 closest distance to " O   HOH Z 128 " =    2.133
peak=    3.487 closest distance to " OG BSER A 210 " =    1.302
peak=    3.487 closest distance to " CB  ARG A 275 " =    1.092
peak=    3.482 closest distance to " O   HOH Z 211 " =    1.167
peak=    3.481 closest distance to " O   HOH Z 403 " =    1.311
peak=    3.480 closest distance to " O   HOH Z 180 " =    2.186
peak=    3.478 closest distance to " O   HOH Z  51 " =    2.312
peak=    3.465 closest distance to " O   HOH Z 236 " =    1.749
peak=    3.463 closest distance to " O   HOH Z 110 " =    1.575
peak=    3.458 closest distance to " CA  SER A  87 " =    0.979
peak=    3.457 closest distance to " O   HOH Z  49 " =    1.031
peak=    3.455 closest distance to " O   ASP A 200 " =    1.432
peak=    3.453 closest distance to " O   HOH Z  88 " =    3.851
peak=    3.453 closest distance to " O   HOH Z   1 " =    2.100
peak=    3.451 closest distance to " O   HOH Z 201 " =    1.867
peak=    3.450 closest distance to " CD1 LEU A   5 " =    1.335
peak=    3.450 closest distance to " O   HOH Z 217 " =    1.584
peak=    3.449 closest distance to " CG  ARG A 159 " =    0.953
peak=    3.447 closest distance to " CG  GLN A  88 " =    1.034
peak=    3.446 closest distance to " CA  ARG A 159 " =    1.344
peak=    3.444 closest distance to " CE3 TRP A 150 " =    1.120
peak=    3.444 closest distance to " O   HOH Z 357 " =    2.003
peak=    3.443 closest distance to " O   HOH Z 173 " =    1.909
peak=    3.429 closest distance to " N   SER A 271 " =    0.970
peak=    3.429 closest distance to " C   VAL A 153 " =    1.171
peak=    3.428 closest distance to " CB  ASN A 142 " =    0.859
peak=    3.425 closest distance to " O   HOH Z 411 " =    1.578
peak=    3.418 closest distance to " CA  VAL A 112 " =    1.227
peak=    3.417 closest distance to " O   HOH Z  85 " =    1.922
peak=    3.405 closest distance to " O   HOH Z 356 " =    1.305
peak=    3.405 closest distance to " O   HOH Z 148 " =    1.981
peak=    3.402 closest distance to " N   GLU A   2 " =    1.526
peak=    3.402 closest distance to " O   HOH Z 359 " =    4.154
peak=    3.400 closest distance to " O   HOH Z 362 " =    1.966
peak=    3.398 closest distance to " O   HOH Z 437 " =    2.186
peak=    3.398 closest distance to " N   ARG A 156 " =    1.342
peak=    3.396 closest distance to " O   HOH Z 193 " =    1.630
peak=    3.395 closest distance to " CD1 LEU A 167 " =    1.269
peak=    3.394 closest distance to " O   HOH Z  43 " =    1.169
peak=    3.394 closest distance to " CZ3 TRP A  92 " =    1.160
peak=    3.389 closest distance to " O   HOH Z 153 " =    3.780
peak=    3.385 closest distance to " CB  GLU A 236 " =    1.427
peak=    3.385 closest distance to " CA  ARG A  36 " =    1.169
peak=    3.379 closest distance to " ND2 ASN A 249 " =    0.728
peak=    3.374 closest distance to " CG  GLN A  89 " =    1.556
peak=    3.374 closest distance to " CB  SER A 210 " =    0.941
peak=    3.372 closest distance to " CA  ARG A 139 " =    1.023
peak=    3.370 closest distance to " O   HOH Z 392 " =    1.936
peak=    3.366 closest distance to " O   HOH Z 156 " =    2.923
peak=    3.366 closest distance to " CB  SER A 276 " =    1.139
peak=    3.364 closest distance to " O   HOH Z 145 " =    2.611
peak=    3.364 closest distance to " O   HOH Z 132 " =    2.416
peak=    3.353 closest distance to " O   HOH Z 168 " =    1.668
peak=    3.348 closest distance to " O   HOH Z 375 " =    0.971
peak=    3.345 closest distance to " O   HOH Z  28 " =    1.297
peak=    3.341 closest distance to " CG BARG A 275 " =    1.268
peak=    3.341 closest distance to " CB  TRP A 179 " =    1.471
peak=    3.338 closest distance to " O   HOH Z 380 " =    1.857
peak=    3.336 closest distance to " O   HOH Z 328 " =    1.689
peak=    3.331 closest distance to " CB  HIS A 108 " =    0.849
peak=    3.330 closest distance to " CG2 VAL A 257 " =    0.941
peak=    3.329 closest distance to " O   HOH Z 193 " =    1.947
peak=    3.326 closest distance to " OG  SER A 276 " =    1.024
peak=    3.320 closest distance to " OG BSER A 212 " =    2.440
peak=    3.317 closest distance to " NE2 HIS A 207 " =    1.043
peak=    3.316 closest distance to " O   HOH Z 115 " =    1.872
peak=    3.313 closest distance to " O   TYR A 116 " =    1.217
peak=    3.311 closest distance to " CE3 TRP A 274 " =    2.549
peak=    3.309 closest distance to " O   HOH Z  57 " =    1.749
peak=    3.302 closest distance to " OE2 GLU A  53 " =    1.892
peak=    3.299 closest distance to " CA  TYR A 116 " =    1.402
peak=    3.295 closest distance to " O   HOH Z 207 " =    2.616
peak=    3.293 closest distance to " O   HOH Z 368 " =    4.358
