# Date 2008-01-16 Time 01:40:18 PST -0800 (1200476418.32 s)
#phil __OFF__

Command line arguments: "../517.param" "adp.set_b_iso=10" "sites.shake=0.5" "main.number_of_macro_cycles=5" "--overwrite"

HOST = idle.lbl.gov
HOSTTYPE = x86_64-linux
USER = phzwart
PID = 26684
JOB_ID = 5158
SGE_ARCH = lx24-amd64
SGE_TASK_FIRST = 1
SGE_TASK_LAST = 1330
SGE_TASK_ID = 517

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

              phenix.refine: Macromolecular Structure Refinement

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

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

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

Processing inputs. This may take a minute or two.

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

  refinement.modify_start_model.sites.shake = 0.5

  refinement.main.number_of_macro_cycles = 5

Working crystal symmetry after inspecting all inputs:
  Unit cell: (69.8988, 46.4607, 84.2302, 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: 3.24, per 1000 atoms: 1.15


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

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

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

Miller array info: /net/cci-filer1/vol1/tmp/phzwart/tassos/trial/1e0w.cns:FOBS,SIGMA
Observation type: xray.amplitude
Type of data: double, size=19589
Type of sigmas: double, size=19589
Number of Miller indices: 19589
Anomalous flag: False
Unit cell: (69.8988, 46.4607, 84.2302, 90, 90, 90)
Space group: P 21 21 21 (No. 19)
Systematic absences: 0
Centric reflections: 2427
Resolution range: 14.8359 1.95116
Completeness in resolution range: 0.954072
Completeness with d_max=infinity: 0.951153

Number of F-obs in resolution range:                   19589
Number of F-obs <= 0:                                  0
Refinement resolution range: d_max =  14.8359
                             d_min =   1.9512

Miller array info: /net/cci-filer1/vol1/tmp/phzwart/tassos/trial/1e0w.cns:TEST
Observation type: None
Type of data: int, size=19589
Type of sigmas: None
Number of Miller indices: 19589
Anomalous flag: False
Unit cell: (69.8988, 46.4607, 84.2302, 90, 90, 90)
Space group: P 21 21 21 (No. 19)
Systematic absences: 0
Centric reflections: 2427
Resolution range: 14.8359 1.95116
Completeness in resolution range: 0.954072
Completeness with d_max=infinity: 0.951153

Test (R-free flags) flag value: 1

Number of work/free reflections by resolution:
                                         work  free  %free
  bin  1: 14.8363 -  4.1753 [2154/2182]  1942   212   9.8%
  bin  2:  4.1753 -  3.3264 [2061/2077]  1852   209  10.1%
  bin  3:  3.3264 -  2.9095 [2048/2067]  1843   205  10.0%
  bin  4:  2.9095 -  2.6451 [2037/2067]  1837   200   9.8%
  bin  5:  2.6451 -  2.4564 [2018/2037]  1818   200   9.9%
  bin  6:  2.4564 -  2.3122 [2007/2043]  1799   208  10.4%
  bin  7:  2.3122 -  2.1968 [1975/2008]  1777   198  10.0%
  bin  8:  2.1968 -  2.1014 [1996/2030]  1798   198   9.9%
  bin  9:  2.1014 -  2.0207 [1972/2000]  1774   198  10.0%
  bin 10:  2.0207 -  1.9512 [1321/2021]  1190   131   9.9%
                                overall 17630  1959  10.0%
Writing MTZ file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/trial/run_517/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: 0.13 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:
        1.63 -     2.29: 30
        2.29 -     2.94: 1679
        2.94 -     3.59: 4624
        3.59 -     4.25: 9323
        4.25 -     4.90: 13221
  Nonbonded interactions sorted by model distance:
             atom i - atom j             model   vdw sym.op. j
  " O   HOH Z 178 " - " O   HOH Z 403 "  1.635 3.040 -x+1,y-1/2,-z+1/2
  " O   HOH Z 110 " - " O   HOH Z 355 "  1.678 3.040 -x+1/2,-y+1,z+1/2
  " NH2 ARG A 259 " - " O   HOH Z   3 "  1.722 3.120 -x,y-1/2,-z+1/2
  " O   HOH Z  52 " - " O   HOH Z 183 "  1.745 3.040 -x+1,y+1/2,-z+1/2
  " O   HOH Z 113 " - " O   HOH Z 350 "  1.763 3.040 -x+1/2,-y+1,z+1/2
  ... (remaining 28872 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_517/model_refine_001.eff

Writing geometry restraints to file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/trial/run_517/model_refine_001.geo

CPU time processing inputs: 8.73


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

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

#phil __ON__
refinement {
  crystal_symmetry {
    unit_cell = 69.89875 46.4607 84.23025 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: 1.95 - 14.84 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.4833   r_free= 0.4774   ksol= 0.00   Bsol= 0.00   scale= 0.802    |
|                                                                             |
| 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:   0.74 A                  |
| x-ray target function (ml) for work reflections: 6.282934                   |
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
| Bin     Resolution   Compl.  No. Refl.    R-factors          Targets        |
|number     range              work test   work   test        work        test|
|  1: 14.8363 -  4.6571 0.99   1390  155 0.4025 0.4076      6.5969      6.6315|
|  2:  4.6571 -  3.7156 0.99   1363  147 0.4103 0.3952       6.797      6.7793|
|  3:  3.7156 -  3.2516 0.99   1316  151 0.4443 0.4181      6.6831      6.7631|
|  4:  3.2516 -  2.9568 0.99   1318  148 0.4625 0.4612      6.5342       6.491|
|  5:  2.9568 -  2.7463 0.99   1308  143 0.5079 0.5080      6.3788      6.3508|
|  6:  2.7463 -  2.5853 0.99   1288  145 0.5025 0.5500      6.2704      6.2689|
|  7:  2.5853 -  2.4564 0.99   1309  137 0.5153 0.4671      6.2528      6.2072|
|  8:  2.4564 -  2.3499 0.98   1276  151 0.5372 0.5336       6.172      6.1722|
|  9:  2.3499 -  2.2598 0.98   1276  145 0.5169 0.5102      6.1219      6.1074|
| 10:  2.2598 -  2.1821 0.98   1289  131 0.5433 0.5188       6.116      6.1298|
| 11:  2.1821 -  2.1140 1.00   1274  146 0.5281 0.5320      6.0493      6.0581|
| 12:  2.1140 -  2.0538 0.97   1270  141 0.5155 0.5058      5.9699      5.9943|
| 13:  2.0538 -  1.9998 0.98   1269  139 0.5429 0.5083       5.885      5.8296|
| 14:  1.9998 -  1.9512 0.53    684   80 0.5594 0.5637      5.8413      5.7741|
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
|R-free likelihood based estimates for figures of merit, absolute phase error,|
|and distribution parameters alpha and beta (Acta Cryst. (1995). A51, 880-887)|
|                                                                             |
| Bin     Resolution      No. Refl.   FOM  Phase Scale    Alpha        Beta   |
|  #        range        work  test        error factor                       |
|  1: 14.8363 -  4.6571  1390   155  0.66  38.10   0.80     0.70      83286.79|
|  2:  4.6571 -  3.7156  1363   147  0.67  37.56   0.88     0.76     118683.32|
|  3:  3.7156 -  3.2516  1316   151  0.57  46.14   0.85     0.72     125404.64|
|  4:  3.2516 -  2.9568  1318   148  0.50  51.89   0.82     0.62     107558.81|
|  5:  2.9568 -  2.7463  1308   143  0.41  59.19   0.75     0.51      86340.19|
|  6:  2.7463 -  2.5853  1288   145  0.38  61.32   0.73     0.45      73283.37|
|  7:  2.5853 -  2.4564  1309   137  0.36  62.90   0.75     0.41      66263.79|
|  8:  2.4564 -  2.3499  1276   151  0.34  64.14   0.72     0.42      60512.03|
|  9:  2.3499 -  2.2598  1276   145  0.36  63.14   0.75     0.42      53966.12|
| 10:  2.2598 -  2.1821  1289   131  0.35  63.54   0.76     0.45      49406.05|
| 11:  2.1821 -  2.1140  1274   146  0.35  63.94   0.78     0.43      45424.89|
| 12:  2.1140 -  2.0538  1270   141  0.32  65.84   0.77     0.41      43809.21|
| 13:  2.0538 -  1.9998  1269   139  0.27  69.61   0.75     0.36      38111.92|
| 14:  1.9998 -  1.9512   684    80  0.25  71.33   0.71     0.29      32378.51|
|alpha:            min =        0.29 max =            0.76 mean =         0.51|
|beta:             min =    32378.51 max =       125404.64 mean =     72159.31|
|figures of merit: min =        0.00 max =            1.00 mean =         0.42|
|phase err.(work): min =        0.00 max =           89.98 mean =        57.77|
|phase err.(test): min =        0.00 max =           89.96 mean =        58.04|
|-----------------------------------------------------------------------------|

