# Date 2008-01-16 Time 02:51:29 PST -0800 (1200480689.30 s)
#phil __OFF__

Command line arguments: "../1003.param" "adp.set_b_iso=10" "sites.shake=0.5" "main.number_of_macro_cycles=5" "--overwrite"

HOST = thunderbird.lbl.gov
HOSTTYPE = x86_64-linux
USER = phzwart
PID = 12917
JOB_ID = 5158
SGE_ARCH = lx24-amd64
SGE_TASK_FIRST = 1
SGE_TASK_LAST = 1330
SGE_TASK_ID = 1003

-------------------------------------------------------------------------------
  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: (71.3037, 46.4607, 85.0941, 90, 90, 90)
  Space group: P 21 21 21 (No. 19)

/net/cci-filer1/vol1/tmp/phzwart/tassos/trial/model.pdb
  Monomer Library directory:
    "/net/rosie/scratch3/phzwart/CCTBX/Sources/mon_lib"
  Total number of atoms: 2823
  Number of models: 1
  Model: 0
    Number of conformers: 2
    Conformer: "A"
      Number of atoms: 2769
      Number of chains: 2
        Number of residues, atoms: 302, 2333
          Classifications: {'peptide': 302}
          Modifications used: {'COO': 1}
          Link IDs: {'PTRANS': 7, 'CIS': 1, 'TRANS': 293}
        Number of residues, atoms: 436, 436
          Classifications: {'water': 436}
          Link IDs: {None: 435}
    Conformer: "B"
      Number of atoms: 2771
      Common with "A": 2717
      Number of chains: 2
        Number of residues, atoms: 302, 2333
          Classifications: {'peptide': 302}
          Modifications used: {'COO': 1}
          Link IDs: {'PTRANS': 7, 'CIS': 1, 'TRANS': 293}
          bond proxies already assigned to first conformer: 2332
        Number of residues, atoms: 438, 438
          Classifications: {'water': 438}
          Link IDs: {None: 437}
  Time building chain proxies: 3.30, per 1000 atoms: 1.17


================================== 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: (71.3037, 46.4607, 85.0941, 90, 90, 90)
Space group: P 21 21 21 (No. 19)
Systematic absences: 0
Centric reflections: 2427
Resolution range: 15.0929 1.97104
Completeness in resolution range: 0.953747
Completeness with d_max=infinity: 0.950876

Number of F-obs in resolution range:                   19589
Number of F-obs <= 0:                                  0
Refinement resolution range: d_max =  15.0929
                             d_min =   1.9710

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: (71.3037, 46.4607, 85.0941, 90, 90, 90)
Space group: P 21 21 21 (No. 19)
Systematic absences: 0
Centric reflections: 2427
Resolution range: 15.0929 1.97104
Completeness in resolution range: 0.953747
Completeness with d_max=infinity: 0.950876

Test (R-free flags) flag value: 1

Number of work/free reflections by resolution:
                                         work  free  %free
  bin  1: 15.0933 -  4.2185 [2155/2181]  1943   212   9.8%
  bin  2:  4.2185 -  3.3605 [2080/2099]  1871   209  10.0%
  bin  3:  3.3605 -  2.9393 [2033/2052]  1827   206  10.1%
  bin  4:  2.9393 -  2.6721 [2025/2055]  1827   198   9.8%
  bin  5:  2.6721 -  2.4815 [2036/2055]  1830   206  10.1%
  bin  6:  2.4815 -  2.3358 [1990/2015]  1786   204  10.3%
  bin  7:  2.3358 -  2.2192 [1997/2025]  1800   197   9.9%
  bin  8:  2.2192 -  2.1228 [1984/2020]  1791   193   9.7%
  bin  9:  2.1228 -  2.0413 [1977/2019]  1778   199  10.1%
  bin 10:  2.0413 -  1.9710 [1312/2018]  1177   135  10.3%
                                overall 17630  1959  10.0%
Writing MTZ file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/trial/run_1003/model_refine_data.mtz


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

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

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

  Number of disulfides: simple=3, symmetry=0
    Simple disulfide: " SG  CYS A 168 " - " SG ACYS A 201 " distance=2.08
    Simple disulfide: " SG  CYS A 168 " - " SG BCYS A 201 " distance=1.98
    Simple disulfide: " SG  CYS A 254 " - " SG  CYS A 260 " distance=2.05
  Time building geometry restraints manager: 0.14 seconds
  Histogram of bond lengths:
        1.21 -     1.38: 943
        1.38 -     1.56: 1465
        1.56 -     1.73: 7
        1.73 -     1.90: 21
        1.90 -     2.08: 3
  Bond restraints sorted by residual:
             atom i - atom j            ideal  model  delta   weight residual
  " SG  CYS A 168 " - " SG BCYS A 201 " 2.031  1.983  0.048 2.50e+03 5.87e+00
  " C   GLN A  88 " - " N   GLN A  89 " 1.329  1.360 -0.031 5.10e+03 4.97e+00
  " SG  CYS A 168 " - " SG ACYS A 201 " 2.031  2.075 -0.044 2.50e+03 4.89e+00
  " CB  CYS A 201 " - " SG ACYS A 201 " 1.808  1.738  0.070 9.18e+02 4.46e+00
  " C   PRO A 198 " - " N   ILE A 199 " 1.329  1.301  0.028 5.10e+03 4.10e+00
  ... (remaining 2434 not shown)
  Histogram of nonbonded interaction distances:
        1.81 -     2.42: 30
        2.42 -     3.04: 2203
        3.04 -     3.66: 4740
        3.66 -     4.28: 9088
        4.28 -     4.90: 12386
  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
  " O   HOH Z 204 " - " O   HOH Z 296 "  1.966 3.040 -x+1/2,-y+1,z+1/2
  " O   HOH Z 206 " - " O   HOH Z 341 "  1.997 3.040 -x+1/2,-y+1,z+1/2
  " O   HOH Z 107 " - " O   HOH Z 340 "  2.028 3.040 -x+1/2,-y+1,z+1/2
  " O   HOH Z 113 " - " O   HOH Z 350 "  2.073 3.040 -x+1/2,-y+1,z+1/2
  ... (remaining 28442 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_1003/model_refine_001.eff

Writing geometry restraints to file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/trial/run_1003/model_refine_001.geo

CPU time processing inputs: 9.22


============================ 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 = 71.30375 46.4607 85.09415 90 90 90
    space_group = "P 21 21 21"
  }
  input {
    pdb {
      file_name = "/net/cci-filer1/vol1/tmp/phzwart/tassos/trial/model.pdb"
    }
    xray_data {
      file_name = "/net/cci-filer1/vol1/tmp/phzwart/tassos/trial/1e0w.cns"
      labels = "FOBS,SIGMA"
      r_free_flags {
        file_name = "/net/cci-filer1/vol1/tmp/phzwart/tassos/trial/1e0w.cns"
        label = "TEST"
        test_flag_value = 1
      }
    }
  }
  output {
    prefix = "model_refine"
    serial = 1
  }
  main {
    number_of_macro_cycles = 5
  }
  modify_start_model {
    adp {
      set_b_iso = 10
    }
    sites {
      shake = 0.5
    }
  }
}
#phil __OFF__


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


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


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

|--(resolution: 1.97 - 15.09 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.4705   r_free= 0.4531   ksol= 0.00   Bsol= 0.00   scale= 0.803    |
|                                                                             |
| 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:   0.68 A                  |
| x-ray target function (ml) for work reflections: 6.268540                   |
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
| Bin     Resolution   Compl.  No. Refl.    R-factors          Targets        |
|number     range              work test   work   test        work        test|
|  1: 15.0933 -  4.7055 0.99   1400  158 0.3929 0.4060      6.5705      6.5855|
|  2:  4.7055 -  3.7538 0.99   1348  143 0.3837 0.3775      6.7645       6.733|
|  3:  3.7538 -  3.2849 0.99   1316  147 0.4288 0.3883      6.6389      6.7031|
|  4:  3.2849 -  2.9871 0.99   1327  157 0.4530 0.4140      6.5187        6.46|
|  5:  2.9871 -  2.7744 0.99   1298  139 0.4961 0.5055      6.3543      6.3437|
|  6:  2.7744 -  2.6117 0.99   1296  148 0.4944 0.5016      6.2692      6.2762|
|  7:  2.6117 -  2.4815 0.99   1313  139 0.5168 0.4525      6.2569      6.1678|
|  8:  2.4815 -  2.3739 0.98   1261  145 0.5281 0.4546      6.1672      6.1542|
|  9:  2.3739 -  2.2829 0.98   1294  149 0.4986 0.4913      6.1153      6.1045|
| 10:  2.2829 -  2.2043 0.99   1281  136 0.5115 0.5170      6.0949      6.1077|
| 11:  2.2043 -  2.1356 0.98   1280  138 0.5215 0.4843      6.0404      6.0198|
| 12:  2.1356 -  2.0747 0.97   1256  144 0.5003 0.5554      5.9643      6.0256|
| 13:  2.0747 -  2.0202 0.99   1274  142 0.5389 0.5018      5.8799      5.8103|
| 14:  2.0202 -  1.9710 0.53    686   74 0.5571 0.5354       5.846      5.8059|
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
|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: 15.0933 -  4.7055  1400   158  0.68  35.84   0.80     0.73      75557.80|
|  2:  4.7055 -  3.7538  1348   143  0.72  33.24   0.89     0.80      99681.36|
|  3:  3.7538 -  3.2849  1316   147  0.63  41.59   0.85     0.76     103876.42|
|  4:  3.2849 -  2.9871  1327   157  0.56  47.46   0.82     0.67      93081.06|
|  5:  2.9871 -  2.7744  1298   139  0.45  56.01   0.74     0.53      77668.85|
|  6:  2.7744 -  2.6117  1296   148  0.42  57.98   0.74     0.49      69617.20|
|  7:  2.6117 -  2.4815  1313   139  0.42  58.38   0.75     0.47      60712.02|
|  8:  2.4815 -  2.3739  1261   145  0.42  58.30   0.71     0.51      54179.65|
|  9:  2.3739 -  2.2829  1294   149  0.45  56.23   0.75     0.51      46915.35|
| 10:  2.2829 -  2.2043  1281   136  0.42  58.49   0.76     0.49      44997.81|
| 11:  2.2043 -  2.1356  1280   138  0.37  62.10   0.77     0.46      44111.55|
| 12:  2.1356 -  2.0747  1256   144  0.34  64.83   0.77     0.41      42828.63|
| 13:  2.0747 -  2.0202  1274   142  0.28  69.25   0.74     0.36      38301.47|
| 14:  2.0202 -  1.9710   686    74  0.26  70.72   0.70     0.30      32617.23|
|alpha:            min =        0.30 max =            0.80 mean =         0.55|
|beta:             min =    32617.23 max =       103876.42 mean =     64618.41|
|figures of merit: min =        0.00 max =            1.00 mean =         0.47|
|phase err.(work): min =        0.00 max =           89.99 mean =        54.23|
|phase err.(test): min =        0.00 max =           89.98 mean =        54.32|
|-----------------------------------------------------------------------------|