peak=    3.291 closest distance to " CA  ASP A 124 " =    0.740
peak=    3.289 closest distance to " CB  TRP A 150 " =    0.999
peak=    3.288 closest distance to " NE AARG A 275 " =    1.680
peak=    3.287 closest distance to " O   HOH Z 357 " =    2.503
peak=    3.286 closest distance to " CG2 ILE A 109 " =    0.947
peak=    3.285 closest distance to " CB  ALA A 114 " =    1.656
peak=    3.276 closest distance to " O   GLY A 302 " =    2.343
peak=    3.275 closest distance to " O   HOH Z 325 " =    2.037
peak=    3.271 closest distance to " O   HOH Z 204 " =    1.488
peak=    3.269 closest distance to " CB  ARG A 138 " =    0.837
peak=    3.268 closest distance to " N   PHE A 130 " =    1.280
peak=    3.267 closest distance to " CA  GLY A 267 " =    1.329
peak=    3.266 closest distance to " CZ3 TRP A 177 " =    1.024
peak=    3.258 closest distance to " O   HOH Z  85 " =    2.491
peak=    3.255 closest distance to " O   THR A 220 " =    1.347
peak=    3.253 closest distance to " CB  TYR A  30 " =    1.383
peak=    3.248 closest distance to " OD2 ASP A  65 " =    3.069
peak=    3.245 closest distance to " O   ALA A 291 " =    1.437
peak=    3.242 closest distance to " O   HOH Z 188 " =    3.015
peak=    3.241 closest distance to " O   HOH Z 214 " =    2.305
peak=    3.240 closest distance to " O   HOH Z 222 " =    1.793
peak=    3.239 closest distance to " CA  ASN A 215 " =    1.142
peak=    3.234 closest distance to " CB  GLU A 152 " =    1.235
peak=    3.234 closest distance to " CA  VAL A 125 " =    1.097
peak=    3.232 closest distance to " O   HOH Z 425 " =    2.059
peak=    3.229 closest distance to " O   HOH Z  76 " =    1.281
peak=    3.228 closest distance to " O   ALA A 233 " =    1.827
peak=    3.227 closest distance to " OD1 ASP A 200 " =    1.604
peak=    3.227 closest distance to " O   HOH Z 175 " =    3.816
peak=    3.226 closest distance to " CA  ARG A 156 " =    1.031
peak=    3.223 closest distance to " CB  ALA A 104 " =    0.786
peak=    3.219 closest distance to " CB  ALA A  10 " =    0.983
peak=    3.219 closest distance to " O   HOH Z  10 " =    1.660
peak=    3.218 closest distance to " NE2 GLN A  58 " =    5.786
peak=    3.215 closest distance to " CA  ALA A 184 " =    1.245
peak=    3.210 closest distance to " NZ  LYS A 117 " =    1.281
peak=    3.209 closest distance to " O   HOH Z 184 " =    1.667
peak=    3.204 closest distance to " CA  LEU A 282 " =    1.123
peak=    3.203 closest distance to " O   HOH Z 353 " =    1.626
peak=    3.197 closest distance to " CA  ALA A 299 " =    0.961
peak=    3.196 closest distance to " CD1 LEU A 300 " =    1.277
peak=    3.191 closest distance to " O   HOH Z  98 " =    1.831
peak=    3.189 closest distance to " CB  PHE A  16 " =    1.028
peak=    3.188 closest distance to " O   HOH Z 185 " =    1.860
peak=    3.188 closest distance to " O   HOH Z  55 " =    1.681
peak=    3.186 closest distance to " O   HOH Z 365 " =    5.713
peak=    3.186 closest distance to " CB  THR A  31 " =    1.520
peak=    3.185 closest distance to " NE2 GLN A  89 " =    1.616
peak=    3.184 closest distance to " CE2 TYR A 186 " =    0.875
peak=    3.182 closest distance to " CA  THR A 264 " =    0.853
peak=    3.180 closest distance to " CA  MET A  47 " =    1.274
peak=    3.178 closest distance to " CG  MET A 188 " =    0.849
peak=    3.177 closest distance to " OG  SER A 135 " =    1.304
peak=    3.174 closest distance to " CB  ARG A 156 " =    1.336
peak=    3.174 closest distance to " O   HOH Z 116 " =    1.494
peak=    3.171 closest distance to " CA  ALA A  21 " =    1.182
peak=    3.170 closest distance to " O   HOH Z 280 " =    3.083
peak=    3.169 closest distance to " OE1 GLN A 278 " =    1.284
peak=    3.167 closest distance to " O   HOH Z 285 " =    2.406
peak=    3.161 closest distance to " CG2 VAL A 202 " =    1.362
peak=    3.159 closest distance to " O   HOH Z 417 " =    2.075
peak=    3.158 closest distance to " CA  GLU A 152 " =    1.024
peak=    3.157 closest distance to " C   PRO A  54 " =    0.801
peak=    3.156 closest distance to " CG  MET A 113 " =    1.573
peak=    3.152 closest distance to " O   HOH Z 405 " =    1.639
peak=    3.141 closest distance to " O   HOH Z 387 " =    2.701
peak=    3.139 closest distance to " O   HOH Z 279 " =    2.384
peak=    3.134 closest distance to " O   MET A 105 " =    1.694
peak=    3.131 closest distance to " O   CYS A 168 " =    1.535
peak=    3.129 closest distance to " O   HOH Z   6 " =    1.530
peak=    3.126 closest distance to " CA  LEU A 222 " =    1.084
peak=    3.123 closest distance to " CB  LYS A 117 " =    1.224
