# Date 2008-01-16 Time 01:21:48 PST -0800 (1200475308.30 s)
#phil __OFF__

Command line arguments: "../388.param" "adp.set_b_iso=10" "sites.shake=0.5" "main.number_of_macro_cycles=5" "--overwrite"

HOST = thunderbird.lbl.gov
HOSTTYPE = x86_64-linux
USER = phzwart
PID = 28107
JOB_ID = 5158
SGE_ARCH = lx24-amd64
SGE_TASK_FIRST = 1
SGE_TASK_LAST = 1330
SGE_TASK_ID = 388

-------------------------------------------------------------------------------
  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: (69.5475, 46.2261, 85.5261, 90, 90, 90)
  Space group: P 21 21 21 (No. 19)

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


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

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

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

Miller array info: /net/cci-filer1/vol1/tmp/phzwart/tassos/trial/1e0w.cns:FOBS,SIGMA
Observation type: xray.amplitude
Type of data: double, size=19589
Type of sigmas: double, size=19589
Number of Miller indices: 19589
Anomalous flag: False
Unit cell: (69.5475, 46.2261, 85.5261, 90, 90, 90)
Space group: P 21 21 21 (No. 19)
Systematic absences: 0
Centric reflections: 2427
Resolution range: 14.844 1.97157
Completeness in resolution range: 0.978227
Completeness with d_max=infinity: 0.975159

Number of F-obs in resolution range:                   19589
Number of F-obs <= 0:                                  0
Refinement resolution range: d_max =  14.8440
                             d_min =   1.9716

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: (69.5475, 46.2261, 85.5261, 90, 90, 90)
Space group: P 21 21 21 (No. 19)
Systematic absences: 0
Centric reflections: 2427
Resolution range: 14.844 1.97157
Completeness in resolution range: 0.978227
Completeness with d_max=infinity: 0.975159

Test (R-free flags) flag value: 1

Number of work/free reflections by resolution:
                                         work  free  %free
  bin  1: 14.8444 -  4.2182 [2103/2127]  1893   210  10.0%
  bin  2:  4.2182 -  3.3609 [2026/2046]  1822   204  10.1%
  bin  3:  3.3609 -  2.9398 [1993/2012]  1794   199  10.0%
  bin  4:  2.9398 -  2.6727 [1963/1993]  1766   197  10.0%
  bin  5:  2.6727 -  2.4821 [1976/1995]  1781   195   9.9%
  bin  6:  2.4821 -  2.3363 [1958/1983]  1758   200  10.2%
  bin  7:  2.3363 -  2.2197 [1940/1968]  1748   192   9.9%
  bin  8:  2.2197 -  2.1234 [1934/1970]  1741   193  10.0%
  bin  9:  2.1234 -  2.0419 [1916/1958]  1725   191  10.0%
  bin 10:  2.0419 -  1.9716 [1780/1973]  1602   178  10.0%
                                overall 17630  1959  10.0%
Writing MTZ file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/trial/run_388/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:
        1.67 -     2.31: 25
        2.31 -     2.96: 1740
        2.96 -     3.61: 4652
        3.61 -     4.25: 9349
        4.25 -     4.90: 13033
  Nonbonded interactions sorted by model distance:
             atom i - atom j             model   vdw sym.op. j
  " O   HOH Z  52 " - " O   HOH Z 183 "  1.666 3.040 -x+1,y+1/2,-z+1/2
  " CE BMET A  47 " - " O  BHOH Z  74 "  1.806 3.460
  " O   HOH Z 271 " - " O   HOH Z 342 "  1.939 3.040 -x+1/2,-y+1,z+1/2
  " O   HOH Z  37 " - " O   HOH Z 416 "  1.950 3.040 -x+1,y-1/2,-z+1/2
  " O   HOH Z 110 " - " O   HOH Z 355 "  1.983 3.040 -x+1/2,-y+1,z+1/2
  ... (remaining 28794 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_388/model_refine_001.eff

Writing geometry restraints to file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/trial/run_388/model_refine_001.geo

CPU time processing inputs: 9.24


============================ 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 = 69.5475 46.22605 85.5261 90 90 90
    space_group = "P 21 21 21"
  }
  input {
    pdb {
      file_name = "/net/cci-filer1/vol1/tmp/phzwart/tassos/trial/model.pdb"
    }
    xray_data {
      file_name = "/net/cci-filer1/vol1/tmp/phzwart/tassos/trial/1e0w.cns"
      labels = "FOBS,SIGMA"
      r_free_flags {
        file_name = "/net/cci-filer1/vol1/tmp/phzwart/tassos/trial/1e0w.cns"
        label = "TEST"
        test_flag_value = 1
      }
    }
  }
  output {
    prefix = "model_refine"
    serial = 1
  }
  main {
    number_of_macro_cycles = 5
  }
  modify_start_model {
    adp {
      set_b_iso = 10
    }
    sites {
      shake = 0.5
    }
  }
}
#phil __OFF__


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


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


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

|--(resolution: 1.97 - 14.84 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.4708   r_free= 0.4593   ksol= 0.00   Bsol= 0.00   scale= 0.810    |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (0.00,0.00,0.00,0.00,0.00,0.00); trace/3= 0.00                              |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.73 A                  |
| x-ray target function (ml) for work reflections: 6.270316                   |
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
| Bin     Resolution   Compl.  No. Refl.    R-factors          Targets        |
|number     range              work test   work   test        work        test|
|  1: 14.8444 -  4.7045 0.99   1374  152 0.3905 0.3942      6.5678      6.5934|
|  2:  4.7045 -  3.7540 0.99   1303  146 0.3935 0.3582      6.7672      6.7202|
|  3:  3.7540 -  3.2853 0.99   1287  144 0.4230 0.4022      6.6586      6.7012|
|  4:  3.2853 -  2.9876 0.99   1284  143 0.4479 0.4135      6.5266      6.4551|
|  5:  2.9876 -  2.7750 0.99   1267  138 0.4995 0.5013      6.3738       6.375|
|  6:  2.7750 -  2.6123 0.99   1272  143 0.5029 0.5547      6.2857      6.2517|
|  7:  2.6123 -  2.4821 0.99   1269  139 0.4945 0.4417      6.2383      6.1832|
|  8:  2.4821 -  2.3745 0.98   1248  141 0.5227 0.4873      6.2014      6.2144|
|  9:  2.3745 -  2.2834 0.98   1258  138 0.5100 0.5515      6.1184      6.1472|
| 10:  2.2834 -  2.2049 1.00   1234  141 0.5140 0.5129      6.1234      6.1042|
| 11:  2.2049 -  2.1361 0.97   1255  135 0.5145 0.4618      6.0436       6.048|
| 12:  2.1361 -  2.0753 0.98   1245  140 0.5034 0.5301      5.9946      6.0407|
| 13:  2.0753 -  2.0208 0.99   1245  136 0.5372 0.5184      5.8997      5.8739|
| 14:  2.0208 -  1.9716 0.86   1089  123 0.5417 0.5044      5.8594      5.7684|
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
|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: 14.8444 -  4.7045  1374   152  0.66  37.32   0.80     0.71      81073.53|
|  2:  4.7045 -  3.7540  1303   146  0.71  34.27   0.89     0.79     102478.39|
|  3:  3.7540 -  3.2853  1287   144  0.63  41.42   0.87     0.75     105346.09|
|  4:  3.2853 -  2.9876  1284   143  0.55  47.60   0.82     0.65      93685.35|
|  5:  2.9876 -  2.7750  1267   138  0.44  56.52   0.75     0.53      79228.89|
|  6:  2.7750 -  2.6123  1272   143  0.40  59.72   0.74     0.46      71692.09|
|  7:  2.6123 -  2.4821  1269   139  0.36  63.26   0.75     0.41      67409.00|
|  8:  2.4821 -  2.3745  1248   141  0.34  64.39   0.75     0.40      62123.30|
|  9:  2.3745 -  2.2834  1258   138  0.36  62.77   0.73     0.42      54298.69|
| 10:  2.2834 -  2.2049  1234   141  0.40  60.17   0.78     0.46      46830.66|
| 11:  2.2049 -  2.1361  1255   135  0.39  60.88   0.77     0.48      43925.08|
| 12:  2.1361 -  2.0753  1245   140  0.36  63.41   0.79     0.44      42191.84|
| 13:  2.0753 -  2.0208  1245   136  0.28  68.85   0.74     0.35      38353.92|
| 14:  2.0208 -  1.9716  1089   123  0.23  72.62   0.73     0.26      32416.32|
|alpha:            min =        0.26 max =            0.79 mean =         0.51|
|beta:             min =    32416.32 max =       105346.09 mean =     66491.64|
|figures of merit: min =        0.00 max =            1.00 mean =         0.44|
|phase err.(work): min =        0.00 max =           89.98 mean =        56.27|
|phase err.(test): min =        0.00 max =           89.99 mean =        56.24|
|-----------------------------------------------------------------------------|

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

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

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 12.810829             wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 80.152   (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 1.340610              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 83.308   (deg)                 |
|-----------------------------------------------------------------------------|