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

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

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 12.642249             wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 78.886   (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 1.069605              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 78.551   (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:       23 |
| 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:      706 |
| 0.560 - 0.700:   237 |  29.802 -  37.251:   338 |  2.677 -  3.048:     1509 |
| 0.700 - 0.840:   127 |  37.251 -  44.699:   241 |  3.048 -  3.418:     2670 |
| 0.840 - 0.980:    59 |  44.699 -  52.147:   125 |  3.418 -  3.789:     3941 |
| 0.980 - 1.120:    17 |  52.147 -  59.595:    51 |  3.789 -  4.159:     5080 |
| 1.120 - 1.260:     9 |  59.595 -  67.044:    13 |  4.159 -  4.530:     6603 |
| 1.260 - 1.400:     1 |  67.044 -  74.492:     3 |  4.530 -  4.900:     7746 |
|-----------------------------------------------------------------------------|
|-Geometry statistics: start--------------------------------------------------|
|      Type |    Count |    Deviation from ideal |     Targets | Target (sum) |
|           |          |    rmsd      max    min |             |              |
|      bond |     2439 |   0.414    1.400  0.000 |     454.651 |              |
|     angle |     3299 |  24.226   74.492  0.009 |     193.752 |              |
| chirality |      348 |   2.119    6.404  0.009 |     112.240 |       53.531 |
| planarity |      436 |   0.145    0.405  0.000 |     250.485 |              |
|  dihedral |      870 |  33.790  144.062  0.019 |      20.704 |              |
| nonbonded |     2439 |   4.089    4.900  1.196 |       1.766 |              |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 11.807)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      10.00   10.00   10.00    None  None   None       |
|    all(noH): 2823   0      10.00   10.00   10.00    None  None   None       |
|    Sol.    : 438    0      10.00   10.00   10.00    None  None   None       |
|    Mac.    : 2385   0      10.00   10.00   10.00    None  None   None       |
|    Hyd.    : 0      0      None    None    None     None  None   None       |
|    - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -      |
|       Distribution of isotropic (or equivalent) ADP for non-H atoms:        |
|    Bin#      value range     #atoms | Bin#      value range     #atoms      |
|      0:    10.000 -  10.000: 2823   |   5:    10.000 -  10.000:    0        |
|      1:    10.000 -  10.000:    0   |   6:    10.000 -  10.000:    0        |
|      2:    10.000 -  10.000:    0   |   7:    10.000 -  10.000:    0        |
|      3:    10.000 -  10.000:    0   |   8:    10.000 -  10.000:    0        |
|      4:    10.000 -  10.000:    0   |   9:    10.000 -  10.000:    0        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|