peak=    3.115 closest distance to " O   HOH Z 112 " =    1.233
peak=    3.114 closest distance to " CG1 ILE A 151 " =    1.107
peak=    3.113 closest distance to " O   HOH Z  78 " =    2.087
peak=    3.109 closest distance to " N   MET A 185 " =    1.168
peak=    3.108 closest distance to " O   HOH Z 438 " =    2.684
peak=    3.107 closest distance to " O   HOH Z 371 " =    2.818
peak=    3.107 closest distance to " N   ALA A 256 " =    0.988
peak=    3.106 closest distance to " CA  MET A 105 " =    0.870
peak=    3.106 closest distance to " O   HOH Z  40 " =    1.925
peak=    3.103 closest distance to " O   ILE A  20 " =    2.072
peak=    3.101 closest distance to " N   ASP A 162 " =    1.221
peak=    3.093 closest distance to " O   HOH Z 104 " =    1.522
peak=    3.091 closest distance to " O   HOH Z 407 " =    1.930
peak=    3.088 closest distance to " NE  ARG A  56 " =    3.722
peak=    3.084 closest distance to " CZ  PHE A  38 " =    1.368
peak=    3.083 closest distance to " CA  ALA A 180 " =    1.252
peak=    3.080 closest distance to " O   THR A 294 " =    1.277
peak=    3.074 closest distance to " C   GLN A  88 " =    1.505
peak=    3.073 closest distance to " O   HOH Z  88 " =    2.456
peak=    3.058 closest distance to " CA  ASN A 284 " =    0.977
peak=    3.051 closest distance to " CB  ALA A 248 " =    1.199
peak=    3.032 closest distance to " CA  ARG A 195 " =    1.320
peak=    3.016 closest distance to " CA  TRP A  92 " =    1.020

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

Number of peaks found at mFobs-DFmodel map (map cutoff=3.00 sigma)= 225         
Filter by distance & map next to the model:
   mapped sites are within: 0.385 - 5.721
   number of sites selected in [dist_min= 0.70, dist_max= 6.00]: 223 from: 225
   mapped sites are within: 0.720 - 5.721

peak=   -5.237 closest distance to " CD  ARG A 138 " =    1.167
peak=   -4.751 closest distance to " CG2 VAL A 230 " =    1.015
peak=   -4.577 closest distance to " O   PRO A 198 " =    1.344
peak=   -4.534 closest distance to " OE1 GLN A  88 " =    0.968
peak=   -4.423 closest distance to " O   HOH Z  39 " =    0.746
peak=   -4.211 closest distance to " CG  ARG A 219 " =    2.460
peak=   -4.082 closest distance to " CG  MET A 105 " =    0.989
peak=   -4.078 closest distance to " CB  PHE A 130 " =    1.290
peak=   -4.070 closest distance to " CB  ASP A  27 " =    2.525
peak=   -4.042 closest distance to " N   THR A 157 " =    1.672
peak=   -4.042 closest distance to " N   ALA A  43 " =    2.737
peak=   -3.969 closest distance to " CD  ARG A  14 " =    3.156
peak=   -3.939 closest distance to " CD  LYS A 289 " =    2.276
peak=   -3.929 closest distance to " OG BSER A 134 " =    1.739
peak=   -3.929 closest distance to " CB  VAL A 230 " =    0.963
peak=   -3.926 closest distance to " CD2 TYR A 116 " =    2.352
peak=   -3.866 closest distance to " OG  SER A  87 " =    1.380
peak=   -3.853 closest distance to " O   HOH Z  32 " =    1.666
peak=   -3.841 closest distance to " CA  GLY A  91 " =    2.281
peak=   -3.823 closest distance to " CB  ALA A 248 " =    1.926
peak=   -3.821 closest distance to " OG  SER A  97 " =    2.008
peak=   -3.811 closest distance to " O   HOH Z 268 " =    0.722
peak=   -3.810 closest distance to " O   HOH Z 163 " =    1.779
peak=   -3.799 closest distance to " CB  ALA A 291 " =    2.113
peak=   -3.767 closest distance to " O   HOH Z 286 " =    1.621
peak=   -3.764 closest distance to " O   HOH Z 216 " =    1.371
peak=   -3.753 closest distance to " CG  GLN A  88 " =    0.854
peak=   -3.750 closest distance to " O   HOH Z 231 " =    0.749
peak=   -3.747 closest distance to " CB  ALA A   9 " =    2.517
peak=   -3.737 closest distance to " CD  ARG A 156 " =    1.931
peak=   -3.726 closest distance to " CD2 LEU A   5 " =    0.973
peak=   -3.718 closest distance to " O   HOH Z 166 " =    1.572
peak=   -3.712 closest distance to " OG  SER A  28 " =    1.958
peak=   -3.711 closest distance to " O   PRO A 163 " =    1.903
peak=   -3.705 closest distance to " O   HOH Z 111 " =    1.754
peak=   -3.699 closest distance to " NH2 ARG A  79 " =    2.055
peak=   -3.691 closest distance to " O   HOH Z 415 " =    1.199
peak=   -3.680 closest distance to " C   ASP A  50 " =    1.623
peak=   -3.661 closest distance to " O   HOH Z 131 " =    3.817
peak=   -3.659 closest distance to " CB  ALA A  43 " =    2.655
peak=   -3.647 closest distance to " NH2AARG A 275 " =    5.721
peak=   -3.638 closest distance to " CG2 THR A  31 " =    2.470
peak=   -3.633 closest distance to " CE1 PHE A  59 " =    2.030
peak=   -3.625 closest distance to " O   SER A  22 " =    2.852