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

|-Geometry statistics: start--------------------------------------------------|
|            Histogram of deviations from ideal values for                    |
| Bonds                | Angles                   |  Nonbonded contacts       |
| 0.000 - 0.140:   597 |   0.009 -   7.457:   713 |  1.196 -  1.566:        4 |
| 0.140 - 0.280:   585 |   7.457 -  14.906:   711 |  1.566 -  1.937:       29 |
| 0.280 - 0.420:   441 |  14.906 -  22.354:   630 |  1.937 -  2.307:      180 |
| 0.420 - 0.560:   366 |  22.354 -  29.802:   474 |  2.307 -  2.677:      709 |
| 0.560 - 0.700:   237 |  29.802 -  37.251:   338 |  2.677 -  3.048:     1552 |
| 0.700 - 0.840:   127 |  37.251 -  44.699:   241 |  3.048 -  3.418:     2685 |
| 0.840 - 0.980:    59 |  44.699 -  52.147:   125 |  3.418 -  3.789:     4008 |
| 0.980 - 1.120:    17 |  52.147 -  59.595:    51 |  3.789 -  4.159:     5155 |
| 1.120 - 1.260:     9 |  59.595 -  67.044:    13 |  4.159 -  4.530:     6653 |
| 1.260 - 1.400:     1 |  67.044 -  74.492:     3 |  4.530 -  4.900:     7827 |
|-----------------------------------------------------------------------------|
|-Geometry statistics: start--------------------------------------------------|
|      Type |    Count |    Deviation from ideal |     Targets | Target (sum) |
|           |          |    rmsd      max    min |             |              |
|      bond |     2439 |   0.414    1.400  0.000 |     454.651 |              |
|     angle |     3299 |  24.226   74.492  0.009 |     193.752 |              |
| chirality |      348 |   2.119    6.404  0.009 |     112.240 |       53.034 |
| 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  1.196 |       2.107 |              |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 11.485)------------------------------------------|
|    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 = 11.485)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.01    19.99   9.86     None  None   None       |
|    all(noH): 2823   0      0.01    19.99   9.86     None  None   None       |
|    Sol.    : 438    0      0.06    19.99   10.10    None  None   None       |
|    Mac.    : 2385   0      0.01    19.98   9.82     None  None   None       |
|    Hyd.    : 0      0      None    None    None     None  None   None       |
|    - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -      |
|       Distribution of isotropic (or equivalent) ADP for non-H atoms:        |
|    Bin#      value range     #atoms | Bin#      value range     #atoms      |
|      0:     0.008 -   2.007:  301   |   5:    10.002 -  12.000:  285        |
|      1:     2.007 -   4.006:  276   |   6:    12.000 -  13.999:  292        |
|      2:     4.006 -   6.004:  309   |   7:    13.999 -  15.998:  289        |
|      3:     6.004 -   8.003:  285   |   8:    15.998 -  17.996:  266        |
|      4:     8.003 -  10.002:  251   |   9:    17.996 -  19.995:  269        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.97 - 14.84 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.4770   r_free= 0.4631   ksol= 0.00   Bsol= 0.00   scale= 0.778    |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (0.00,0.00,0.00,0.00,0.00,0.00); trace/3= 0.00                              |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.73 A                  |
| x-ray target function (ml) for work reflections: 6.272983                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.97 - 14.84 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.4616   r_free= 0.4477   ksol= 0.37   Bsol= 5.27   scale= 1.012    |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (7.21,10.00,8.06,0.00,0.00,0.00); trace/3= 8.42                             |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.73 A                  |
| x-ray target function (ml) for work reflections: 6.262062                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 10.793542             wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 81.337   (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 1.174444              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 79.263   (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.4616      final r-factor (work) = 0.3779          |
| start r-factor (free) = 0.4477      final r-factor (free) = 0.3988          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 86.8817 = 10.79 * 0.50 * 6.2719 + 1.00 * 53.0338                            |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 33.4548 = 10.79 * 0.50 * 6.1743 + 1.00 * 0.1335                             |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 26     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.3779      final r-factor (work) = 0.3305          |
| start r-factor (free) = 0.3988      final r-factor (free) = 0.3740          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 7.2657 = 1.17 * 1.00 * 6.1743 + 1.00 * 0.0143                               |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 7.1495 = 1.17 * 1.00 * 6.0733 + 1.00 * 0.0167                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 28     |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 11.485)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.00    89.01   12.74    None  None   None       |
|    all(noH): 2823   0      0.00    89.01   12.74    None  None   None       |
|    Sol.    : 438    0      0.00    82.86   26.35    None  None   None       |
|    Mac.    : 2385   0      0.00    89.01   10.24    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 -   8.901: 1330   |   5:    44.507 -  53.408:   42        |
|      1:     8.901 -  17.803:  794   |   6:    53.408 -  62.310:   15        |
|      2:    17.803 -  26.704:  367   |   7:    62.310 -  71.211:    7        |
|      3:    26.704 -  35.606:  187   |   8:    71.211 -  80.113:    2        |
|      4:    35.606 -  44.507:   77   |   9:    80.113 -  89.014:    2        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.3305 r_free = 0.3740             target_work(ml) = 6.048         |
| occupancies: max = 1.00  min = 0.30   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.3300 r_free = 0.3745             target_work(ml) = 6.047         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        7 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.97 - 14.84 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.3300   r_free= 0.3745   ksol= 0.37   Bsol= 5.27   scale= 1.112    |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (7.21,10.00,8.06,0.00,0.00,0.00); trace/3= 8.42                             |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.47 A                  |
| x-ray target function (ml) for work reflections: 6.047325                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.97 - 14.84 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.3263   r_free= 0.3673   ksol= 0.35   Bsol= 27.17   scale= 1.014   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (3.60,5.44,4.73,0.00,0.00,0.00); trace/3= 4.59                              |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.48 A                  |
| x-ray target function (ml) for work reflections: 6.046067                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 8.122068              wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 97.602   (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 0.504515              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 133.863  (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.3263      final r-factor (work) = 0.2243          |
| start r-factor (free) = 0.3673      final r-factor (free) = 0.2745          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 24.7832 = 8.12 * 0.50 * 6.0698 + 1.00 * 0.1335                              |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 23.9986 = 8.12 * 0.50 * 5.8883 + 1.00 * 0.0860                              |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 27     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.2243      final r-factor (work) = 0.1998          |
| start r-factor (free) = 0.2745      final r-factor (free) = 0.2550          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 2.9876 = 0.50 * 1.00 * 5.8883 + 1.00 * 0.0169                               |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 2.8790 = 0.50 * 1.00 * 5.6727 + 1.00 * 0.0170                               |
|-----------------------------------------------------------------------------|
| number of iterations = 7       |    number of function evaluations = 15     |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 11.485)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.00    89.34   12.59    None  None   None       |
|    all(noH): 2823   0      0.00    89.34   12.59    None  None   None       |
|    Sol.    : 438    0      0.00    83.80   29.74    None  None   None       |
|    Mac.    : 2385   0      0.00    89.34   9.44     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 -   8.934: 1465   |   5:    44.669 -  53.603:   42        |
|      1:     8.934 -  17.868:  710   |   6:    53.603 -  62.536:   13        |
|      2:    17.868 -  26.801:  277   |   7:    62.536 -  71.470:    5        |
|      3:    26.801 -  35.735:  214   |   8:    71.470 -  80.404:    2        |
|      4:    35.735 -  44.669:   93   |   9:    80.404 -  89.338:    2        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.1998 r_free = 0.2550             target_work(ml) = 5.636         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        7 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.1993 r_free = 0.2550             target_work(ml) = 5.635         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        4 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.97 - 14.84 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1993   r_free= 0.2550   ksol= 0.35   Bsol= 27.17   scale= 1.062   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (3.60,5.44,4.73,0.00,0.00,0.00); trace/3= 4.59                              |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.24 A                  |
| x-ray target function (ml) for work reflections: 5.634767                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.97 - 14.84 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1974   r_free= 0.2542   ksol= 0.33   Bsol= 27.17   scale= 1.024   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (2.55,3.20,3.74,0.00,0.00,0.00); trace/3= 3.16                              |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.24 A                  |
| x-ray target function (ml) for work reflections: 5.630622                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 2.327300              wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 103.349  (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 0.292903              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 94.814   (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1974      final r-factor (work) = 0.1588          |
| start r-factor (free) = 0.2542      final r-factor (free) = 0.2144          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 6.6879 = 2.33 * 0.50 * 5.6740 + 1.00 * 0.0853                               |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 6.4999 = 2.33 * 0.50 * 5.5389 + 1.00 * 0.0546                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 28     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1588      final r-factor (work) = 0.1447          |
| start r-factor (free) = 0.2144      final r-factor (free) = 0.1937          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 1.6368 = 0.29 * 1.00 * 5.5389 + 1.00 * 0.0144                               |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 1.5935 = 0.29 * 1.00 * 5.4078 + 1.00 * 0.0095                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 28     |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 11.485)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.00    87.91   12.43    None  None   None       |
|    all(noH): 2823   0      0.00    87.91   12.43    None  None   None       |
|    Sol.    : 438    0      1.71    82.50   33.36    None  None   None       |
|    Mac.    : 2385   0      0.00    87.91   8.59     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 -   8.791: 1647   |   5:    43.956 -  52.747:   76        |
|      1:     8.791 -  17.582:  602   |   6:    52.747 -  61.538:   36        |
|      2:    17.582 -  26.373:  179   |   7:    61.538 -  70.329:    5        |
|      3:    26.373 -  35.165:  140   |   8:    70.329 -  79.120:    0        |
|      4:    35.165 -  43.956:  136   |   9:    79.120 -  87.911:    2        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.1447 r_free = 0.1937             target_work(ml) = 5.356         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        4 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.1446 r_free = 0.1933             target_work(ml) = 5.355         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        6 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.97 - 14.84 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1446   r_free= 0.1933   ksol= 0.33   Bsol= 27.17   scale= 1.033   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (2.55,3.20,3.74,0.00,0.00,0.00); trace/3= 3.16                              |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.17 A                  |
| x-ray target function (ml) for work reflections: 5.355129                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.97 - 14.84 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1443   r_free= 0.1929   ksol= 0.32   Bsol= 31.96   scale= 1.013   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (1.93,2.25,3.21,0.00,0.00,0.00); trace/3= 2.46                              |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.17 A                  |
| x-ray target function (ml) for work reflections: 5.352281                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 2.065437              wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 113.418  (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 0.539685              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 145.167  (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1443      final r-factor (work) = 0.1244          |
