# Date 2008-01-16 Time 02:02:21 PST -0800 (1200477741.69 s)
#phil __OFF__

Command line arguments: "../663.param" "adp.set_b_iso=10" "sites.shake=0.5" "main.number_of_macro_cycles=5" "--overwrite"

HOST = moonbird.lbl.gov
HOSTTYPE = x86_64-linux
USER = phzwart
PID = 24921
JOB_ID = 5158
SGE_ARCH = lx24-amd64
SGE_TASK_FIRST = 1
SGE_TASK_LAST = 1330
SGE_TASK_ID = 663

-------------------------------------------------------------------------------
  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: (70.25, 46.93, 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: 3.26, per 1000 atoms: 1.15


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

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

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

Miller array info: /net/cci-filer1/vol1/tmp/phzwart/tassos/trial/1e0w.cns:FOBS,SIGMA
Observation type: xray.amplitude
Type of data: double, size=19589
Type of sigmas: double, size=19589
Number of Miller indices: 19589
Anomalous flag: False
Unit cell: (70.25, 46.93, 85.5261, 90, 90, 90)
Space group: P 21 21 21 (No. 19)
Systematic absences: 0
Centric reflections: 2427
Resolution range: 14.9529 1.98108
Completeness in resolution range: 0.967836
Completeness with d_max=infinity: 0.964785

Number of F-obs in resolution range:                   19589
Number of F-obs <= 0:                                  0
Refinement resolution range: d_max =  14.9529
                             d_min =   1.9811

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: (70.25, 46.93, 85.5261, 90, 90, 90)
Space group: P 21 21 21 (No. 19)
Systematic absences: 0
Centric reflections: 2427
Resolution range: 14.9529 1.98108
Completeness in resolution range: 0.967836
Completeness with d_max=infinity: 0.964785

Test (R-free flags) flag value: 1

Number of work/free reflections by resolution:
                                         work  free  %free
  bin  1: 14.9533 -  4.2387 [2117/2144]  1906   211  10.0%
  bin  2:  4.2387 -  3.3772 [2041/2057]  1836   205  10.0%
  bin  3:  3.3772 -  2.9540 [2019/2038]  1815   204  10.1%
  bin  4:  2.9540 -  2.6856 [2000/2030]  1805   195   9.8%
  bin  5:  2.6856 -  2.4941 [1986/2005]  1786   200  10.1%
  bin  6:  2.4941 -  2.3476 [1953/1978]  1761   192   9.8%
  bin  7:  2.3476 -  2.2304 [1970/2003]  1769   201  10.2%
  bin  8:  2.2304 -  2.1336 [1958/1989]  1762   196  10.0%
  bin  9:  2.1336 -  2.0517 [1962/2004]  1766   196  10.0%
  bin 10:  2.0517 -  1.9811 [1583/1992]  1424   159  10.0%
                                overall 17630  1959  10.0%
Writing MTZ file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/trial/run_663/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: 0.15 seconds
  Histogram of bond lengths:
        1.21 -     1.38: 943
        1.38 -     1.56: 1465
        1.56 -     1.73: 7
        1.73 -     1.90: 21
        1.90 -     2.08: 3
  Bond restraints sorted by residual:
             atom i - atom j            ideal  model  delta   weight residual
  " SG  CYS A 168 " - " SG BCYS A 201 " 2.031  1.983  0.048 2.50e+03 5.87e+00
  " C   GLN A  88 " - " N   GLN A  89 " 1.329  1.360 -0.031 5.10e+03 4.97e+00
  " SG  CYS A 168 " - " SG ACYS A 201 " 2.031  2.075 -0.044 2.50e+03 4.89e+00
  " CB  CYS A 201 " - " SG ACYS A 201 " 1.808  1.738  0.070 9.18e+02 4.46e+00
  " C   PRO A 198 " - " N   ILE A 199 " 1.329  1.301  0.028 5.10e+03 4.10e+00
  ... (remaining 2434 not shown)
  Histogram of nonbonded interaction distances:
        1.81 -     2.42: 13
        2.42 -     3.04: 2211
        3.04 -     3.66: 4700
        3.66 -     4.28: 9070
        4.28 -     4.90: 12419
  Nonbonded interactions sorted by model distance:
             atom i - atom j             model   vdw sym.op. j
  " CE BMET A  47 " - " O  BHOH Z  74 "  1.806 3.460
  " O   HOH Z 100 " - " O   HOH Z 352 "  2.177 3.040 -x+1/2,-y+1,z+1/2
  " O   HOH Z 113 " - " O   HOH Z 350 "  2.207 3.040 -x+1/2,-y+1,z+1/2
  " CZ BARG A 275 " - " O  BHOH Z 338 "  2.218 3.270
  " O   HOH Z 178 " - " O   HOH Z 403 "  2.327 3.040 -x+1,y-1/2,-z+1/2
  ... (remaining 28408 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_663/model_refine_001.eff

Writing geometry restraints to file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/trial/run_663/model_refine_001.geo