peak=   -3.615 closest distance to " O   HOH Z 350 " =    1.668
peak=   -3.614 closest distance to " O   HOH Z 198 " =    2.440
peak=   -3.611 closest distance to " CG  ARG A 138 " =    1.177
peak=   -3.609 closest distance to " CB  PRO A 163 " =    2.321
peak=   -3.603 closest distance to " CB  ALA A 291 " =    1.900
peak=   -3.596 closest distance to " O   HOH Z 389 " =    1.214
peak=   -3.594 closest distance to " O   HOH Z 282 " =    4.573
peak=   -3.592 closest distance to " CG1 VAL A 112 " =    3.134
peak=   -3.584 closest distance to " CB  GLN A  55 " =    1.205
peak=   -3.582 closest distance to " O   SER A 141 " =    1.831
peak=   -3.581 closest distance to " OE1 GLU A 277 " =    2.363
peak=   -3.576 closest distance to " O   HOH Z  61 " =    1.348
peak=   -3.574 closest distance to " ND2 ASN A  69 " =    1.632
peak=   -3.574 closest distance to " O   HOH Z 377 " =    1.876
peak=   -3.565 closest distance to " O   HOH Z 275 " =    1.877
peak=   -3.564 closest distance to " CG  PRO A 163 " =    2.645
peak=   -3.562 closest distance to " OH  TYR A 214 " =    1.087
peak=   -3.560 closest distance to " O   HOH Z 389 " =    2.437
peak=   -3.559 closest distance to " CD1 LEU A   5 " =    2.483
peak=   -3.550 closest distance to " O   ARG A 145 " =    1.353
peak=   -3.547 closest distance to " O   HOH Z 292 " =    1.822
peak=   -3.539 closest distance to " O   ASP A 191 " =    1.970
peak=   -3.538 closest distance to " C   ASN A 285 " =    2.371
peak=   -3.537 closest distance to " O   HOH Z 298 " =    2.790
peak=   -3.535 closest distance to " O   HOH Z  52 " =    0.901
peak=   -3.534 closest distance to " O   HOH Z 411 " =    5.102
peak=   -3.530 closest distance to " OE1 GLN A 278 " =    1.133
peak=   -3.521 closest distance to " O   HOH Z 255 " =    1.024
peak=   -3.519 closest distance to " O   HOH Z 318 " =    1.672
peak=   -3.505 closest distance to " OH  TYR A 247 " =    1.497
peak=   -3.500 closest distance to " O   GLY A  80 " =    2.573
peak=   -3.491 closest distance to " CE2 TYR A  30 " =    2.528
peak=   -3.486 closest distance to " CG  ARG A 259 " =    2.525
peak=   -3.485 closest distance to " O   HOH Z 105 " =    2.041
peak=   -3.484 closest distance to " CB  ALA A 227 " =    2.313
peak=   -3.482 closest distance to " O   SER A 135 " =    1.463
peak=   -3.479 closest distance to " O   HOH Z  68 " =    1.376
peak=   -3.478 closest distance to " CG  LEU A   5 " =    0.960
peak=   -3.478 closest distance to " CA  GLY A 133 " =    2.011
peak=   -3.478 closest distance to " O   HOH Z 275 " =    1.648
peak=   -3.477 closest distance to " O   HOH Z 385 " =    0.872
peak=   -3.470 closest distance to " C   ALA A 158 " =    1.379
peak=   -3.463 closest distance to " CD1 LEU A 297 " =    2.338
peak=   -3.462 closest distance to " CG2 VAL A 202 " =    2.887
peak=   -3.461 closest distance to " CB  PRO A 243 " =    2.607
peak=   -3.461 closest distance to " CA  GLY A 203 " =    2.426
peak=   -3.456 closest distance to " CG2 VAL A 296 " =    1.668
peak=   -3.452 closest distance to " CB  TRP A  85 " =    2.461
peak=   -3.446 closest distance to " CD  GLU A 277 " =    1.134
peak=   -3.442 closest distance to " O   HOH Z 211 " =    0.987
peak=   -3.441 closest distance to " O   HOH Z 389 " =    4.995
peak=   -3.438 closest distance to " O   HOH Z 368 " =    1.251
peak=   -3.437 closest distance to " O   HOH Z 407 " =    3.306
peak=   -3.435 closest distance to " CG  TRP A 266 " =    1.803
peak=   -3.430 closest distance to " NE2 GLN A 223 " =    1.553
peak=   -3.430 closest distance to " OG ASER A 134 " =    1.076
peak=   -3.419 closest distance to " OG  SER A  87 " =    1.529
peak=   -3.413 closest distance to " O   HOH Z 108 " =    1.480
peak=   -3.411 closest distance to " O   GLY A 203 " =    2.421
peak=   -3.411 closest distance to " CG1 VAL A 125 " =    2.368
peak=   -3.408 closest distance to " O   HOH Z 392 " =    1.715
peak=   -3.407 closest distance to " CG  GLN A 278 " =    2.259
peak=   -3.404 closest distance to " CZ2 TRP A  92 " =    2.848
peak=   -3.403 closest distance to " O   HOH Z 435 " =    2.347
peak=   -3.401 closest distance to " O   HOH Z 186 " =    1.572
peak=   -3.394 closest distance to " CE1 TYR A 169 " =    2.642
peak=   -3.391 closest distance to " O   HOH Z 231 " =    2.003
peak=   -3.390 closest distance to " O   HOH Z 359 " =    3.328
peak=   -3.385 closest distance to " O   HOH Z 200 " =    3.484
peak=   -3.376 closest distance to " OE1 GLN A  88 " =    1.257
peak=   -3.374 closest distance to " CZ3 TRP A 179 " =    1.163
peak=   -3.371 closest distance to " CA  TYR A  68 " =    1.106