| start r-factor (free) = 0.1929      final r-factor (free) = 0.1681          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 5.6420 = 2.07 * 0.50 * 5.4103 + 1.00 * 0.0546                               |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 5.5186 = 2.07 * 0.50 * 5.2876 + 1.00 * 0.0580                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 27     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1244      final r-factor (work) = 0.1192          |
| start r-factor (free) = 0.1681      final r-factor (free) = 0.1638          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 2.8631 = 0.54 * 1.00 * 5.2876 + 1.00 * 0.0095                               |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 2.8176 = 0.54 * 1.00 * 5.2004 + 1.00 * 0.0110                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 28     |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 11.485)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.00    90.56   12.68    None  None   None       |
|    all(noH): 2823   0      0.00    90.56   12.68    None  None   None       |
|    Sol.    : 438    0      2.12    83.55   35.79    None  None   None       |
|    Mac.    : 2385   0      0.00    90.56   8.44     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 -   9.057: 1714   |   5:    45.282 -  54.339:   91        |
|      1:     9.057 -  18.113:  559   |   6:    54.339 -  63.395:   49        |
|      2:    18.113 -  27.169:  150   |   7:    63.395 -  72.452:   11        |
|      3:    27.169 -  36.226:  129   |   8:    72.452 -  81.508:    3        |
|      4:    36.226 -  45.282:  115   |   9:    81.508 -  90.565:    2        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.1192 r_free = 0.1638             target_work(ml) = 5.186         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        6 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.1191 r_free = 0.1636             target_work(ml) = 5.186         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        5 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.97 - 14.84 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1191   r_free= 0.1636   ksol= 0.32   Bsol= 31.96   scale= 1.016   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (1.93,2.25,3.21,0.00,0.00,0.00); trace/3= 2.46                              |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.15 A                  |
| x-ray target function (ml) for work reflections: 5.185688                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.97 - 14.84 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1191   r_free= 0.1635   ksol= 0.31   Bsol= 34.65   scale= 1.013   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (1.86,2.10,3.15,0.00,0.00,0.00); trace/3= 2.37                              |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.15 A                  |
| x-ray target function (ml) for work reflections: 5.184974                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 2.209707              wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 112.886  (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 0.551903              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 127.584  (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1191      final r-factor (work) = 0.1128          |
| start r-factor (free) = 0.1635      final r-factor (free) = 0.1590          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 5.8031 = 2.21 * 0.50 * 5.2000 + 1.00 * 0.0579                               |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 5.7619 = 2.21 * 0.50 * 5.1622 + 1.00 * 0.0584                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 27     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1128      final r-factor (work) = 0.1118          |
| start r-factor (free) = 0.1590      final r-factor (free) = 0.1585          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 2.8601 = 0.55 * 1.00 * 5.1622 + 1.00 * 0.0110                               |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 2.8518 = 0.55 * 1.00 * 5.1431 + 1.00 * 0.0133                               |
|-----------------------------------------------------------------------------|
| number of iterations = 21      |    number of function evaluations = 22     |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 11.485)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.00    93.01   12.60    None  None   None       |
|    all(noH): 2823   0      0.00    93.01   12.60    None  None   None       |
|    Sol.    : 438    0      2.04    83.98   35.70    None  None   None       |
|    Mac.    : 2385   0      0.00    93.01   8.35     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 -   9.301: 1760   |   5:    46.505 -  55.806:   90        |
|      1:     9.301 -  18.602:  539   |   6:    55.806 -  65.107:   39        |
|      2:    18.602 -  27.903:  140   |   7:    65.107 -  74.408:   11        |
|      3:    27.903 -  37.204:  130   |   8:    74.408 -  83.709:    3        |
|      4:    37.204 -  46.505:  109   |   9:    83.709 -  93.010:    2        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.1118 r_free = 0.1585             target_work(ml) = 5.142         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        5 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.1117 r_free = 0.1584             target_work(ml) = 5.142         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        5 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.97 - 14.84 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1117   r_free= 0.1584   ksol= 0.31   Bsol= 34.65   scale= 1.011   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (1.86,2.10,3.15,0.00,0.00,0.00); trace/3= 2.37                              |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.14 A                  |
| x-ray target function (ml) for work reflections: 5.141801                   |
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
| Bin     Resolution   Compl.  No. Refl.    R-factors          Targets        |
|number     range              work test   work   test        work        test|
|  1: 14.8444 -  4.7045 0.99   1374  152 0.1018 0.1251      5.3955      5.5111|
|  2:  4.7045 -  3.7540 0.99   1303  146 0.0859 0.1160      5.4421      5.6511|
|  3:  3.7540 -  3.2853 0.99   1287  144 0.1078 0.1488      5.4972      5.8479|
|  4:  3.2853 -  2.9876 0.99   1284  143 0.1218 0.1635      5.4627      5.6174|
|  5:  2.9876 -  2.7750 0.99   1267  138 0.1267 0.1711      5.3141      5.5131|
|  6:  2.7750 -  2.6123 0.99   1272  143 0.1177 0.1777      5.1909      5.4501|
|  7:  2.6123 -  2.4821 0.99   1269  139 0.1263 0.1621      5.1651      5.3623|
|  8:  2.4821 -  2.3745 0.98   1248  141 0.1164 0.1754      5.0829      5.3852|
|  9:  2.3745 -  2.2834 0.98   1258  138 0.1160 0.1725        5.04      5.2516|
| 10:  2.2834 -  2.2049 1.00   1234  141 0.1099 0.1792      4.9625      5.2579|
| 11:  2.2049 -  2.1361 0.97   1255  135 0.1137 0.1660      4.9393      5.2366|
| 12:  2.1361 -  2.0753 0.98   1245  140 0.1132 0.1796      4.8925      5.2609|
| 13:  2.0753 -  2.0208 0.99   1245  136 0.1123 0.1694        4.81      5.0605|
| 14:  2.0208 -  1.9716 0.86   1089  123 0.1003 0.1771       4.665      4.9599|
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
|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: 14.8444 -  4.7045  1374   152  0.94   9.08   0.98     0.96       7033.46|
|  2:  4.7045 -  3.7540  1303   146  0.95   7.79   1.03     1.02       8971.46|
|  3:  3.7540 -  3.2853  1287   144  0.93  11.30   1.04     1.03      10597.71|
|  4:  3.2853 -  2.9876  1284   143  0.92  13.34   1.02     1.01      10270.05|
|  5:  2.9876 -  2.7750  1267   138  0.90  15.47   1.00     0.97       8133.25|
|  6:  2.7750 -  2.6123  1272   143  0.90  15.39   0.99     0.96       6743.44|
|  7:  2.6123 -  2.4821  1269   139  0.90  15.91   0.99     0.97       6214.26|
|  8:  2.4821 -  2.3745  1248   141  0.91  14.84   1.00     0.98       5325.74|
|  9:  2.3745 -  2.2834  1258   138  0.91  15.32   1.01     0.99       5136.45|
| 10:  2.2834 -  2.2049  1234   141  0.91  15.15   1.01     0.96       4365.90|
| 11:  2.2049 -  2.1361  1255   135  0.90  16.26   1.01     0.98       4442.80|
| 12:  2.1361 -  2.0753  1245   140  0.91  15.62   1.02     1.01       4058.12|
| 13:  2.0753 -  2.0208  1245   136  0.90  15.81   1.02     1.01       3459.29|
| 14:  2.0208 -  1.9716  1089   123  0.92  14.48   1.00     0.97       2619.44|
|alpha:            min =        0.96 max =            1.03 mean =         0.99|
|beta:             min =     2619.44 max =        10597.71 mean =      6309.21|
|figures of merit: min =        0.00 max =            1.00 mean =         0.92|
|phase err.(work): min =        0.00 max =           89.95 mean =        13.92|
|phase err.(test): min =        0.00 max =           89.80 mean =        13.42|
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.97 - 14.84 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1118   r_free= 0.1587   ksol= 0.32   Bsol= 39.04   scale= 1.012   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-0.50,-0.31,0.82,0.00,0.00,0.00); trace/3= 0.00                            |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.14 A                  |
| x-ray target function (ml) for work reflections: 5.142216                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.97 - 14.84 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1118   r_free= 0.1587   ksol= 0.32   Bsol= 39.04   scale= 1.012   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-0.50,-0.31,0.82,0.00,0.00,0.00); trace/3= 0.00                            |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.14 A                  |
| x-ray target function (ml) for work reflections: 5.142216                   |
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
| Bin     Resolution   Compl.  No. Refl.    R-factors          Targets        |
|number     range              work test   work   test        work        test|
|  1: 14.8444 -  4.7045 0.99   1374  152 0.1011 0.1290      5.3969      5.5294|
|  2:  4.7045 -  3.7540 0.99   1303  146 0.0875 0.1155      5.4534      5.6403|
|  3:  3.7540 -  3.2853 0.99   1287  144 0.1087 0.1473      5.4988      5.8434|
|  4:  3.2853 -  2.9876 0.99   1284  143 0.1220 0.1639      5.4619      5.6176|
|  5:  2.9876 -  2.7750 0.99   1267  138 0.1267 0.1706      5.3147       5.511|
|  6:  2.7750 -  2.6123 0.99   1272  143 0.1174 0.1777      5.1903      5.4515|
|  7:  2.6123 -  2.4821 0.99   1269  139 0.1261 0.1629      5.1633      5.3622|
|  8:  2.4821 -  2.3745 0.98   1248  141 0.1162 0.1748      5.0816      5.3814|
|  9:  2.3745 -  2.2834 0.98   1258  138 0.1157 0.1725      5.0385       5.253|
| 10:  2.2834 -  2.2049 1.00   1234  141 0.1097 0.1786      4.9628      5.2562|
| 11:  2.2049 -  2.1361 0.97   1255  135 0.1132 0.1659      4.9388      5.2371|
| 12:  2.1361 -  2.0753 0.98   1245  140 0.1128 0.1797      4.8917      5.2637|
| 13:  2.0753 -  2.0208 0.99   1245  136 0.1120 0.1695       4.809       5.058|
| 14:  2.0208 -  1.9716 0.86   1089  123 0.1003 0.1765       4.663      4.9582|
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
|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: 14.8444 -  4.7045  1374   152  0.94   9.27   0.98     0.96       7346.80|
|  2:  4.7045 -  3.7540  1303   146  0.95   7.91   1.03     1.02       9075.64|
|  3:  3.7540 -  3.2853  1287   144  0.93  11.27   1.04     1.03      10507.57|
|  4:  3.2853 -  2.9876  1284   143  0.92  13.35   1.02     1.01      10228.18|
|  5:  2.9876 -  2.7750  1267   138  0.90  15.47   1.01     0.97       8131.19|
|  6:  2.7750 -  2.6123  1272   143  0.91  15.36   0.99     0.96       6739.44|
|  7:  2.6123 -  2.4821  1269   139  0.90  15.88   0.99     0.97       6192.46|
|  8:  2.4821 -  2.3745  1248   141  0.91  14.84   1.00     0.98       5318.58|
|  9:  2.3745 -  2.2834  1258   138  0.91  15.30   1.01     1.00       5128.36|
| 10:  2.2834 -  2.2049  1234   141  0.91  15.16   1.01     0.96       4366.07|
| 11:  2.2049 -  2.1361  1255   135  0.90  16.26   1.01     0.98       4447.43|
| 12:  2.1361 -  2.0753  1245   140  0.91  15.62   1.03     1.01       4061.48|
| 13:  2.0753 -  2.0208  1245   136  0.91  15.77   1.02     1.01       3454.89|
| 14:  2.0208 -  1.9716  1089   123  0.92  14.41   1.00     0.97       2606.23|
|alpha:            min =        0.96 max =            1.03 mean =         0.99|
|beta:             min =     2606.23 max =        10507.57 mean =      6328.06|
|figures of merit: min =        0.00 max =            1.00 mean =         0.92|
|phase err.(work): min =        0.00 max =           89.97 mean =        13.93|
|phase err.(test): min =        0.00 max =           88.51 mean =        13.47|
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 11.485)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      2.41    95.42   15.00    None  None   None       |
|    all(noH): 2823   0      2.41    95.42   15.00    None  None   None       |
|    Sol.    : 438    0      4.44    86.39   38.11    None  None   None       |
|    Mac.    : 2385   0      2.41    95.42   10.76    None  None   None       |
|    Hyd.    : 0      0      None    None    None     None  None   None       |
|    - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -      |
|       Distribution of isotropic (or equivalent) ADP for non-H atoms:        |
|    Bin#      value range     #atoms | Bin#      value range     #atoms      |
|      0:     2.406 -  11.707: 1760   |   5:    48.911 -  58.212:   90        |
|      1:    11.707 -  21.008:  539   |   6:    58.212 -  67.513:   39        |
|      2:    21.008 -  30.309:  140   |   7:    67.513 -  76.814:   11        |
|      3:    30.309 -  39.610:  130   |   8:    76.814 -  86.115:    3        |
|      4:    39.610 -  48.911:  109   |   9:    86.115 -  95.416:    2        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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