============================== 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 = 13.418913             wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 80.615   (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 1.421851              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 82.710   (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 |  1.108 -  1.487:        4 |
| 0.140 - 0.280:   585 |   7.457 -  14.906:   711 |  1.487 -  1.866:       16 |
| 0.280 - 0.420:   441 |  14.906 -  22.354:   630 |  1.866 -  2.245:      148 |
| 0.420 - 0.560:   366 |  22.354 -  29.802:   474 |  2.245 -  2.624:      621 |
| 0.560 - 0.700:   237 |  29.802 -  37.251:   338 |  2.624 -  3.004:     1447 |
| 0.700 - 0.840:   127 |  37.251 -  44.699:   241 |  3.004 -  3.383:     2603 |
| 0.840 - 0.980:    59 |  44.699 -  52.147:   125 |  3.383 -  3.762:     4027 |
| 0.980 - 1.120:    17 |  52.147 -  59.595:    51 |  3.762 -  4.141:     5217 |
| 1.120 - 1.260:     9 |  59.595 -  67.044:    13 |  4.141 -  4.521:     6794 |
| 1.260 - 1.400:     1 |  67.044 -  74.492:     3 |  4.521 -  4.900:     8007 |
|-----------------------------------------------------------------------------|
|-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 |       52.919 |
| planarity |      436 |   0.145    0.405  0.000 |     250.485 |              |
|  dihedral |      870 |  33.790  144.062  0.019 |      20.704 |              |
| nonbonded |     2439 |   4.087    4.900  1.108 |       2.184 |              |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 11.436)------------------------------------------|
|    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 = 11.436)------------------------------------------|
|    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: 1.95 - 14.84 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.4895   r_free= 0.4822   ksol= 0.00   Bsol= 0.00   scale= 0.771    |
|                                                                             |
| 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:   0.76 A                  |
| x-ray target function (ml) for work reflections: 6.284987                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.95 - 14.84 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.4748   r_free= 0.4674   ksol= 0.36   Bsol= 0.00   scale= 1.004    |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (6.84,8.68,9.95,0.00,0.00,0.00); trace/3= 8.49                              |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.75 A                  |
| x-ray target function (ml) for work reflections: 6.277700                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 11.214587             wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 81.850   (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 1.254271              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 77.424   (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.4748      final r-factor (work) = 0.4060          |
| start r-factor (free) = 0.4674      final r-factor (free) = 0.4214          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 88.1389 = 11.21 * 0.50 * 6.2811 + 1.00 * 52.9191                            |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 34.9474 = 11.21 * 0.50 * 6.2091 + 1.00 * 0.1314                             |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 26     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.4060      final r-factor (work) = 0.3636          |
| start r-factor (free) = 0.4214      final r-factor (free) = 0.4131          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 7.8021 = 1.25 * 1.00 * 6.2091 + 1.00 * 0.0143                               |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 7.7114 = 1.25 * 1.00 * 6.1340 + 1.00 * 0.0176                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 27     |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 11.436)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.00    93.23   13.83    None  None   None       |
|    all(noH): 2823   0      0.00    93.23   13.83    None  None   None       |
|    Sol.    : 438    0      0.00    93.23   26.04    None  None   None       |
|    Mac.    : 2385   0      0.00    87.68   11.59    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 -   9.323: 1257   |   5:    46.617 -  55.940:   39        |
|      1:     9.323 -  18.647:  830   |   6:    55.940 -  65.263:   12        |
|      2:    18.647 -  27.970:  386   |   7:    65.263 -  74.587:    4        |
|      3:    27.970 -  37.293:  197   |   8:    74.587 -  83.910:    3        |
|      4:    37.293 -  46.617:   91   |   9:    83.910 -  93.233:    4        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.3636 r_free = 0.4131             target_work(ml) = 6.124         |
| occupancies: max = 1.00  min = 0.30   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.3630 r_free = 0.4136             target_work(ml) = 6.124         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:       12 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.95 - 14.84 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.3630   r_free= 0.4136   ksol= 0.36   Bsol= 0.00   scale= 1.118    |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (6.84,8.68,9.95,0.00,0.00,0.00); trace/3= 8.49                              |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.56 A                  |
| x-ray target function (ml) for work reflections: 6.123826                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.95 - 14.84 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.3588   r_free= 0.4084   ksol= 0.34   Bsol= 22.92   scale= 1.015   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (3.00,4.08,6.11,0.00,0.00,0.00); trace/3= 4.40                              |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.57 A                  |
| x-ray target function (ml) for work reflections: 6.122572                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 9.354565              wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 98.126   (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 0.539867              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 126.897  (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.3588      final r-factor (work) = 0.2683          |
| start r-factor (free) = 0.4084      final r-factor (free) = 0.3251          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 28.8014 = 9.35 * 0.50 * 6.1296 + 1.00 * 0.1314                              |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 28.1911 = 9.35 * 0.50 * 6.0074 + 1.00 * 0.0927                              |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 28     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.2683      final r-factor (work) = 0.2425          |
| start r-factor (free) = 0.3251      final r-factor (free) = 0.3015          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 3.2603 = 0.54 * 1.00 * 6.0074 + 1.00 * 0.0170                               |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 3.1669 = 0.54 * 1.00 * 5.8436 + 1.00 * 0.0122                               |
|-----------------------------------------------------------------------------|
| number of iterations = 22      |    number of function evaluations = 23     |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 11.436)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.00    88.72   13.66    None  None   None       |
|    all(noH): 2823   0      0.00    88.72   13.66    None  None   None       |
|    Sol.    : 438    0      0.00    84.73   32.65    None  None   None       |
|    Mac.    : 2385   0      0.00    88.72   10.18    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 -   8.872: 1394   |   5:    44.360 -  53.232:   67        |
|      1:     8.872 -  17.744:  728   |   6:    53.232 -  62.104:   27        |
|      2:    17.744 -  26.616:  279   |   7:    62.104 -  70.976:    8        |
|      3:    26.616 -  35.488:  191   |   8:    70.976 -  79.848:    4        |
|      4:    35.488 -  44.360:  121   |   9:    79.848 -  88.720:    4        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.2425 r_free = 0.3015             target_work(ml) = 5.812         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:       12 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.2422 r_free = 0.3020             target_work(ml) = 5.812         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:       12 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.95 - 14.84 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.2422   r_free= 0.3020   ksol= 0.34   Bsol= 22.92   scale= 1.065   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (3.00,4.08,6.11,0.00,0.00,0.00); trace/3= 4.40                              |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.32 A                  |
| x-ray target function (ml) for work reflections: 5.811666                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.95 - 14.84 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.2405   r_free= 0.3013   ksol= 0.33   Bsol= 30.59   scale= 1.017   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (1.88,2.22,3.65,0.00,0.00,0.00); trace/3= 2.58                              |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.33 A                  |
| x-ray target function (ml) for work reflections: 5.810103                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 5.972762              wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 102.917  (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 0.336287              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 99.116   (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.2405      final r-factor (work) = 0.1708          |
| start r-factor (free) = 0.3013      final r-factor (free) = 0.2245          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 17.5503 = 5.97 * 0.50 * 5.8457 + 1.00 * 0.0927                              |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 17.0402 = 5.97 * 0.50 * 5.6810 + 1.00 * 0.0746                              |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 27     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1708      final r-factor (work) = 0.1521          |
| start r-factor (free) = 0.2245      final r-factor (free) = 0.2021          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 1.9221 = 0.34 * 1.00 * 5.6810 + 1.00 * 0.0117                               |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 1.8456 = 0.34 * 1.00 * 5.4589 + 1.00 * 0.0099                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 27     |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 11.436)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.00    85.97   13.47    None  None   None       |
|    all(noH): 2823   0      0.00    85.97   13.47    None  None   None       |
|    Sol.    : 438    0      2.72    80.25   35.78    None  None   None       |
|    Mac.    : 2385   0      0.00    85.97   9.37     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 -   8.597: 1508   |   5:    42.986 -  51.584:   96        |
|      1:     8.597 -  17.195:  680   |   6:    51.584 -  60.181:   51        |
|      2:    17.195 -  25.792:  200   |   7:    60.181 -  68.778:   17        |
|      3:    25.792 -  34.389:  145   |   8:    68.778 -  77.375:    5        |
|      4:    34.389 -  42.986:  117   |   9:    77.375 -  85.972:    4        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.1521 r_free = 0.2021             target_work(ml) = 5.400         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:       12 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.1517 r_free = 0.2016             target_work(ml) = 5.398         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:       12 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.95 - 14.84 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1517   r_free= 0.2016   ksol= 0.33   Bsol= 30.59   scale= 1.038   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (1.88,2.22,3.65,0.00,0.00,0.00); trace/3= 2.58                              |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.18 A                  |
| x-ray target function (ml) for work reflections: 5.397956                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.95 - 14.84 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1507   r_free= 0.1994   ksol= 0.31   Bsol= 33.09   scale= 1.011   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (1.24,1.41,2.31,0.00,0.00,0.00); trace/3= 1.65                              |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.18 A                  |
| x-ray target function (ml) for work reflections: 5.390515                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 3.537987              wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 106.850  (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 0.293310              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 114.936  (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1507      final r-factor (work) = 0.1248          |
| start r-factor (free) = 0.1994      final r-factor (free) = 0.1687          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 9.7375 = 3.54 * 0.50 * 5.4624 + 1.00 * 0.0746                               |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 9.4709 = 3.54 * 0.50 * 5.3153 + 1.00 * 0.0681                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 27     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1248      final r-factor (work) = 0.1196          |