peak=   -3.366 closest distance to " O   ALA A   1 " =    1.250
peak=   -3.360 closest distance to " O   HOH Z 181 " =    2.168
peak=   -3.355 closest distance to " C   ALA A  10 " =    1.779
peak=   -3.353 closest distance to " OG  SER A 245 " =    1.410
peak=   -3.352 closest distance to " CZ  TYR A 169 " =    1.854
peak=   -3.350 closest distance to " O   HOH Z  53 " =    1.795
peak=   -3.349 closest distance to " O   HOH Z  11 " =    1.707
peak=   -3.349 closest distance to " CD2 TYR A 169 " =    2.572
peak=   -3.348 closest distance to " OD1 ASP A 171 " =    1.550
peak=   -3.346 closest distance to " CD2 TYR A 247 " =    2.408
peak=   -3.336 closest distance to " CD  PRO A 213 " =    2.148
peak=   -3.333 closest distance to " O   HOH Z 155 " =    1.070
peak=   -3.328 closest distance to " CB  SER A 271 " =    1.111
peak=   -3.327 closest distance to " O   HOH Z 300 " =    1.200
peak=   -3.320 closest distance to " CB  PRO A  54 " =    2.469
peak=   -3.313 closest distance to " O   HOH Z 165 " =    1.734
peak=   -3.312 closest distance to " O   HOH Z 359 " =    1.665
peak=   -3.311 closest distance to " O   HOH Z 300 " =    2.109
peak=   -3.307 closest distance to " C   ARG A 269 " =    1.446
peak=   -3.305 closest distance to " ND2 ASN A 285 " =    2.035
peak=   -3.304 closest distance to " O   SER A 206 " =    1.740
peak=   -3.300 closest distance to " O   HOH Z 297 " =    1.024
peak=   -3.297 closest distance to " CG  LEU A 228 " =    0.901
peak=   -3.296 closest distance to " CA  GLY A 241 " =    2.287
peak=   -3.292 closest distance to " O   GLY A 211 " =    1.232
peak=   -3.289 closest distance to " O   HOH Z 133 " =    1.540
peak=   -3.281 closest distance to " O   HOH Z 185 " =    2.176
peak=   -3.277 closest distance to " O   HOH Z 177 " =    2.596
peak=   -3.276 closest distance to " CB  ALA A 114 " =    2.421
peak=   -3.275 closest distance to " O   HOH Z  73 " =    1.939
peak=   -3.274 closest distance to " O   HOH Z  22 " =    2.781
peak=   -3.271 closest distance to " O   HOH Z 165 " =    2.308
peak=   -3.269 closest distance to " N   PRO A 163 " =    1.334
peak=   -3.264 closest distance to " O   HOH Z 121 " =    3.768
peak=   -3.263 closest distance to " CB  SER A  63 " =    3.289
peak=   -3.253 closest distance to " CA  GLY A  98 " =    1.897
peak=   -3.253 closest distance to " OG  SER A  62 " =    4.456
peak=   -3.250 closest distance to " O   TRP A  70 " =    1.527
peak=   -3.249 closest distance to " O   HOH Z 401 " =    0.989
peak=   -3.240 closest distance to " O   HOH Z  60 " =    1.584
peak=   -3.239 closest distance to " O   ASP A 162 " =    2.326
peak=   -3.238 closest distance to " O   HOH Z 313 " =    1.608
peak=   -3.236 closest distance to " C   MET A 188 " =    1.465
peak=   -3.234 closest distance to " O   HOH Z 114 " =    1.847
peak=   -3.232 closest distance to " O   HOH Z 385 " =    1.494
peak=   -3.229 closest distance to " CB  ALA A 161 " =    1.638
peak=   -3.226 closest distance to " CD2 TYR A 293 " =    1.890
peak=   -3.225 closest distance to " CB  ALA A 129 " =    2.644
peak=   -3.224 closest distance to " O   HOH Z 353 " =    1.510
peak=   -3.223 closest distance to " CZ  PHE A 225 " =    1.213
peak=   -3.221 closest distance to " O   HOH Z 221 " =    1.312
peak=   -3.220 closest distance to " O   HOH Z  15 " =    1.314
peak=   -3.219 closest distance to " OH  TYR A 169 " =    1.112
peak=   -3.217 closest distance to " O   HOH Z  52 " =    1.921
peak=   -3.217 closest distance to " O   ALA A  51 " =    1.426
peak=   -3.214 closest distance to " CG BLYS A 290 " =    0.972
peak=   -3.212 closest distance to " N   ARG A 138 " =    1.537
peak=   -3.208 closest distance to " O   HOH Z 183 " =    1.532
peak=   -3.207 closest distance to " CA  ARG A 156 " =    1.091
peak=   -3.207 closest distance to " O   HOH Z 139 " =    3.269
peak=   -3.205 closest distance to " O   HOH Z 201 " =    1.162
peak=   -3.201 closest distance to " CG  LEU A 281 " =    1.769
peak=   -3.201 closest distance to " O   HOH Z 398 " =    0.893
peak=   -3.201 closest distance to " NE2 GLN A 240 " =    1.360
peak=   -3.195 closest distance to " O   HOH Z 325 " =    1.640
peak=   -3.192 closest distance to " O   HOH Z 337 " =    1.520
peak=   -3.191 closest distance to " CA  ASN A 127 " =    1.094
peak=   -3.190 closest distance to " CD  LYS A 166 " =    2.447
peak=   -3.187 closest distance to " NZ  LYS A 166 " =    1.447
peak=   -3.175 closest distance to " O   HOH Z 426 " =    1.676
peak=   -3.173 closest distance to " OG  SER A 206 " =    1.883
peak=   -3.171 closest distance to " O   HOH Z 276 " =    1.144
peak=   -3.170 closest distance to " O   HOH Z 368 " =    1.846