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

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

Randomizing
|-ADP statistics (Wilson B = 11.807)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.01    19.99   9.86     None  None   None       |
|    all(noH): 2823   0      0.01    19.99   9.86     None  None   None       |
|    Sol.    : 438    0      0.06    19.99   10.10    None  None   None       |
|    Mac.    : 2385   0      0.01    19.98   9.82     None  None   None       |
|    Hyd.    : 0      0      None    None    None     None  None   None       |
|    - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -      |
|       Distribution of isotropic (or equivalent) ADP for non-H atoms:        |
|    Bin#      value range     #atoms | Bin#      value range     #atoms      |
|      0:     0.008 -   2.007:  301   |   5:    10.002 -  12.000:  285        |
|      1:     2.007 -   4.006:  276   |   6:    12.000 -  13.999:  292        |
|      2:     4.006 -   6.004:  309   |   7:    13.999 -  15.998:  289        |
|      3:     6.004 -   8.003:  285   |   8:    15.998 -  17.996:  266        |
|      4:     8.003 -  10.002:  251   |   9:    17.996 -  19.995:  269        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.97 - 15.09 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.4762   r_free= 0.4598   ksol= 0.00   Bsol= 0.00   scale= 0.772    |
|                                                                             |
| 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:   0.70 A                  |
| x-ray target function (ml) for work reflections: 6.271279                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.97 - 15.09 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.4623   r_free= 0.4453   ksol= 0.37   Bsol= 20.00   scale= 1.000   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (8.25,8.39,8.09,0.00,0.00,0.00); trace/3= 8.24                              |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.70 A                  |
| x-ray target function (ml) for work reflections: 6.263335                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 10.858253             wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 80.368   (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 0.953096              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 77.394   (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.4623      final r-factor (work) = 0.3727          |
| start r-factor (free) = 0.4453      final r-factor (free) = 0.3976          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 87.5614 = 10.86 * 0.50 * 6.2680 + 1.00 * 53.5314                            |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 33.6084 = 10.86 * 0.50 * 6.1649 + 1.00 * 0.1385                             |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 26     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.3727      final r-factor (work) = 0.3268          |
| start r-factor (free) = 0.3976      final r-factor (free) = 0.3794          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 5.8901 = 0.95 * 1.00 * 6.1649 + 1.00 * 0.0144                               |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 5.7921 = 0.95 * 1.00 * 6.0624 + 1.00 * 0.0140                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 30     |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 11.807)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.00    92.03   12.36    None  None   None       |
|    all(noH): 2823   0      0.00    92.03   12.36    None  None   None       |
|    Sol.    : 438    0      0.00    79.98   27.14    None  None   None       |
|    Mac.    : 2385   0      0.00    92.03   9.64     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 -   9.203: 1438   |   5:    46.016 -  55.219:   46        |
|      1:     9.203 -  18.406:  786   |   6:    55.219 -  64.422:   13        |
|      2:    18.406 -  27.610:  308   |   7:    64.422 -  73.625:    2        |
|      3:    27.610 -  36.813:  163   |   8:    73.625 -  82.828:    3        |
|      4:    36.813 -  46.016:   62   |   9:    82.828 -  92.032:    2        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.3268 r_free = 0.3794             target_work(ml) = 6.039         |
| occupancies: max = 1.00  min = 0.30   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.3261 r_free = 0.3803             target_work(ml) = 6.038         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        3 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.97 - 15.09 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.3261   r_free= 0.3803   ksol= 0.37   Bsol= 20.00   scale= 1.098   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (8.25,8.39,8.09,0.00,0.00,0.00); trace/3= 8.24                              |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.46 A                  |
| x-ray target function (ml) for work reflections: 6.038268                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.97 - 15.09 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.3231   r_free= 0.3750   ksol= 0.35   Bsol= 50.00   scale= 1.004   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (4.55,4.26,5.05,0.00,0.00,0.00); trace/3= 4.62                              |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.48 A                  |
| x-ray target function (ml) for work reflections: 6.037696                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 7.025578              wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 96.940   (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 0.441386              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 134.148  (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.3231      final r-factor (work) = 0.2182          |
| start r-factor (free) = 0.3750      final r-factor (free) = 0.2702          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 21.4290 = 7.03 * 0.50 * 6.0609 + 1.00 * 0.1385                              |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 20.7571 = 7.03 * 0.50 * 5.8867 + 1.00 * 0.0782                              |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 29     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.2182      final r-factor (work) = 0.1923          |
| start r-factor (free) = 0.2702      final r-factor (free) = 0.2494          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 2.6125 = 0.44 * 1.00 * 5.8867 + 1.00 * 0.0142                               |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 2.5042 = 0.44 * 1.00 * 5.6487 + 1.00 * 0.0109                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 27     |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 11.807)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.00    84.97   12.59    None  None   None       |
|    all(noH): 2823   0      0.00    84.97   12.59    None  None   None       |
|    Sol.    : 438    0      0.76    76.81   33.94    None  None   None       |
|    Mac.    : 2385   0      0.00    84.97   8.66     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 -   8.497: 1559   |   5:    42.483 -  50.980:  101        |
|      1:     8.497 -  16.993:  636   |   6:    50.980 -  59.476:   40        |
|      2:    16.993 -  25.490:  211   |   7:    59.476 -  67.973:    7        |
|      3:    25.490 -  33.986:  126   |   8:    67.973 -  76.469:    1        |
|      4:    33.986 -  42.483:  138   |   9:    76.469 -  84.966:    4        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.1923 r_free = 0.2494             target_work(ml) = 5.606         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        3 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.1921 r_free = 0.2491             target_work(ml) = 5.605         |
| occupancies: max = 1.00  min = 0.02   number of occupancies < 0.1:        2 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.97 - 15.09 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1921   r_free= 0.2491   ksol= 0.35   Bsol= 50.00   scale= 1.049   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (4.55,4.26,5.05,0.00,0.00,0.00); trace/3= 4.62                              |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.24 A                  |
| x-ray target function (ml) for work reflections: 5.604832                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.97 - 15.09 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1909   r_free= 0.2464   ksol= 0.33   Bsol= 49.26   scale= 1.003   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (2.87,2.43,3.37,0.00,0.00,0.00); trace/3= 2.89                              |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.25 A                  |
| x-ray target function (ml) for work reflections: 5.603796                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 3.906713              wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 102.683  (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 0.439536              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 139.438  (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1909      final r-factor (work) = 0.1407          |
| start r-factor (free) = 0.2464      final r-factor (free) = 0.1859          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 11.1324 = 3.91 * 0.50 * 5.6592 + 1.00 * 0.0780                              |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 10.7845 = 3.91 * 0.50 * 5.4867 + 1.00 * 0.0669                              |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 28     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1407      final r-factor (work) = 0.1303          |
| start r-factor (free) = 0.1859      final r-factor (free) = 0.1749          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 2.4224 = 0.44 * 1.00 * 5.4867 + 1.00 * 0.0108                               |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 2.3389 = 0.44 * 1.00 * 5.2960 + 1.00 * 0.0111                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 26     |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 11.807)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.00    87.72   12.93    None  None   None       |
|    all(noH): 2823   0      0.00    87.72   12.93    None  None   None       |
|    Sol.    : 438    0      1.84    79.10   36.45    None  None   None       |
|    Mac.    : 2385   0      0.00    87.72   8.61     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 -   8.772: 1638   |   5:    43.861 -  52.633:  103        |
|      1:     8.772 -  17.544:  612   |   6:    52.633 -  61.405:   62        |
|      2:    17.544 -  26.317:  159   |   7:    61.405 -  70.178:   15        |
|      3:    26.317 -  35.089:  126   |   8:    70.178 -  78.950:    5        |
|      4:    35.089 -  43.861:  100   |   9:    78.950 -  87.722:    3        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.1303 r_free = 0.1749             target_work(ml) = 5.262         |
| occupancies: max = 1.00  min = 0.02   number of occupancies < 0.1:        2 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.1302 r_free = 0.1745             target_work(ml) = 5.261         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        2 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.97 - 15.09 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1302   r_free= 0.1745   ksol= 0.33   Bsol= 49.26   scale= 1.019   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (2.87,2.43,3.37,0.00,0.00,0.00); trace/3= 2.89                              |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.14 A                  |
| x-ray target function (ml) for work reflections: 5.261188                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.97 - 15.09 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1300   r_free= 0.1748   ksol= 0.33   Bsol= 46.39   scale= 1.004   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (2.40,1.92,2.82,0.00,0.00,0.00); trace/3= 2.38                              |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.15 A                  |
| x-ray target function (ml) for work reflections: 5.261297                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 2.626286              wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 127.859  (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 0.161774              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 139.879  (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1300      final r-factor (work) = 0.1177          |
| start r-factor (free) = 0.1748      final r-factor (free) = 0.1634          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 7.0235 = 2.63 * 0.50 * 5.2977 + 1.00 * 0.0669                               |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 6.9221 = 2.63 * 0.50 * 5.2203 + 1.00 * 0.0671                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 28     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1177      final r-factor (work) = 0.1178          |