| start r-factor (free) = 0.1687      final r-factor (free) = 0.1643          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 1.5687 = 0.29 * 1.00 * 5.3153 + 1.00 * 0.0097                               |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 1.5366 = 0.29 * 1.00 * 5.2070 + 1.00 * 0.0094                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 27     |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 11.436)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.00    86.65   13.38    None  None   None       |
|    all(noH): 2823   0      0.00    86.65   13.38    None  None   None       |
|    Sol.    : 438    0      3.18    82.13   36.28    None  None   None       |
|    Mac.    : 2385   0      0.00    86.65   9.18     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 -   8.665: 1555   |   5:    43.325 -  51.990:   96        |
|      1:     8.665 -  17.330:  689   |   6:    51.990 -  60.656:   57        |
|      2:    17.330 -  25.995:  165   |   7:    60.656 -  69.321:   17        |
|      3:    25.995 -  34.660:  121   |   8:    69.321 -  77.986:    9        |
|      4:    34.660 -  43.325:  108   |   9:    77.986 -  86.651:    6        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.1196 r_free = 0.1643             target_work(ml) = 5.190         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:       12 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.1195 r_free = 0.1639             target_work(ml) = 5.189         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:       11 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.95 - 14.84 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1195   r_free= 0.1639   ksol= 0.31   Bsol= 33.09   scale= 1.017   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (1.24,1.41,2.31,0.00,0.00,0.00); trace/3= 1.65                              |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.15 A                  |
| x-ray target function (ml) for work reflections: 5.188931                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.95 - 14.84 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1196   r_free= 0.1644   ksol= 0.32   Bsol= 34.46   scale= 1.012   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (1.12,1.30,1.98,0.00,0.00,0.00); trace/3= 1.47                              |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.15 A                  |
| x-ray target function (ml) for work reflections: 5.190362                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 2.496349              wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 123.978  (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 0.562635              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 154.765  (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1196      final r-factor (work) = 0.1131          |
| start r-factor (free) = 0.1644      final r-factor (free) = 0.1594          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 6.5674 = 2.50 * 0.50 * 5.2070 + 1.00 * 0.0681                               |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 6.5161 = 2.50 * 0.50 * 5.1683 + 1.00 * 0.0651                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 28     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1131      final r-factor (work) = 0.1114          |
| start r-factor (free) = 0.1594      final r-factor (free) = 0.1602          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 2.9172 = 0.56 * 1.00 * 5.1683 + 1.00 * 0.0093                               |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 2.9043 = 0.56 * 1.00 * 5.1434 + 1.00 * 0.0104                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 27     |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 11.436)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.00    93.73   13.42    None  None   None       |
|    all(noH): 2823   0      0.00    93.73   13.42    None  None   None       |
|    Sol.    : 438    0      3.00    86.12   36.68    None  None   None       |
|    Mac.    : 2385   0      0.00    93.73   9.14     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 -   9.373: 1667   |   5:    46.866 -  56.240:   81        |
|      1:     9.373 -  18.747:  625   |   6:    56.240 -  65.613:   40        |
|      2:    18.747 -  28.120:  145   |   7:    65.613 -  74.986:   18        |
|      3:    28.120 -  37.493:  135   |   8:    74.986 -  84.360:    5        |
|      4:    37.493 -  46.866:  104   |   9:    84.360 -  93.733:    3        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.1114 r_free = 0.1602             target_work(ml) = 5.146         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:       11 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.1113 r_free = 0.1601             target_work(ml) = 5.145         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:       11 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.95 - 14.84 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1113   r_free= 0.1601   ksol= 0.32   Bsol= 34.46   scale= 1.011   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (1.12,1.30,1.98,0.00,0.00,0.00); trace/3= 1.47                              |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.15 A                  |
| x-ray target function (ml) for work reflections: 5.145248                   |
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
| Bin     Resolution   Compl.  No. Refl.    R-factors          Targets        |
|number     range              work test   work   test        work        test|
|  1: 14.8363 -  4.6571 0.99   1390  155 0.0983 0.1256      5.3715      5.5201|
|  2:  4.6571 -  3.7156 0.99   1363  147 0.0862 0.1207      5.4369      5.6682|
|  3:  3.7156 -  3.2516 0.99   1316  151 0.1077 0.1515      5.4829      5.8248|
|  4:  3.2516 -  2.9568 0.99   1318  148 0.1218 0.1649      5.4593      5.6199|
|  5:  2.9568 -  2.7463 0.99   1308  143 0.1293 0.1683      5.3167       5.488|
|  6:  2.7463 -  2.5853 0.99   1288  145 0.1200 0.1838      5.1932      5.4767|
|  7:  2.5853 -  2.4564 0.99   1309  137 0.1243 0.1653      5.1691      5.3682|
|  8:  2.4564 -  2.3499 0.98   1276  151 0.1130 0.1714      5.0552      5.3228|
|  9:  2.3499 -  2.2598 0.98   1276  145 0.1129 0.1916      5.0308      5.3317|
| 10:  2.2598 -  2.1821 0.98   1289  131 0.1101 0.1690      4.9561      5.2028|
| 11:  2.1821 -  2.1140 1.00   1274  146 0.1144 0.1793      4.9437      5.3045|
| 12:  2.1140 -  2.0538 0.97   1270  141 0.1082 0.1661      4.8664      5.1162|
| 13:  2.0538 -  1.9998 0.98   1269  139 0.1148 0.1882      4.7909      5.0653|
| 14:  1.9998 -  1.9512 0.53    684   80 0.1037 0.1565      4.6742      4.8846|
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
|R-free likelihood based estimates for figures of merit, absolute phase error,|
|and distribution parameters alpha and beta (Acta Cryst. (1995). A51, 880-887)|
|                                                                             |
| Bin     Resolution      No. Refl.   FOM  Phase Scale    Alpha        Beta   |
|  #        range        work  test        error factor                       |
|  1: 14.8363 -  4.6571  1390   155  0.94   8.71   0.99     0.97       6880.18|
|  2:  4.6571 -  3.7156  1363   147  0.95   7.76   1.03     1.01       8803.67|
|  3:  3.7156 -  3.2516  1316   151  0.93  11.81   1.04     1.03      10668.10|
|  4:  3.2516 -  2.9568  1318   148  0.92  13.73   1.02     1.00      10423.09|
|  5:  2.9568 -  2.7463  1308   143  0.90  16.11   0.99     0.96       8178.31|
|  6:  2.7463 -  2.5853  1288   145  0.90  15.89   0.99     0.96       6963.89|
|  7:  2.5853 -  2.4564  1309   137  0.90  15.72   0.99     0.95       6316.82|
|  8:  2.4564 -  2.3499  1276   151  0.91  15.58   1.00     0.97       5388.39|
|  9:  2.3499 -  2.2598  1276   145  0.91  15.46   1.02     1.00       5184.27|
| 10:  2.2598 -  2.1821  1289   131  0.90  15.76   1.01     0.97       4432.38|
| 11:  2.1821 -  2.1140  1274   146  0.90  16.39   1.01     0.98       4453.49|
| 12:  2.1140 -  2.0538  1270   141  0.91  15.25   1.01     0.99       3980.00|
| 13:  2.0538 -  1.9998  1269   139  0.89  16.81   1.01     1.00       3405.54|
| 14:  1.9998 -  1.9512   684    80  0.91  15.09   1.01     0.98       2672.49|
|alpha:            min =        0.95 max =            1.03 mean =         0.98|
|beta:             min =     2672.49 max =        10668.10 mean =      6429.79|
|figures of merit: min =        0.00 max =            1.00 mean =         0.91|
|phase err.(work): min =        0.00 max =           89.99 mean =        14.20|
|phase err.(test): min =        0.00 max =           89.79 mean =        13.71|
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.95 - 14.84 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1113   r_free= 0.1601   ksol= 0.32   Bsol= 37.23   scale= 1.013   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-0.30,-0.15,0.46,0.00,0.00,0.00); trace/3= 0.00                            |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.15 A                  |
| x-ray target function (ml) for work reflections: 5.145214                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.95 - 14.84 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1113   r_free= 0.1601   ksol= 0.32   Bsol= 37.23   scale= 1.013   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-0.30,-0.15,0.46,0.00,0.00,0.00); trace/3= 0.00                            |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.15 A                  |
| x-ray target function (ml) for work reflections: 5.145214                   |
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
| Bin     Resolution   Compl.  No. Refl.    R-factors          Targets        |
|number     range              work test   work   test        work        test|
|  1: 14.8363 -  4.6571 0.99   1390  155 0.0984 0.1258      5.3728      5.5218|
|  2:  4.6571 -  3.7156 0.99   1363  147 0.0863 0.1209       5.438      5.6692|
|  3:  3.7156 -  3.2516 0.99   1316  151 0.1078 0.1516      5.4835      5.8256|
|  4:  3.2516 -  2.9568 0.99   1318  148 0.1218 0.1648      5.4593      5.6199|
|  5:  2.9568 -  2.7463 0.99   1308  143 0.1293 0.1683      5.3163      5.4869|
|  6:  2.7463 -  2.5853 0.99   1288  145 0.1199 0.1839      5.1929      5.4771|
|  7:  2.5853 -  2.4564 0.99   1309  137 0.1242 0.1653       5.169      5.3684|
|  8:  2.4564 -  2.3499 0.98   1276  151 0.1130 0.1712      5.0549       5.322|
|  9:  2.3499 -  2.2598 0.98   1276  145 0.1129 0.1918      5.0305      5.3319|
| 10:  2.2598 -  2.1821 0.98   1289  131 0.1100 0.1690      4.9557      5.2015|
| 11:  2.1821 -  2.1140 1.00   1274  146 0.1144 0.1791      4.9433      5.3042|
| 12:  2.1140 -  2.0538 0.97   1270  141 0.1081 0.1661      4.8656      5.1157|
| 13:  2.0538 -  1.9998 0.98   1269  139 0.1148 0.1879      4.7904      5.0637|
| 14:  1.9998 -  1.9512 0.53    684   80 0.1037 0.1564       4.674       4.885|
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
|R-free likelihood based estimates for figures of merit, absolute phase error,|
|and distribution parameters alpha and beta (Acta Cryst. (1995). A51, 880-887)|
|                                                                             |
| Bin     Resolution      No. Refl.   FOM  Phase Scale    Alpha        Beta   |
|  #        range        work  test        error factor                       |
|  1: 14.8363 -  4.6571  1390   155  0.94   8.73   0.99     0.97       6904.62|
|  2:  4.6571 -  3.7156  1363   147  0.95   7.77   1.03     1.02       8826.17|
|  3:  3.7156 -  3.2516  1316   151  0.93  11.83   1.04     1.03      10685.58|
|  4:  3.2516 -  2.9568  1318   148  0.92  13.73   1.02     1.01      10422.17|
|  5:  2.9568 -  2.7463  1308   143  0.90  16.11   1.00     0.96       8177.07|
|  6:  2.7463 -  2.5853  1288   145  0.90  15.88   0.99     0.96       6960.08|
|  7:  2.5853 -  2.4564  1309   137  0.90  15.72   1.00     0.96       6316.34|
|  8:  2.4564 -  2.3499  1276   151  0.91  15.57   1.00     0.97       5383.71|
|  9:  2.3499 -  2.2598  1276   145  0.91  15.46   1.02     1.01       5181.35|
| 10:  2.2598 -  2.1821  1289   131  0.90  15.76   1.01     0.97       4428.90|
| 11:  2.1821 -  2.1140  1274   146  0.90  16.38   1.02     0.99       4450.43|
| 12:  2.1140 -  2.0538  1270   141  0.91  15.22   1.02     1.00       3971.79|
| 13:  2.0538 -  1.9998  1269   139  0.89  16.80   1.02     1.00       3400.52|
| 14:  1.9998 -  1.9512   684    80  0.91  15.08   1.01     0.99       2671.02|
|alpha:            min =        0.96 max =            1.03 mean =         0.99|
|beta:             min =     2671.02 max =        10685.58 mean =      6432.25|
|figures of merit: min =        0.00 max =            1.00 mean =         0.91|
|phase err.(work): min =        0.00 max =           89.93 mean =        14.19|
|phase err.(test): min =        0.00 max =           89.93 mean =        13.71|
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 11.436)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      1.56    95.29   14.98    None  None   None       |
|    all(noH): 2823   0      1.56    95.29   14.98    None  None   None       |
|    Sol.    : 438    0      4.57    87.68   38.24    None  None   None       |
|    Mac.    : 2385   0      1.56    95.29   10.71    None  None   None       |
|    Hyd.    : 0      0      None    None    None     None  None   None       |
|    - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -      |
|       Distribution of isotropic (or equivalent) ADP for non-H atoms:        |
|    Bin#      value range     #atoms | Bin#      value range     #atoms      |
|      0:     1.562 -  10.935: 1667   |   5:    48.428 -  57.802:   81        |
|      1:    10.935 -  20.308:  625   |   6:    57.802 -  67.175:   40        |
|      2:    20.308 -  29.682:  145   |   7:    67.175 -  76.548:   18        |
|      3:    29.682 -  39.055:  135   |   8:    76.548 -  85.921:    5        |
|      4:    39.055 -  48.428:  104   |   9:    85.921 -  95.295:    3        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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