CPU time processing inputs: 9.29


============================ 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 = 70.25 46.93 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: 1.98 - 14.95 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.4153   r_free= 0.4047   ksol= 0.00   Bsol= 0.00   scale= 0.835    |
|                                                                             |
| 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:   0.55 A                  |
| x-ray target function (ml) for work reflections: 6.201892                   |
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
| Bin     Resolution   Compl.  No. Refl.    R-factors          Targets        |
|number     range              work test   work   test        work        test|
|  1: 14.9533 -  4.7275 0.99   1378  154 0.3561 0.3390      6.4986       6.445|
|  2:  4.7275 -  3.7722 0.99   1334  145 0.3100 0.3099      6.5923      6.6022|
|  3:  3.7722 -  3.3012 0.99   1302  146 0.3548 0.3378       6.515      6.5523|
|  4:  3.3012 -  3.0021 0.99   1291  145 0.3824 0.3683      6.4133      6.3306|
|  5:  3.0021 -  2.7884 0.99   1281  141 0.4248 0.4392      6.2824      6.3119|
|  6:  2.7884 -  2.6249 0.99   1283  144 0.4374 0.5003      6.2062      6.2346|
|  7:  2.6249 -  2.4941 0.99   1279  140 0.4628 0.4147      6.2047      6.1091|
|  8:  2.4941 -  2.3860 0.98   1264  144 0.4621 0.4447      6.1288      6.1244|
|  9:  2.3860 -  2.2944 0.98   1271  139 0.4673 0.4376      6.0778      6.0287|
| 10:  2.2944 -  2.2155 0.99   1246  142 0.4688 0.4803      6.0764      6.0734|
| 11:  2.2155 -  2.1465 0.99   1275  139 0.4787 0.4039      6.0198      5.9533|
| 12:  2.1465 -  2.0853 0.97   1243  137 0.4733 0.4539      5.9562      5.9735|
| 13:  2.0853 -  2.0305 0.99   1253  142 0.4879 0.5214       5.863      5.8647|
| 14:  2.0305 -  1.9811 0.72    930  101 0.4913 0.4855      5.8214      5.7431|
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
|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: 14.9533 -  4.7275  1378   154  0.74  30.86   0.82     0.76      57582.38|
|  2:  4.7275 -  3.7722  1334   145  0.79  27.28   0.92     0.84      67972.24|
|  3:  3.7722 -  3.3012  1302   146  0.72  33.18   0.89     0.82      69841.08|
|  4:  3.3012 -  3.0021  1291   145  0.67  37.78   0.85     0.74      63765.14|
|  5:  3.0021 -  2.7884  1281   141  0.57  46.02   0.79     0.65      58334.27|
|  6:  2.7884 -  2.6249  1283   144  0.55  47.96   0.78     0.62      52663.12|
|  7:  2.6249 -  2.4941  1279   140  0.55  48.24   0.76     0.61      47918.29|
|  8:  2.4941 -  2.3860  1264   144  0.55  48.49   0.78     0.62      42597.71|
|  9:  2.3860 -  2.2944  1271   139  0.56  47.16   0.77     0.63      36885.11|
| 10:  2.2944 -  2.2155  1246   142  0.57  47.03   0.79     0.64      33277.75|
| 11:  2.2155 -  2.1465  1275   139  0.55  48.42   0.79     0.63      31367.81|
| 12:  2.1465 -  2.0853  1243   137  0.50  52.68   0.79     0.58      33051.71|
| 13:  2.0853 -  2.0305  1253   142  0.44  57.38   0.77     0.52      30908.71|
| 14:  2.0305 -  1.9811   930   101  0.43  57.62   0.75     0.47      26126.78|
|alpha:            min =        0.47 max =            0.84 mean =         0.66|
|beta:             min =    26126.78 max =        69841.08 mean =     47257.52|
|figures of merit: min =        0.00 max =            1.00 mean =         0.59|
|phase err.(work): min =        0.00 max =           89.98 mean =        44.56|
|phase err.(test): min =        0.00 max =           89.90 mean =        44.64|
|-----------------------------------------------------------------------------|

============================== 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 = 6.817299              wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 73.237   (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 0.542956              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 77.918   (deg)                 |
|-----------------------------------------------------------------------------|