| start r-factor (free) = 0.1634      final r-factor (free) = 0.1615          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 0.8556 = 0.16 * 1.00 * 5.2203 + 1.00 * 0.0111                               |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 0.8478 = 0.16 * 1.00 * 5.1859 + 1.00 * 0.0088                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 29     |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 11.807)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.00    85.82   12.44    None  None   None       |
|    all(noH): 2823   0      0.00    85.82   12.44    None  None   None       |
|    Sol.    : 438    0      2.17    76.01   33.90    None  None   None       |
|    Mac.    : 2385   0      0.00    85.82   8.50     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 -   8.582: 1632   |   5:    42.909 -  51.491:   81        |
|      1:     8.582 -  17.164:  645   |   6:    51.491 -  60.073:   48        |
|      2:    17.164 -  25.746:  151   |   7:    60.073 -  68.655:   12        |
|      3:    25.746 -  34.328:  137   |   8:    68.655 -  77.237:    6        |
|      4:    34.328 -  42.909:  109   |   9:    77.237 -  85.819:    2        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.1178 r_free = 0.1615             target_work(ml) = 5.178         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        2 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.1177 r_free = 0.1612             target_work(ml) = 5.177         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        2 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.97 - 15.09 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1177   r_free= 0.1612   ksol= 0.33   Bsol= 46.39   scale= 1.007   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (2.40,1.92,2.82,0.00,0.00,0.00); trace/3= 2.38                              |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.13 A                  |
| x-ray target function (ml) for work reflections: 5.177455                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.97 - 15.09 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1177   r_free= 0.1610   ksol= 0.33   Bsol= 46.39   scale= 1.001   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (2.11,1.73,2.62,0.00,0.00,0.00); trace/3= 2.15                              |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.14 A                  |
| x-ray target function (ml) for work reflections: 5.177340                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 1.959220              wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 139.160  (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 0.159418              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 149.593  (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1177      final r-factor (work) = 0.1151          |
| start r-factor (free) = 0.1610      final r-factor (free) = 0.1586          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 5.1469 = 1.96 * 0.50 * 5.1856 + 1.00 * 0.0671                               |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 5.1238 = 1.96 * 0.50 * 5.1688 + 1.00 * 0.0604                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 27     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1151      final r-factor (work) = 0.1152          |
| start r-factor (free) = 0.1586      final r-factor (free) = 0.1584          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 0.8328 = 0.16 * 1.00 * 5.1688 + 1.00 * 0.0088                               |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 0.8324 = 0.16 * 1.00 * 5.1624 + 1.00 * 0.0094                               |
|-----------------------------------------------------------------------------|
| number of iterations = 20      |    number of function evaluations = 22     |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 11.807)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.00    84.73   12.28    None  None   None       |
|    all(noH): 2823   0      0.00    84.73   12.28    None  None   None       |
|    Sol.    : 438    0      2.35    74.38   33.02    None  None   None       |
|    Mac.    : 2385   0      0.00    84.73   8.47     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 -   8.473: 1614   |   5:    42.363 -  50.835:   86        |
|      1:     8.473 -  16.945:  665   |   6:    50.835 -  59.308:   40        |
|      2:    16.945 -  25.418:  146   |   7:    59.308 -  67.780:    8        |
|      3:    25.418 -  33.890:  142   |   8:    67.780 -  76.253:    6        |
|      4:    33.890 -  42.363:  114   |   9:    76.253 -  84.725:    2        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.1152 r_free = 0.1584             target_work(ml) = 5.163         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        2 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.1151 r_free = 0.1582             target_work(ml) = 5.162         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        2 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.97 - 15.09 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1151   r_free= 0.1582   ksol= 0.33   Bsol= 46.39   scale= 1.001   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (2.11,1.73,2.62,0.00,0.00,0.00); trace/3= 2.15                              |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.14 A                  |
| x-ray target function (ml) for work reflections: 5.162026                   |
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
| Bin     Resolution   Compl.  No. Refl.    R-factors          Targets        |
|number     range              work test   work   test        work        test|
|  1: 15.0933 -  4.7055 0.99   1400  158 0.1020 0.1352      5.4023      5.5771|
|  2:  4.7055 -  3.7538 0.99   1348  143 0.0904 0.1160      5.4767      5.6469|
|  3:  3.7538 -  3.2849 0.99   1316  147 0.1102 0.1540      5.4992      5.8619|
|  4:  3.2849 -  2.9871 0.99   1327  157 0.1244 0.1563      5.4701      5.5901|
|  5:  2.9871 -  2.7744 0.99   1298  139 0.1353 0.1720      5.3342      5.5384|
|  6:  2.7744 -  2.6117 0.99   1296  148 0.1231 0.1710      5.2121      5.4562|
|  7:  2.6117 -  2.4815 0.99   1313  139 0.1304 0.1607      5.1963        5.35|
|  8:  2.4815 -  2.3739 0.98   1261  145 0.1174 0.1833       5.059      5.3987|
|  9:  2.3739 -  2.2829 0.98   1294  149 0.1209 0.1783      5.0551      5.3371|
| 10:  2.2829 -  2.2043 0.99   1281  136 0.1158 0.1735      4.9587      5.1894|
| 11:  2.2043 -  2.1356 0.98   1280  138 0.1186 0.1765      4.9609      5.3053|
| 12:  2.1356 -  2.0747 0.97   1256  144 0.1101 0.1575      4.8809      5.0675|
| 13:  2.0747 -  2.0202 0.99   1274  142 0.1243 0.1805      4.8096      5.0817|
| 14:  2.0202 -  1.9710 0.53    686   74 0.1029 0.1549      4.6401      4.8647|
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
|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: 15.0933 -  4.7055  1400   158  0.94   8.91   0.98     0.96       7269.98|
|  2:  4.7055 -  3.7538  1348   143  0.95   8.18   1.01     1.00       9347.99|
|  3:  3.7538 -  3.2849  1316   147  0.93  11.52   1.02     1.02      10706.22|
|  4:  3.2849 -  2.9871  1327   157  0.92  13.80   1.00     0.97      10262.64|
|  5:  2.9871 -  2.7744  1298   139  0.90  15.83   0.99     0.97       8095.24|
|  6:  2.7744 -  2.6117  1296   148  0.90  15.72   0.98     0.96       6958.83|
|  7:  2.6117 -  2.4815  1313   139  0.91  15.54   0.99     0.97       6423.58|
|  8:  2.4815 -  2.3739  1261   145  0.90  15.65   0.98     0.95       5167.85|
|  9:  2.3739 -  2.2829  1294   149  0.91  15.32   1.01     0.99       5130.63|
| 10:  2.2829 -  2.2043  1281   136  0.91  15.21   1.01     0.97       4254.10|
| 11:  2.2043 -  2.1356  1280   138  0.90  16.52   1.00     0.96       4430.18|
| 12:  2.1356 -  2.0747  1256   144  0.92  14.88   1.02     1.02       3986.70|
| 13:  2.0747 -  2.0202  1274   142  0.90  16.40   1.01     1.00       3322.75|
| 14:  2.0202 -  1.9710   686    74  0.92  14.41   0.99     0.97       2441.91|
|alpha:            min =        0.95 max =            1.02 mean =         0.98|
|beta:             min =     2441.91 max =        10706.22 mean =      6445.77|
|figures of merit: min =        0.00 max =            1.00 mean =         0.91|
|phase err.(work): min =        0.00 max =           89.97 mean =        14.06|
|phase err.(test): min =        0.00 max =           87.76 mean =        13.55|
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.97 - 15.09 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1151   r_free= 0.1582   ksol= 0.33   Bsol= 48.49   scale= 1.000   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-0.07,-0.42,0.48,0.00,0.00,0.00); trace/3= 0.00                            |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.14 A                  |
| x-ray target function (ml) for work reflections: 5.162006                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.97 - 15.09 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1151   r_free= 0.1582   ksol= 0.33   Bsol= 48.49   scale= 1.000   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-0.07,-0.42,0.48,0.00,0.00,0.00); trace/3= 0.00                            |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.14 A                  |
| x-ray target function (ml) for work reflections: 5.162006                   |
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
| Bin     Resolution   Compl.  No. Refl.    R-factors          Targets        |
|number     range              work test   work   test        work        test|
|  1: 15.0933 -  4.7055 0.99   1400  158 0.1019 0.1352       5.402      5.5767|
|  2:  4.7055 -  3.7538 0.99   1348  143 0.0904 0.1160      5.4766      5.6469|
|  3:  3.7538 -  3.2849 0.99   1316  147 0.1102 0.1540      5.4992      5.8618|
|  4:  3.2849 -  2.9871 0.99   1327  157 0.1244 0.1563        5.47      5.5901|
|  5:  2.9871 -  2.7744 0.99   1298  139 0.1353 0.1720      5.3343      5.5386|
|  6:  2.7744 -  2.6117 0.99   1296  148 0.1231 0.1710      5.2121       5.456|
|  7:  2.6117 -  2.4815 0.99   1313  139 0.1303 0.1607      5.1962      5.3499|
|  8:  2.4815 -  2.3739 0.98   1261  145 0.1174 0.1833      5.0589      5.3987|
|  9:  2.3739 -  2.2829 0.98   1294  149 0.1209 0.1783      5.0551       5.337|
| 10:  2.2829 -  2.2043 0.99   1281  136 0.1158 0.1734      4.9587      5.1895|
| 11:  2.2043 -  2.1356 0.98   1280  138 0.1186 0.1765      4.9609      5.3054|
| 12:  2.1356 -  2.0747 0.97   1256  144 0.1102 0.1575      4.8812      5.0677|
| 13:  2.0747 -  2.0202 0.99   1274  142 0.1242 0.1806      4.8097      5.0819|
| 14:  2.0202 -  1.9710 0.53    686   74 0.1029 0.1549      4.6401      4.8647|
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
|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: 15.0933 -  4.7055  1400   158  0.94   8.90   0.98     0.96       7264.81|
|  2:  4.7055 -  3.7538  1348   143  0.95   8.17   1.01     1.00       9343.15|
|  3:  3.7538 -  3.2849  1316   147  0.93  11.52   1.02     1.02      10702.91|
|  4:  3.2849 -  2.9871  1327   157  0.92  13.80   1.00     0.97      10263.36|
|  5:  2.9871 -  2.7744  1298   139  0.90  15.83   0.99     0.97       8095.66|
|  6:  2.7744 -  2.6117  1296   148  0.90  15.72   0.98     0.96       6958.50|
|  7:  2.6117 -  2.4815  1313   139  0.91  15.54   0.99     0.97       6422.02|
|  8:  2.4815 -  2.3739  1261   145  0.90  15.65   0.98     0.95       5167.41|
|  9:  2.3739 -  2.2829  1294   149  0.91  15.32   1.01     0.99       5130.08|
| 10:  2.2829 -  2.2043  1281   136  0.91  15.21   1.00     0.97       4253.74|
| 11:  2.2043 -  2.1356  1280   138  0.90  16.52   1.00     0.96       4429.96|
| 12:  2.1356 -  2.0747  1256   144  0.92  14.89   1.02     1.02       3989.03|
| 13:  2.0747 -  2.0202  1274   142  0.90  16.41   1.00     1.00       3323.82|
| 14:  2.0202 -  1.9710   686    74  0.92  14.41   0.99     0.96       2441.87|
|alpha:            min =        0.95 max =            1.02 mean =         0.98|
|beta:             min =     2441.87 max =        10702.91 mean =      6444.81|
|figures of merit: min =        0.00 max =            1.00 mean =         0.91|
|phase err.(work): min =        0.00 max =           89.97 mean =        14.06|
|phase err.(test): min =        0.00 max =           87.76 mean =        13.55|
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 11.807)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      2.10    86.83   14.38    None  None   None       |
|    all(noH): 2823   0      2.10    86.83   14.38    None  None   None       |
|    Sol.    : 438    0      4.45    76.49   35.12    None  None   None       |
|    Mac.    : 2385   0      2.10    86.83   10.57    None  None   None       |
|    Hyd.    : 0      0      None    None    None     None  None   None       |
|    - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -      |
|       Distribution of isotropic (or equivalent) ADP for non-H atoms:        |
|    Bin#      value range     #atoms | Bin#      value range     #atoms      |
|      0:     2.102 -  10.574: 1614   |   5:    44.464 -  52.937:   86        |
|      1:    10.574 -  19.047:  665   |   6:    52.937 -  61.409:   40        |
|      2:    19.047 -  27.519:  146   |   7:    61.409 -  69.882:    8        |
|      3:    27.519 -  35.992:  142   |   8:    69.882 -  78.354:    6        |
|      4:    35.992 -  44.464:  114   |   9:    78.354 -  86.827:    2        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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