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

Number of peaks found at mFobs-DFmodel map (map cutoff=3.00 sigma)= 304         
Filter by distance & map next to the model:
   mapped sites are within: 0.345 - 5.591
   number of sites selected in [dist_min= 0.70, dist_max= 6.00]: 302 from: 304
   mapped sites are within: 0.721 - 5.591

peak=   10.991 closest distance to " CB  VAL A 230 " =    1.427
peak=   10.857 closest distance to " CB  VAL A 296 " =    1.549
peak=    7.115 closest distance to " O   HOH Z 130 " =    1.297
peak=    5.968 closest distance to " O   HOH Z 124 " =    1.623
peak=    5.903 closest distance to " NE2 GLN A  11 " =    1.202
peak=    5.874 closest distance to " CG  LEU A   5 " =    1.140
peak=    5.834 closest distance to " CD2 LEU A   5 " =    1.232
peak=    5.801 closest distance to " NH2 ARG A  56 " =    2.061
peak=    5.777 closest distance to " O   HOH Z 142 " =    2.011
peak=    5.408 closest distance to " CG  PRO A  54 " =    1.297
peak=    5.172 closest distance to " CG  LEU A 228 " =    1.199
peak=    5.118 closest distance to " O   HOH Z   9 " =    1.411
peak=    5.018 closest distance to " CB  PRO A  54 " =    1.032
peak=    5.005 closest distance to " O   HOH Z 193 " =    1.680
peak=    4.879 closest distance to " O   HOH Z 209 " =    2.282
peak=    4.867 closest distance to " O   HOH Z 126 " =    1.820
peak=    4.814 closest distance to " O   HOH Z 427 " =    2.521
peak=    4.756 closest distance to " CB  SER A   3 " =    1.355
peak=    4.741 closest distance to " CG  PRO A 213 " =    1.235
peak=    4.737 closest distance to " CB  ARG A 275 " =    0.912
peak=    4.669 closest distance to " O   HOH Z   7 " =    1.385
peak=    4.630 closest distance to " CB  GLN A 183 " =    1.223
peak=    4.609 closest distance to " O   HOH Z 263 " =    1.626
peak=    4.587 closest distance to " O   HOH Z 272 " =    1.832
peak=    4.577 closest distance to " CB  VAL A 230 " =    1.141
peak=    4.518 closest distance to " O   HOH Z  78 " =    1.652
peak=    4.494 closest distance to " O   HOH Z 298 " =    1.772
peak=    4.487 closest distance to " CB BVAL A  41 " =    0.944
peak=    4.486 closest distance to " CB  GLN A 223 " =    1.571
peak=    4.444 closest distance to " O   HOH Z 369 " =    2.252
peak=    4.422 closest distance to " O   HOH Z 232 " =    2.441
peak=    4.413 closest distance to " O   HOH Z 380 " =    1.698
peak=    4.332 closest distance to " O   SER A  87 " =    2.321
peak=    4.312 closest distance to " O   HOH Z 423 " =    1.408
peak=    4.304 closest distance to " O   HOH Z 316 " =    2.912
peak=    4.278 closest distance to " CG  PRO A 243 " =    1.177
peak=    4.270 closest distance to " CB  SER A  63 " =    1.210
peak=    4.259 closest distance to " CB  GLU A 152 " =    1.232
peak=    4.257 closest distance to " O   HOH Z 236 " =    1.391
peak=    4.255 closest distance to " CG  PRO A 198 " =    1.181
peak=    4.238 closest distance to " O   HOH Z 403 " =    1.723
peak=    4.185 closest distance to " O   HOH Z 425 " =    1.444
peak=    4.172 closest distance to " NZ  LYS A 117 " =    3.048
peak=    4.170 closest distance to " O   HOH Z  68 " =    2.172
peak=    4.136 closest distance to " CA  PHE A 283 " =    1.343
peak=    4.126 closest distance to " N   PHE A 130 " =    1.317
peak=    4.115 closest distance to " O   HOH Z 346 " =    1.529
peak=    4.101 closest distance to " CD2 LEU A 228 " =    1.184
peak=    4.085 closest distance to " O   HOH Z 411 " =    3.583
peak=    4.082 closest distance to " O   HOH Z 130 " =    2.335
peak=    4.080 closest distance to " ND2 ASN A 187 " =    1.646
peak=    4.079 closest distance to " O   HOH Z 203 " =    1.705
peak=    4.064 closest distance to " CG  ARG A 138 " =    1.154
peak=    4.030 closest distance to " O   HOH Z  85 " =    1.303
peak=    4.030 closest distance to " CB  ARG A  79 " =    1.354
peak=    4.025 closest distance to " O   HOH Z  61 " =    1.579
peak=    4.012 closest distance to " O   HOH Z 422 " =    2.441
peak=    4.011 closest distance to " O   HOH Z  44 " =    1.765
peak=    4.006 closest distance to " CB  TRP A 179 " =    1.284
peak=    3.993 closest distance to " O   HOH Z  78 " =    1.902
peak=    3.985 closest distance to " CB  ASN A 148 " =    1.370
peak=    3.978 closest distance to " C   PRO A 198 " =    1.530
peak=    3.973 closest distance to " O   HOH Z 405 " =    1.367
peak=    3.971 closest distance to " CG1BVAL A  72 " =    1.280
peak=    3.970 closest distance to " O   HOH Z   3 " =    2.160
peak=    3.965 closest distance to " CB  VAL A 202 " =    1.687
peak=    3.945 closest distance to " O   HOH Z 419 " =    2.085
peak=    3.944 closest distance to " CB  VAL A 265 " =    1.297
peak=    3.940 closest distance to " O   HOH Z  30 " =    1.529
peak=    3.932 closest distance to " O   HOH Z  93 " =    2.322
peak=    3.932 closest distance to " CB  TRP A 266 " =    1.043
peak=    3.931 closest distance to " OD1 ASN A  69 " =    2.558
peak=    3.927 closest distance to " O   HOH Z 287 " =    1.735
peak=    3.919 closest distance to " O   HOH Z 117 " =    1.998
peak=    3.910 closest distance to " O   HOH Z  59 " =    1.666
peak=    3.899 closest distance to " CB  ARG A 139 " =    1.053
peak=    3.899 closest distance to " O   HOH Z 234 " =    3.432
peak=    3.893 closest distance to " O   HOH Z 250 " =    1.336
peak=    3.889 closest distance to " CD1AILE A 234 " =    0.987
peak=    3.881 closest distance to " O   HOH Z  55 " =    2.111
peak=    3.875 closest distance to " O   HOH Z 261 " =    2.276
peak=    3.875 closest distance to " O   HOH Z 189 " =    2.598
peak=    3.873 closest distance to " CB  GLU A 277 " =    3.462
peak=    3.846 closest distance to " O   HOH Z 303 " =    2.244
peak=    3.823 closest distance to " CG  LEU A 167 " =    1.177
peak=    3.802 closest distance to " CA  TYR A  30 " =    1.011
peak=    3.801 closest distance to " O   HOH Z  43 " =    1.869
peak=    3.795 closest distance to " OG  SER A  62 " =    2.974
peak=    3.794 closest distance to " NH1BARG A 145 " =    1.423
peak=    3.793 closest distance to " O   HOH Z 371 " =    2.792
peak=    3.761 closest distance to " CB  ASN A 187 " =    1.320
peak=    3.745 closest distance to " O   HOH Z 345 " =    3.197
peak=    3.743 closest distance to " CG2 THR A 221 " =    1.359
peak=    3.734 closest distance to " O   HOH Z   2 " =    1.677
peak=    3.717 closest distance to " O   HOH Z 145 " =    1.335
peak=    3.708 closest distance to " O   HOH Z  89 " =    2.218
peak=    3.695 closest distance to " O   HOH Z 366 " =    2.720
peak=    3.692 closest distance to " CB  THR A 157 " =    1.048
peak=    3.690 closest distance to " O   HOH Z 112 " =    1.074
peak=    3.686 closest distance to " O   HOH Z 368 " =    2.165
peak=    3.686 closest distance to " O   HOH Z 146 " =    1.604
peak=    3.685 closest distance to " O   HOH Z 359 " =    1.193
peak=    3.682 closest distance to " O   HOH Z 193 " =    1.937
peak=    3.675 closest distance to " CB  TYR A 169 " =    0.872
peak=    3.671 closest distance to " CG2 VAL A 257 " =    0.837
peak=    3.670 closest distance to " N   ARG A 156 " =    1.295
peak=    3.667 closest distance to " CB  SER A 216 " =    0.781
peak=    3.660 closest distance to " O   HOH Z  10 " =    1.711
peak=    3.659 closest distance to " CB  ARG A 138 " =    0.767
peak=    3.650 closest distance to " OD2 ASP A 286 " =    2.571
peak=    3.649 closest distance to " CB  GLN A  88 " =    1.297
peak=    3.644 closest distance to " O   HOH Z 272 " =    2.260
peak=    3.639 closest distance to " O   HOH Z 222 " =    2.266
peak=    3.638 closest distance to " NH2AARG A 190 " =    1.797
peak=    3.618 closest distance to " OG BSER A 164 " =    2.144
peak=    3.606 closest distance to " CA  ASN A 127 " =    1.019
peak=    3.598 closest distance to " CB  GLU A 128 " =    1.002
peak=    3.595 closest distance to " O   HOH Z  61 " =    1.522
peak=    3.590 closest distance to " NH2BARG A 145 " =    1.960
peak=    3.584 closest distance to " O   HOH Z 368 " =    3.621
peak=    3.581 closest distance to " CD  PRO A 243 " =    1.386
peak=    3.567 closest distance to " O   HOH Z 371 " =    1.711
peak=    3.564 closest distance to " O   HOH Z  63 " =    1.188
peak=    3.562 closest distance to " OE1 GLU A   2 " =    2.116
peak=    3.549 closest distance to " O   HOH Z 425 " =    2.015
peak=    3.542 closest distance to " O   HOH Z   9 " =    1.850
peak=    3.541 closest distance to " CG  GLN A  88 " =    1.115
peak=    3.539 closest distance to " O   PRO A 198 " =    1.267
peak=    3.538 closest distance to " O   HOH Z  39 " =    1.205
peak=    3.537 closest distance to " CB  LEU A 255 " =    0.830
peak=    3.536 closest distance to " O   HOH Z  65 " =    0.915
peak=    3.528 closest distance to " O   HOH Z 227 " =    1.796
peak=    3.528 closest distance to " CD1 ILE A  33 " =    1.701
peak=    3.518 closest distance to " N   ASN A  39 " =    1.099
peak=    3.516 closest distance to " O   HOH Z 126 " =    1.452
peak=    3.516 closest distance to " CA  ASN A 215 " =    1.051
peak=    3.515 closest distance to " O   HOH Z 389 " =    1.275
peak=    3.513 closest distance to " O   HOH Z  88 " =    2.555
peak=    3.506 closest distance to " CB  ASN A 142 " =    0.994
peak=    3.496 closest distance to " CD  ARG A 138 " =    0.892
peak=    3.490 closest distance to " CB  ASN A 148 " =    1.899
peak=    3.478 closest distance to " CG1 ILE A  33 " =    1.339
peak=    3.473 closest distance to " O   HOH Z  22 " =    2.107
peak=    3.469 closest distance to " C   ALA A 299 " =    0.985
peak=    3.468 closest distance to " CA  ALA A  21 " =    1.191
peak=    3.459 closest distance to " CE1 TYR A 186 " =    1.235
peak=    3.453 closest distance to " O   HOH Z 374 " =    2.424
peak=    3.453 closest distance to " O   HOH Z 222 " =    2.348