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

|-Geometry statistics: start--------------------------------------------------|
|            Histogram of deviations from ideal values for                    |
| Bonds                | Angles                   |  Nonbonded contacts       |
| 0.000 - 0.140:   597 |   0.009 -   7.457:   713 |  1.196 -  1.566:        2 |
| 0.140 - 0.280:   585 |   7.457 -  14.906:   711 |  1.566 -  1.937:       24 |
| 0.280 - 0.420:   441 |  14.906 -  22.354:   630 |  1.937 -  2.307:      164 |
| 0.420 - 0.560:   366 |  22.354 -  29.802:   474 |  2.307 -  2.677:      684 |
| 0.560 - 0.700:   237 |  29.802 -  37.251:   338 |  2.677 -  3.048:     1528 |
| 0.700 - 0.840:   127 |  37.251 -  44.699:   241 |  3.048 -  3.418:     2639 |
| 0.840 - 0.980:    59 |  44.699 -  52.147:   125 |  3.418 -  3.789:     3939 |
| 0.980 - 1.120:    17 |  52.147 -  59.595:    51 |  3.789 -  4.159:     5083 |
| 1.120 - 1.260:     9 |  59.595 -  67.044:    13 |  4.159 -  4.530:     6596 |
| 1.260 - 1.400:     1 |  67.044 -  74.492:     3 |  4.530 -  4.900:     7757 |
|-----------------------------------------------------------------------------|
|-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 |       53.577 |
| planarity |      436 |   0.145    0.405  0.000 |     250.485 |              |
|  dihedral |      870 |  33.790  144.062  0.019 |      20.704 |              |
| nonbonded |     2439 |   4.091    4.900  1.196 |       1.691 |              |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 11.805)------------------------------------------|
|    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 = 11.805)------------------------------------------|
|    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: 1.98 - 14.95 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.4249   r_free= 0.4154   ksol= 0.00   Bsol= 0.00   scale= 0.802    |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (0.00,0.00,0.00,0.00,0.00,0.00); trace/3= 0.00                              |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.55 A                  |
| x-ray target function (ml) for work reflections: 6.210239                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.98 - 14.95 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.4068   r_free= 0.3963   ksol= 0.34   Bsol= 10.36   scale= 1.036   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (7.48,8.37,8.72,0.00,0.00,0.00); trace/3= 8.19                              |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.55 A                  |
| x-ray target function (ml) for work reflections: 6.198234                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 6.196277              wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 75.365   (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 0.552695              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 75.952   (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.4068      final r-factor (work) = 0.2960          |
| start r-factor (free) = 0.3963      final r-factor (free) = 0.3203          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 72.8502 = 6.20 * 0.50 * 6.2209 + 1.00 * 53.5771                             |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 18.7756 = 6.20 * 0.50 * 6.0248 + 1.00 * 0.1100                              |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 26     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.2960      final r-factor (work) = 0.2241          |
| start r-factor (free) = 0.3203      final r-factor (free) = 0.2590          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 3.3446 = 0.55 * 1.00 * 6.0248 + 1.00 * 0.0147                               |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 3.2205 = 0.55 * 1.00 * 5.8073 + 1.00 * 0.0108                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 31     |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 11.805)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.00    61.26   10.33    None  None   None       |
|    all(noH): 2823   0      0.00    61.26   10.33    None  None   None       |
|    Sol.    : 438    0      0.00    61.26   27.89    None  None   None       |
|    Mac.    : 2385   0      0.00    60.46   7.10     None  None   None       |
|    Hyd.    : 0      0      None    None    None     None  None   None       |
|    - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -      |
|       Distribution of isotropic (or equivalent) ADP for non-H atoms:        |
|    Bin#      value range     #atoms | Bin#      value range     #atoms      |
|      0:     0.000 -   6.126: 1404   |   5:    30.630 -  36.756:  115        |
|      1:     6.126 -  12.252:  707   |   6:    36.756 -  42.882:   77        |
|      2:    12.252 -  18.378:  217   |   7:    42.882 -  49.008:   37        |
|      3:    18.378 -  24.504:  123   |   8:    49.008 -  55.134:    7        |
|      4:    24.504 -  30.630:  128   |   9:    55.134 -  61.260:    8        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.2241 r_free = 0.2590             target_work(ml) = 5.708         |
| occupancies: max = 1.00  min = 0.30   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.2236 r_free = 0.2593             target_work(ml) = 5.707         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        2 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.98 - 14.95 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.2236   r_free= 0.2593   ksol= 0.34   Bsol= 10.36   scale= 1.096   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (7.48,8.37,8.72,0.00,0.00,0.00); trace/3= 8.19                              |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.24 A                  |
| x-ray target function (ml) for work reflections: 5.707081                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.98 - 14.95 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.2172   r_free= 0.2517   ksol= 0.33   Bsol= 33.64   scale= 1.004   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (3.98,4.44,5.61,0.00,0.00,0.00); trace/3= 4.68                              |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.27 A                  |
| x-ray target function (ml) for work reflections: 5.702366                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 2.134181              wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 93.172   (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 0.267884              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 118.109  (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.2172      final r-factor (work) = 0.1540          |
| start r-factor (free) = 0.2517      final r-factor (free) = 0.1908          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 6.3227 = 2.13 * 0.50 * 5.8227 + 1.00 * 0.1094                               |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 5.9651 = 2.13 * 0.50 * 5.5393 + 1.00 * 0.0542                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 28     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1540      final r-factor (work) = 0.1426          |