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

Number of peaks found at mFobs-DFmodel map (map cutoff=3.00 sigma)= 319         
Filter by distance & map next to the model:
   mapped sites are within: 0.402 - 5.716
   number of sites selected in [dist_min= 0.70, dist_max= 6.00]: 317 from: 319
   mapped sites are within: 0.741 - 5.716

peak=   10.868 closest distance to " CB  VAL A 230 " =    1.422
peak=    8.546 closest distance to " CG2 VAL A 296 " =    1.221
peak=    6.312 closest distance to " O   HOH Z 278 " =    1.843
peak=    6.118 closest distance to " NE2 GLN A  11 " =    1.190
peak=    6.097 closest distance to " CG  LEU A   5 " =    1.194
peak=    5.479 closest distance to " O   HOH Z 124 " =    1.601
peak=    5.399 closest distance to " O   HOH Z 236 " =    1.469
peak=    5.354 closest distance to " O   HOH Z 202 " =    1.575
peak=    5.238 closest distance to " NH2 ARG A  56 " =    2.038
peak=    5.235 closest distance to " CG  PRO A  54 " =    1.216
peak=    5.191 closest distance to " O   HOH Z 132 " =    1.423
peak=    5.191 closest distance to " CD2 LEU A   5 " =    1.156
peak=    5.178 closest distance to " CB  ASN A 187 " =    2.015
peak=    5.108 closest distance to " O   HOH Z 142 " =    1.804
peak=    5.094 closest distance to " O   HOH Z 193 " =    1.654
peak=    4.995 closest distance to " O   HOH Z 260 " =    1.372
peak=    4.958 closest distance to " CD1AILE A 234 " =    0.976
peak=    4.945 closest distance to " CB  VAL A 230 " =    1.135
peak=    4.941 closest distance to " CB  VAL A 296 " =    1.076
peak=    4.916 closest distance to " CG  LEU A 228 " =    1.175
peak=    4.895 closest distance to " O   HOH Z 143 " =    1.299
peak=    4.767 closest distance to " O   HOH Z 427 " =    2.696
peak=    4.742 closest distance to " O   HOH Z 108 " =    1.430
peak=    4.724 closest distance to " CB  ARG A 275 " =    0.896
peak=    4.719 closest distance to " CG  PRO A 213 " =    1.229
peak=    4.715 closest distance to " O   HOH Z 203 " =    1.671
peak=    4.702 closest distance to " O   HOH Z 373 " =    2.145
peak=    4.687 closest distance to " O   HOH Z 263 " =    1.436
peak=    4.686 closest distance to " O   HOH Z 232 " =    2.300
peak=    4.673 closest distance to " O   HOH Z 272 " =    1.871
peak=    4.641 closest distance to " CB  GLN A 223 " =    1.499
peak=    4.612 closest distance to " CB  GLN A 183 " =    1.303
peak=    4.611 closest distance to " CB  SER A  63 " =    1.288
peak=    4.607 closest distance to " C   PRO A 198 " =    1.547
peak=    4.534 closest distance to " CB  PRO A  54 " =    0.957
peak=    4.510 closest distance to " CD2 LEU A 228 " =    1.206
peak=    4.460 closest distance to " CA  GLY A 241 " =    3.764
peak=    4.458 closest distance to " CB  SER A   3 " =    1.364
peak=    4.413 closest distance to " CB  ASN A 148 " =    1.357
peak=    4.372 closest distance to " O   HOH Z 326 " =    1.499
peak=    4.300 closest distance to " OD1 ASN A  69 " =    2.547
peak=    4.275 closest distance to " CG  PRO A 198 " =    1.274
peak=    4.258 closest distance to " O   SER A  87 " =    2.296
peak=    4.257 closest distance to " CB  TRP A 179 " =    1.314
peak=    4.252 closest distance to " O   HOH Z 117 " =    2.068
peak=    4.247 closest distance to " CB  GLU A 152 " =    1.237
peak=    4.225 closest distance to " O   HOH Z 316 " =    2.932
peak=    4.207 closest distance to " O   HOH Z 234 " =    3.574
peak=    4.204 closest distance to " OD2 ASP A 286 " =    2.645
peak=    4.156 closest distance to " O   HOH Z  78 " =    1.711
peak=    4.147 closest distance to " CA  TYR A  30 " =    1.019
peak=    4.130 closest distance to " NZ  LYS A 117 " =    3.139
peak=    4.120 closest distance to " CB  TYR A 169 " =    1.053
peak=    4.094 closest distance to " O   HOH Z  61 " =    1.599
peak=    4.090 closest distance to " O   HOH Z   9 " =    2.267
peak=    4.040 closest distance to " CB  GLN A  88 " =    1.272
peak=    4.035 closest distance to " CG1BVAL A  72 " =    1.358
peak=    4.026 closest distance to " CB  ARG A  79 " =    1.357
peak=    4.008 closest distance to " OE1 GLU A   2 " =    2.075
peak=    4.002 closest distance to " O   HOH Z  59 " =    1.648
peak=    4.001 closest distance to " O   HOH Z 133 " =    1.514
peak=    3.983 closest distance to " O   HOH Z 196 " =    3.290
peak=    3.982 closest distance to " O   HOH Z 322 " =    2.185
peak=    3.955 closest distance to " O   HOH Z 346 " =    1.539
peak=    3.952 closest distance to " O   HOH Z 134 " =    1.304
peak=    3.951 closest distance to " O   HOH Z 344 " =    1.261
peak=    3.942 closest distance to " CB  VAL A 265 " =    1.265
peak=    3.925 closest distance to " O   HOH Z 209 " =    2.404
peak=    3.923 closest distance to " O   HOH Z  54 " =    1.620
peak=    3.922 closest distance to " O   HOH Z 227 " =    1.714
peak=    3.921 closest distance to " O   HOH Z 280 " =    2.967
peak=    3.918 closest distance to " O   HOH Z 371 " =    3.126
peak=    3.904 closest distance to " O   HOH Z 189 " =    2.346
peak=    3.902 closest distance to " O   HOH Z 287 " =    1.654
peak=    3.889 closest distance to " O   HOH Z 209 " =    2.280
peak=    3.889 closest distance to " O   HOH Z  93 " =    2.339
peak=    3.887 closest distance to " CB  ARG A 139 " =    1.049
peak=    3.887 closest distance to " O   HOH Z 345 " =    3.146
peak=    3.869 closest distance to " CA  VAL A 126 " =    1.061
peak=    3.838 closest distance to " CG  LEU A 167 " =    1.162
peak=    3.829 closest distance to " O   HOH Z  59 " =    2.086
peak=    3.828 closest distance to " O   HOH Z  44 " =    1.908
peak=    3.823 closest distance to " CB BVAL A  41 " =    1.123
peak=    3.823 closest distance to " O   HOH Z 303 " =    2.088
peak=    3.814 closest distance to " CG1 ILE A  33 " =    1.325
peak=    3.811 closest distance to " C   ALA A 299 " =    0.941
peak=    3.806 closest distance to " O   HOH Z 193 " =    1.888
peak=    3.805 closest distance to " O   HOH Z 423 " =    1.865
peak=    3.788 closest distance to " CA  ASN A 215 " =    1.146
peak=    3.779 closest distance to " CB  LEU A 228 " =    1.340
peak=    3.764 closest distance to " O   HOH Z 380 " =    1.693
peak=    3.751 closest distance to " CB  ASN A 148 " =    1.865
peak=    3.747 closest distance to " CG  ARG A  66 " =    2.861
peak=    3.746 closest distance to " O   HOH Z  68 " =    1.711
peak=    3.745 closest distance to " O   HOH Z 374 " =    2.420
peak=    3.743 closest distance to " CB  VAL A 202 " =    1.659
peak=    3.731 closest distance to " O   HOH Z 118 " =    1.526
peak=    3.729 closest distance to " O   HOH Z 368 " =    2.068
peak=    3.728 closest distance to " CG2 VAL A 257 " =    0.789
peak=    3.723 closest distance to " O   HOH Z 298 " =    1.760
peak=    3.716 closest distance to " O   HOH Z 284 " =    1.491
peak=    3.715 closest distance to " O   HOH Z 369 " =    2.096
peak=    3.714 closest distance to " O   HOH Z  85 " =    1.310
peak=    3.710 closest distance to " O   HOH Z 248 " =    1.719
peak=    3.692 closest distance to " O   HOH Z 250 " =    1.379
peak=    3.685 closest distance to " O   HOH Z  43 " =    1.955
peak=    3.683 closest distance to " CA  VAL A  41 " =    0.864
peak=    3.679 closest distance to " O   HOH Z 145 " =    1.350
peak=    3.678 closest distance to " CG  GLN A  88 " =    1.072
peak=    3.668 closest distance to " O   HOH Z  10 " =    1.747
peak=    3.662 closest distance to " O   HOH Z 357 " =    1.791
peak=    3.658 closest distance to " O   HOH Z 425 " =    2.052
peak=    3.654 closest distance to " O   HOH Z 192 " =    1.428
peak=    3.653 closest distance to " CG  PRO A 243 " =    1.257
peak=    3.643 closest distance to " O   HOH Z  89 " =    2.129
peak=    3.642 closest distance to " O   HOH Z 180 " =    2.206
peak=    3.642 closest distance to " O   HOH Z  11 " =    1.500
peak=    3.641 closest distance to " O   HOH Z 148 " =    1.521
peak=    3.634 closest distance to " O   HOH Z 426 " =    1.489
peak=    3.633 closest distance to " O   HOH Z  48 " =    1.501
peak=    3.628 closest distance to " CB  ARG A 102 " =    0.741
peak=    3.628 closest distance to " OG BSER A 164 " =    2.239
peak=    3.625 closest distance to " CG  GLU A 277 " =    2.139
peak=    3.624 closest distance to " CG2 THR A 221 " =    1.170
peak=    3.623 closest distance to " CB  THR A 157 " =    1.000
peak=    3.620 closest distance to " CA  LYS A 290 " =    1.271
peak=    3.618 closest distance to " CB  GLU A 277 " =    3.454
peak=    3.605 closest distance to " O   HOH Z 403 " =    1.326
peak=    3.593 closest distance to " CA  THR A 264 " =    0.798
peak=    3.592 closest distance to " CB  GLU A 128 " =    1.123
peak=    3.588 closest distance to " O   HOH Z  61 " =    1.567
peak=    3.584 closest distance to " CB  LEU A 255 " =    0.819
peak=    3.576 closest distance to " CG2 ILE A 120 " =    1.284
peak=    3.572 closest distance to " O   HOH Z 213 " =    1.729
peak=    3.572 closest distance to " O   HOH Z  88 " =    3.161
peak=    3.571 closest distance to " CA  ALA A  21 " =    1.108
peak=    3.569 closest distance to " O   HOH Z 193 " =    1.651
peak=    3.564 closest distance to " N   ARG A 156 " =    1.269
peak=    3.564 closest distance to " O   HOH Z 261 " =    2.208
peak=    3.563 closest distance to " O   HOH Z 273 " =    2.774
peak=    3.556 closest distance to " O   HOH Z  97 " =    1.496
peak=    3.554 closest distance to " O   HOH Z 425 " =    1.346
peak=    3.547 closest distance to " ND2 ASN A 187 " =    1.719
peak=    3.542 closest distance to " O   HOH Z 214 " =    1.162
peak=    3.541 closest distance to " O   HOH Z  48 " =    1.408
peak=    3.538 closest distance to " CG1BVAL A 121 " =    1.102
peak=    3.538 closest distance to " O   HOH Z 407 " =    2.202
peak=    3.537 closest distance to " O   HOH Z 158 " =    2.935
peak=    3.533 closest distance to " O   HOH Z 130 " =    2.236
peak=    3.526 closest distance to " O   HOH Z 112 " =    1.622
peak=    3.525 closest distance to " CZ AARG A 102 " =    1.717
peak=    3.523 closest distance to " O   HOH Z 128 " =    2.113
peak=    3.523 closest distance to " O   HOH Z 430 " =    1.721
peak=    3.513 closest distance to " CA  PHE A 283 " =    1.391
peak=    3.511 closest distance to " CB  SER A 273 " =    0.853
peak=    3.508 closest distance to " O   HOH Z 247 " =    1.186