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

Number of peaks found at mFobs-DFmodel map (map cutoff=3.00 sigma)= 330         
Filter by distance & map next to the model:
   mapped sites are within: 0.444 - 5.600
   number of sites selected in [dist_min= 0.70, dist_max= 6.00]: 325 from: 330
   mapped sites are within: 0.719 - 5.600

peak=   11.103 closest distance to " CB  VAL A 230 " =    1.474
peak=    6.847 closest distance to " CG2 VAL A 296 " =    1.087
peak=    6.164 closest distance to " NH2 ARG A  56 " =    2.187
peak=    5.737 closest distance to " CG  LEU A   5 " =    1.206
peak=    5.594 closest distance to " CD2 LEU A   5 " =    1.286
peak=    5.464 closest distance to " NE2 GLN A  11 " =    1.193
peak=    5.423 closest distance to " CG  LEU A 228 " =    1.204
peak=    5.209 closest distance to " O   HOH Z 232 " =    2.282
peak=    5.149 closest distance to " CB  SER A  63 " =    1.322
peak=    5.071 closest distance to " CB  VAL A 296 " =    1.177
peak=    5.011 closest distance to " O   HOH Z 126 " =    1.880
peak=    4.941 closest distance to " CB  GLN A 223 " =    1.399
peak=    4.854 closest distance to " CD2 LEU A 228 " =    1.193
peak=    4.836 closest distance to " O   HOH Z 144 " =    1.753
peak=    4.804 closest distance to " CG  PRO A 198 " =    1.306
peak=    4.760 closest distance to " CG  PRO A 213 " =    1.210
peak=    4.753 closest distance to " CB  GLN A 183 " =    1.180
peak=    4.723 closest distance to " C   PRO A 198 " =    1.587
peak=    4.704 closest distance to " CB  SER A   3 " =    1.451
peak=    4.681 closest distance to " O   HOH Z 236 " =    1.875
peak=    4.619 closest distance to " CB  GLU A 152 " =    1.212
peak=    4.503 closest distance to " CB  ASN A 148 " =    1.410
peak=    4.467 closest distance to " CB  VAL A 230 " =    1.203
peak=    4.456 closest distance to " OD1 ASN A  69 " =    2.647
peak=    4.452 closest distance to " CB  ARG A 275 " =    0.882
peak=    4.434 closest distance to " O   HOH Z 427 " =    2.878
peak=    4.394 closest distance to " O   HOH Z 316 " =    3.017
peak=    4.394 closest distance to " O   HOH Z 193 " =    1.995
peak=    4.374 closest distance to " O   HOH Z 263 " =    1.609
peak=    4.307 closest distance to " CB  GLU A 128 " =    1.017
peak=    4.262 closest distance to " O   HOH Z 298 " =    1.790
peak=    4.219 closest distance to " CG  PRO A 243 " =    1.130
peak=    4.216 closest distance to " ND2 ASN A 187 " =    1.547
peak=    4.205 closest distance to " CB  VAL A 265 " =    1.284
peak=    4.169 closest distance to " O   HOH Z 132 " =    2.502
peak=    4.125 closest distance to " CE3 TRP A 274 " =    2.482
peak=    4.123 closest distance to " CB  ARG A  79 " =    1.377
peak=    4.116 closest distance to " OD2 ASP A 286 " =    2.806
peak=    4.113 closest distance to " N   PHE A 130 " =    1.320
peak=    4.107 closest distance to " O   SER A  87 " =    2.360
peak=    4.105 closest distance to " O   HOH Z 278 " =    0.906
peak=    4.087 closest distance to " O   HOH Z   9 " =    2.131
peak=    4.081 closest distance to " O   HOH Z 411 " =    3.702
peak=    4.076 closest distance to " CB  SER A 216 " =    0.766
peak=    4.075 closest distance to " O   HOH Z 371 " =    2.773
peak=    4.036 closest distance to " CD  ARG A  66 " =    2.559
peak=    4.035 closest distance to " O   HOH Z 303 " =    2.175
peak=    4.031 closest distance to " CG  GLN A  88 " =    1.085
peak=    4.027 closest distance to " CB  TYR A 169 " =    0.825
peak=    4.022 closest distance to " O   HOH Z 425 " =    1.408
peak=    4.014 closest distance to " CA  ALA A  51 " =    1.062
peak=    4.014 closest distance to " CD  ARG A 159 " =    0.757
peak=    3.988 closest distance to " CA  SER A  87 " =    0.939
peak=    3.986 closest distance to " O   HOH Z 346 " =    1.602
peak=    3.946 closest distance to " CB  ASN A  39 " =    0.866
peak=    3.941 closest distance to " NH1AARG A 145 " =    1.106
peak=    3.937 closest distance to " O   HOH Z  78 " =    1.861
peak=    3.937 closest distance to " O   HOH Z 368 " =    2.069
peak=    3.930 closest distance to " O   HOH Z  37 " =    1.312
peak=    3.923 closest distance to " O   HOH Z 124 " =    1.408
peak=    3.922 closest distance to " CB  TRP A 266 " =    0.957
peak=    3.920 closest distance to " O   HOH Z   2 " =    1.751
peak=    3.909 closest distance to " O   HOH Z   7 " =    1.243
peak=    3.903 closest distance to " O   HOH Z 272 " =    1.899
peak=    3.901 closest distance to " CB  ASN A 187 " =    1.001
peak=    3.889 closest distance to " O   HOH Z 234 " =    3.712
peak=    3.885 closest distance to " O   HOH Z  88 " =    3.233
peak=    3.875 closest distance to " O   HOH Z 369 " =    2.051
peak=    3.874 closest distance to " CA  ASN A 215 " =    1.160
peak=    3.871 closest distance to " O   HOH Z 193 " =    1.754
peak=    3.861 closest distance to " O   HOH Z 280 " =    2.952
peak=    3.835 closest distance to " CD BLYS A 290 " =    1.135
peak=    3.832 closest distance to " ND2 ASN A 249 " =    1.918
peak=    3.830 closest distance to " CD1 LEU A 300 " =    1.263
peak=    3.811 closest distance to " O   HOH Z  61 " =    1.628
peak=    3.804 closest distance to " O   HOH Z 248 " =    1.814
peak=    3.801 closest distance to " CB  ASN A 148 " =    1.887
peak=    3.795 closest distance to " O   HOH Z  10 " =    1.817
peak=    3.794 closest distance to " O   HOH Z 265 " =    2.233
peak=    3.794 closest distance to " O   HOH Z 403 " =    1.660
peak=    3.765 closest distance to " O   HOH Z 193 " =    1.815
peak=    3.763 closest distance to " O   HOH Z 203 " =    1.704
peak=    3.760 closest distance to " CB  MET A  40 " =    0.860
peak=    3.758 closest distance to " O   HOH Z  58 " =    1.700
peak=    3.751 closest distance to " O   HOH Z 158 " =    2.870
peak=    3.749 closest distance to " CG  ARG A 138 " =    1.104
peak=    3.734 closest distance to " CA  THR A 264 " =    0.823
peak=    3.732 closest distance to " ND1 HIS A  86 " =    1.685
peak=    3.728 closest distance to " CG  LEU A 167 " =    1.168
peak=    3.721 closest distance to " CB  ASN A 142 " =    0.949
peak=    3.716 closest distance to " O   HOH Z 108 " =    1.343
peak=    3.716 closest distance to " O   HOH Z  30 " =    1.504
peak=    3.713 closest distance to " O   HOH Z 271 " =    2.035
peak=    3.710 closest distance to " CB  VAL A 202 " =    1.563
peak=    3.705 closest distance to " C   ALA A 299 " =    0.972
peak=    3.704 closest distance to " O   HOH Z 437 " =    2.131
peak=    3.702 closest distance to " CD2 LEU A 255 " =    1.453
peak=    3.690 closest distance to " O   HOH Z 286 " =    2.303
peak=    3.686 closest distance to " CA  TYR A  30 " =    0.977
peak=    3.685 closest distance to " O   HOH Z  61 " =    1.601
peak=    3.682 closest distance to " CG2 VAL A 257 " =    0.972
peak=    3.677 closest distance to " CA  ALA A  21 " =    1.168
peak=    3.659 closest distance to " CG1BVAL A  72 " =    1.579
peak=    3.657 closest distance to " O   HOH Z  97 " =    1.989
peak=    3.655 closest distance to " CB  LEU A 143 " =    1.129
peak=    3.655 closest distance to " CB  LEU A 228 " =    1.235
peak=    3.646 closest distance to " O   HOH Z 112 " =    1.443
peak=    3.644 closest distance to " O   HOH Z 334 " =    1.482
peak=    3.644 closest distance to " NE AARG A 275 " =    1.396
peak=    3.642 closest distance to " O   HOH Z 344 " =    2.895
peak=    3.640 closest distance to " O   HOH Z 128 " =    1.922
peak=    3.636 closest distance to " N   ARG A 156 " =    1.287
peak=    3.631 closest distance to " O   HOH Z 171 " =    3.920
peak=    3.630 closest distance to " O   HOH Z 130 " =    2.197
peak=    3.627 closest distance to " O   HOH Z 350 " =    1.563
peak=    3.626 closest distance to " CA  ALA A 154 " =    1.075
peak=    3.625 closest distance to " CG  PRO A 280 " =    0.788
peak=    3.623 closest distance to " OG BSER A 164 " =    2.263
peak=    3.620 closest distance to " CB  ARG A 139 " =    0.981
peak=    3.615 closest distance to " O   HOH Z 217 " =    3.135
peak=    3.613 closest distance to " O   HOH Z   1 " =    1.832
peak=    3.609 closest distance to " O   HOH Z 197 " =    3.174
peak=    3.609 closest distance to " O   HOH Z  43 " =    1.903
peak=    3.606 closest distance to " O   HOH Z 189 " =    2.704
peak=    3.602 closest distance to " OD1BASN A 224 " =    2.271
peak=    3.599 closest distance to " CA  VAL A  41 " =    0.901
peak=    3.590 closest distance to " CB  TRP A 179 " =    1.452
peak=    3.588 closest distance to " NH1 ARG A  56 " =    0.961
peak=    3.586 closest distance to " CG2 THR A 221 " =    1.104
peak=    3.577 closest distance to " NH2 ARG A 156 " =    1.106
peak=    3.574 closest distance to " O   HOH Z 209 " =    2.366
peak=    3.571 closest distance to " CA  LEU A 282 " =    1.080
peak=    3.571 closest distance to " O   HOH Z 273 " =    2.701
peak=    3.563 closest distance to " O   HOH Z 280 " =    1.782
peak=    3.560 closest distance to " CB  PRO A  54 " =    0.749
peak=    3.551 closest distance to " O   HOH Z 227 " =    2.110
peak=    3.544 closest distance to " O   HOH Z 260 " =    1.260
peak=    3.543 closest distance to " CA  THR A 221 " =    0.905
peak=    3.539 closest distance to " CB  ILE A 234 " =    0.939
peak=    3.538 closest distance to " CB  GLN A  88 " =    1.271
peak=    3.516 closest distance to " CB  VAL A 250 " =    1.142
peak=    3.506 closest distance to " O   HOH Z 247 " =    1.325
peak=    3.504 closest distance to " CB  ASP A 140 " =    0.758
peak=    3.502 closest distance to " OG  SER A  22 " =    2.868
peak=    3.493 closest distance to " CB  GLU A 236 " =    1.227
peak=    3.493 closest distance to " O   HOH Z   3 " =    1.878
peak=    3.488 closest distance to " O   HOH Z 216 " =    2.469
peak=    3.488 closest distance to " O   HOH Z 126 " =    1.498
peak=    3.484 closest distance to " CB  PRO A 198 " =    0.852
peak=    3.481 closest distance to " CB  GLU A 277 " =    3.485
peak=    3.476 closest distance to " O   HOH Z  21 " =    1.704
peak=    3.472 closest distance to " N   ASN A  39 " =    1.104
peak=    3.471 closest distance to " CZ  PHE A 218 " =    1.024
peak=    3.468 closest distance to " O   HOH Z 425 " =    2.088
peak=    3.467 closest distance to " CB  THR A 157 " =    1.111
peak=    3.464 closest distance to " CB  ALA A 291 " =    1.372
peak=    3.458 closest distance to " CG BARG A 275 " =    1.508
peak=    3.458 closest distance to " CZ3 TRP A 123 " =    1.282
peak=    3.449 closest distance to " O   HOH Z 227 " =    1.627
peak=    3.437 closest distance to " O   HOH Z 135 " =    1.812