| start r-factor (free) = 0.1908      final r-factor (free) = 0.1802          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 1.4945 = 0.27 * 1.00 * 5.5393 + 1.00 * 0.0106                               |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 1.4445 = 0.27 * 1.00 * 5.3552 + 1.00 * 0.0099                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 28     |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 11.805)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.00    64.39   10.84    None  None   None       |
|    all(noH): 2823   0      0.00    64.39   10.84    None  None   None       |
|    Sol.    : 438    0      1.54    59.31   31.13    None  None   None       |
|    Mac.    : 2385   0      0.00    64.39   7.11     None  None   None       |
|    Hyd.    : 0      0      None    None    None     None  None   None       |
|    - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -      |
|       Distribution of isotropic (or equivalent) ADP for non-H atoms:        |
|    Bin#      value range     #atoms | Bin#      value range     #atoms      |
|      0:     0.000 -   6.439: 1502   |   5:    32.197 -  38.636:  120        |
|      1:     6.439 -  12.879:  632   |   6:    38.636 -  45.075:   96        |
|      2:    12.879 -  19.318:  209   |   7:    45.075 -  51.514:   48        |
|      3:    19.318 -  25.757:   98   |   8:    51.514 -  57.954:   11        |
|      4:    25.757 -  32.197:  101   |   9:    57.954 -  64.393:    6        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.1426 r_free = 0.1802             target_work(ml) = 5.328         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        2 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.1425 r_free = 0.1802             target_work(ml) = 5.328         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        3 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.98 - 14.95 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1425   r_free= 0.1802   ksol= 0.33   Bsol= 33.64   scale= 1.027   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (3.98,4.44,5.61,0.00,0.00,0.00); trace/3= 4.68                              |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.16 A                  |
| x-ray target function (ml) for work reflections: 5.327984                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.98 - 14.95 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1421   r_free= 0.1796   ksol= 0.32   Bsol= 39.75   scale= 1.001   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (3.17,3.59,4.50,0.00,0.00,0.00); trace/3= 3.75                              |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.16 A                  |
| x-ray target function (ml) for work reflections: 5.327409                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 2.028156              wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 107.477  (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 0.727950              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 133.885  (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1421      final r-factor (work) = 0.1214          |
| start r-factor (free) = 0.1796      final r-factor (free) = 0.1591          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 5.4906 = 2.03 * 0.50 * 5.3610 + 1.00 * 0.0542                               |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 5.3833 = 2.03 * 0.50 * 5.2512 + 1.00 * 0.0581                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 28     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1214      final r-factor (work) = 0.1169          |
| start r-factor (free) = 0.1591      final r-factor (free) = 0.1570          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 3.8324 = 0.73 * 1.00 * 5.2512 + 1.00 * 0.0098                               |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 3.7771 = 0.73 * 1.00 * 5.1716 + 1.00 * 0.0124                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 32     |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 11.805)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.00    76.53   11.42    None  None   None       |
|    all(noH): 2823   0      0.00    76.53   11.42    None  None   None       |
|    Sol.    : 438    0      0.87    71.10   34.02    None  None   None       |
|    Mac.    : 2385   0      0.00    76.53   7.27     None  None   None       |
|    Hyd.    : 0      0      None    None    None     None  None   None       |
|    - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -      |
|       Distribution of isotropic (or equivalent) ADP for non-H atoms:        |
|    Bin#      value range     #atoms | Bin#      value range     #atoms      |
|      0:     0.000 -   7.653: 1685   |   5:    38.264 -  45.916:   98        |
|      1:     7.653 -  15.305:  551   |   6:    45.916 -  53.569:   76        |
|      2:    15.305 -  22.958:  152   |   7:    53.569 -  61.222:   38        |
|      3:    22.958 -  30.611:  105   |   8:    61.222 -  68.874:    8        |
|      4:    30.611 -  38.264:  104   |   9:    68.874 -  76.527:    6        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.1169 r_free = 0.1570             target_work(ml) = 5.166         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        3 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.1169 r_free = 0.1570             target_work(ml) = 5.166         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        4 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.98 - 14.95 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1169   r_free= 0.1570   ksol= 0.32   Bsol= 39.75   scale= 1.009   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (3.17,3.59,4.50,0.00,0.00,0.00); trace/3= 3.75                              |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.14 A                  |
| x-ray target function (ml) for work reflections: 5.166108                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.98 - 14.95 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1169   r_free= 0.1570   ksol= 0.32   Bsol= 39.75   scale= 1.005   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (3.09,3.48,4.24,0.00,0.00,0.00); trace/3= 3.60                              |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.14 A                  |
| x-ray target function (ml) for work reflections: 5.165930                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 1.822975              wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 131.161  (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 0.221301              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 139.423  (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1169      final r-factor (work) = 0.1124          |