peak=    3.505 closest distance to " OG1 THR A 294 " =    2.380
peak=    3.497 closest distance to " O   HOH Z 344 " =    2.709
peak=    3.493 closest distance to " O   HOH Z 366 " =    3.260
peak=    3.489 closest distance to " O   HOH Z 389 " =    1.658
peak=    3.487 closest distance to " CG  MET A 188 " =    1.297
peak=    3.487 closest distance to " O   HOH Z 128 " =    1.914
peak=    3.487 closest distance to " O   HOH Z 222 " =    2.340
peak=    3.481 closest distance to " O   HOH Z  80 " =    1.699
peak=    3.473 closest distance to " O   HOH Z 303 " =    1.769
peak=    3.472 closest distance to " CD ALYS A 290 " =    1.239
peak=    3.464 closest distance to " NH1 ARG A  14 " =    1.009
peak=    3.449 closest distance to " CD1 LEU A 228 " =    1.588
peak=    3.447 closest distance to " O   HOH Z 152 " =    2.663
peak=    3.447 closest distance to " CA  LYS A 117 " =    1.224
peak=    3.438 closest distance to " O   HOH Z 116 " =    1.590
peak=    3.433 closest distance to " O   HOH Z 422 " =    2.545
peak=    3.425 closest distance to " O   HOH Z 392 " =    2.965
peak=    3.423 closest distance to " O   HOH Z 130 " =    2.532
peak=    3.421 closest distance to " O   HOH Z 276 " =    1.296
peak=    3.416 closest distance to " CA  ALA A 248 " =    1.263
peak=    3.414 closest distance to " NZ  LYS A  76 " =    1.298
peak=    3.407 closest distance to " N   PHE A 130 " =    1.347
peak=    3.404 closest distance to " O   HOH Z 265 " =    2.198
peak=    3.400 closest distance to " OD1 ASP A 286 " =    1.558
peak=    3.394 closest distance to " O   HOH Z 327 " =    1.603
peak=    3.394 closest distance to " CB  GLN A 278 " =    0.817
peak=    3.393 closest distance to " O   HOH Z 411 " =    1.737
peak=    3.389 closest distance to " O   HOH Z  63 " =    1.011
peak=    3.385 closest distance to " CB  SER A 216 " =    0.778
peak=    3.385 closest distance to " CA  ALA A  51 " =    0.974
peak=    3.382 closest distance to " O   HOH Z 281 " =    4.484
peak=    3.379 closest distance to " NH2BARG A 145 " =    2.187
peak=    3.377 closest distance to " O   HOH Z 438 " =    2.319
peak=    3.374 closest distance to " O   HOH Z 194 " =    2.144
peak=    3.365 closest distance to " N   TRP A 177 " =    1.648
peak=    3.365 closest distance to " O   HOH Z 329 " =    3.349
peak=    3.361 closest distance to " CE1 TYR A 186 " =    1.208
peak=    3.356 closest distance to " CB  ALA A 291 " =    1.497
peak=    3.353 closest distance to " CA  THR A 221 " =    0.910
peak=    3.351 closest distance to " O   MET A 105 " =    1.763
peak=    3.351 closest distance to " CA  SER A 271 " =    1.064
peak=    3.351 closest distance to " CE BMET A  47 " =    1.088
peak=    3.350 closest distance to " CZ2 TRP A 274 " =    1.674
peak=    3.346 closest distance to " CG2 ILE A  20 " =    1.625
peak=    3.341 closest distance to " O   HOH Z 263 " =    1.951
peak=    3.341 closest distance to " O   HOH Z 108 " =    1.719
peak=    3.338 closest distance to " O   HOH Z  71 " =    3.017
peak=    3.338 closest distance to " O   HOH Z 217 " =    1.272
peak=    3.335 closest distance to " CA  ASN A 127 " =    1.045
peak=    3.330 closest distance to " CD1 LEU A 300 " =    1.278
peak=    3.330 closest distance to " O   HOH Z 214 " =    2.039
peak=    3.330 closest distance to " CE AMET A  47 " =    1.449
peak=    3.326 closest distance to " O   HOH Z 285 " =    1.763
peak=    3.326 closest distance to " O   HOH Z 280 " =    1.542
peak=    3.324 closest distance to " O   HOH Z 280 " =    2.388
peak=    3.323 closest distance to " CB  ILE A  20 " =    1.463
peak=    3.322 closest distance to " CA  LEU A 101 " =    1.454
peak=    3.315 closest distance to " O   HOH Z 271 " =    1.796
peak=    3.315 closest distance to " O   HOH Z 406 " =    1.620
peak=    3.315 closest distance to " N   SER A 135 " =    1.410
peak=    3.311 closest distance to " CB  ARG A 190 " =    1.750
peak=    3.303 closest distance to " O   HOH Z 148 " =    3.179
peak=    3.300 closest distance to " CD  LYS A 289 " =    0.843
peak=    3.298 closest distance to " O   HOH Z 123 " =    1.035
peak=    3.292 closest distance to " O   HOH Z 283 " =    1.593
peak=    3.289 closest distance to " N   ASN A  39 " =    1.103
peak=    3.288 closest distance to " O   HOH Z 255 " =    1.658
peak=    3.287 closest distance to " CB  SER A  62 " =    1.217
peak=    3.286 closest distance to " CG  LEU A 281 " =    0.998
peak=    3.285 closest distance to " O   HOH Z   1 " =    1.558
peak=    3.284 closest distance to " CB  SER A  26 " =    1.540
peak=    3.284 closest distance to " O   HOH Z  78 " =    2.255
peak=    3.284 closest distance to " O   HOH Z  66 " =    2.144
peak=    3.284 closest distance to " CB  ALA A 180 " =    1.193
peak=    3.283 closest distance to " CG  LYS A 166 " =    1.514
peak=    3.281 closest distance to " NH2BARG A 190 " =    1.618
peak=    3.278 closest distance to " O   HOH Z  59 " =    2.128
peak=    3.276 closest distance to " CB  ILE A 234 " =    0.933
peak=    3.275 closest distance to " O   HOH Z 251 " =    1.559
peak=    3.275 closest distance to " CD  PRO A 243 " =    1.543
peak=    3.274 closest distance to " OG  SER A  62 " =    3.081
peak=    3.273 closest distance to " CG  MET A 185 " =    1.100
peak=    3.273 closest distance to " O   HOH Z  59 " =    1.881
peak=    3.270 closest distance to " CD2 TYR A 186 " =    1.002
peak=    3.267 closest distance to " NH1BARG A 145 " =    1.365
peak=    3.263 closest distance to " O   HOH Z 280 " =    3.004
peak=    3.262 closest distance to " O   HOH Z 172 " =    5.716
peak=    3.261 closest distance to " CB  ALA A 114 " =    1.442
peak=    3.260 closest distance to " O   HOH Z 332 " =    1.508
peak=    3.254 closest distance to " O   SER A  26 " =    1.509
peak=    3.246 closest distance to " O   HOH Z 140 " =    2.395
peak=    3.244 closest distance to " OG  SER A  22 " =    2.771
peak=    3.243 closest distance to " O   HOH Z 356 " =    1.257
peak=    3.243 closest distance to " NH2AARG A 190 " =    1.848
peak=    3.238 closest distance to " CB  TRP A 266 " =    1.080
peak=    3.229 closest distance to " NE2 GLN A  58 " =    5.579
peak=    3.229 closest distance to " O   HOH Z  68 " =    2.584
peak=    3.225 closest distance to " NH2 ARG A 219 " =    1.883
peak=    3.225 closest distance to " O   HOH Z 172 " =    3.549
peak=    3.224 closest distance to " CD  LYS A 119 " =    1.495
peak=    3.222 closest distance to " O   GLN A  58 " =    1.473
peak=    3.218 closest distance to " CD2 TYR A  30 " =    1.007
peak=    3.218 closest distance to " O   ASN A 217 " =    1.231
peak=    3.217 closest distance to " O   HOH Z 245 " =    1.345
peak=    3.213 closest distance to " OE2 GLU A  53 " =    1.964
peak=    3.213 closest distance to " O   HOH Z 368 " =    3.731
peak=    3.212 closest distance to " O   HOH Z 367 " =    3.632
peak=    3.211 closest distance to " O   HOH Z 141 " =    1.531
peak=    3.211 closest distance to " CB  ASN A 142 " =    1.030
peak=    3.208 closest distance to " O   HOH Z 153 " =    3.607
peak=    3.207 closest distance to " CA  ARG A 275 " =    1.898
peak=    3.200 closest distance to " CB  LEU A 143 " =    1.184
peak=    3.200 closest distance to " CD2 TRP A 179 " =    1.415
peak=    3.198 closest distance to " O   HOH Z   7 " =    1.486
peak=    3.192 closest distance to " O   HOH Z 114 " =    3.755
peak=    3.191 closest distance to " O   HOH Z 189 " =    2.641
peak=    3.191 closest distance to " CG  GLN A  77 " =    2.308
peak=    3.189 closest distance to " CG  ASN A  60 " =    1.133
peak=    3.189 closest distance to " O   HOH Z   1 " =    1.673
peak=    3.187 closest distance to " CA  GLN A 194 " =    1.199
peak=    3.185 closest distance to " CE  LYS A  76 " =    0.936
peak=    3.184 closest distance to " CD  ARG A 269 " =    1.058
peak=    3.180 closest distance to " CA  ASN A 176 " =    1.113
peak=    3.178 closest distance to " CB  ASP A 140 " =    0.837
peak=    3.177 closest distance to " O   HOH Z 419 " =    1.596
peak=    3.176 closest distance to " CG  GLN A  89 " =    1.473
peak=    3.176 closest distance to " O   HOH Z 125 " =    2.409
peak=    3.174 closest distance to " NZ  LYS A 117 " =    1.109
peak=    3.172 closest distance to " O   HOH Z  15 " =    1.395
peak=    3.169 closest distance to " CD2 HIS A  81 " =    1.119
peak=    3.168 closest distance to " O   HOH Z 383 " =    1.757
peak=    3.167 closest distance to " O   HOH Z  21 " =    1.741
peak=    3.161 closest distance to " O   HOH Z 409 " =    3.313
peak=    3.160 closest distance to " O   HOH Z 213 " =    1.861
peak=    3.159 closest distance to " O   HOH Z 151 " =    1.660
peak=    3.156 closest distance to " CA  ASN A  74 " =    1.258
peak=    3.155 closest distance to " SD  MET A 185 " =    1.479
peak=    3.151 closest distance to " O   HOH Z  40 " =    2.017
peak=    3.149 closest distance to " O   HOH Z 145 " =    1.903
peak=    3.146 closest distance to " CB  ARG A 138 " =    0.921
peak=    3.135 closest distance to " CD2 LEU A 255 " =    1.191
peak=    3.134 closest distance to " O   GLY A  57 " =    2.485
peak=    3.131 closest distance to " O   HOH Z 359 " =    1.902
peak=    3.129 closest distance to " O   HOH Z  50 " =    1.584
peak=    3.124 closest distance to " CA  ALA A 154 " =    1.098
peak=    3.123 closest distance to " O   HOH Z  88 " =    2.341
peak=    3.121 closest distance to " CG1 ILE A 120 " =    1.252
peak=    3.120 closest distance to " O   HOH Z 222 " =    2.404
peak=    3.120 closest distance to " O   HOH Z 250 " =    1.846
peak=    3.112 closest distance to " O   ALA A 158 " =    1.339
peak=    3.099 closest distance to " OG ASER A 134 " =    1.434
peak=    3.084 closest distance to " CD2 LEU A 297 " =    0.960
peak=    3.083 closest distance to " CB  PRO A 198 " =    0.930
peak=    3.080 closest distance to " CB  ASN A 215 " =    0.972
peak=    3.077 closest distance to " O   THR A  31 " =    1.553
peak=    3.076 closest distance to " CB  ASN A  39 " =    0.809
peak=    3.074 closest distance to " O   HOH Z 207 " =    1.975
peak=    3.061 closest distance to " ND1 HIS A  81 " =    1.486
peak=    3.042 closest distance to " OE2 GLU A   2 " =    1.630
peak=    3.031 closest distance to " O   HOH Z 127 " =    1.812
peak=    3.013 closest distance to " O   HOH Z 134 " =    1.352