peak=    3.453 closest distance to " O   HOH Z   1 " =    1.767
peak=    3.452 closest distance to " O   HOH Z 196 " =    1.430
peak=    3.446 closest distance to " O   HOH Z 303 " =    1.731
peak=    3.440 closest distance to " O   HOH Z 273 " =    2.750
peak=    3.436 closest distance to " O   HOH Z 344 " =    2.799
peak=    3.428 closest distance to " CB  ALA A 248 " =    1.356
peak=    3.428 closest distance to " CB  ASN A  39 " =    0.872
peak=    3.426 closest distance to " O   HOH Z 284 " =    1.559
peak=    3.424 closest distance to " O   HOH Z 344 " =    1.148
peak=    3.421 closest distance to " O   HOH Z 383 " =    1.916
peak=    3.420 closest distance to " O   HOH Z 392 " =    1.357
peak=    3.413 closest distance to " O   HOH Z 193 " =    1.773
peak=    3.412 closest distance to " CA  LYS A 290 " =    1.252
peak=    3.410 closest distance to " CG2 ILE A  20 " =    1.643
peak=    3.409 closest distance to " O   HOH Z 423 " =    1.685
peak=    3.408 closest distance to " O   HOH Z 357 " =    1.920
peak=    3.408 closest distance to " O   HOH Z 213 " =    1.969
peak=    3.400 closest distance to " CG  GLN A  89 " =    1.397
peak=    3.399 closest distance to " CG BARG A 102 " =    1.820
peak=    3.398 closest distance to " O   HOH Z  58 " =    1.669
peak=    3.395 closest distance to " CD BLYS A 290 " =    1.250
peak=    3.394 closest distance to " O   HOH Z 132 " =    2.243
peak=    3.393 closest distance to " O   HOH Z 284 " =    2.836
peak=    3.381 closest distance to " CA  LYS A 117 " =    1.218
peak=    3.377 closest distance to " CG  LEU A 281 " =    1.016
peak=    3.374 closest distance to " O   HOH Z 145 " =    1.917
peak=    3.371 closest distance to " CA  ILE A 234 " =    0.966
peak=    3.366 closest distance to " O   HOH Z 261 " =    1.560
peak=    3.366 closest distance to " O   HOH Z 106 " =    2.561
peak=    3.363 closest distance to " CB  ARG A 190 " =    1.767
peak=    3.361 closest distance to " CD  GLN A 194 " =    1.371
peak=    3.360 closest distance to " O   HOH Z 118 " =    1.365
peak=    3.358 closest distance to " OG  SER A  62 " =    2.768
peak=    3.357 closest distance to " O   HOH Z 180 " =    2.102
peak=    3.351 closest distance to " CB  LEU A 143 " =    1.116
peak=    3.345 closest distance to " O  BHOH Z 338 " =    2.468
peak=    3.341 closest distance to " O   HOH Z 145 " =    3.367
peak=    3.339 closest distance to " O   HOH Z  48 " =    1.631
peak=    3.338 closest distance to " ND2 ASN A 110 " =    1.680
peak=    3.336 closest distance to " O   HOH Z 406 " =    1.529
peak=    3.329 closest distance to " O   HOH Z  59 " =    1.934
peak=    3.323 closest distance to " CB  HIS A 108 " =    0.865
peak=    3.323 closest distance to " O   HOH Z 281 " =    1.632
peak=    3.321 closest distance to " O   HOH Z   6 " =    1.951
peak=    3.317 closest distance to " CG2 ILE A 120 " =    1.211
peak=    3.315 closest distance to " OE2 GLU A  53 " =    2.034
peak=    3.312 closest distance to " NH2BARG A 190 " =    1.605
peak=    3.310 closest distance to " CB  SER A  26 " =    1.556
peak=    3.308 closest distance to " O   HOH Z 389 " =    1.677
peak=    3.307 closest distance to " O   HOH Z 255 " =    1.746
peak=    3.306 closest distance to " O   HOH Z 353 " =    2.484
peak=    3.299 closest distance to " CB  SER A 276 " =    1.096
peak=    3.298 closest distance to " O   HOH Z 123 " =    1.114
peak=    3.297 closest distance to " O   HOH Z 148 " =    3.404
peak=    3.294 closest distance to " ND1 HIS A  86 " =    1.838
peak=    3.294 closest distance to " O   HOH Z   1 " =    4.511
peak=    3.294 closest distance to " CB  ASN A 215 " =    1.016
peak=    3.294 closest distance to " O   HOH Z  71 " =    1.155
peak=    3.293 closest distance to " CA  THR A 264 " =    0.762
peak=    3.293 closest distance to " OG  SER A  22 " =    2.677
peak=    3.287 closest distance to " CA  ALA A  51 " =    0.999
peak=    3.286 closest distance to " O   HOH Z  40 " =    2.082
peak=    3.285 closest distance to " CD2 TRP A 179 " =    1.363
peak=    3.284 closest distance to " O   HOH Z 305 " =    3.391
peak=    3.283 closest distance to " O   HOH Z 427 " =    1.441
peak=    3.283 closest distance to " OE1 GLN A  58 " =    4.136
peak=    3.278 closest distance to " CE AMET A  47 " =    1.437
peak=    3.275 closest distance to " O   HOH Z 137 " =    1.535
peak=    3.274 closest distance to " CD  ARG A 269 " =    1.071
peak=    3.273 closest distance to " CB  ASP A 140 " =    0.916
peak=    3.271 closest distance to " O   HOH Z 108 " =    2.234
peak=    3.270 closest distance to " O   HOH Z  47 " =    1.684
peak=    3.267 closest distance to " O   HOH Z 209 " =    2.384
peak=    3.265 closest distance to " CA  SER A  87 " =    0.942
peak=    3.265 closest distance to " O   HOH Z 128 " =    1.971
peak=    3.264 closest distance to " CB  LEU A 300 " =    0.906
peak=    3.259 closest distance to " O   HOH Z   1 " =    1.565
peak=    3.259 closest distance to " O   HOH Z 432 " =    1.623
peak=    3.257 closest distance to " O   HOH Z 130 " =    1.831
peak=    3.252 closest distance to " O   HOH Z 109 " =    2.382
peak=    3.250 closest distance to " O   HOH Z 128 " =    2.063
peak=    3.249 closest distance to " NH1AARG A 145 " =    1.126
peak=    3.248 closest distance to " O   HOH Z 110 " =    1.579
peak=    3.246 closest distance to " CB  ALA A 114 " =    1.521
peak=    3.246 closest distance to " O   HOH Z 214 " =    2.267
peak=    3.246 closest distance to " OG1 THR A 294 " =    2.404
peak=    3.245 closest distance to " CA  ASN A  74 " =    1.220
peak=    3.241 closest distance to " O   HOH Z 257 " =    2.301
peak=    3.240 closest distance to " N   SER A 135 " =    1.393
peak=    3.237 closest distance to " CG  MET A 185 " =    1.202
peak=    3.237 closest distance to " N   VAL A 126 " =    1.131
peak=    3.234 closest distance to " O   HOH Z 158 " =    3.048
peak=    3.232 closest distance to " CG AARG A 275 " =    1.073
peak=    3.227 closest distance to " CD1 ILE A 263 " =    1.324
peak=    3.226 closest distance to " O   HOH Z 329 " =    3.797
peak=    3.226 closest distance to " CA  VAL A 126 " =    1.049
peak=    3.225 closest distance to " C   GLU A 277 " =    1.234
peak=    3.221 closest distance to " O   HOH Z 280 " =    2.410
peak=    3.219 closest distance to " O   HOH Z 417 " =    1.807
peak=    3.218 closest distance to " O   HOH Z 148 " =    2.271
peak=    3.213 closest distance to " O   HOH Z 128 " =    2.116
peak=    3.209 closest distance to " NE2 GLN A  58 " =    3.406
peak=    3.207 closest distance to " O   HOH Z 359 " =    1.955
peak=    3.206 closest distance to " N   TYR A  15 " =    1.044
peak=    3.205 closest distance to " O   HOH Z 197 " =    3.139
peak=    3.202 closest distance to " CE  MET A  93 " =    1.536
peak=    3.200 closest distance to " O   HOH Z 238 " =    5.180
peak=    3.192 closest distance to " O   HOH Z 324 " =    1.352
peak=    3.190 closest distance to " CA  GLY A 267 " =    0.930
peak=    3.187 closest distance to " OG BSER A 134 " =    3.158
peak=    3.173 closest distance to " NH1 ARG A  14 " =    1.053
peak=    3.173 closest distance to " O   HOH Z 248 " =    1.571
peak=    3.171 closest distance to " CD2 LEU A 297 " =    0.979
peak=    3.169 closest distance to " O   HOH Z 234 " =    1.894
peak=    3.167 closest distance to " CB  ILE A  20 " =    1.513
peak=    3.166 closest distance to " CB  PRO A  90 " =    1.224
peak=    3.166 closest distance to " NZ  LYS A  76 " =    1.507
peak=    3.163 closest distance to " CD2 HIS A  81 " =    1.070
peak=    3.156 closest distance to " N   ASN A 127 " =    1.362
peak=    3.155 closest distance to " N   VAL A 257 " =    1.633
peak=    3.149 closest distance to " O   HOH Z 172 " =    5.591
peak=    3.146 closest distance to " CB  ALA A 291 " =    1.472
peak=    3.145 closest distance to " CA  LEU A 282 " =    1.208
peak=    3.145 closest distance to " O   HOH Z 423 " =    2.166
peak=    3.144 closest distance to " CB  GLN A 278 " =    0.895
peak=    3.143 closest distance to " N   ALA A   1 " =    1.863
peak=    3.142 closest distance to " CB  ALA A  10 " =    0.770
peak=    3.140 closest distance to " O   HOH Z 118 " =    1.528
peak=    3.137 closest distance to " CB  ALA A   9 " =    1.456
peak=    3.136 closest distance to " CG  LYS A  76 " =    1.513
peak=    3.134 closest distance to " CB  MET A  40 " =    0.859
peak=    3.129 closest distance to " O   HOH Z  89 " =    1.623
peak=    3.129 closest distance to " O   HOH Z 245 " =    1.340
peak=    3.128 closest distance to " CG1AVAL A 121 " =    0.774
peak=    3.126 closest distance to " O   HOH Z 365 " =    1.768
peak=    3.122 closest distance to " O   HOH Z 148 " =    1.490
peak=    3.122 closest distance to " CB  LYS A 117 " =    1.195
peak=    3.116 closest distance to " O   HOH Z 366 " =    3.366
peak=    3.110 closest distance to " O   HOH Z  66 " =    2.090
peak=    3.105 closest distance to " O   HOH Z  43 " =    2.692
peak=    3.100 closest distance to " CA  ALA A 158 " =    1.193
peak=    3.083 closest distance to " O   ARG A 145 " =    1.833
peak=    3.079 closest distance to " O   HOH Z 251 " =    1.596
peak=    3.078 closest distance to " O   HOH Z 438 " =    2.326
peak=    3.071 closest distance to " CB  VAL A 268 " =    0.800
peak=    3.068 closest distance to " NH1BARG A 190 " =    2.025
peak=    3.068 closest distance to " CD  ARG A 159 " =    0.721
peak=    3.067 closest distance to " O   HOH Z 151 " =    1.532
peak=    3.065 closest distance to " CG  LEU A   5 " =    0.730
peak=    3.052 closest distance to " O   HOH Z 141 " =    1.565
peak=    3.044 closest distance to " CD2 LEU A 255 " =    1.518
peak=    3.043 closest distance to " O   HOH Z 128 " =    2.645
peak=    3.024 closest distance to " CB  LYS A 290 " =    1.172
peak=    3.013 closest distance to " OG ASER A 134 " =    1.495