peak=   -3.164 closest distance to " O   HOH Z 128 " =    2.452
peak=   -3.162 closest distance to " N   VAL A  72 " =    2.178
peak=   -3.155 closest distance to " C   LEU A 101 " =    1.198
peak=   -3.154 closest distance to " CG2BVAL A  41 " =    2.485
peak=   -3.151 closest distance to " CE2 PHE A 218 " =    2.465
peak=   -3.150 closest distance to " O   HOH Z  51 " =    1.052
peak=   -3.149 closest distance to " C   GLY A  13 " =    0.908
peak=   -3.149 closest distance to " CB  ASP A 132 " =    2.329
peak=   -3.145 closest distance to " ND2 ASN A 173 " =    1.822
peak=   -3.143 closest distance to " CD2 LEU A 237 " =    2.505
peak=   -3.135 closest distance to " O   HOH Z  10 " =    1.551
peak=   -3.134 closest distance to " OD2 ASP A 171 " =    1.880
peak=   -3.128 closest distance to " O   HOH Z  83 " =    1.594
peak=   -3.127 closest distance to " NH2 ARG A 219 " =    1.865
peak=   -3.126 closest distance to " NE2 GLN A 223 " =    1.975
peak=   -3.125 closest distance to " N   PRO A  54 " =    1.128
peak=   -3.125 closest distance to " O   HOH Z 133 " =    1.395
peak=   -3.121 closest distance to " CD2 LEU A 237 " =    2.884
peak=   -3.119 closest distance to " O   HOH Z  60 " =    1.612
peak=   -3.118 closest distance to " O   HOH Z 238 " =    0.827
peak=   -3.116 closest distance to " OE2 GLU A 152 " =    1.105
peak=   -3.112 closest distance to " OG  SER A  26 " =    1.024
peak=   -3.101 closest distance to " CD1 TRP A  85 " =    1.016
peak=   -3.098 closest distance to " SG ACYS A 201 " =    2.231
peak=   -3.096 closest distance to " O   HOH Z  49 " =    1.636
peak=   -3.088 closest distance to " O   HOH Z 189 " =    3.694
peak=   -3.080 closest distance to " N   ASP A 191 " =    1.089
peak=   -3.077 closest distance to " CZ  ARG A  24 " =    1.867
peak=   -3.072 closest distance to " O   HOH Z 348 " =    2.113
peak=   -3.068 closest distance to " CD2 HIS A 207 " =    2.284
peak=   -3.058 closest distance to " O   ALA A   1 " =    1.899
peak=   -3.033 closest distance to " CG2 VAL A 296 " =    0.881
peak=   -3.032 closest distance to " CB  GLN A  55 " =    1.071
peak=   -3.020 closest distance to " OD1 ASN A  60 " =    0.720

================= 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    :  0.5098 0.4993   6.309642e+00   6.295526e+00
   1_bss:  0.5021 0.4890   6.305894e+00   6.290300e+00
   1_xyz:  0.4399 0.4594   6.238493e+00   6.258909e+00
   1_adp:  0.3988 0.4622   6.196570e+00   6.261657e+00
   1_occ:  0.3983 0.4623   6.195896e+00   6.261766e+00
   2_bss:  0.3973 0.4601   6.197617e+00   6.262121e+00
   2_xyz:  0.3384 0.4062   6.075932e+00   6.189089e+00
   2_adp:  0.3214 0.3893   6.046719e+00   6.162261e+00
   2_occ:  0.3213 0.3882   6.045630e+00   6.161468e+00
   3_bss:  0.3202 0.3857   6.045893e+00   6.160322e+00
   3_xyz:  0.2556 0.3187   5.861463e+00   6.015130e+00
   3_adp:  0.2383 0.3058   5.813159e+00   5.984658e+00
   3_occ:  0.2379 0.3054   5.812122e+00   5.983786e+00
   4_bss:  0.2374 0.3055   5.812526e+00   5.983533e+00
   4_xyz:  0.1845 0.2443   5.585129e+00   5.794575e+00
   4_adp:  0.1631 0.2217   5.483770e+00   5.708985e+00
   4_occ:  0.1630 0.2218   5.483345e+00   5.708751e+00
   5_bss:  0.1631 0.2212   5.481343e+00   5.706101e+00
   5_xyz:  0.1387 0.1913   5.339942e+00   5.576797e+00
   5_adp:  0.1316 0.1842   5.299547e+00   5.537651e+00
   5_occ:  0.1315 0.1840   5.298951e+00   5.537081e+00
   5_bss:  0.1320 0.1836   5.298930e+00   5.536242e+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:  0.300  20.000   7.250   7.627   8.263   0.000   0.000   0.000
   1_xyz:  0.300  20.000   7.250   7.627   8.263   0.000   0.000   0.000
   1_adp:  0.300  20.000   7.250   7.627   8.263   0.000   0.000   0.000
   1_occ:  0.300  20.000   7.250   7.627   8.263   0.000   0.000   0.000
   2_bss:  0.348  59.335   4.413   4.190   5.000   0.000   0.000   0.000
   2_xyz:  0.348  59.335   4.413   4.190   5.000   0.000   0.000   0.000
   2_adp:  0.348  59.335   4.413   4.190   5.000   0.000   0.000   0.000
   2_occ:  0.348  59.335   4.413   4.190   5.000   0.000   0.000   0.000
   3_bss:  0.351  67.520   1.945   1.671   2.915   0.000   0.000   0.000
   3_xyz:  0.351  67.520   1.945   1.671   2.915   0.000   0.000   0.000
   3_adp:  0.351  67.520   1.945   1.671   2.915   0.000   0.000   0.000
   3_occ:  0.351  67.520   1.945   1.671   2.915   0.000   0.000   0.000
   4_bss:  0.337  60.852   0.712   0.452   1.852   0.000   0.000   0.000
   4_xyz:  0.337  60.852   0.712   0.452   1.852   0.000   0.000   0.000
   4_adp:  0.337  60.852   0.712   0.452   1.852   0.000   0.000   0.000