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

Number of peaks found at mFobs-DFmodel map (map cutoff=3.00 sigma)= 191         
Filter by distance & map next to the model:
   mapped sites are within: 0.667 - 5.271
   number of sites selected in [dist_min= 0.70, dist_max= 6.00]: 189 from: 191
   mapped sites are within: 0.761 - 5.271

peak=   -4.866 closest distance to " CG2 VAL A 230 " =    0.778
peak=   -4.699 closest distance to " SG  CYS A 254 " =    3.162
peak=   -4.401 closest distance to " CD  ARG A 156 " =    2.015
peak=   -4.362 closest distance to " O   PRO A 198 " =    1.319
peak=   -4.333 closest distance to " O   HOH Z  11 " =    1.926
peak=   -4.253 closest distance to " O   HOH Z 231 " =    1.707
peak=   -4.239 closest distance to " N   GLN A  58 " =    1.632
peak=   -4.236 closest distance to " CG2 VAL A 296 " =    1.434
peak=   -4.190 closest distance to " O   PRO A 163 " =    1.994
peak=   -4.158 closest distance to " O   HOH Z 388 " =    2.080
peak=   -4.145 closest distance to " O   HOH Z  43 " =    1.994
peak=   -4.097 closest distance to " O   HOH Z  98 " =    1.691
peak=   -3.995 closest distance to " CB  TYR A  15 " =    2.097
peak=   -3.983 closest distance to " NH2 ARG A  79 " =    1.851
peak=   -3.982 closest distance to " O   HOH Z 266 " =    4.388
peak=   -3.971 closest distance to " CB  CYS A 201 " =    2.556
peak=   -3.955 closest distance to " N   HIS A 115 " =    1.969
peak=   -3.940 closest distance to " CB  PRO A 280 " =    2.092
peak=   -3.933 closest distance to " CE2 TYR A  30 " =    2.890
peak=   -3.923 closest distance to " O   VAL A  67 " =    2.804
peak=   -3.903 closest distance to " CD1 LEU A 255 " =    2.795
peak=   -3.881 closest distance to " C   HIS A 108 " =    1.197
peak=   -3.859 closest distance to " O   ALA A 161 " =    1.640
peak=   -3.856 closest distance to " N   SER A 276 " =    1.208
peak=   -3.850 closest distance to " NH1 ARG A  56 " =    2.489
peak=   -3.828 closest distance to " CB  ALA A 161 " =    2.544
peak=   -3.820 closest distance to " N   ALA A 248 " =    1.657
peak=   -3.806 closest distance to " CB  PRO A 243 " =    2.602
peak=   -3.775 closest distance to " O   PRO A 198 " =    1.298
peak=   -3.751 closest distance to " O   HOH Z 198 " =    2.257
peak=   -3.749 closest distance to " O   HOH Z 166 " =    1.401
peak=   -3.736 closest distance to " OG ASER A 134 " =    1.200
peak=   -3.736 closest distance to " OG BSER A 134 " =    1.311
peak=   -3.734 closest distance to " CG  LYS A 193 " =    2.113
peak=   -3.703 closest distance to " O   VAL A  67 " =    2.621
peak=   -3.701 closest distance to " CA  GLY A 133 " =    1.935
peak=   -3.697 closest distance to " CD1 LEU A 101 " =    2.319
peak=   -3.691 closest distance to " O   HOH Z 290 " =    1.083
peak=   -3.673 closest distance to " O   HOH Z 426 " =    2.273
peak=   -3.669 closest distance to " O   HOH Z 389 " =    4.693
peak=   -3.656 closest distance to " OG BSER A 134 " =    1.603
peak=   -3.650 closest distance to " O   HOH Z 389 " =    1.755
peak=   -3.649 closest distance to " CG  ASP A 231 " =    0.761
peak=   -3.646 closest distance to " CB  ALA A  51 " =    1.779
peak=   -3.638 closest distance to " CD  LYS A 289 " =    2.540
peak=   -3.631 closest distance to " O   HOH Z 166 " =    2.026
peak=   -3.629 closest distance to " CD1 PHE A  59 " =    1.915
peak=   -3.628 closest distance to " CB  ASP A 132 " =    2.229
peak=   -3.626 closest distance to " CB  ALA A 248 " =    1.932
peak=   -3.603 closest distance to " O   HOH Z  63 " =    0.901
peak=   -3.596 closest distance to " O   ASN A 187 " =    1.479
peak=   -3.596 closest distance to " O   HOH Z 191 " =    5.271
peak=   -3.594 closest distance to " O   HOH Z 175 " =    4.354
peak=   -3.584 closest distance to " C   ASN A 285 " =    2.276
peak=   -3.582 closest distance to " O   HOH Z 102 " =    1.692
peak=   -3.580 closest distance to " CG  LEU A 228 " =    1.025
peak=   -3.572 closest distance to " O   HOH Z 103 " =    1.700
peak=   -3.572 closest distance to " O   HOH Z 339 " =    1.710
peak=   -3.566 closest distance to " OXT GLY A 302 " =    2.767
peak=   -3.564 closest distance to " OG1 THR A  82 " =    1.439
peak=   -3.558 closest distance to " CG  PHE A 283 " =    2.599
peak=   -3.551 closest distance to " CA  ASP A 298 " =    1.066
peak=   -3.516 closest distance to " O   HOH Z 410 " =    2.046
peak=   -3.516 closest distance to " CE  LYS A  76 " =    2.922
peak=   -3.515 closest distance to " O   ALA A  51 " =    1.315
peak=   -3.512 closest distance to " CD  GLN A  88 " =    0.857
peak=   -3.506 closest distance to " CD  GLU A 152 " =    2.427
peak=   -3.488 closest distance to " O   HOH Z  13 " =    1.577
peak=   -3.487 closest distance to " O   HOH Z 148 " =    1.876
peak=   -3.483 closest distance to " O   ASP A 231 " =    2.375
peak=   -3.479 closest distance to " ND2 ASN A  45 " =    0.959
peak=   -3.478 closest distance to " O   HOH Z 385 " =    2.084
peak=   -3.470 closest distance to " CZ  PHE A  59 " =    1.541
peak=   -3.467 closest distance to " OD2 ASP A 270 " =    1.383
peak=   -3.467 closest distance to " N   MET A 188 " =    1.887
peak=   -3.464 closest distance to " CB  PRO A 163 " =    2.650
peak=   -3.458 closest distance to " OH  TYR A 214 " =    1.316
peak=   -3.457 closest distance to " O   HOH Z 184 " =    1.090
peak=   -3.456 closest distance to " O   TRP A  70 " =    1.477
peak=   -3.455 closest distance to " CG  PRO A 163 " =    2.709
peak=   -3.448 closest distance to " N   ALA A   9 " =    1.439
peak=   -3.445 closest distance to " OXT GLY A 302 " =    3.700
peak=   -3.444 closest distance to " CG1 VAL A 112 " =    2.765
peak=   -3.439 closest distance to " O   HOH Z 423 " =    2.123
peak=   -3.435 closest distance to " CD1 LEU A 228 " =    2.110
peak=   -3.433 closest distance to " O   HOH Z  11 " =    1.955
peak=   -3.432 closest distance to " O   HOH Z  93 " =    1.477
peak=   -3.431 closest distance to " O   HOH Z 351 " =    1.450
peak=   -3.430 closest distance to " CB  ASN A  39 " =    2.048
peak=   -3.421 closest distance to " ND2 ASN A  60 " =    1.306
peak=   -3.421 closest distance to " NH2AARG A 275 " =    5.227
peak=   -3.420 closest distance to " O   HOH Z 385 " =    1.818
peak=   -3.419 closest distance to " CE  MET A 105 " =    1.968
peak=   -3.403 closest distance to " O   SER A 135 " =    1.536
peak=   -3.399 closest distance to " OG  SER A 206 " =    1.659
peak=   -3.391 closest distance to " O   HOH Z 198 " =    1.520
peak=   -3.391 closest distance to " O   HOH Z 308 " =    1.669
peak=   -3.384 closest distance to " O   HOH Z 423 " =    1.110
peak=   -3.373 closest distance to " CG  TRP A 266 " =    1.746
peak=   -3.367 closest distance to " ND2 ASN A  39 " =    1.352
peak=   -3.360 closest distance to " O   HOH Z 165 " =    2.192
peak=   -3.359 closest distance to " O   HOH Z 143 " =    0.992
peak=   -3.356 closest distance to " O   HOH Z 436 " =    1.433
peak=   -3.352 closest distance to " CE3 TRP A 274 " =    2.335
peak=   -3.350 closest distance to " C   LEU A 143 " =    1.187
peak=   -3.348 closest distance to " CG  GLN A 223 " =    1.921
peak=   -3.348 closest distance to " OG  SER A   3 " =    1.485
peak=   -3.338 closest distance to " CA  TYR A  30 " =    2.907
peak=   -3.335 closest distance to " O   MET A  40 " =    2.662
peak=   -3.335 closest distance to " O   HOH Z 407 " =    2.986
peak=   -3.335 closest distance to " O   HOH Z 427 " =    1.487
peak=   -3.334 closest distance to " CA  GLY A  35 " =    2.023
peak=   -3.330 closest distance to " O   ASP A 191 " =    1.720
peak=   -3.316 closest distance to " N   GLN A  58 " =    1.326
peak=   -3.310 closest distance to " C   ALA A 158 " =    1.248
peak=   -3.306 closest distance to " O   HOH Z 350 " =    1.971
peak=   -3.304 closest distance to " O   HOH Z 364 " =    2.703
peak=   -3.304 closest distance to " O   HOH Z 137 " =    1.523
peak=   -3.299 closest distance to " OD1 ASP A 191 " =    1.402
peak=   -3.299 closest distance to " O   HOH Z  47 " =    1.438
peak=   -3.296 closest distance to " O   VAL A 153 " =    2.310
peak=   -3.289 closest distance to " O   ALA A   8 " =    1.709
peak=   -3.285 closest distance to " O   HOH Z 411 " =    3.629
peak=   -3.281 closest distance to " CD1 PHE A  59 " =    2.209
peak=   -3.278 closest distance to " OE1 GLN A  73 " =    2.229
peak=   -3.277 closest distance to " O   SER A  22 " =    2.350
peak=   -3.275 closest distance to " O   HOH Z 344 " =    2.496
peak=   -3.274 closest distance to " CE2 PHE A 218 " =    2.553
peak=   -3.273 closest distance to " O   HOH Z 281 " =    2.984
peak=   -3.265 closest distance to " CG  GLU A 277 " =    1.161
peak=   -3.265 closest distance to " CD1 ILE A 239 " =    2.506
peak=   -3.263 closest distance to " NE2 GLN A 278 " =    1.865
peak=   -3.262 closest distance to " OD1 ASP A 191 " =    1.639
peak=   -3.257 closest distance to " CZ  TYR A 169 " =    1.707
peak=   -3.254 closest distance to " O   PHE A 218 " =    1.412
peak=   -3.254 closest distance to " C   LEU A 282 " =    1.659
peak=   -3.247 closest distance to " O   HOH Z 234 " =    3.990
peak=   -3.245 closest distance to " O   HOH Z  44 " =    2.214
peak=   -3.245 closest distance to " OD2 ASP A 191 " =    1.402
peak=   -3.245 closest distance to " O   SER A 146 " =    0.906
peak=   -3.242 closest distance to " CG  ASP A  50 " =    2.213
peak=   -3.238 closest distance to " O   HOH Z 313 " =    1.747
peak=   -3.237 closest distance to " CD2 LEU A 237 " =    2.690
peak=   -3.236 closest distance to " O   HOH Z  15 " =    1.604
peak=   -3.235 closest distance to " O   HOH Z  97 " =    0.803
peak=   -3.235 closest distance to " ND2 ASN A 142 " =    1.922
peak=   -3.235 closest distance to " CG  GLU A 152 " =    1.360
peak=   -3.231 closest distance to " CG  MET A 105 " =    0.888
peak=   -3.226 closest distance to " O   HOH Z 134 " =    2.680
peak=   -3.225 closest distance to " NH2 ARG A 159 " =    2.283
peak=   -3.220 closest distance to " OD1 ASP A 200 " =    1.152
peak=   -3.219 closest distance to " CD  ARG A 139 " =    1.707
peak=   -3.213 closest distance to " O   TRP A  92 " =    1.769
peak=   -3.209 closest distance to " OD1 ASP A 171 " =    1.653
peak=   -3.206 closest distance to " OE2 GLU A 152 " =    1.183
peak=   -3.204 closest distance to " OD1 ASN A 249 " =    1.178
peak=   -3.199 closest distance to " N   ALA A  43 " =    2.615
peak=   -3.194 closest distance to " OG  SER A  26 " =    1.111
peak=   -3.194 closest distance to " CG2 VAL A 189 " =    1.904
peak=   -3.177 closest distance to " N   GLN A  77 " =    1.611
peak=   -3.177 closest distance to " CD1 TYR A 247 " =    2.700
peak=   -3.176 closest distance to " CG2AVAL A  41 " =    2.834
peak=   -3.176 closest distance to " CB  SER A 245 " =    2.518
peak=   -3.173 closest distance to " O   HOH Z 131 " =    3.949
peak=   -3.167 closest distance to " O   HOH Z 193 " =    1.889
peak=   -3.165 closest distance to " CZ2 TRP A  92 " =    2.680
peak=   -3.160 closest distance to " O   HOH Z 426 " =    1.608
peak=   -3.156 closest distance to " O   HOH Z  90 " =    2.609
peak=   -3.154 closest distance to " O   HOH Z 211 " =    1.527
peak=   -3.145 closest distance to " O   HOH Z  68 " =    1.965
peak=   -3.145 closest distance to " ND2 ASN A  45 " =    1.068
peak=   -3.142 closest distance to " O   GLU A  44 " =    1.712
peak=   -3.139 closest distance to " O   GLY A 118 " =    1.408
peak=   -3.139 closest distance to " ND2 ASN A 249 " =    2.325
peak=   -3.132 closest distance to " O   HOH Z  88 " =    2.131
peak=   -3.111 closest distance to " CB  TYR A 172 " =    2.132
peak=   -3.108 closest distance to " O   HOH Z 210 " =    1.098
peak=   -3.106 closest distance to " O   HOH Z 405 " =    2.801
peak=   -3.102 closest distance to " CE2 TRP A 179 " =    1.383
peak=   -3.096 closest distance to " O   HOH Z 402 " =    1.358
peak=   -3.087 closest distance to " CA  ALA A 227 " =    2.316
peak=   -3.084 closest distance to " O   LYS A 289 " =    2.938
peak=   -3.074 closest distance to " OG BSER A  99 " =    0.928
peak=   -3.069 closest distance to " CG1 VAL A 125 " =    2.188
peak=   -3.067 closest distance to " CG  GLU A   2 " =    2.031
peak=   -3.062 closest distance to " CD2 TYR A 293 " =    2.056
peak=   -3.046 closest distance to " CB  ASP A 132 " =    1.987
peak=   -3.014 closest distance to " O   HOH Z  96 " =    1.525
peak=   -2.999 closest distance to " CA  ASP A  27 " =    2.346