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

Number of peaks found at mFobs-DFmodel map (map cutoff=3.00 sigma)= 185         
Filter by distance & map next to the model:
   mapped sites are within: 0.748 - 5.311
   number of sites selected in [dist_min= 0.70, dist_max= 6.00]: 184 from: 185
   mapped sites are within: 0.748 - 5.311

peak=   -4.814 closest distance to " CD  ARG A 156 " =    1.992
peak=   -4.664 closest distance to " CG2 VAL A 230 " =    0.748
peak=   -4.469 closest distance to " CD  ARG A  14 " =    3.213
peak=   -4.361 closest distance to " CA  GLY A  23 " =    1.992
peak=   -4.270 closest distance to " CD1 LEU A 255 " =    2.799
peak=   -4.264 closest distance to " O   VAL A  67 " =    2.661
peak=   -4.261 closest distance to " OG BSER A 134 " =    1.221
peak=   -4.232 closest distance to " CB  PRO A 243 " =    2.621
peak=   -4.126 closest distance to " C   HIS A 108 " =    1.177
peak=   -4.097 closest distance to " O   ALA A 161 " =    1.681
peak=   -4.070 closest distance to " O   HOH Z 290 " =    1.087
peak=   -4.036 closest distance to " NH2 ARG A  79 " =    1.932
peak=   -4.016 closest distance to " O   ALA A 292 " =    2.134
peak=   -4.007 closest distance to " O   HOH Z 191 " =    5.311
peak=   -4.000 closest distance to " O   HOH Z 266 " =    4.784
peak=   -3.986 closest distance to " O   HOH Z 429 " =    2.061
peak=   -3.973 closest distance to " O   PRO A 198 " =    1.221
peak=   -3.957 closest distance to " O   HOH Z  65 " =    1.108
peak=   -3.934 closest distance to " O   HOH Z 231 " =    2.002
peak=   -3.917 closest distance to " O   HOH Z  11 " =    1.926
peak=   -3.885 closest distance to " O   HOH Z 351 " =    1.471
peak=   -3.868 closest distance to " OD2 ASP A 191 " =    1.296
peak=   -3.850 closest distance to " CA  GLY A 133 " =    1.973
peak=   -3.846 closest distance to " CA  VAL A  67 " =    2.826
peak=   -3.821 closest distance to " N   GLN A  58 " =    1.876
peak=   -3.819 closest distance to " OG  SER A   3 " =    1.377
peak=   -3.806 closest distance to " CE2 PHE A 218 " =    2.509
peak=   -3.784 closest distance to " C   ASN A 285 " =    2.209
peak=   -3.773 closest distance to " CB  TYR A  15 " =    2.101
peak=   -3.769 closest distance to " N   HIS A 115 " =    2.058
peak=   -3.762 closest distance to " O   PRO A 163 " =    2.009
peak=   -3.749 closest distance to " O   HOH Z 388 " =    2.161
peak=   -3.748 closest distance to " CB  ASN A  39 " =    2.221
peak=   -3.745 closest distance to " O   HOH Z 102 " =    1.561
peak=   -3.737 closest distance to " CG  GLN A  58 " =    1.126
peak=   -3.720 closest distance to " CG2AVAL A  41 " =    2.962
peak=   -3.710 closest distance to " CD1 PHE A  59 " =    1.973
peak=   -3.703 closest distance to " CB  ALA A   7 " =    2.055
peak=   -3.695 closest distance to " O   HOH Z 385 " =    2.090
peak=   -3.690 closest distance to " CG2 THR A 178 " =    2.147
peak=   -3.686 closest distance to " CG1 VAL A 112 " =    2.750
peak=   -3.671 closest distance to " O   ALA A  51 " =    1.289
peak=   -3.666 closest distance to " CZ  PHE A  59 " =    1.400
peak=   -3.661 closest distance to " O   HOH Z  47 " =    1.531
peak=   -3.657 closest distance to " O   HOH Z 313 " =    1.733
peak=   -3.648 closest distance to " N   THR A 157 " =    1.346
peak=   -3.646 closest distance to " CG  GLN A 223 " =    1.839
peak=   -3.638 closest distance to " CB  ALA A 100 " =    2.472
peak=   -3.635 closest distance to " O   SER A 135 " =    1.490
peak=   -3.623 closest distance to " CA  GLY A  98 " =    1.849
peak=   -3.604 closest distance to " CD2 LEU A 237 " =    2.743
peak=   -3.602 closest distance to " O   HOH Z 114 " =    2.966
peak=   -3.597 closest distance to " O   HOH Z 140 " =    1.401
peak=   -3.593 closest distance to " CG1 VAL A 197 " =    2.204
peak=   -3.586 closest distance to " CB  ALA A 244 " =    2.092
peak=   -3.552 closest distance to " C   ASN A 187 " =    1.866
peak=   -3.547 closest distance to " CD1 LEU A 228 " =    2.065
peak=   -3.537 closest distance to " O   HOH Z 377 " =    2.150
peak=   -3.535 closest distance to " O   HOH Z 423 " =    2.265
peak=   -3.527 closest distance to " O   HOH Z 211 " =    1.501
peak=   -3.522 closest distance to " O   PRO A 243 " =    2.536
peak=   -3.521 closest distance to " CB  ALA A 161 " =    2.475
peak=   -3.514 closest distance to " CD1 LEU A 101 " =    2.236
peak=   -3.513 closest distance to " O   SER A  22 " =    2.321
peak=   -3.513 closest distance to " O   HOH Z 166 " =    1.684
peak=   -3.511 closest distance to " CB  ALA A 291 " =    2.296
peak=   -3.501 closest distance to " O   HOH Z 185 " =    2.041
peak=   -3.498 closest distance to " O   HOH Z 377 " =    0.962
peak=   -3.497 closest distance to " O   HOH Z 193 " =    2.316
peak=   -3.495 closest distance to " CE2 TYR A  30 " =    2.852
peak=   -3.490 closest distance to " O   HOH Z 134 " =    2.900
peak=   -3.487 closest distance to " O   HOH Z 348 " =    1.687
peak=   -3.486 closest distance to " CB  ASP A 132 " =    2.317
peak=   -3.485 closest distance to " O   HOH Z 389 " =    1.976
peak=   -3.484 closest distance to " O   ALA A 292 " =    1.995
peak=   -3.476 closest distance to " O   HOH Z 111 " =    4.513
peak=   -3.462 closest distance to " CA  GLY A 241 " =    2.183
peak=   -3.456 closest distance to " CB  PHE A 192 " =    1.792
peak=   -3.455 closest distance to " CB  ALA A  43 " =    2.266
peak=   -3.449 closest distance to " O   HOH Z 407 " =    2.994
peak=   -3.448 closest distance to " N   ALA A 248 " =    1.625
peak=   -3.438 closest distance to " CD  LYS A 289 " =    2.458
peak=   -3.431 closest distance to " CB  CYS A 201 " =    2.548
peak=   -3.428 closest distance to " O   HOH Z 131 " =    3.966
peak=   -3.424 closest distance to " OG ASER A 134 " =    1.204
peak=   -3.420 closest distance to " O   PRO A 198 " =    1.223
peak=   -3.419 closest distance to " OE1 GLN A  88 " =    1.180
peak=   -3.417 closest distance to " CG  PHE A 283 " =    2.554
peak=   -3.412 closest distance to " O   HOH Z 359 " =    3.380
peak=   -3.407 closest distance to " CD1 LEU A 101 " =    2.739
peak=   -3.405 closest distance to " CG  GLN A 278 " =    2.043
peak=   -3.378 closest distance to " ND2 ASN A 187 " =    1.621
peak=   -3.372 closest distance to " O   GLY A  80 " =    2.492
peak=   -3.371 closest distance to " O   HOH Z 427 " =    1.485
peak=   -3.364 closest distance to " O   HOH Z 130 " =    2.120
peak=   -3.363 closest distance to " OG  SER A  97 " =    2.155
peak=   -3.361 closest distance to " OG  SER A  87 " =    1.273
peak=   -3.359 closest distance to " ND2 ASN A  45 " =    1.037
peak=   -3.359 closest distance to " O   HOH Z  51 " =    1.147
peak=   -3.358 closest distance to " O   HOH Z 165 " =    2.164
peak=   -3.355 closest distance to " O   HOH Z 103 " =    1.690
peak=   -3.353 closest distance to " OE2 GLU A 152 " =    1.123
peak=   -3.352 closest distance to " O   MET A  40 " =    2.658
peak=   -3.351 closest distance to " OD1 ASN A 301 " =    1.963
peak=   -3.350 closest distance to " CZ2 TRP A 274 " =    0.916
peak=   -3.349 closest distance to " O   HOH Z 143 " =    1.207
peak=   -3.347 closest distance to " CG  ASP A 231 " =    0.789
peak=   -3.339 closest distance to " CG  TRP A 266 " =    1.806
peak=   -3.332 closest distance to " N   VAL A  72 " =    1.641
peak=   -3.332 closest distance to " O   HOH Z 158 " =    2.092
peak=   -3.328 closest distance to " CA  GLY A 203 " =    2.262
peak=   -3.326 closest distance to " O   HOH Z 250 " =    1.371
peak=   -3.325 closest distance to " CD  GLN A  88 " =    1.007
peak=   -3.321 closest distance to " O   HOH Z 198 " =    2.053
peak=   -3.318 closest distance to " O   HOH Z 438 " =    0.978
peak=   -3.304 closest distance to " OG BSER A 134 " =    1.659
peak=   -3.300 closest distance to " CG  ARG A 219 " =    2.815
peak=   -3.300 closest distance to " CG  MET A 105 " =    0.875
peak=   -3.299 closest distance to " O   HOH Z 222 " =    3.057
peak=   -3.290 closest distance to " CA  ASP A  27 " =    2.434
peak=   -3.287 closest distance to " CG  GLU A 152 " =    1.322
peak=   -3.286 closest distance to " O   GLN A 240 " =    1.792
peak=   -3.286 closest distance to " O   HOH Z 298 " =    1.254
peak=   -3.274 closest distance to " CA  ASN A 127 " =    1.294
peak=   -3.271 closest distance to " CD2 TYR A 293 " =    1.931
peak=   -3.269 closest distance to " CZ  TYR A 169 " =    1.705
peak=   -3.264 closest distance to " O   HOH Z 426 " =    1.677
peak=   -3.263 closest distance to " CA  ASP A 298 " =    1.094
peak=   -3.249 closest distance to " O   HOH Z 166 " =    1.695
peak=   -3.246 closest distance to " ND2BASN A 224 " =    1.658
peak=   -3.246 closest distance to " O   HOH Z 234 " =    3.776
peak=   -3.245 closest distance to " N   ALA A  43 " =    2.606
peak=   -3.244 closest distance to " O   ALA A   1 " =    1.729
peak=   -3.240 closest distance to " N   THR A  52 " =    1.719
peak=   -3.230 closest distance to " CD2 LEU A   5 " =    1.137
peak=   -3.230 closest distance to " OE1 GLU A 277 " =    2.160
peak=   -3.230 closest distance to " CE3 TRP A 274 " =    2.273
peak=   -3.228 closest distance to " OXT GLY A 302 " =    2.890
peak=   -3.227 closest distance to " O   HOH Z  63 " =    1.499
peak=   -3.226 closest distance to " O   ALA A   8 " =    1.828
peak=   -3.226 closest distance to " O   HOH Z 368 " =    2.319
peak=   -3.226 closest distance to " O   HOH Z 389 " =    1.420
peak=   -3.225 closest distance to " N   ALA A 226 " =    1.973
peak=   -3.225 closest distance to " C   MET A 188 " =    1.538
peak=   -3.223 closest distance to " ND2 ASN A  69 " =    1.670
peak=   -3.222 closest distance to " NH2BARG A 275 " =    1.507
peak=   -3.221 closest distance to " CG1 VAL A 230 " =    1.850
peak=   -3.221 closest distance to " CE  MET A 105 " =    2.024
peak=   -3.218 closest distance to " O   HOH Z  90 " =    2.690
peak=   -3.214 closest distance to " O   HOH Z 210 " =    1.112
peak=   -3.206 closest distance to " OE2 GLU A   2 " =    1.004
peak=   -3.205 closest distance to " CG1 VAL A 296 " =    2.058
peak=   -3.202 closest distance to " O   HOH Z 350 " =    1.996
peak=   -3.201 closest distance to " O   ASN A 187 " =    1.508
peak=   -3.200 closest distance to " C   VAL A 265 " =    0.863
peak=   -3.199 closest distance to " O   HOH Z  71 " =    1.289
peak=   -3.197 closest distance to " O   HOH Z 393 " =    3.427
peak=   -3.192 closest distance to " O   HOH Z 210 " =    1.972
peak=   -3.192 closest distance to " O   HOH Z  60 " =    2.206
peak=   -3.191 closest distance to " CZ3 TRP A 179 " =    1.298
peak=   -3.186 closest distance to " CG1 VAL A 268 " =    2.828
peak=   -3.184 closest distance to " CB  ALA A 248 " =    2.353
peak=   -3.181 closest distance to " O   HOH Z 137 " =    1.708
peak=   -3.179 closest distance to " O   GLY A  75 " =    1.947
peak=   -3.176 closest distance to " O   HOH Z  13 " =    1.710
peak=   -3.175 closest distance to " O   HOH Z 435 " =    1.936
peak=   -3.164 closest distance to " CB  PRO A 163 " =    2.435
peak=   -3.159 closest distance to " CB  TYR A 172 " =    2.212
peak=   -3.153 closest distance to " CG  LEU A 228 " =    1.035
peak=   -3.149 closest distance to " O   HOH Z 359 " =    1.658
peak=   -3.140 closest distance to " CD  GLU A 277 " =    1.164
peak=   -3.139 closest distance to " CB  ASP A 132 " =    2.269
peak=   -3.139 closest distance to " OG  SER A 206 " =    1.604
peak=   -3.135 closest distance to " ND2 ASN A 209 " =    1.899
peak=   -3.132 closest distance to " OH  TYR A 214 " =    1.179
peak=   -3.129 closest distance to " CD2 TRP A 150 " =    0.837
peak=   -3.124 closest distance to " CE  MET A 105 " =    2.250
peak=   -3.122 closest distance to " O   HOH Z 357 " =    1.914
peak=   -3.112 closest distance to " CD1 TYR A 247 " =    2.593
peak=   -3.105 closest distance to " ND2 ASN A  45 " =    1.831
peak=   -3.101 closest distance to " C   ALA A 158 " =    1.288
peak=   -3.091 closest distance to " N   GLN A  77 " =    1.664
peak=   -3.077 closest distance to " O   HOH Z 231 " =    1.401
peak=   -3.008 closest distance to " O   HOH Z 364 " =    1.932