peak=    3.432 closest distance to " O   HOH Z  44 " =    1.709
peak=    3.424 closest distance to " CB  ALA A 248 " =    0.992
peak=    3.423 closest distance to " O   HOH Z   1 " =    1.686
peak=    3.420 closest distance to " NH2AARG A 190 " =    1.572
peak=    3.418 closest distance to " O   HOH Z 133 " =    1.688
peak=    3.417 closest distance to " OG  SER A 206 " =    1.217
peak=    3.415 closest distance to " NZ ALYS A 290 " =    1.117
peak=    3.415 closest distance to " CD1 ILE A  33 " =    1.690
peak=    3.413 closest distance to " O   HOH Z 281 " =    4.516
peak=    3.413 closest distance to " O   HOH Z 329 " =    3.822
peak=    3.412 closest distance to " CE1 TYR A 186 " =    1.336
peak=    3.411 closest distance to " O   HOH Z  68 " =    2.081
peak=    3.409 closest distance to " O   HOH Z 108 " =    2.447
peak=    3.403 closest distance to " CG1 VAL A 153 " =    0.959
peak=    3.401 closest distance to " CB  LEU A 255 " =    0.890
peak=    3.395 closest distance to " O   HOH Z 410 " =    1.608
peak=    3.394 closest distance to " O   HOH Z 261 " =    2.237
peak=    3.393 closest distance to " CB BVAL A  41 " =    1.249
peak=    3.392 closest distance to " CE  LYS A  76 " =    0.908
peak=    3.391 closest distance to " O   HOH Z 209 " =    2.480
peak=    3.388 closest distance to " CD2 LEU A 167 " =    0.719
peak=    3.387 closest distance to " O   HOH Z 327 " =    2.050
peak=    3.387 closest distance to " CA  TYR A 186 " =    1.478
peak=    3.383 closest distance to " O   HOH Z 109 " =    2.579
peak=    3.382 closest distance to " CG1 ILE A 151 " =    1.073
peak=    3.381 closest distance to " O   HOH Z 217 " =    1.534
peak=    3.367 closest distance to " NH2BARG A 145 " =    1.931
peak=    3.365 closest distance to " CZ  PHE A 192 " =    0.943
peak=    3.363 closest distance to " CB  ALA A 161 " =    0.890
peak=    3.361 closest distance to " O   HOH Z 133 " =    2.566
peak=    3.360 closest distance to " O   HOH Z 184 " =    1.462
peak=    3.359 closest distance to " CA  GLY A 267 " =    1.070
peak=    3.358 closest distance to " O   HOH Z 423 " =    2.607
peak=    3.354 closest distance to " O   HOH Z 148 " =    3.318
peak=    3.342 closest distance to " O   HOH Z  71 " =    1.273
peak=    3.341 closest distance to " O   HOH Z 145 " =    1.626
peak=    3.340 closest distance to " CA  ALA A 295 " =    0.952
peak=    3.339 closest distance to " NH1 ARG A  14 " =    0.932
peak=    3.336 closest distance to " O   HOH Z 175 " =    2.140
peak=    3.334 closest distance to " O   HOH Z  48 " =    1.464
peak=    3.334 closest distance to " OG BSER A 134 " =    3.032
peak=    3.334 closest distance to " CB  LYS A 117 " =    1.210
peak=    3.333 closest distance to " O   HOH Z 345 " =    3.376
peak=    3.331 closest distance to " O   HOH Z 303 " =    1.826
peak=    3.330 closest distance to " CG1 VAL A 296 " =    1.110
peak=    3.329 closest distance to " O   HOH Z 355 " =    1.733
peak=    3.329 closest distance to " CB  HIS A 108 " =    0.826
peak=    3.329 closest distance to " CG  ARG A 159 " =    0.969
peak=    3.327 closest distance to " CB  ALA A  34 " =    1.008
peak=    3.324 closest distance to " O   HOH Z 417 " =    2.019
peak=    3.323 closest distance to " CB  THR A  82 " =    1.320
peak=    3.323 closest distance to " O   HOH Z 423 " =    1.538
peak=    3.321 closest distance to " CG1 ILE A  33 " =    1.335
peak=    3.315 closest distance to " O   HOH Z  88 " =    2.582
peak=    3.315 closest distance to " O   HOH Z  59 " =    1.905
peak=    3.313 closest distance to " O   HOH Z 188 " =    1.977
peak=    3.311 closest distance to " CD2 TYR A 186 " =    0.970
peak=    3.308 closest distance to " O   HOH Z 371 " =    1.779
peak=    3.308 closest distance to " CB  ALA A 114 " =    1.306
peak=    3.308 closest distance to " C   LYS A 290 " =    1.308
peak=    3.306 closest distance to " O   HOH Z 214 " =    1.857
peak=    3.306 closest distance to " O   GLN A 278 " =    1.325
peak=    3.304 closest distance to " O   HOH Z 357 " =    1.836
peak=    3.304 closest distance to " O   HOH Z 407 " =    2.110
peak=    3.304 closest distance to " N   ALA A   1 " =    2.029
peak=    3.295 closest distance to " O   HOH Z 252 " =    1.830
peak=    3.292 closest distance to " O   HOH Z 255 " =    1.749
peak=    3.291 closest distance to " N   VAL A 126 " =    1.102
peak=    3.290 closest distance to " CA  ALA A 158 " =    1.180
peak=    3.287 closest distance to " O   HOH Z 250 " =    1.297
peak=    3.276 closest distance to " CB  SER A 210 " =    0.794
peak=    3.273 closest distance to " CG  MET A 185 " =    1.264
peak=    3.270 closest distance to " N   SER A 135 " =    1.325
peak=    3.269 closest distance to " CD  ARG A 269 " =    0.998
peak=    3.269 closest distance to " O   HOH Z 145 " =    3.443
peak=    3.264 closest distance to " CB  TRP A 150 " =    1.516
peak=    3.264 closest distance to " ND1 HIS A  81 " =    1.717
peak=    3.261 closest distance to " CD  PRO A 243 " =    1.496
peak=    3.259 closest distance to " O   HOH Z 380 " =    1.927
peak=    3.252 closest distance to " CG1 ILE A  49 " =    1.278
peak=    3.250 closest distance to " CA  ILE A 234 " =    1.030
peak=    3.250 closest distance to " O   MET A 105 " =    1.765
peak=    3.247 closest distance to " O  BHOH Z 338 " =    2.548
peak=    3.245 closest distance to " NH2BARG A 190 " =    1.658
peak=    3.244 closest distance to " CB  ASN A 110 " =    1.172
peak=    3.244 closest distance to " O   HOH Z  40 " =    2.015
peak=    3.240 closest distance to " CA  VAL A 126 " =    0.911
peak=    3.238 closest distance to " O   HOH Z 313 " =    1.756
peak=    3.237 closest distance to " NH1BARG A 190 " =    1.895
peak=    3.236 closest distance to " O   HOH Z 291 " =    1.890
peak=    3.236 closest distance to " CB  SER A 212 " =    1.200
peak=    3.233 closest distance to " O   HOH Z 374 " =    2.617
peak=    3.231 closest distance to " CE  MET A  93 " =    1.497
peak=    3.224 closest distance to " CB  ALA A 248 " =    1.321
peak=    3.224 closest distance to " O   HOH Z 419 " =    1.802
peak=    3.218 closest distance to " O   HOH Z  64 " =    1.974
peak=    3.216 closest distance to " CA  MET A  40 " =    1.085
peak=    3.214 closest distance to " CG  MET A 185 " =    1.032
peak=    3.214 closest distance to " O   TRP A 274 " =    1.838
peak=    3.214 closest distance to " O   HOH Z 302 " =    1.861
peak=    3.212 closest distance to " CD  LYS A 166 " =    1.280
peak=    3.212 closest distance to " O   HOH Z 285 " =    1.975
peak=    3.208 closest distance to " CA  PHE A 283 " =    1.184
peak=    3.204 closest distance to " CD  ARG A 219 " =    1.055
peak=    3.204 closest distance to " N   TRP A 177 " =    1.661
peak=    3.200 closest distance to " OG  SER A  62 " =    2.879
peak=    3.197 closest distance to " O   HOH Z 244 " =    1.606
peak=    3.196 closest distance to " CG  GLN A 278 " =    1.290
peak=    3.193 closest distance to " O   HOH Z 435 " =    2.133
peak=    3.185 closest distance to " CA  GLN A 223 " =    0.803
peak=    3.185 closest distance to " CD1 ILE A 106 " =    1.029
peak=    3.179 closest distance to " O   HOH Z 380 " =    1.644
peak=    3.179 closest distance to " CE  LYS A 166 " =    1.740
peak=    3.178 closest distance to " CB  ARG A 190 " =    1.777
peak=    3.178 closest distance to " O   THR A  31 " =    1.548
peak=    3.175 closest distance to " N   GLN A 278 " =    0.957
peak=    3.174 closest distance to " O   HOH Z 291 " =    1.604
peak=    3.173 closest distance to " O   HOH Z 411 " =    1.955
peak=    3.169 closest distance to " CB  ALA A   9 " =    1.558
peak=    3.167 closest distance to " O   HOH Z 409 " =    2.906
peak=    3.167 closest distance to " O   HOH Z 207 " =    1.718
peak=    3.166 closest distance to " O   HOH Z 344 " =    1.139
peak=    3.159 closest distance to " O   HOH Z 345 " =    1.786
peak=    3.158 closest distance to " CE2 TYR A 186 " =    0.963
peak=    3.156 closest distance to " O   HOH Z  44 " =    2.992
peak=    3.155 closest distance to " N   SER A 134 " =    1.360
peak=    3.154 closest distance to " CA  ASN A 284 " =    0.880
peak=    3.153 closest distance to " O   HOH Z 282 " =    1.996
peak=    3.152 closest distance to " CG2 VAL A 174 " =    1.389
peak=    3.152 closest distance to " O   HOH Z 305 " =    3.440
peak=    3.151 closest distance to " O   HOH Z 383 " =    1.867
peak=    3.150 closest distance to " O   HOH Z 118 " =    1.630
peak=    3.148 closest distance to " CG2 THR A 220 " =    1.019
peak=    3.145 closest distance to " O   HOH Z 151 " =    1.861
peak=    3.143 closest distance to " O   HOH Z 276 " =    1.285
peak=    3.143 closest distance to " O   HOH Z 128 " =    1.766
peak=    3.143 closest distance to " O   ALA A 233 " =    1.760
peak=    3.142 closest distance to " CD1 ILE A 263 " =    1.293
peak=    3.141 closest distance to " CG  MET A 188 " =    1.126
peak=    3.140 closest distance to " CA  LYS A  48 " =    1.284
peak=    3.140 closest distance to " O   ALA A 158 " =    1.389
peak=    3.140 closest distance to " CD  LYS A 119 " =    1.564
peak=    3.139 closest distance to " O   HOH Z  49 " =    2.389
peak=    3.138 closest distance to " O   HOH Z  63 " =    2.277
peak=    3.132 closest distance to " O   HOH Z 128 " =    1.995
peak=    3.126 closest distance to " NE2 GLN A  58 " =    5.600
peak=    3.117 closest distance to " OG  SER A  62 " =    5.457
peak=    3.116 closest distance to " O   HOH Z 422 " =    2.635
peak=    3.115 closest distance to " CA  ILE A 106 " =    0.799
peak=    3.114 closest distance to " CA  ARG A  56 " =    2.100
peak=    3.108 closest distance to " O   HOH Z 238 " =    5.106
peak=    3.106 closest distance to " CA  PHE A 218 " =    1.034
peak=    3.105 closest distance to " O   HOH Z 388 " =    2.068
peak=    3.100 closest distance to " O   HOH Z 147 " =    1.663
peak=    3.099 closest distance to " NZ  LYS A  76 " =    1.227
peak=    3.099 closest distance to " O   HOH Z 332 " =    1.514
peak=    3.098 closest distance to " O   HOH Z 367 " =    3.596
peak=    3.087 closest distance to " O   HOH Z 353 " =    2.591
peak=    3.084 closest distance to " CB  ILE A  20 " =    1.414
peak=    3.081 closest distance to " O   HOH Z 180 " =    2.046
peak=    3.079 closest distance to " CB  LEU A 237 " =    0.830
peak=    3.069 closest distance to " O   HOH Z 272 " =    2.441
peak=    3.066 closest distance to " O   GLY A  57 " =    2.663
peak=    3.053 closest distance to " O   HOH Z 328 " =    1.768
peak=    3.049 closest distance to " O   HOH Z 213 " =    2.025