================= 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    :  0.4833 0.4774   6.282934e+00   6.276852e+00
   1_bss:  0.4748 0.4674   6.277700e+00   6.266326e+00
   1_xyz:  0.4060 0.4214   6.189484e+00   6.213551e+00
   1_adp:  0.3636 0.4131   6.123938e+00   6.198119e+00
   1_occ:  0.3630 0.4136   6.123826e+00   6.198663e+00
   2_bss:  0.3588 0.4084   6.122572e+00   6.195134e+00
   2_xyz:  0.2683 0.3251   5.887826e+00   6.032949e+00
   2_adp:  0.2425 0.3015   5.811901e+00   5.978210e+00
   2_occ:  0.2422 0.3020   5.811666e+00   5.978454e+00
   3_bss:  0.2405 0.3013   5.810103e+00   5.977303e+00
   3_xyz:  0.1708 0.2245   5.511743e+00   5.717985e+00
   3_adp:  0.1521 0.2021   5.399591e+00   5.615546e+00
   3_occ:  0.1517 0.2016   5.397956e+00   5.613658e+00
   4_bss:  0.1507 0.1994   5.390515e+00   5.605433e+00
   4_xyz:  0.1248 0.1687   5.225665e+00   5.453487e+00
   4_adp:  0.1196 0.1643   5.190368e+00   5.420510e+00
   4_occ:  0.1195 0.1639   5.188931e+00   5.418741e+00
   5_bss:  0.1196 0.1644   5.190362e+00   5.420424e+00
   5_xyz:  0.1131 0.1594   5.150352e+00   5.390293e+00
   5_adp:  0.1114 0.1602   5.145871e+00   5.393073e+00
   5_occ:  0.1113 0.1601   5.145248e+00   5.392313e+00
   5_bss:  0.1113 0.1601   5.145214e+00   5.392277e+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:  0.357   0.000   6.844   8.679   9.953   0.000   0.000   0.000
   1_xyz:  0.357   0.000   6.844   8.679   9.953   0.000   0.000   0.000
   1_adp:  0.357   0.000   6.844   8.679   9.953   0.000   0.000   0.000
   1_occ:  0.357   0.000   6.844   8.679   9.953   0.000   0.000   0.000
   2_bss:  0.341  22.920   2.999   4.079   6.111   0.000   0.000   0.000
   2_xyz:  0.341  22.920   2.999   4.079   6.111   0.000   0.000   0.000
   2_adp:  0.341  22.920   2.999   4.079   6.111   0.000   0.000   0.000
   2_occ:  0.341  22.920   2.999   4.079   6.111   0.000   0.000   0.000
   3_bss:  0.334  30.585   1.878   2.221   3.653   0.000   0.000   0.000
   3_xyz:  0.334  30.585   1.878   2.221   3.653   0.000   0.000   0.000
   3_adp:  0.334  30.585   1.878   2.221   3.653   0.000   0.000   0.000
   3_occ:  0.334  30.585   1.878   2.221   3.653   0.000   0.000   0.000
   4_bss:  0.315  33.087   1.238   1.412   2.306   0.000   0.000   0.000
   4_xyz:  0.315  33.087   1.238   1.412   2.306   0.000   0.000   0.000
   4_adp:  0.315  33.087   1.238   1.412   2.306   0.000   0.000   0.000
   4_occ:  0.315  33.087   1.238   1.412   2.306   0.000   0.000   0.000
   5_bss:  0.321  34.461   1.122   1.304   1.978   0.000   0.000   0.000
   5_xyz:  0.321  34.461   1.122   1.304   1.978   0.000   0.000   0.000
   5_adp:  0.321  34.461   1.122   1.304   1.978   0.000   0.000   0.000
   5_occ:  0.321  34.461   1.122   1.304   1.978   0.000   0.000   0.000
   5_bss:  0.323  37.232  -0.304  -0.151   0.456   0.000   0.000   0.000
------------------------------------------------------------------------
 stage     <pher>    fom   alpha         beta
   0    :  57.798 0.4228  0.5062    72161.002
   1_bss:  58.394 0.4127  0.6225    68977.818
   1_xyz:  48.875 0.5337  0.7950    53061.087
   1_adp:  46.855 0.5593  0.8893    50823.992
   1_occ:  47.041 0.5570  0.8848    51050.689
   2_bss:  46.578 0.5625  0.7777    50283.281
   2_xyz:  34.711 0.7037  0.9506    28661.824
   2_adp:  31.258 0.7436  0.9944    24466.770
   2_occ:  31.266 0.7435  0.9941    24503.463
   3_bss:  31.126 0.7450  0.9335    24388.105
   3_xyz:  22.166 0.8402  1.0012    13097.111
   3_adp:  19.232 0.8694  1.0139    10559.844
   3_occ:  19.182 0.8699  1.0138    10497.602
   4_bss:  18.941 0.8718  0.9799    10185.140
   4_xyz:  15.500 0.9021  0.9942     7232.907
   4_adp:  14.794 0.9082  0.9935     6805.763
   4_occ:  14.753 0.9086  0.9935     6776.996
   5_bss:  14.788 0.9084  0.9867     6842.392
   5_xyz:  14.127 0.9139  0.9892     6418.990
   5_adp:  14.163 0.9137  0.9848     6442.670
   5_occ:  14.147 0.9139  0.9847     6430.163
   5_bss:  14.146 0.9139  0.9882     6432.621
------------------------------------------------------------------------
 stage       angl   bond   chir   dihe   plan   repu  geom_target
   0    :  24.226  0.414  2.119 33.790  0.145  4.087   5.2919e+01
   1_bss:  24.226  0.414  2.119 33.790  0.145  4.087   5.2919e+01
   1_xyz:   1.610  0.012  0.103 18.288  0.006  4.108   1.3143e-01
   1_adp:   1.610  0.012  0.103 18.288  0.006  4.108   1.3143e-01
   1_occ:   1.610  0.012  0.103 18.288  0.006  4.108   1.3143e-01
   2_bss:   1.610  0.012  0.103 18.288  0.006  4.108   1.3143e-01
   2_xyz:   1.234  0.009  0.089 16.554  0.005  4.105   9.2670e-02
   2_adp:   1.234  0.009  0.089 16.554  0.005  4.105   9.2670e-02
   2_occ:   1.234  0.009  0.089 16.554  0.005  4.105   9.2670e-02
   3_bss:   1.234  0.009  0.089 16.554  0.005  4.105   9.2670e-02
   3_xyz:   1.129  0.008  0.081 16.210  0.004  4.116   7.4577e-02
   3_adp:   1.129  0.008  0.081 16.210  0.004  4.116   7.4577e-02
   3_occ:   1.129  0.008  0.081 16.210  0.004  4.116   7.4577e-02
   4_bss:   1.129  0.008  0.081 16.210  0.004  4.116   7.4577e-02
   4_xyz:   1.060  0.007  0.080 15.820  0.004  4.106   6.8143e-02
   4_adp:   1.060  0.007  0.080 15.820  0.004  4.106   6.8143e-02
   4_occ:   1.060  0.007  0.080 15.820  0.004  4.106   6.8143e-02
   5_bss:   1.060  0.007  0.080 15.820  0.004  4.106   6.8143e-02
   5_xyz:   1.034  0.007  0.078 15.729  0.004  4.107   6.5104e-02
   5_adp:   1.034  0.007  0.078 15.729  0.004  4.107   6.5104e-02
   5_occ:   1.034  0.007  0.078 15.729  0.004  4.107   6.5104e-02
   5_bss:   1.034  0.007  0.078 15.729  0.004  4.107   6.5104e-02
------------------------------------------------------------------------
                      Maximal deviations:
 stage       angl   bond   chir   dihe   plan   repu       |grad|
   0    :  74.492  1.400  6.404144.062  0.405  1.108   6.8576e+00
   1_bss:  74.492  1.400  6.404144.062  0.405  1.108   6.8576e+00
   1_xyz:  12.689  0.159  0.404 84.620  0.050  2.197   8.9094e-02
   1_adp:  12.689  0.159  0.404 84.620  0.050  2.197   8.9094e-02
   1_occ:  12.689  0.159  0.404 84.620  0.050  2.197   8.9094e-02
   2_bss:  12.689  0.159  0.404 84.620  0.050  2.197   8.9094e-02
   2_xyz:   7.548  0.090  0.375 80.598  0.047  2.210   6.9065e-02
   2_adp:   7.548  0.090  0.375 80.598  0.047  2.210   6.9065e-02
   2_occ:   7.548  0.090  0.375 80.598  0.047  2.210   6.9065e-02
   3_bss:   7.548  0.090  0.375 80.598  0.047  2.210   6.9065e-02
   3_xyz:   7.024  0.054  0.463 85.856  0.028  2.282   6.3423e-02
   3_adp:   7.024  0.054  0.463 85.856  0.028  2.282   6.3423e-02
   3_occ:   7.024  0.054  0.463 85.856  0.028  2.282   6.3423e-02
   4_bss:   7.024  0.054  0.463 85.856  0.028  2.282   6.3423e-02
   4_xyz:   6.622  0.046  0.518 83.269  0.037  2.243   7.0699e-02
   4_adp:   6.622  0.046  0.518 83.269  0.037  2.243   7.0699e-02
   4_occ:   6.622  0.046  0.518 83.269  0.037  2.243   7.0699e-02
   5_bss:   6.622  0.046  0.518 83.269  0.037  2.243   7.0699e-02
   5_xyz:   6.468  0.042  0.540 83.916  0.038  2.279   6.7091e-02
   5_adp:   6.468  0.042  0.540 83.916  0.038  2.279   6.7091e-02
   5_occ:   6.468  0.042  0.540 83.916  0.038  2.279   6.7091e-02
   5_bss:   6.468  0.042  0.540 83.916  0.038  2.279   6.7091e-02
------------------------------------------------------------------------
           |-----overall-----|---macromolecule----|------solvent-------|
  stage    b_max  b_min  b_ave  b_max  b_min  b_ave  b_max  b_min  b_ave
   0    :  10.00  10.00  10.00  10.00  10.00  10.00  10.00  10.00  10.00
   1_bss:  19.99   0.01   9.86  19.98   0.01   9.82  19.99   0.06  10.10
   1_xyz:  19.99   0.01   9.86  19.98   0.01   9.82  19.99   0.06  10.10
   1_adp:  93.23   0.00  13.83  87.68   0.00  11.59  93.23   0.00  26.04
   1_occ:  93.23   0.00  13.83  87.68   0.00  11.59  93.23   0.00  26.04
   2_bss:  93.23   0.00  13.83  87.68   0.00  11.59  93.23   0.00  26.04
   2_xyz:  93.23   0.00  13.83  87.68   0.00  11.59  93.23   0.00  26.04
   2_adp:  88.72   0.00  13.66  88.72   0.00  10.18  84.73   0.00  32.65
   2_occ:  88.72   0.00  13.66  88.72   0.00  10.18  84.73   0.00  32.65
   3_bss:  88.72   0.00  13.66  88.72   0.00  10.18  84.73   0.00  32.65
   3_xyz:  88.72   0.00  13.66  88.72   0.00  10.18  84.73   0.00  32.65
   3_adp:  85.97   0.00  13.47  85.97   0.00   9.37  80.25   2.72  35.78
   3_occ:  85.97   0.00  13.47  85.97   0.00   9.37  80.25   2.72  35.78
   4_bss:  85.97   0.00  13.47  85.97   0.00   9.37  80.25   2.72  35.78
   4_xyz:  85.97   0.00  13.47  85.97   0.00   9.37  80.25   2.72  35.78
   4_adp:  86.65   0.00  13.38  86.65   0.00   9.18  82.13   3.18  36.28
   4_occ:  86.65   0.00  13.38  86.65   0.00   9.18  82.13   3.18  36.28
   5_bss:  86.65   0.00  13.38  86.65   0.00   9.18  82.13   3.18  36.28
   5_xyz:  86.65   0.00  13.38  86.65   0.00   9.18  82.13   3.18  36.28
   5_adp:  93.73   0.00  13.42  93.73   0.00   9.14  86.12   3.00  36.68
   5_occ:  93.73   0.00  13.42  93.73   0.00   9.14  86.12   3.00  36.68
   5_bss:  95.29   1.56  14.98  95.29   1.56  10.71  87.68   4.57  38.24
------------------------------------------------------------------------
 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:    1.227    0.022    0.402
   1_adp:    1.227    0.022    0.402
   1_occ:    1.227    0.022    0.402
   2_bss:    1.227    0.022    0.402
   2_xyz:    1.655    0.022    0.593
   2_adp:    1.655    0.022    0.593
   2_occ:    1.655    0.022    0.593
   3_bss:    1.655    0.022    0.593
   3_xyz:    1.518    0.039    0.697
   3_adp:    1.518    0.039    0.697
   3_occ:    1.518    0.039    0.697
   4_bss:    1.518    0.039    0.697
   4_xyz:    1.713    0.060    0.739
   4_adp:    1.713    0.060    0.739
   4_occ:    1.713    0.060    0.739
   5_bss:    1.713    0.060    0.739
   5_xyz:    1.780    0.025    0.752
   5_adp:    1.780    0.025    0.752
   5_occ:    1.780    0.025    0.752
   5_bss:    1.780    0.025    0.752
------------------------------------------------------------------------