   4_occ:  0.337  60.852   0.712   0.452   1.852   0.000   0.000   0.000
   5_bss:  0.324  60.852   0.160  -0.545   1.353  -0.000   0.000   0.000
   5_xyz:  0.324  60.852   0.160  -0.545   1.353  -0.000   0.000   0.000
   5_adp:  0.324  60.852   0.160  -0.545   1.353  -0.000   0.000   0.000
   5_occ:  0.324  60.852   0.160  -0.545   1.353  -0.000   0.000   0.000
   5_bss:  0.320  64.824  -0.181  -0.862   1.044  -0.000   0.000   0.000
------------------------------------------------------------------------
 stage     <pher>    fom   alpha         beta
   0    :  64.393 0.3361  0.4064    82226.263
   1_bss:  63.338 0.3496  0.5279    81134.552
   1_xyz:  56.952 0.4310  0.6305    67374.417
   1_adp:  57.020 0.4297  0.7070    68330.740
   1_occ:  56.980 0.4302  0.7066    68379.000
   2_bss:  56.795 0.4325  0.6423    68110.617
   2_xyz:  47.159 0.5538  0.8159    49489.234
   2_adp:  44.065 0.5927  0.8655    45070.246
   2_occ:  44.001 0.5933  0.8654    44839.844
   3_bss:  43.781 0.5959  0.8015    44533.133
   3_xyz:  34.068 0.7104  0.9306    28349.495
   3_adp:  31.927 0.7354  0.9484    25624.817
   3_occ:  31.900 0.7357  0.9476    25557.295
   4_bss:  31.869 0.7361  0.9101    25544.491
   4_xyz:  24.475 0.8157  0.9745    15555.469
   4_adp:  21.904 0.8423  0.9814    12796.256
   4_occ:  21.897 0.8424  0.9810    12772.191
   5_bss:  21.813 0.8431  0.9582    12669.337
   5_xyz:  18.397 0.8762  0.9754     9462.230
   5_adp:  17.425 0.8855  0.9718     8759.531
   5_occ:  17.410 0.8856  0.9716     8736.690
   5_bss:  17.373 0.8859  0.9667     8697.666
------------------------------------------------------------------------
 stage       angl   bond   chir   dihe   plan   repu  geom_target
   0    :  24.226  0.414  2.119 33.790  0.145  4.088   5.4035e+01
   1_bss:  24.226  0.414  2.119 33.790  0.145  4.088   5.4035e+01
   1_xyz:   1.795  0.014  0.112 18.580  0.007  4.107   1.5904e-01
   1_adp:   1.795  0.014  0.112 18.580  0.007  4.107   1.5904e-01
   1_occ:   1.795  0.014  0.112 18.580  0.007  4.107   1.5904e-01
   2_bss:   1.795  0.014  0.112 18.580  0.007  4.107   1.5904e-01
   2_xyz:   1.250  0.009  0.083 16.747  0.005  4.108   9.5873e-02
   2_adp:   1.250  0.009  0.083 16.747  0.005  4.108   9.5873e-02
   2_occ:   1.250  0.009  0.083 16.747  0.005  4.108   9.5873e-02
   3_bss:   1.250  0.009  0.083 16.747  0.005  4.108   9.5873e-02
   3_xyz:   1.193  0.010  0.083 15.790  0.006  4.128   9.1898e-02
   3_adp:   1.193  0.010  0.083 15.790  0.006  4.128   9.1898e-02
   3_occ:   1.193  0.010  0.083 15.790  0.006  4.128   9.1898e-02
   4_bss:   1.193  0.010  0.083 15.790  0.006  4.128   9.1898e-02
   4_xyz:   1.104  0.009  0.082 15.539  0.005  4.112   7.5605e-02
   4_adp:   1.104  0.009  0.082 15.539  0.005  4.112   7.5605e-02
   4_occ:   1.104  0.009  0.082 15.539  0.005  4.112   7.5605e-02
   5_bss:   1.104  0.009  0.082 15.539  0.005  4.112   7.5605e-02
   5_xyz:   1.079  0.009  0.081 15.406  0.004  4.123   7.0011e-02
   5_adp:   1.079  0.009  0.081 15.406  0.004  4.123   7.0011e-02
   5_occ:   1.079  0.009  0.081 15.406  0.004  4.123   7.0011e-02
   5_bss:   1.079  0.009  0.081 15.406  0.004  4.123   7.0011e-02
------------------------------------------------------------------------
                      Maximal deviations:
 stage       angl   bond   chir   dihe   plan   repu       |grad|
   0    :  74.492  1.400  6.404144.062  0.405  1.196   7.0040e+00
   1_bss:  74.492  1.400  6.404144.062  0.405  1.196   7.0040e+00
   1_xyz:  14.080  0.196  0.445 86.862  0.037  2.162   1.0998e-01
   1_adp:  14.080  0.196  0.445 86.862  0.037  2.162   1.0998e-01
   1_occ:  14.080  0.196  0.445 86.862  0.037  2.162   1.0998e-01
   2_bss:  14.080  0.196  0.445 86.862  0.037  2.162   1.0998e-01
   2_xyz:   6.978  0.065  0.277 87.586  0.045  2.060   7.4645e-02
   2_adp:   6.978  0.065  0.277 87.586  0.045  2.060   7.4645e-02
   2_occ:   6.978  0.065  0.277 87.586  0.045  2.060   7.4645e-02
   3_bss:   6.978  0.065  0.277 87.586  0.045  2.060   7.4645e-02
   3_xyz:   9.104  0.115  0.420 86.126  0.039  2.229   1.7750e-01
   3_adp:   9.104  0.115  0.420 86.126  0.039  2.229   1.7750e-01
   3_occ:   9.104  0.115  0.420 86.126  0.039  2.229   1.7750e-01
   4_bss:   9.104  0.115  0.420 86.126  0.039  2.229   1.7750e-01
   4_xyz:   8.145  0.052  0.325 87.507  0.051  2.248   5.9170e-02
   4_adp:   8.145  0.052  0.325 87.507  0.051  2.248   5.9170e-02
   4_occ:   8.145  0.052  0.325 87.507  0.051  2.248   5.9170e-02
   5_bss:   8.145  0.052  0.325 87.507  0.051  2.248   5.9170e-02
   5_xyz:   8.268  0.071  0.434 80.744  0.035  2.305   5.0379e-02
   5_adp:   8.268  0.071  0.434 80.744  0.035  2.305   5.0379e-02