| start r-factor (free) = 0.1570      final r-factor (free) = 0.1553          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 4.7716 = 1.82 * 0.50 * 5.1713 + 1.00 * 0.0581                               |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 4.7507 = 1.82 * 0.50 * 5.1496 + 1.00 * 0.0569                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 29     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1124      final r-factor (work) = 0.1130          |
| start r-factor (free) = 0.1553      final r-factor (free) = 0.1547          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 1.1519 = 0.22 * 1.00 * 5.1496 + 1.00 * 0.0123                               |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 1.1491 = 0.22 * 1.00 * 5.1464 + 1.00 * 0.0102                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 27     |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 11.805)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.00    76.80   11.07    None  None   None       |
|    all(noH): 2823   0      0.00    76.80   11.07    None  None   None       |
|    Sol.    : 438    0      0.89    65.82   32.34    None  None   None       |
|    Mac.    : 2385   0      0.00    76.80   7.16     None  None   None       |
|    Hyd.    : 0      0      None    None    None     None  None   None       |
|    - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -      |
|       Distribution of isotropic (or equivalent) ADP for non-H atoms:        |
|    Bin#      value range     #atoms | Bin#      value range     #atoms      |
|      0:     0.000 -   7.680: 1700   |   5:    38.399 -  46.078:   88        |
|      1:     7.680 -  15.360:  563   |   6:    46.078 -  53.758:   70        |
|      2:    15.360 -  23.039:  143   |   7:    53.758 -  61.438:   19        |
|      3:    23.039 -  30.719:  118   |   8:    61.438 -  69.118:    7        |
|      4:    30.719 -  38.399:  110   |   9:    69.118 -  76.797:    5        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.1130 r_free = 0.1547             target_work(ml) = 5.142         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        4 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.1130 r_free = 0.1546             target_work(ml) = 5.142         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        4 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.98 - 14.95 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1130   r_free= 0.1546   ksol= 0.32   Bsol= 39.75   scale= 1.004   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (3.09,3.48,4.24,0.00,0.00,0.00); trace/3= 3.60                              |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.14 A                  |
| x-ray target function (ml) for work reflections: 5.141637                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.98 - 14.95 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1133   r_free= 0.1545   ksol= 0.32   Bsol= 39.75   scale= 1.002   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (3.03,3.41,4.15,0.00,0.00,0.00); trace/3= 3.53                              |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.14 A                  |
| x-ray target function (ml) for work reflections: 5.142607                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 1.979322              wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 157.978  (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 0.455980              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 158.486  (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1133      final r-factor (work) = 0.1104          |
| start r-factor (free) = 0.1545      final r-factor (free) = 0.1540          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 5.1500 = 1.98 * 0.50 * 5.1463 + 1.00 * 0.0569                               |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 5.1379 = 1.98 * 0.50 * 5.1309 + 1.00 * 0.0601                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 27     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1104      final r-factor (work) = 0.1097          |
| start r-factor (free) = 0.1540      final r-factor (free) = 0.1549          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 2.3498 = 0.46 * 1.00 * 5.1309 + 1.00 * 0.0102                               |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 2.3483 = 0.46 * 1.00 * 5.1255 + 1.00 * 0.0112                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 27     |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 11.805)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.00    77.66   11.07    None  None   None       |
|    all(noH): 2823   0      0.00    77.66   11.07    None  None   None       |
|    Sol.    : 438    0      1.06    65.94   32.45    None  None   None       |
|    Mac.    : 2385   0      0.00    77.66   7.15     None  None   None       |
|    Hyd.    : 0      0      None    None    None     None  None   None       |
|    - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -      |
|       Distribution of isotropic (or equivalent) ADP for non-H atoms:        |
|    Bin#      value range     #atoms | Bin#      value range     #atoms      |
|      0:     0.000 -   7.766: 1710   |   5:    38.828 -  46.594:   89        |
|      1:     7.766 -  15.531:  546   |   6:    46.594 -  54.359:   68        |
|      2:    15.531 -  23.297:  149   |   7:    54.359 -  62.125:   16        |
|      3:    23.297 -  31.062:  117   |   8:    62.125 -  69.890:    7        |
|      4:    31.062 -  38.828:  116   |   9:    69.890 -  77.656:    5        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.1097 r_free = 0.1549             target_work(ml) = 5.130         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        4 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.1097 r_free = 0.1550             target_work(ml) = 5.130         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        4 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.98 - 14.95 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1097   r_free= 0.1550   ksol= 0.32   Bsol= 39.75   scale= 1.001   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (3.03,3.41,4.15,0.00,0.00,0.00); trace/3= 3.53                              |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.15 A                  |
| x-ray target function (ml) for work reflections: 5.129988                   |
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
| Bin     Resolution   Compl.  No. Refl.    R-factors          Targets        |
|number     range              work test   work   test        work        test|
|  1: 14.9533 -  4.7275 0.99   1378  154 0.0999 0.1291      5.3822      5.5205|
|  2:  4.7275 -  3.7722 0.99   1334  145 0.0869 0.1092      5.4389      5.6204|
|  3:  3.7722 -  3.3012 0.99   1302  146 0.1035 0.1497       5.459      5.8501|
|  4:  3.3012 -  3.0021 0.99   1291  145 0.1176 0.1514      5.4393      5.5784|