================= 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    :  0.4708 0.4593   6.270316e+00   6.258498e+00
   1_bss:  0.4616 0.4477   6.262062e+00   6.245027e+00
   1_xyz:  0.3779 0.3988   6.142002e+00   6.168992e+00
   1_adp:  0.3305 0.3740   6.048071e+00   6.132893e+00
   1_occ:  0.3300 0.3745   6.047325e+00   6.134040e+00
   2_bss:  0.3263 0.3673   6.046067e+00   6.127953e+00
   2_xyz:  0.2243 0.2745   5.731187e+00   5.894548e+00
   2_adp:  0.1998 0.2550   5.635743e+00   5.827424e+00
   2_occ:  0.1993 0.2550   5.634767e+00   5.827341e+00
   3_bss:  0.1974 0.2542   5.630622e+00   5.823143e+00
   3_xyz:  0.1588 0.2144   5.447804e+00   5.667980e+00
   3_adp:  0.1447 0.1937   5.355878e+00   5.575123e+00
   3_occ:  0.1446 0.1933   5.355129e+00   5.574218e+00
   4_bss:  0.1443 0.1929   5.352281e+00   5.570360e+00
   4_xyz:  0.1244 0.1681   5.219423e+00   5.448418e+00
   4_adp:  0.1192 0.1638   5.186357e+00   5.421142e+00
   4_occ:  0.1191 0.1636   5.185688e+00   5.419901e+00
   5_bss:  0.1191 0.1635   5.184974e+00   5.419236e+00
   5_xyz:  0.1128 0.1590   5.147026e+00   5.394392e+00
   5_adp:  0.1118 0.1585   5.142454e+00   5.391923e+00
   5_occ:  0.1117 0.1584   5.141801e+00   5.390939e+00
   5_bss:  0.1118 0.1587   5.142216e+00   5.390840e+00
------------------------------------------------------------------------
 stage     k_sol   b_sol     b11     b22     b33     b12     b13     b23
   0    :  0.000   0.000   0.000   0.000   0.000   0.000   0.000   0.000
   1_bss:  0.366   5.271   7.210  10.001   8.056   0.000   0.000   0.000
   1_xyz:  0.366   5.271   7.210  10.001   8.056   0.000   0.000   0.000
   1_adp:  0.366   5.271   7.210  10.001   8.056   0.000   0.000   0.000
   1_occ:  0.366   5.271   7.210  10.001   8.056   0.000   0.000   0.000
   2_bss:  0.350  27.170   3.603   5.443   4.730   0.000   0.000   0.000
   2_xyz:  0.350  27.170   3.603   5.443   4.730   0.000   0.000   0.000
   2_adp:  0.350  27.170   3.603   5.443   4.730   0.000   0.000   0.000
   2_occ:  0.350  27.170   3.603   5.443   4.730   0.000   0.000   0.000
   3_bss:  0.333  27.170   2.553   3.199   3.736   0.000   0.000   0.000
   3_xyz:  0.333  27.170   2.553   3.199   3.736   0.000   0.000   0.000
   3_adp:  0.333  27.170   2.553   3.199   3.736   0.000   0.000   0.000
   3_occ:  0.333  27.170   2.553   3.199   3.736   0.000   0.000   0.000
   4_bss:  0.316  31.964   1.932   2.250   3.211   0.000   0.000   0.000
   4_xyz:  0.316  31.964   1.932   2.250   3.211   0.000   0.000   0.000
   4_adp:  0.316  31.964   1.932   2.250   3.211   0.000   0.000   0.000
   4_occ:  0.316  31.964   1.932   2.250   3.211   0.000   0.000   0.000
   5_bss:  0.311  34.649   1.865   2.097   3.153   0.000   0.000   0.000
   5_xyz:  0.311  34.649   1.865   2.097   3.153   0.000   0.000   0.000
   5_adp:  0.311  34.649   1.865   2.097   3.153   0.000   0.000   0.000
   5_occ:  0.311  34.649   1.865   2.097   3.153   0.000   0.000   0.000
   5_bss:  0.320  39.038  -0.502  -0.313   0.816   0.000   0.000   0.000
------------------------------------------------------------------------
 stage     <pher>    fom   alpha         beta
   0    :  56.263 0.4420  0.5141    66493.986
   1_bss:  55.898 0.4447  0.6559    63119.839
   1_xyz:  45.204 0.5789  0.8425    45898.815
   1_adp:  40.251 0.6404  0.9689    39998.361
   1_occ:  40.373 0.6389  0.9656    40073.941
   2_bss:  39.837 0.6451  0.8511    39183.581
   2_xyz:  27.997 0.7791  0.9931    19654.188
   2_adp:  25.028 0.8116  1.0237    16659.025
   2_occ:  25.002 0.8119  1.0238    16655.209
   3_bss:  24.851 0.8131  0.9731    16403.886
   3_xyz:  20.359 0.8579  1.0001    11360.330
   3_adp:  17.984 0.8808  1.0083     9396.585
   3_occ:  17.967 0.8809  1.0081     9363.308
   4_bss:  17.861 0.8818  0.9825     9271.793
   4_xyz:  15.203 0.9048  0.9931     7121.137
   4_adp:  14.584 0.9102  0.9911     6764.504
   4_occ:  14.564 0.9103  0.9911     6741.969
   5_bss:  14.549 0.9105  0.9880     6729.616
   5_xyz:  13.971 0.9153  0.9901     6365.930
   5_adp:  13.888 0.9161  0.9866     6324.693
   5_occ:  13.873 0.9162  0.9866     6309.222
   5_bss:  13.886 0.9161  0.9880     6328.064
------------------------------------------------------------------------
 stage       angl   bond   chir   dihe   plan   repu  geom_target
   0    :  24.226  0.414  2.119 33.790  0.145  4.087   5.3034e+01
   1_bss:  24.226  0.414  2.119 33.790  0.145  4.087   5.3034e+01
   1_xyz:   1.651  0.013  0.104 18.086  0.006  4.106   1.3349e-01
   1_adp:   1.651  0.013  0.104 18.086  0.006  4.106   1.3349e-01
   1_occ:   1.651  0.013  0.104 18.086  0.006  4.106   1.3349e-01
   2_bss:   1.651  0.013  0.104 18.086  0.006  4.106   1.3349e-01
   2_xyz:   1.190  0.009  0.089 16.059  0.005  4.116   8.5963e-02
   2_adp:   1.190  0.009  0.089 16.059  0.005  4.116   8.5963e-02
   2_occ:   1.190  0.009  0.089 16.059  0.005  4.116   8.5963e-02
   3_bss:   1.190  0.009  0.089 16.059  0.005  4.116   8.5963e-02
   3_xyz:   0.912  0.005  0.066 15.670  0.003  4.112   5.4619e-02
   3_adp:   0.912  0.005  0.066 15.670  0.003  4.112   5.4619e-02
   3_occ:   0.912  0.005  0.066 15.670  0.003  4.112   5.4619e-02
   4_bss:   0.912  0.005  0.066 15.670  0.003  4.112   5.4619e-02
   4_xyz:   0.959  0.005  0.072 15.678  0.004  4.115   5.8008e-02
   4_adp:   0.959  0.005  0.072 15.678  0.004  4.115   5.8008e-02
   4_occ:   0.959  0.005  0.072 15.678  0.004  4.115   5.8008e-02
   5_bss:   0.959  0.005  0.072 15.678  0.004  4.115   5.8008e-02
   5_xyz:   0.965  0.006  0.073 15.519  0.004  4.109   5.8431e-02
   5_adp:   0.965  0.006  0.073 15.519  0.004  4.109   5.8431e-02
   5_occ:   0.965  0.006  0.073 15.519  0.004  4.109   5.8431e-02
   5_bss:   0.965  0.006  0.073 15.519  0.004  4.109   5.8431e-02
------------------------------------------------------------------------
                      Maximal deviations:
 stage       angl   bond   chir   dihe   plan   repu       |grad|
   0    :  74.492  1.400  6.404144.062  0.405  1.196   6.8731e+00
   1_bss:  74.492  1.400  6.404144.062  0.405  1.196   6.8731e+00
   1_xyz:  13.389  0.163  0.436 88.061  0.037  2.250   9.4705e-02
   1_adp:  13.389  0.163  0.436 88.061  0.037  2.250   9.4705e-02
   1_occ:  13.389  0.163  0.436 88.061  0.037  2.250   9.4705e-02
   2_bss:  13.389  0.163  0.436 88.061  0.037  2.250   9.4705e-02
   2_xyz:   8.939  0.133  0.312 85.631  0.043  2.245   7.2493e-02
   2_adp:   8.939  0.133  0.312 85.631  0.043  2.245   7.2493e-02
   2_occ:   8.939  0.133  0.312 85.631  0.043  2.245   7.2493e-02
   3_bss:   8.939  0.133  0.312 85.631  0.043  2.245   7.2493e-02
   3_xyz:   7.313  0.047  0.272 84.604  0.028  2.330   3.7174e-02
   3_adp:   7.313  0.047  0.272 84.604  0.028  2.330   3.7174e-02
   3_occ:   7.313  0.047  0.272 84.604  0.028  2.330   3.7174e-02
   4_bss:   7.313  0.047  0.272 84.604  0.028  2.330   3.7174e-02
   4_xyz:   7.529  0.045  0.276 84.049  0.031  2.313   6.1785e-02
   4_adp:   7.529  0.045  0.276 84.049  0.031  2.313   6.1785e-02
   4_occ:   7.529  0.045  0.276 84.049  0.031  2.313   6.1785e-02
   5_bss:   7.529  0.045  0.276 84.049  0.031  2.313   6.1785e-02
   5_xyz:   6.664  0.040  0.303 84.459  0.035  2.278   5.0917e-02
   5_adp:   6.664  0.040  0.303 84.459  0.035  2.278   5.0917e-02
   5_occ:   6.664  0.040  0.303 84.459  0.035  2.278   5.0917e-02
   5_bss:   6.664  0.040  0.303 84.459  0.035  2.278   5.0917e-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:  89.01   0.00  12.74  89.01   0.00  10.24  82.86   0.00  26.35
   1_occ:  89.01   0.00  12.74  89.01   0.00  10.24  82.86   0.00  26.35
   2_bss:  89.01   0.00  12.74  89.01   0.00  10.24  82.86   0.00  26.35
   2_xyz:  89.01   0.00  12.74  89.01   0.00  10.24  82.86   0.00  26.35
   2_adp:  89.34   0.00  12.59  89.34   0.00   9.44  83.80   0.00  29.74
   2_occ:  89.34   0.00  12.59  89.34   0.00   9.44  83.80   0.00  29.74
   3_bss:  89.34   0.00  12.59  89.34   0.00   9.44  83.80   0.00  29.74
   3_xyz:  89.34   0.00  12.59  89.34   0.00   9.44  83.80   0.00  29.74
   3_adp:  87.91   0.00  12.43  87.91   0.00   8.59  82.50   1.71  33.36
   3_occ:  87.91   0.00  12.43  87.91   0.00   8.59  82.50   1.71  33.36
   4_bss:  87.91   0.00  12.43  87.91   0.00   8.59  82.50   1.71  33.36
   4_xyz:  87.91   0.00  12.43  87.91   0.00   8.59  82.50   1.71  33.36
   4_adp:  90.56   0.00  12.68  90.56   0.00   8.44  83.55   2.12  35.79
   4_occ:  90.56   0.00  12.68  90.56   0.00   8.44  83.55   2.12  35.79
   5_bss:  90.56   0.00  12.68  90.56   0.00   8.44  83.55   2.12  35.79
   5_xyz:  90.56   0.00  12.68  90.56   0.00   8.44  83.55   2.12  35.79
   5_adp:  93.01   0.00  12.60  93.01   0.00   8.35  83.98   2.04  35.70
   5_occ:  93.01   0.00  12.60  93.01   0.00   8.35  83.98   2.04  35.70
   5_bss:  95.42   2.41  15.00  95.42   2.41  10.76  86.39   4.44  38.11
------------------------------------------------------------------------
 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:    1.238    0.017    0.408
   1_adp:    1.238    0.017    0.408
   1_occ:    1.238    0.017    0.408
   2_bss:    1.238    0.017    0.408
   2_xyz:    1.415    0.053    0.600
   2_adp:    1.415    0.053    0.600
   2_occ:    1.415    0.053    0.600
   3_bss:    1.415    0.053    0.600
   3_xyz:    1.541    0.047    0.635
   3_adp:    1.541    0.047    0.635
   3_occ:    1.541    0.047    0.635
   4_bss:    1.541    0.047    0.635
   4_xyz:    1.685    0.042    0.684
   4_adp:    1.685    0.042    0.684
   4_occ:    1.685    0.042    0.684
   5_bss:    1.685    0.042    0.684
   5_xyz:    1.705    0.053    0.694
   5_adp:    1.705    0.053    0.694
   5_occ:    1.705    0.053    0.694
   5_bss:    1.705    0.053    0.694
------------------------------------------------------------------------