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

Number of peaks found at mFobs-DFmodel map (map cutoff=3.00 sigma)= 218         
Filter by distance & map next to the model:
   mapped sites are within: 0.454 - 5.384
   number of sites selected in [dist_min= 0.70, dist_max= 6.00]: 213 from: 218
   mapped sites are within: 0.742 - 5.384

peak=   -5.918 closest distance to " CG2 VAL A 230 " =    0.742
peak=   -4.908 closest distance to " O   HOH Z 290 " =    1.020
peak=   -4.446 closest distance to " CD  ARG A  14 " =    3.285
peak=   -4.247 closest distance to " O   HOH Z 231 " =    1.369
peak=   -4.244 closest distance to " CD  ARG A 156 " =    1.941
peak=   -4.144 closest distance to " O   HOH Z 231 " =    0.827
peak=   -4.091 closest distance to " CG  LEU A 101 " =    2.578
peak=   -4.015 closest distance to " CB  PRO A 243 " =    2.586
peak=   -4.013 closest distance to " CB  PRO A 163 " =    2.619
peak=   -3.979 closest distance to " CZ3 TRP A 179 " =    1.193
peak=   -3.962 closest distance to " CG  GLN A 223 " =    1.837
peak=   -3.949 closest distance to " O   PRO A 163 " =    1.907
peak=   -3.929 closest distance to " N   GLN A  58 " =    1.859
peak=   -3.915 closest distance to " O   HOH Z 351 " =    1.336
peak=   -3.890 closest distance to " CG  ASP A 231 " =    0.777
peak=   -3.849 closest distance to " O   PRO A 198 " =    1.190
peak=   -3.843 closest distance to " CG2 VAL A 296 " =    1.233
peak=   -3.843 closest distance to " O   HOH Z 388 " =    2.148
peak=   -3.817 closest distance to " N   THR A 157 " =    1.493
peak=   -3.807 closest distance to " O   HOH Z 435 " =    2.860
peak=   -3.804 closest distance to " O   HOH Z 211 " =    1.549
peak=   -3.783 closest distance to " CG1 VAL A 296 " =    1.350
peak=   -3.735 closest distance to " O   HOH Z 266 " =    4.670
peak=   -3.716 closest distance to " O   HOH Z 166 " =    1.435
peak=   -3.701 closest distance to " O   TYR A 247 " =    2.780
peak=   -3.698 closest distance to " O   HOH Z 389 " =    1.941
peak=   -3.689 closest distance to " C   ALA A 158 " =    1.324
peak=   -3.685 closest distance to " O   HOH Z  52 " =    1.464
peak=   -3.671 closest distance to " NH2 ARG A  79 " =    1.818
peak=   -3.661 closest distance to " CG  PRO A 163 " =    2.494
peak=   -3.656 closest distance to " CB  VAL A 296 " =    1.174
peak=   -3.651 closest distance to " O   HOH Z 417 " =    2.852
peak=   -3.650 closest distance to " CD  LYS A 289 " =    2.622
peak=   -3.638 closest distance to " O   ALA A 161 " =    1.496
peak=   -3.636 closest distance to " CB  ALA A 248 " =    2.005
peak=   -3.636 closest distance to " N   HIS A 115 " =    2.243
peak=   -3.635 closest distance to " CG  MET A 105 " =    0.954
peak=   -3.634 closest distance to " O   HOH Z  60 " =    2.168
peak=   -3.632 closest distance to " O   HOH Z  43 " =    1.780
peak=   -3.628 closest distance to " C   HIS A 108 " =    1.179
peak=   -3.626 closest distance to " CA  ASP A  27 " =    2.394
peak=   -3.622 closest distance to " OG BSER A 134 " =    1.219
peak=   -3.612 closest distance to " CE2 TYR A  30 " =    2.961
peak=   -3.607 closest distance to " CD1 LEU A 101 " =    2.377
peak=   -3.600 closest distance to " CD1 LEU A 228 " =    2.271
peak=   -3.598 closest distance to " OG  SER A  87 " =    1.348
peak=   -3.598 closest distance to " CE BMET A  47 " =    1.636
peak=   -3.581 closest distance to " C   ASN A 285 " =    2.440
peak=   -3.578 closest distance to " CG  TRP A 266 " =    1.682
peak=   -3.569 closest distance to " O   HOH Z 168 " =    1.957
peak=   -3.566 closest distance to " O   HOH Z  92 " =    1.645
peak=   -3.564 closest distance to " O   HOH Z 407 " =    3.102
peak=   -3.561 closest distance to " O   HOH Z  22 " =    2.612
peak=   -3.555 closest distance to " OG BSER A 134 " =    1.637
peak=   -3.542 closest distance to " O   HOH Z 377 " =    1.955
peak=   -3.539 closest distance to " CA  GLY A 241 " =    2.266
peak=   -3.536 closest distance to " ND2 ASN A  45 " =    1.094
peak=   -3.531 closest distance to " N   ALA A  43 " =    2.288
peak=   -3.528 closest distance to " O   HOH Z 275 " =    1.572
peak=   -3.526 closest distance to " O   HOH Z 185 " =    2.200
peak=   -3.516 closest distance to " C   LEU A 222 " =    0.743
peak=   -3.515 closest distance to " O   HOH Z  38 " =    1.933
peak=   -3.511 closest distance to " CG2 THR A   4 " =    1.933
peak=   -3.498 closest distance to " CG  PHE A 283 " =    2.673
peak=   -3.492 closest distance to " O   ILE A 109 " =    2.621
peak=   -3.490 closest distance to " CD1 LEU A 101 " =    2.719
peak=   -3.487 closest distance to " CD2 TYR A 293 " =    2.173
peak=   -3.485 closest distance to " NE2 GLN A  88 " =    2.147
peak=   -3.481 closest distance to " CZ  PHE A  59 " =    1.497
peak=   -3.478 closest distance to " O   HOH Z 309 " =    2.416
peak=   -3.477 closest distance to " O   ARG A 145 " =    1.634
peak=   -3.470 closest distance to " CE2 PHE A 218 " =    2.564
peak=   -3.469 closest distance to " O   HOH Z 281 " =    2.825
peak=   -3.469 closest distance to " OG  SER A   3 " =    1.647
peak=   -3.469 closest distance to " O   GLY A 196 " =    1.150
peak=   -3.460 closest distance to " O   VAL A  67 " =    2.633
peak=   -3.456 closest distance to " C   ASP A 231 " =    2.549
peak=   -3.455 closest distance to " C   VAL A 174 " =    1.825
peak=   -3.452 closest distance to " O   HOH Z 103 " =    1.953
peak=   -3.447 closest distance to " O   GLY A 211 " =    1.316
peak=   -3.431 closest distance to " CB  ASN A  39 " =    2.137
peak=   -3.428 closest distance to " O   HOH Z 423 " =    1.098
peak=   -3.426 closest distance to " O   HOH Z 241 " =    1.372
peak=   -3.425 closest distance to " O   HOH Z  98 " =    1.993
peak=   -3.421 closest distance to " CG1 VAL A 197 " =    2.286
peak=   -3.418 closest distance to " O   GLY A 203 " =    2.459
peak=   -3.416 closest distance to " NH2AARG A 275 " =    5.328
peak=   -3.414 closest distance to " CE1 TYR A 169 " =    2.535
peak=   -3.396 closest distance to " N   SER A 212 " =    1.828
peak=   -3.394 closest distance to " CB  PHE A 192 " =    1.742
peak=   -3.391 closest distance to " O   VAL A  67 " =    2.537
peak=   -3.387 closest distance to " CD2 LEU A 300 " =    2.689
peak=   -3.384 closest distance to " O   HOH Z 134 " =    2.665
peak=   -3.383 closest distance to " O   GLY A  80 " =    2.496
peak=   -3.382 closest distance to " C   MET A 188 " =    1.527
peak=   -3.382 closest distance to " CD1 PHE A  59 " =    1.925
peak=   -3.381 closest distance to " O   HOH Z 426 " =    1.640
peak=   -3.376 closest distance to " CD1 ILE A 239 " =    2.058
peak=   -3.366 closest distance to " OD1 ASN A 148 " =    1.520
peak=   -3.366 closest distance to " O   HOH Z  71 " =    0.935
peak=   -3.366 closest distance to " O   HOH Z 191 " =    5.384
peak=   -3.362 closest distance to " N   SER A 276 " =    1.263
peak=   -3.354 closest distance to " CD  GLN A  58 " =    0.894
peak=   -3.353 closest distance to " CG1 VAL A 250 " =    2.767
peak=   -3.350 closest distance to " CG2 THR A 178 " =    2.200
peak=   -3.349 closest distance to " O   HOH Z  98 " =    2.341
peak=   -3.343 closest distance to " O   HOH Z 426 " =    2.242
peak=   -3.343 closest distance to " OE1 GLN A  88 " =    1.112
peak=   -3.341 closest distance to " NH1AARG A 275 " =    1.879
peak=   -3.340 closest distance to " OXT GLY A 302 " =    2.929
peak=   -3.336 closest distance to " O   VAL A 153 " =    2.182
peak=   -3.335 closest distance to " CG  LEU A 228 " =    0.936
peak=   -3.333 closest distance to " SG BCYS A 201 " =    2.260
peak=   -3.333 closest distance to " CE  MET A 105 " =    2.130
peak=   -3.333 closest distance to " CA  GLY A 203 " =    2.225
peak=   -3.333 closest distance to " C   ASN A 187 " =    1.776
peak=   -3.333 closest distance to " O   HOH Z 111 " =    4.441
peak=   -3.330 closest distance to " CB  TYR A  15 " =    2.159
peak=   -3.328 closest distance to " CG1 VAL A 112 " =    2.779
peak=   -3.323 closest distance to " O   HOH Z 148 " =    1.897
peak=   -3.321 closest distance to " CG1 VAL A 112 " =    2.597
peak=   -3.314 closest distance to " O   HOH Z 171 " =    1.954
peak=   -3.313 closest distance to " O   HOH Z  97 " =    1.502
peak=   -3.312 closest distance to " CB  ASP A 132 " =    2.282
peak=   -3.306 closest distance to " O   HOH Z 410 " =    2.102
peak=   -3.298 closest distance to " CZ  ARG A 259 " =    0.797
peak=   -3.298 closest distance to " O   HOH Z 423 " =    2.217
peak=   -3.297 closest distance to " CB  ALA A   9 " =    2.598
peak=   -3.291 closest distance to " CG  LYS A 193 " =    2.264
peak=   -3.291 closest distance to " O   HOH Z 377 " =    1.207
peak=   -3.291 closest distance to " CD  GLN A  88 " =    0.767
peak=   -3.289 closest distance to " O   HOH Z 371 " =    1.241
peak=   -3.285 closest distance to " CA  GLY A 241 " =    2.974
peak=   -3.285 closest distance to " CE  LYS A  76 " =    2.773
peak=   -3.282 closest distance to " N   GLY A  23 " =    2.123
peak=   -3.278 closest distance to " O   HOH Z 322 " =    0.876
peak=   -3.275 closest distance to " O   HOH Z 175 " =    4.242
peak=   -3.271 closest distance to " CD  ARG A 139 " =    1.577
peak=   -3.270 closest distance to " C   ALA A   8 " =    1.518
peak=   -3.268 closest distance to " CB  ALA A 248 " =    2.434
peak=   -3.268 closest distance to " O   HOH Z  65 " =    1.208
peak=   -3.265 closest distance to " ND2 ASN A  60 " =    1.734
peak=   -3.264 closest distance to " OG1 THR A 178 " =    1.227
peak=   -3.255 closest distance to " ND2 ASN A  60 " =    1.664
peak=   -3.254 closest distance to " O   SER A 135 " =    1.446
peak=   -3.249 closest distance to " CG2 VAL A 112 " =    2.636
peak=   -3.248 closest distance to " OG  SER A  62 " =    1.453
peak=   -3.243 closest distance to " CB  ALA A 244 " =    2.047
peak=   -3.240 closest distance to " CB  ASP A  27 " =    2.479
peak=   -3.239 closest distance to " CD2 PHE A  61 " =    1.870
peak=   -3.238 closest distance to " O   HOH Z 359 " =    3.336
peak=   -3.238 closest distance to " CB  ALA A  43 " =    2.421
peak=   -3.237 closest distance to " O   HOH Z 311 " =    3.759
peak=   -3.235 closest distance to " CD2 LEU A   5 " =    1.016
peak=   -3.231 closest distance to " N   PHE A  59 " =    2.163
peak=   -3.228 closest distance to " CB  ALA A 291 " =    2.144
peak=   -3.224 closest distance to " O   HOH Z 234 " =    4.198
peak=   -3.222 closest distance to " O   PRO A 198 " =    1.268
peak=   -3.220 closest distance to " O   SER A  22 " =    2.225
peak=   -3.219 closest distance to " O   HOH Z 128 " =    4.022
peak=   -3.218 closest distance to " O   HOH Z 198 " =    1.452
peak=   -3.210 closest distance to " O   HOH Z 359 " =    1.578
peak=   -3.210 closest distance to " O   HOH Z  90 " =    2.876
peak=   -3.209 closest distance to " N   GLN A  77 " =    1.703
peak=   -3.204 closest distance to " O   HOH Z 295 " =    1.419
peak=   -3.203 closest distance to " O   HOH Z 278 " =    1.171
peak=   -3.201 closest distance to " NH2 ARG A 159 " =    2.335
peak=   -3.196 closest distance to " O   HOH Z 176 " =    0.766
peak=   -3.194 closest distance to " CB  TYR A 172 " =    2.270
peak=   -3.193 closest distance to " O   HOH Z 436 " =    1.355
peak=   -3.189 closest distance to " O   HOH Z 210 " =    0.892
peak=   -3.182 closest distance to " O   VAL A 197 " =    1.334
peak=   -3.179 closest distance to " OXT GLY A 302 " =    3.508
peak=   -3.177 closest distance to " CD  GLU A 277 " =    0.899
peak=   -3.173 closest distance to " O   SER A  62 " =    2.305
peak=   -3.171 closest distance to " CZ  TYR A 169 " =    1.592
peak=   -3.168 closest distance to " O   HOH Z 390 " =    2.482
peak=   -3.167 closest distance to " O   HOH Z 222 " =    1.434
peak=   -3.160 closest distance to " N   ALA A 226 " =    2.129
peak=   -3.154 closest distance to " O   LYS A 117 " =    1.805
peak=   -3.149 closest distance to " CE3 TRP A 123 " =    1.226
peak=   -3.142 closest distance to " O   GLN A 240 " =    2.127
peak=   -3.141 closest distance to " O   HOH Z  51 " =    1.068
peak=   -3.140 closest distance to " O   HOH Z 116 " =    4.308
peak=   -3.137 closest distance to " CD1 TRP A 179 " =    0.866
peak=   -3.136 closest distance to " CD  ARG A 259 " =    2.504
peak=   -3.135 closest distance to " N   GLN A 122 " =    1.466
peak=   -3.130 closest distance to " O   HOH Z  63 " =    1.327
peak=   -3.125 closest distance to " O   HOH Z 139 " =    3.062
peak=   -3.121 closest distance to " O   HOH Z 298 " =    1.239
peak=   -3.116 closest distance to " O   HOH Z 174 " =    2.521
peak=   -3.114 closest distance to " O   VAL A 197 " =    1.088
peak=   -3.106 closest distance to " O   HOH Z 137 " =    1.801
peak=   -3.105 closest distance to " O   LYS A 289 " =    3.103
peak=   -3.104 closest distance to " CZ BARG A 275 " =    1.699
peak=   -3.099 closest distance to " CB  VAL A 230 " =    1.014
peak=   -3.098 closest distance to " O   HOH Z 140 " =    1.585
peak=   -3.098 closest distance to " N   ALA A 248 " =    1.633
peak=   -3.095 closest distance to " CD1 ILE A 199 " =    2.559
peak=   -3.094 closest distance to " OD1 ASP A 191 " =    1.640
peak=   -3.083 closest distance to " C   GLN A 240 " =    2.240
peak=   -3.082 closest distance to " OG  SER A 206 " =    1.727
peak=   -3.082 closest distance to " O   HOH Z 350 " =    1.957
peak=   -3.080 closest distance to " CB  TRP A  85 " =    2.368
peak=   -3.080 closest distance to " CG1 VAL A 296 " =    1.248
peak=   -3.075 closest distance to " CB  ALA A 114 " =    2.421
peak=   -3.067 closest distance to " O   HOH Z 179 " =    2.309
peak=   -3.066 closest distance to " O   HOH Z 219 " =    1.126
peak=   -3.061 closest distance to " OD1 ASN A 301 " =    1.819
peak=   -3.055 closest distance to " CG  GLU A 152 " =    0.759
peak=   -3.046 closest distance to " O   HOH Z 417 " =    2.650
peak=   -3.043 closest distance to " N   ALA A 248 " =    2.553
peak=   -3.031 closest distance to " CD2 LEU A 143 " =    2.591