|  5:  3.0021 -  2.7884 0.99   1281  141 0.1281 0.1728      5.3061      5.5448|
|  6:  2.7884 -  2.6249 0.99   1283  144 0.1158 0.1751      5.1896      5.4313|
|  7:  2.6249 -  2.4941 0.99   1279  140 0.1231 0.1630      5.1561      5.3685|
|  8:  2.4941 -  2.3860 0.98   1264  144 0.1150 0.1769      5.0662      5.3517|
|  9:  2.3860 -  2.2944 0.98   1271  139 0.1162 0.1781      5.0345      5.3233|
| 10:  2.2944 -  2.2155 0.99   1246  142 0.1075 0.1596      4.9434      5.1382|
| 11:  2.2155 -  2.1465 0.99   1275  139 0.1117 0.1752      4.9211      5.2874|
| 12:  2.1465 -  2.0853 0.97   1243  137 0.1070 0.1606      4.8563      5.1304|
| 13:  2.0853 -  2.0305 0.99   1253  142 0.1124 0.1733      4.7796      5.0799|
| 14:  2.0305 -  1.9811 0.72    930  101 0.1036 0.1691      4.6539      4.8875|
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
|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: 14.9533 -  4.7275  1378   154  0.94   8.86   0.98     0.96       6981.32|
|  2:  4.7275 -  3.7722  1334   145  0.95   7.78   1.02     1.00       8842.05|
|  3:  3.7722 -  3.3012  1302   146  0.94  11.05   1.02     1.02      10128.38|
|  4:  3.3012 -  3.0021  1291   145  0.92  13.15   1.00     0.99      10113.75|
|  5:  3.0021 -  2.7884  1281   141  0.90  15.60   0.99     0.96       7961.91|
|  6:  2.7884 -  2.6249  1283   144  0.91  15.42   0.98     0.95       6863.45|
|  7:  2.6249 -  2.4941  1279   140  0.91  15.45   0.99     0.95       6063.96|
|  8:  2.4941 -  2.3860  1264   144  0.91  14.88   0.99     0.97       5290.53|
|  9:  2.3860 -  2.2944  1271   139  0.91  15.31   1.01     0.99       5053.78|
| 10:  2.2944 -  2.2155  1246   142  0.91  15.06   1.00     0.97       4265.50|
| 11:  2.2155 -  2.1465  1275   139  0.90  16.12   1.00     0.96       4226.67|
| 12:  2.1465 -  2.0853  1243   137  0.92  14.43   1.01     0.99       3749.10|
| 13:  2.0853 -  2.0305  1253   142  0.90  15.84   1.01     1.00       3283.85|
| 14:  2.0305 -  1.9811   930   101  0.92  14.25   0.99     0.95       2465.65|
|alpha:            min =        0.95 max =            1.02 mean =         0.98|
|beta:             min =     2465.65 max =        10128.38 mean =      6199.81|
|figures of merit: min =        0.00 max =            1.00 mean =         0.92|
|phase err.(work): min =        0.00 max =           89.92 mean =        13.73|
|phase err.(test): min =        0.00 max =           88.93 mean =        13.28|
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.98 - 14.95 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1097   r_free= 0.1550   ksol= 0.32   Bsol= 43.33   scale= 1.003   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-0.49,-0.13,0.61,-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: 5.129998                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.98 - 14.95 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1097   r_free= 0.1550   ksol= 0.32   Bsol= 43.33   scale= 1.003   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-0.49,-0.13,0.61,-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: 5.129998                   |
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
| Bin     Resolution   Compl.  No. Refl.    R-factors          Targets        |
|number     range              work test   work   test        work        test|
|  1: 14.9533 -  4.7275 0.99   1378  154 0.0999 0.1291      5.3824      5.5209|
|  2:  4.7275 -  3.7722 0.99   1334  145 0.0869 0.1092       5.439      5.6204|
|  3:  3.7722 -  3.3012 0.99   1302  146 0.1035 0.1498       5.459      5.8503|
|  4:  3.3012 -  3.0021 0.99   1291  145 0.1176 0.1514      5.4393      5.5783|
|  5:  3.0021 -  2.7884 0.99   1281  141 0.1281 0.1727       5.306      5.5446|
|  6:  2.7884 -  2.6249 0.99   1283  144 0.1158 0.1751      5.1896      5.4312|
|  7:  2.6249 -  2.4941 0.99   1279  140 0.1231 0.1631      5.1562      5.3688|
|  8:  2.4941 -  2.3860 0.98   1264  144 0.1151 0.1769      5.0663      5.3516|
|  9:  2.3860 -  2.2944 0.98   1271  139 0.1162 0.1781      5.0345      5.3233|
| 10:  2.2944 -  2.2155 0.99   1246  142 0.1075 0.1596      4.9434      5.1382|
| 11:  2.2155 -  2.1465 0.99   1275  139 0.1117 0.1751       4.921      5.2873|
| 12:  2.1465 -  2.0853 0.97   1243  137 0.1070 0.1606      4.8562      5.1303|
| 13:  2.0853 -  2.0305 0.99   1253  142 0.1124 0.1732      4.7795      5.0797|
| 14:  2.0305 -  1.9811 0.72    930  101 0.1036 0.1691      4.6538      4.8874|
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
|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: 14.9533 -  4.7275  1378   154  0.94   8.86   0.98     0.96       6986.48|
|  2:  4.7275 -  3.7722  1334   145  0.95   7.78   1.02     1.01       8846.31|
|  3:  3.7722 -  3.3012  1302   146  0.94  11.06   1.03     1.02      10130.84|
|  4:  3.3012 -  3.0021  1291   145  0.92  13.15   1.01     0.99      10113.27|
|  5:  3.0021 -  2.7884  1281   141  0.90  15.60   0.99     0.96       7960.88|
|  6:  2.7884 -  2.6249  1283   144  0.91  15.41   0.98     0.95       6862.69|
|  7:  2.6249 -  2.4941  1279   140  0.91  15.45   0.99     0.96       6064.55|
|  8:  2.4941 -  2.3860  1264   144  0.91  14.88   0.99     0.97       5290.26|
|  9:  2.3860 -  2.2944  1271   139  0.91  15.32   1.01     0.99       5054.50|
| 10:  2.2944 -  2.2155  1246   142  0.91  15.05   1.00     0.97       4264.96|
| 11:  2.2155 -  2.1465  1275   139  0.90  16.11   1.00     0.96       4226.25|
| 12:  2.1465 -  2.0853  1243   137  0.92  14.42   1.01     0.99       3748.14|
| 13:  2.0853 -  2.0305  1253   142  0.90  15.84   1.01     1.00       3282.85|
| 14:  2.0305 -  1.9811   930   101  0.92  14.25   0.99     0.95       2464.92|
|alpha:            min =        0.95 max =            1.02 mean =         0.98|
|beta:             min =     2464.92 max =        10130.84 mean =      6200.38|
|figures of merit: min =        0.00 max =            1.00 mean =         0.92|
|phase err.(work): min =        0.00 max =           89.92 mean =        13.73|
|phase err.(test): min =        0.00 max =           88.93 mean =        13.29|
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 11.805)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      3.58    81.24   14.65    None  None   None       |
|    all(noH): 2823   0      3.58    81.24   14.65    None  None   None       |
|    Sol.    : 438    0      4.64    69.52   36.03    None  None   None       |
|    Mac.    : 2385   0      3.58    81.24   10.73    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:     3.579 -  11.345: 1710   |   5:    42.407 -  50.173:   89        |
|      1:    11.345 -  19.111:  546   |   6:    50.173 -  57.939:   68        |
|      2:    19.111 -  26.876:  149   |   7:    57.939 -  65.704:   16        |
|      3:    26.876 -  34.642:  117   |   8:    65.704 -  73.470:    7        |
|      4:    34.642 -  42.407:  116   |   9:    73.470 -  81.235:    5        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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