CPU time actual refinement: 339.23


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

Writing refined structure to PDB file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/trial/run_388/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_388/model_refine_001_2mFobs-DFmodel.map
Writing mFobs-DFmodel XPLOR map to file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/trial/run_388/model_refine_001_mFobs-DFmodel.map
Writing map coefficients to MTZ file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/trial/run_388/model_refine_001_map_coeffs.mtz

Writing default parameters for subsequent refinement:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/trial/run_388/model_refine_002.def


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

Pure refinement (no I/O, processing, etc)= 339.07 
  Macro-tasks:
    bulk solvent and scale       = 42.20  
    individual site refinement   = 138.46 
    weights calculation          = 32.95  
    collect and process          = 6.60   
    model show statistics        = 0.11   
    TOTAL for macro-tasks        = 220.32 
  Micro-tasks:
    mask                            = 2.32   
    f_calc                          = 104.22 
    alpha_beta                      = 8.21   
    target                          = 1.17   
    gradients_wrt_atomic_parameters = 114.80 
    fmodel                         = 7.36   
    r_factors                      = 0.27   
    phase_errors                   = 10.70  
    foms                           = 0.25   
    TOTAL for micro-tasks          = 249.30 
NUMBER OF MASK CALCS=  5
Time per interpreted Python bytecode instruction: 4.748 micro seconds
Total CPU time: 5.88 minutes
from_scatterers_fft:    660 calls, 103.88 s
gradients_fft:          604 calls, 101.30 s

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

# Date 2008-01-16 Time 01:27:40 PST -0800 (1200475660.88 s)
Start R-work = 0.4708, R-free = 0.4593 (no bulk solvent and anisotropic scale)
Final R-work = 0.1289, R-free = 0.1750 (no bulk solvent and anisotropic scale)

Start R-work = 0.4616, R-free = 0.4477
Final R-work = 0.1118, R-free = 0.1587