   5_occ:   8.268  0.071  0.434 80.744  0.035  2.305   5.0379e-02
   5_bss:   8.268  0.071  0.434 80.744  0.035  2.305   5.0379e-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:  93.25   0.00  17.49  85.98   0.00  15.82  93.25   0.00  26.60
   1_occ:  93.25   0.00  17.49  85.98   0.00  15.82  93.25   0.00  26.60
   2_bss:  93.25   0.00  17.49  85.98   0.00  15.82  93.25   0.00  26.60
   2_xyz:  93.25   0.00  17.49  85.98   0.00  15.82  93.25   0.00  26.60
   2_adp:  77.78   0.00  16.29  69.79   0.00  13.61  77.78   0.00  30.87
   2_occ:  77.78   0.00  16.29  69.79   0.00  13.61  77.78   0.00  30.87
   3_bss:  77.78   0.00  16.29  69.79   0.00  13.61  77.78   0.00  30.87
   3_xyz:  77.78   0.00  16.29  69.79   0.00  13.61  77.78   0.00  30.87
   3_adp: 217.17   0.00  16.09 217.17   0.00  12.84  76.95   0.00  33.78
   3_occ: 217.17   0.00  16.09 217.17   0.00  12.84  76.95   0.00  33.78
   4_bss: 217.17   0.00  16.09 217.17   0.00  12.84  76.95   0.00  33.78
   4_xyz: 217.17   0.00  16.09 217.17   0.00  12.84  76.95   0.00  33.78
   4_adp: 135.98   0.00  16.19 135.98   0.00  11.71  78.35   3.20  40.60
   4_occ: 135.98   0.00  16.19 135.98   0.00  11.71  78.35   3.20  40.60
   5_bss: 135.98   0.00  16.19 135.98   0.00  11.71  78.35   3.20  40.60
   5_xyz: 135.98   0.00  16.19 135.98   0.00  11.71  78.35   3.20  40.60
   5_adp: 101.78   0.00  16.42 101.78   0.00  11.39  92.82   3.91  43.81
   5_occ: 101.78   0.00  16.42 101.78   0.00  11.39  92.82   3.91  43.81
   5_bss: 101.96   0.18  16.60 101.96   0.18  11.56  93.00   4.09  43.99
------------------------------------------------------------------------
 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:    1.292    0.023    0.415
   1_adp:    1.292    0.023    0.415
   1_occ:    1.292    0.023    0.415
   2_bss:    1.292    0.023    0.415
   2_xyz:    1.637    0.048    0.576
   2_adp:    1.637    0.048    0.576
   2_occ:    1.637    0.048    0.576
   3_bss:    1.637    0.048    0.576
   3_xyz:    1.640    0.053    0.704
   3_adp:    1.640    0.053    0.704
   3_occ:    1.640    0.053    0.704
   4_bss:    1.640    0.053    0.704
   4_xyz:    1.993    0.068    0.822
   4_adp:    1.993    0.068    0.822
   4_occ:    1.993    0.068    0.822
   5_bss:    1.993    0.068    0.822
   5_xyz:    2.055    0.108    0.867
   5_adp:    2.055    0.108    0.867
   5_occ:    2.055    0.108    0.867
   5_bss:    2.055    0.108    0.867
------------------------------------------------------------------------

CPU time actual refinement: 293.52


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

Writing refined structure to PDB file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/trial/run_1108/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_1108/model_refine_001_2mFobs-DFmodel.map
Writing mFobs-DFmodel XPLOR map to file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/trial/run_1108/model_refine_001_mFobs-DFmodel.map
Writing map coefficients to MTZ file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/trial/run_1108/model_refine_001_map_coeffs.mtz

Writing default parameters for subsequent refinement:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/trial/run_1108/model_refine_002.def


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

Pure refinement (no I/O, processing, etc)= 293.40 
  Macro-tasks:
    bulk solvent and scale       = 34.24  
    individual site refinement   = 124.26 
    weights calculation          = 26.82  
    collect and process          = 5.25   
    model show statistics        = 0.12   
    TOTAL for macro-tasks        = 190.69 
  Micro-tasks:
    mask                            = 2.59   
    f_calc                          = 93.95  
    alpha_beta                      = 6.70   
    target                          = 0.95   
    gradients_wrt_atomic_parameters = 101.98 
    fmodel                         = 5.99   
    r_factors                      = 0.18   
    phase_errors                   = 8.30   
    foms                           = 0.22   
    TOTAL for micro-tasks          = 220.86 
NUMBER OF MASK CALCS=  6
Time per interpreted Python bytecode instruction: 4.184 micro seconds
Total CPU time: 5.09 minutes
from_scatterers_fft:    620 calls, 93.71 s
gradients_fft:          566 calls, 91.09 s

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

# Date 2008-01-16 Time 03:12:49 PST -0800 (1200481969.68 s)
Start R-work = 0.5098, R-free = 0.4993 (no bulk solvent and anisotropic scale)
Final R-work = 0.1474, R-free = 0.2002 (no bulk solvent and anisotropic scale)

Start R-work = 0.5021, R-free = 0.4890
Final R-work = 0.1320, R-free = 0.1836