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

Number of peaks found at mFobs-DFmodel map (map cutoff=3.00 sigma)= 313         
Filter by distance & map next to the model:
   mapped sites are within: 0.338 - 4.296
   number of sites selected in [dist_min= 0.70, dist_max= 6.00]: 310 from: 313
   mapped sites are within: 0.715 - 4.296

peak=   11.220 closest distance to " CB  VAL A 230 " =    1.470
peak=    7.352 closest distance to " CG2 VAL A 296 " =    1.132
peak=    6.463 closest distance to " CG  LEU A   5 " =    1.227
peak=    5.693 closest distance to " CD2 LEU A   5 " =    1.173
peak=    5.606 closest distance to " CG  LEU A 228 " =    1.181
peak=    5.451 closest distance to " NH2 ARG A  56 " =    2.177
peak=    5.354 closest distance to " CG  PRO A  54 " =    1.270
peak=    5.340 closest distance to " CB  VAL A 296 " =    1.097
peak=    5.284 closest distance to " CB  GLN A 223 " =    1.452
peak=    5.212 closest distance to " NE2 GLN A  11 " =    1.139
peak=    5.111 closest distance to " O   HOH Z 126 " =    1.953
peak=    5.046 closest distance to " CB  SER A  63 " =    1.273
peak=    5.026 closest distance to " CB  GLN A 183 " =    1.276
peak=    4.975 closest distance to " CB  ARG A 275 " =    0.891
peak=    4.820 closest distance to " CB  PRO A  54 " =    0.948
peak=    4.780 closest distance to " O   HOH Z 142 " =    1.688
peak=    4.752 closest distance to " CG  PRO A 213 " =    1.236
peak=    4.722 closest distance to " CB  VAL A 230 " =    1.166
peak=    4.715 closest distance to " O   HOH Z 272 " =    1.910
peak=    4.557 closest distance to " CB  GLU A 152 " =    1.186
peak=    4.505 closest distance to " O   HOH Z 209 " =    2.319
peak=    4.496 closest distance to " C   PRO A 198 " =    1.492
peak=    4.461 closest distance to " O   HOH Z 193 " =    1.756
peak=    4.451 closest distance to " O   HOH Z 298 " =    1.803
peak=    4.448 closest distance to " OD1 ASN A  69 " =    2.621
peak=    4.429 closest distance to " O   HOH Z 369 " =    2.083
peak=    4.421 closest distance to " O   HOH Z 232 " =    2.399
peak=    4.402 closest distance to " CB  SER A   3 " =    1.274
peak=    4.354 closest distance to " O   HOH Z 427 " =    2.976
peak=    4.347 closest distance to " O   HOH Z 316 " =    3.060
peak=    4.331 closest distance to " CB  TYR A 169 " =    0.727
peak=    4.308 closest distance to " CD2 LEU A 228 " =    1.178
peak=    4.303 closest distance to " O   HOH Z 236 " =    1.938
peak=    4.274 closest distance to " O   SER A  87 " =    2.290
peak=    4.258 closest distance to " CB  ASN A 148 " =    1.336
peak=    4.254 closest distance to " O   HOH Z 303 " =    2.021
peak=    4.227 closest distance to " ND2 ASN A 187 " =    1.533
peak=    4.215 closest distance to " O   HOH Z  78 " =    1.717
peak=    4.200 closest distance to " O   HOH Z 158 " =    3.143
peak=    4.176 closest distance to " O   HOH Z  43 " =    2.038
peak=    4.171 closest distance to " CB  VAL A 265 " =    1.302
peak=    4.163 closest distance to " O   HOH Z 203 " =    1.696
peak=    4.152 closest distance to " O   HOH Z  61 " =    1.649
peak=    4.130 closest distance to " CB  GLU A 128 " =    1.038
peak=    4.114 closest distance to " O   HOH Z 368 " =    2.131
peak=    4.109 closest distance to " O   HOH Z 423 " =    1.769
peak=    4.105 closest distance to " O   HOH Z 346 " =    1.602
peak=    4.093 closest distance to " O   HOH Z  59 " =    2.058
peak=    4.090 closest distance to " O   HOH Z 263 " =    1.632
peak=    4.084 closest distance to " O   HOH Z 234 " =    3.585
peak=    4.043 closest distance to " CG  PRO A 243 " =    1.109
peak=    4.023 closest distance to " O   HOH Z 389 " =    1.913
peak=    4.013 closest distance to " O   HOH Z 402 " =    1.471
peak=    4.005 closest distance to " CB  ARG A 139 " =    0.955
peak=    4.001 closest distance to " O   HOH Z  68 " =    2.224
peak=    3.976 closest distance to " CA  TYR A  30 " =    0.938
peak=    3.961 closest distance to " CB  TRP A 179 " =    1.342
peak=    3.958 closest distance to " CB  ARG A  79 " =    1.410
peak=    3.956 closest distance to " O   HOH Z  15 " =    2.159
peak=    3.943 closest distance to " CG  PRO A 198 " =    1.198
peak=    3.940 closest distance to " O   HOH Z 411 " =    3.774
peak=    3.939 closest distance to " CB  TRP A 266 " =    0.958
peak=    3.936 closest distance to " O   HOH Z 265 " =    2.462
peak=    3.922 closest distance to " O   HOH Z 197 " =    3.152
peak=    3.906 closest distance to " O   HOH Z 124 " =    1.397
peak=    3.902 closest distance to " CB  GLU A 277 " =    3.526
peak=    3.897 closest distance to " CG1BVAL A  72 " =    1.630
peak=    3.891 closest distance to " O   HOH Z  97 " =    2.536
peak=    3.882 closest distance to " OD2 ASP A 286 " =    2.780
peak=    3.872 closest distance to " O   HOH Z 403 " =    1.662
peak=    3.862 closest distance to " O   HOH Z 261 " =    2.216
peak=    3.860 closest distance to " O   HOH Z 280 " =    2.929
peak=    3.855 closest distance to " O   HOH Z 126 " =    2.087
peak=    3.854 closest distance to " CA  ASN A 215 " =    1.180
peak=    3.850 closest distance to " O   HOH Z  97 " =    1.981
peak=    3.850 closest distance to " O   HOH Z 248 " =    1.682
peak=    3.831 closest distance to " O   HOH Z 371 " =    3.147
peak=    3.818 closest distance to " O   HOH Z 189 " =    2.595
peak=    3.795 closest distance to " CA  ALA A  21 " =    1.174
peak=    3.783 closest distance to " O   HOH Z 250 " =    1.348
peak=    3.757 closest distance to " O   HOH Z 128 " =    2.018
peak=    3.752 closest distance to " O   HOH Z  88 " =    3.060
peak=    3.744 closest distance to " O   HOH Z 145 " =    2.119
peak=    3.736 closest distance to " O   HOH Z 245 " =    1.387
peak=    3.719 closest distance to " O   HOH Z 344 " =    2.930
peak=    3.710 closest distance to " CB  ASN A  39 " =    0.876
peak=    3.704 closest distance to " CD BLYS A 290 " =    1.142
peak=    3.702 closest distance to " OG BSER A 164 " =    2.207
peak=    3.699 closest distance to " NH2 ARG A 156 " =    1.113
peak=    3.698 closest distance to " O   MET A 105 " =    1.836
peak=    3.691 closest distance to " CG  ARG A  66 " =    2.705
peak=    3.686 closest distance to " CB  ASP A 140 " =    0.897
peak=    3.681 closest distance to " O   HOH Z 193 " =    1.893
peak=    3.665 closest distance to " CB  ALA A 248 " =    1.373