CPU time actual refinement: 341.89


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

Writing refined structure to PDB file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/trial/run_517/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_517/model_refine_001_2mFobs-DFmodel.map
Writing mFobs-DFmodel XPLOR map to file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/trial/run_517/model_refine_001_mFobs-DFmodel.map
Writing map coefficients to MTZ file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/trial/run_517/model_refine_001_map_coeffs.mtz

Writing default parameters for subsequent refinement:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/trial/run_517/model_refine_002.def


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

Pure refinement (no I/O, processing, etc)= 341.75 
  Macro-tasks:
    bulk solvent and scale       = 51.38  
    individual site refinement   = 136.56 
    weights calculation          = 31.94  
    collect and process          = 6.53   
    model show statistics        = 0.10   
    TOTAL for macro-tasks        = 226.51 
  Micro-tasks:
    mask                            = 2.26   
    f_calc                          = 103.49 
    alpha_beta                      = 8.26   
    target                          = 1.19   
    gradients_wrt_atomic_parameters = 108.92 
    fmodel                         = 7.75   
    r_factors                      = 0.36   
    phase_errors                   = 11.17  
    foms                           = 0.29   
    TOTAL for micro-tasks          = 243.69 
NUMBER OF MASK CALCS=  5
Time per interpreted Python bytecode instruction: 4.811 micro seconds
Total CPU time: 5.91 minutes
from_scatterers_fft:    634 calls, 103.05 s
gradients_fft:          579 calls,  97.56 s

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

# Date 2008-01-16 Time 01:46:13 PST -0800 (1200476773.49 s)
Start R-work = 0.4833, R-free = 0.4774 (no bulk solvent and anisotropic scale)
Final R-work = 0.1286, R-free = 0.1776 (no bulk solvent and anisotropic scale)

Start R-work = 0.4748, R-free = 0.4674
Final R-work = 0.1113, R-free = 0.1601