================= 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    :  0.4705 0.4531   6.268540e+00   6.256563e+00
   1_bss:  0.4623 0.4453   6.263335e+00   6.250027e+00
   1_xyz:  0.3727 0.3976   6.131971e+00   6.172016e+00
   1_adp:  0.3268 0.3794   6.038936e+00   6.135667e+00
   1_occ:  0.3261 0.3803   6.038268e+00   6.135839e+00
   2_bss:  0.3231 0.3750   6.037696e+00   6.133692e+00
   2_xyz:  0.2182 0.2702   5.710236e+00   5.883253e+00
   2_adp:  0.1923 0.2494   5.605707e+00   5.801968e+00
   2_occ:  0.1921 0.2491   5.604832e+00   5.801062e+00
   3_bss:  0.1909 0.2464   5.603796e+00   5.798018e+00
   3_xyz:  0.1407 0.1859   5.330465e+00   5.554457e+00
   3_adp:  0.1303 0.1749   5.262320e+00   5.491864e+00
   3_occ:  0.1302 0.1745   5.261188e+00   5.490283e+00
   4_bss:  0.1300 0.1748   5.261297e+00   5.490239e+00
   4_xyz:  0.1177 0.1634   5.183704e+00   5.425694e+00
   4_adp:  0.1178 0.1615   5.178244e+00   5.413556e+00
   4_occ:  0.1177 0.1612   5.177455e+00   5.412592e+00
   5_bss:  0.1177 0.1610   5.177340e+00   5.412469e+00
   5_xyz:  0.1151 0.1586   5.161951e+00   5.398656e+00
   5_adp:  0.1152 0.1584   5.162743e+00   5.399833e+00
   5_occ:  0.1151 0.1582   5.162026e+00   5.398812e+00
   5_bss:  0.1151 0.1582   5.162006e+00   5.398790e+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:  0.366  20.001   8.255   8.392   8.085   0.000   0.000   0.000
   1_xyz:  0.366  20.001   8.255   8.392   8.085   0.000   0.000   0.000
   1_adp:  0.366  20.001   8.255   8.392   8.085   0.000   0.000   0.000
   1_occ:  0.366  20.001   8.255   8.392   8.085   0.000   0.000   0.000
   2_bss:  0.349  50.000   4.552   4.260   5.052   0.000   0.000   0.000
   2_xyz:  0.349  50.000   4.552   4.260   5.052   0.000   0.000   0.000
   2_adp:  0.349  50.000   4.552   4.260   5.052   0.000   0.000   0.000
   2_occ:  0.349  50.000   4.552   4.260   5.052   0.000   0.000   0.000
   3_bss:  0.334  49.264   2.872   2.431   3.366   0.000   0.000   0.000
   3_xyz:  0.334  49.264   2.872   2.431   3.366   0.000   0.000   0.000
   3_adp:  0.334  49.264   2.872   2.431   3.366   0.000   0.000   0.000
   3_occ:  0.334  49.264   2.872   2.431   3.366   0.000   0.000   0.000
   4_bss:  0.329  46.387   2.399   1.924   2.815   0.000   0.000   0.000
   4_xyz:  0.329  46.387   2.399   1.924   2.815   0.000   0.000   0.000
   4_adp:  0.329  46.387   2.399   1.924   2.815   0.000   0.000   0.000
   4_occ:  0.329  46.387   2.399   1.924   2.815   0.000   0.000   0.000
   5_bss:  0.330  46.387   2.108   1.732   2.622   0.000   0.000   0.000
   5_xyz:  0.330  46.387   2.108   1.732   2.622   0.000   0.000   0.000
   5_adp:  0.330  46.387   2.108   1.732   2.622   0.000   0.000   0.000
   5_occ:  0.330  46.387   2.108   1.732   2.622   0.000   0.000   0.000
   5_bss:  0.330  48.489  -0.068  -0.416   0.484   0.000   0.000   0.000
------------------------------------------------------------------------
 stage     <pher>    fom   alpha         beta
   0    :  54.237 0.4679  0.5465    64623.528
   1_bss:  54.502 0.4626  0.6835    62215.199
   1_xyz:  44.979 0.5814  0.8441    45719.072
   1_adp:  40.694 0.6342  0.9547    39994.360
   1_occ:  40.812 0.6327  0.9517    40112.739
   2_bss:  40.530 0.6358  0.8410    39628.350
   2_xyz:  27.456 0.7850  0.9911    19068.742
   2_adp:  24.396 0.8181  1.0147    15966.511
   2_occ:  24.387 0.8181  1.0144    15924.880
   3_bss:  24.245 0.8193  0.9536    15707.442
   3_xyz:  17.575 0.8841  0.9934     8899.174
   3_adp:  16.049 0.8980  1.0003     7899.705
   3_occ:  16.012 0.8983  1.0003     7864.169
   4_bss:  16.021 0.8982  0.9812     7881.726
   4_xyz:  14.647 0.9097  0.9857     6811.767
   4_adp:  14.319 0.9127  0.9875     6666.118
   4_occ:  14.297 0.9129  0.9874     6644.879
   5_bss:  14.293 0.9129  0.9794     6641.105
   5_xyz:  14.030 0.9151  0.9795     6444.860
   5_adp:  14.030 0.9152  0.9799     6461.893
   5_occ:  14.013 0.9153  0.9798     6446.867
   5_bss:  14.012 0.9153  0.9780     6445.914
------------------------------------------------------------------------
 stage       angl   bond   chir   dihe   plan   repu  geom_target
   0    :  24.226  0.414  2.119 33.790  0.145  4.089   5.3531e+01
   1_bss:  24.226  0.414  2.119 33.790  0.145  4.089   5.3531e+01
   1_xyz:   1.670  0.013  0.106 18.328  0.006  4.109   1.3846e-01
   1_adp:   1.670  0.013  0.106 18.328  0.006  4.109   1.3846e-01
   1_occ:   1.670  0.013  0.106 18.328  0.006  4.109   1.3846e-01
   2_bss:   1.670  0.013  0.106 18.328  0.006  4.109   1.3846e-01
   2_xyz:   1.107  0.008  0.079 16.560  0.006  4.123   7.8189e-02
   2_adp:   1.107  0.008  0.079 16.560  0.006  4.123   7.8189e-02
   2_occ:   1.107  0.008  0.079 16.560  0.006  4.123   7.8189e-02
   3_bss:   1.107  0.008  0.079 16.560  0.006  4.123   7.8189e-02
   3_xyz:   1.052  0.007  0.080 15.988  0.004  4.121   6.6938e-02
   3_adp:   1.052  0.007  0.080 15.988  0.004  4.121   6.6938e-02
   3_occ:   1.052  0.007  0.080 15.988  0.004  4.121   6.6938e-02
   4_bss:   1.052  0.007  0.080 15.988  0.004  4.121   6.6938e-02
   4_xyz:   1.049  0.007  0.083 16.107  0.004  4.125   6.7059e-02
   4_adp:   1.049  0.007  0.083 16.107  0.004  4.125   6.7059e-02
   4_occ:   1.049  0.007  0.083 16.107  0.004  4.125   6.7059e-02
   5_bss:   1.049  0.007  0.083 16.107  0.004  4.125   6.7059e-02
   5_xyz:   0.983  0.007  0.078 15.661  0.003  4.115   6.0406e-02
   5_adp:   0.983  0.007  0.078 15.661  0.003  4.115   6.0406e-02
   5_occ:   0.983  0.007  0.078 15.661  0.003  4.115   6.0406e-02
   5_bss:   0.983  0.007  0.078 15.661  0.003  4.115   6.0406e-02
------------------------------------------------------------------------
                      Maximal deviations:
 stage       angl   bond   chir   dihe   plan   repu       |grad|
   0    :  74.492  1.400  6.404144.062  0.405  1.196   6.9402e+00
   1_bss:  74.492  1.400  6.404144.062  0.405  1.196   6.9402e+00
   1_xyz:  13.870  0.169  0.462 86.794  0.037  2.261   1.0011e-01
   1_adp:  13.870  0.169  0.462 86.794  0.037  2.261   1.0011e-01
   1_occ:  13.870  0.169  0.462 86.794  0.037  2.261   1.0011e-01
   2_bss:  13.870  0.169  0.462 86.794  0.037  2.261   1.0011e-01
   2_xyz:   7.330  0.059  0.325 87.992  0.054  2.291   6.5309e-02
   2_adp:   7.330  0.059  0.325 87.992  0.054  2.291   6.5309e-02
   2_occ:   7.330  0.059  0.325 87.992  0.054  2.291   6.5309e-02
   3_bss:   7.330  0.059  0.325 87.992  0.054  2.291   6.5309e-02
   3_xyz:   8.026  0.057  0.490 83.073  0.028  2.274   4.5613e-02
   3_adp:   8.026  0.057  0.490 83.073  0.028  2.274   4.5613e-02
   3_occ:   8.026  0.057  0.490 83.073  0.028  2.274   4.5613e-02
   4_bss:   8.026  0.057  0.490 83.073  0.028  2.274   4.5613e-02
   4_xyz:   8.546  0.054  0.547 84.695  0.031  2.308   4.7211e-02
   4_adp:   8.546  0.054  0.547 84.695  0.031  2.308   4.7211e-02
   4_occ:   8.546  0.054  0.547 84.695  0.031  2.308   4.7211e-02
   5_bss:   8.546  0.054  0.547 84.695  0.031  2.308   4.7211e-02
   5_xyz:   7.526  0.044  0.533 84.347  0.027  2.301   3.8673e-02
   5_adp:   7.526  0.044  0.533 84.347  0.027  2.301   3.8673e-02
   5_occ:   7.526  0.044  0.533 84.347  0.027  2.301   3.8673e-02
   5_bss:   7.526  0.044  0.533 84.347  0.027  2.301   3.8673e-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:  92.03   0.00  12.36  92.03   0.00   9.64  79.98   0.00  27.14
   1_occ:  92.03   0.00  12.36  92.03   0.00   9.64  79.98   0.00  27.14
   2_bss:  92.03   0.00  12.36  92.03   0.00   9.64  79.98   0.00  27.14
   2_xyz:  92.03   0.00  12.36  92.03   0.00   9.64  79.98   0.00  27.14
   2_adp:  84.97   0.00  12.59  84.97   0.00   8.66  76.81   0.76  33.94
   2_occ:  84.97   0.00  12.59  84.97   0.00   8.66  76.81   0.76  33.94
   3_bss:  84.97   0.00  12.59  84.97   0.00   8.66  76.81   0.76  33.94
   3_xyz:  84.97   0.00  12.59  84.97   0.00   8.66  76.81   0.76  33.94
   3_adp:  87.72   0.00  12.93  87.72   0.00   8.61  79.10   1.84  36.45
   3_occ:  87.72   0.00  12.93  87.72   0.00   8.61  79.10   1.84  36.45
   4_bss:  87.72   0.00  12.93  87.72   0.00   8.61  79.10   1.84  36.45
   4_xyz:  87.72   0.00  12.93  87.72   0.00   8.61  79.10   1.84  36.45
   4_adp:  85.82   0.00  12.44  85.82   0.00   8.50  76.01   2.17  33.90
   4_occ:  85.82   0.00  12.44  85.82   0.00   8.50  76.01   2.17  33.90
   5_bss:  85.82   0.00  12.44  85.82   0.00   8.50  76.01   2.17  33.90
   5_xyz:  85.82   0.00  12.44  85.82   0.00   8.50  76.01   2.17  33.90
   5_adp:  84.73   0.00  12.28  84.73   0.00   8.47  74.38   2.35  33.02
   5_occ:  84.73   0.00  12.28  84.73   0.00   8.47  74.38   2.35  33.02
   5_bss:  86.83   2.10  14.38  86.83   2.10  10.57  76.49   4.45  35.12
------------------------------------------------------------------------
 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:    1.224    0.018    0.411
   1_adp:    1.224    0.018    0.411
   1_occ:    1.224    0.018    0.411
   2_bss:    1.224    0.018    0.411
   2_xyz:    1.392    0.032    0.584
   2_adp:    1.392    0.032    0.584
   2_occ:    1.392    0.032    0.584
   3_bss:    1.392    0.032    0.584
   3_xyz:    1.634    0.032    0.651
   3_adp:    1.634    0.032    0.651
   3_occ:    1.634    0.032    0.651
   4_bss:    1.634    0.032    0.651
   4_xyz:    1.854    0.044    0.676
   4_adp:    1.854    0.044    0.676
   4_occ:    1.854    0.044    0.676
   5_bss:    1.854    0.044    0.676
   5_xyz:    1.917    0.028    0.685
   5_adp:    1.917    0.028    0.685
   5_occ:    1.917    0.028    0.685
   5_bss:    1.917    0.028    0.685
------------------------------------------------------------------------

CPU time actual refinement: 343.47


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

Writing refined structure to PDB file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/trial/run_1003/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_1003/model_refine_001_2mFobs-DFmodel.map
Writing mFobs-DFmodel XPLOR map to file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/trial/run_1003/model_refine_001_mFobs-DFmodel.map
Writing map coefficients to MTZ file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/trial/run_1003/model_refine_001_map_coeffs.mtz

Writing default parameters for subsequent refinement:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/trial/run_1003/model_refine_002.def


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

Pure refinement (no I/O, processing, etc)= 343.32 
  Macro-tasks:
    bulk solvent and scale       = 40.07  
    individual site refinement   = 143.15 
    weights calculation          = 33.19  
    collect and process          = 6.52   
    model show statistics        = 0.13   
    TOTAL for macro-tasks        = 223.06 
  Micro-tasks:
    mask                            = 1.85   
    f_calc                          = 109.09 
    alpha_beta                      = 8.09   
    target                          = 1.17   
    gradients_wrt_atomic_parameters = 117.99 
    fmodel                         = 7.43   
    r_factors                      = 0.22   
    phase_errors                   = 10.71  
    foms                           = 0.21   
    TOTAL for micro-tasks          = 256.76 
NUMBER OF MASK CALCS=  4
Time per interpreted Python bytecode instruction: 4.837 micro seconds
Total CPU time: 5.95 minutes
from_scatterers_fft:    634 calls, 108.63 s
gradients_fft:          578 calls, 104.79 s

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

# Date 2008-01-16 Time 02:57:27 PST -0800 (1200481047.43 s)
Start R-work = 0.4705, R-free = 0.4531 (no bulk solvent and anisotropic scale)
Final R-work = 0.1320, R-free = 0.1754 (no bulk solvent and anisotropic scale)

Start R-work = 0.4623, R-free = 0.4453
Final R-work = 0.1151, R-free = 0.1582