peak=    3.664 closest distance to " CA  VAL A  41 " =    0.828
peak=    3.664 closest distance to " CA  ALA A 158 " =    1.222
peak=    3.660 closest distance to " CA  THR A 264 " =    0.786
peak=    3.660 closest distance to " O   TRP A 274 " =    1.902
peak=    3.660 closest distance to " CB  LEU A 228 " =    1.275
peak=    3.656 closest distance to " O   HOH Z 407 " =    2.445
peak=    3.652 closest distance to " O   HOH Z 128 " =    2.121
peak=    3.651 closest distance to " CZ  PHE A 218 " =    1.092
peak=    3.645 closest distance to " O   HOH Z 273 " =    2.587
peak=    3.639 closest distance to " CG1 ILE A  33 " =    1.316
peak=    3.638 closest distance to " O   HOH Z  54 " =    1.583
peak=    3.631 closest distance to " CB  VAL A 202 " =    1.571
peak=    3.630 closest distance to " O   HOH Z 322 " =    2.053
peak=    3.611 closest distance to " CA  ALA A  51 " =    0.944
peak=    3.577 closest distance to " CB  ALA A   9 " =    1.577
peak=    3.577 closest distance to " CA  LYS A 117 " =    1.223
peak=    3.570 closest distance to " O   HOH Z 147 " =    1.694
peak=    3.565 closest distance to " O   HOH Z 345 " =    3.290
peak=    3.562 closest distance to " CD1 ILE A 106 " =    1.051
peak=    3.561 closest distance to " CG  LEU A 167 " =    1.189
peak=    3.555 closest distance to " CB  THR A 157 " =    1.152
peak=    3.553 closest distance to " CG2 VAL A 257 " =    0.867
peak=    3.552 closest distance to " CB  ARG A 190 " =    1.651
peak=    3.535 closest distance to " N   ASN A  39 " =    1.150
peak=    3.533 closest distance to " CB  SER A 212 " =    1.174
peak=    3.530 closest distance to " CB  HIS A 108 " =    0.807
peak=    3.527 closest distance to " O   HOH Z  10 " =    1.836
peak=    3.521 closest distance to " CG1 ILE A  49 " =    1.402
peak=    3.517 closest distance to " O   HOH Z 207 " =    1.749
peak=    3.508 closest distance to " CA  THR A 221 " =    0.940
peak=    3.507 closest distance to " O   HOH Z 329 " =    3.835
peak=    3.506 closest distance to " CG1 VAL A 296 " =    1.220
peak=    3.504 closest distance to " O   HOH Z 214 " =    2.081
peak=    3.504 closest distance to " O   HOH Z 112 " =    1.623
peak=    3.503 closest distance to " CB  ALA A 291 " =    1.403
peak=    3.501 closest distance to " O   HOH Z 132 " =    2.704
peak=    3.501 closest distance to " O   HOH Z 291 " =    1.602
peak=    3.499 closest distance to " CD1 LEU A 300 " =    1.265
peak=    3.496 closest distance to " O   HOH Z   9 " =    2.050
peak=    3.496 closest distance to " CB  GLN A 278 " =    0.880
peak=    3.495 closest distance to " O   HOH Z  48 " =    1.719
peak=    3.492 closest distance to " CB  LEU A 143 " =    1.137
peak=    3.489 closest distance to " O   HOH Z 299 " =    4.296
peak=    3.489 closest distance to " CD2 TRP A 179 " =    1.398
peak=    3.486 closest distance to " O   HOH Z 227 " =    2.091
peak=    3.483 closest distance to " CB  SER A 216 " =    0.715
peak=    3.480 closest distance to " CB  ASN A 142 " =    1.068
peak=    3.478 closest distance to " O   HOH Z 286 " =    2.363
peak=    3.470 closest distance to " CB  THR A  31 " =    1.658
peak=    3.461 closest distance to " CB BVAL A  41 " =    1.150
peak=    3.457 closest distance to " N   VAL A 126 " =    1.329
peak=    3.454 closest distance to " CE1 TYR A 186 " =    1.321
peak=    3.453 closest distance to " CG2 ILE A  20 " =    1.467
peak=    3.447 closest distance to " CD  ARG A 269 " =    1.011
peak=    3.445 closest distance to " NZ  LYS A 117 " =    3.215
peak=    3.442 closest distance to " O   HOH Z 426 " =    1.539
peak=    3.441 closest distance to " CB  SER A  26 " =    1.615
peak=    3.435 closest distance to " O   HOH Z 148 " =    3.274
peak=    3.431 closest distance to " O   HOH Z 425 " =    1.293
peak=    3.430 closest distance to " O   HOH Z 154 " =    2.043
peak=    3.427 closest distance to " O   HOH Z 366 " =    3.011
peak=    3.425 closest distance to " CA  ASP A 140 " =    1.230
peak=    3.423 closest distance to " CG  MET A 185 " =    1.155
peak=    3.419 closest distance to " O   HOH Z 368 " =    3.580
peak=    3.418 closest distance to " O   HOH Z 417 " =    3.204
peak=    3.418 closest distance to " CD  LYS A 166 " =    1.323
peak=    3.417 closest distance to " CA  ALA A 233 " =    1.293
peak=    3.416 closest distance to " O   HOH Z 425 " =    2.027
peak=    3.413 closest distance to " N   PHE A 130 " =    1.304
peak=    3.399 closest distance to " CD1 ILE A  33 " =    1.582
peak=    3.399 closest distance to " CD  LYS A 119 " =    1.460
peak=    3.391 closest distance to " CB  GLN A  88 " =    1.196
peak=    3.391 closest distance to " CG1 VAL A 153 " =    0.929
peak=    3.389 closest distance to " CB  SER A 273 " =    0.872
peak=    3.389 closest distance to " O   ASP A 124 " =    1.118
peak=    3.386 closest distance to " O   HOH Z  40 " =    1.399
peak=    3.385 closest distance to " O   GLN A 278 " =    1.315
peak=    3.379 closest distance to " CG2 THR A 221 " =    1.218
peak=    3.378 closest distance to " O   HOH Z 193 " =    1.611
peak=    3.377 closest distance to " O   HOH Z  48 " =    1.400
peak=    3.377 closest distance to " O   HOH Z 189 " =    2.709
peak=    3.375 closest distance to " O   HOH Z 423 " =    2.960
peak=    3.369 closest distance to " CG2 ILE A 120 " =    1.282
peak=    3.367 closest distance to " CD1 LEU A  96 " =    0.715
peak=    3.367 closest distance to " CE  LYS A  76 " =    0.920
peak=    3.365 closest distance to " O   HOH Z 135 " =    1.763
peak=    3.364 closest distance to " CB  TRP A 150 " =    1.510
peak=    3.359 closest distance to " CA  PHE A 283 " =    1.214
peak=    3.354 closest distance to " CD  ARG A 159 " =    0.729
peak=    3.353 closest distance to " CA  ALA A 291 " =    0.934
peak=    3.347 closest distance to " CA  ARG A 195 " =    1.230
peak=    3.345 closest distance to " CA  SER A  87 " =    1.024
peak=    3.344 closest distance to " O   HOH Z 172 " =    3.737
peak=    3.344 closest distance to " CA  ARG A  36 " =    1.025
peak=    3.341 closest distance to " CB  GLN A 205 " =    1.140
peak=    3.339 closest distance to " N   SER A 135 " =    1.342
peak=    3.339 closest distance to " O   ALA A 158 " =    1.388
peak=    3.337 closest distance to " O   HOH Z 437 " =    2.004
peak=    3.332 closest distance to " CB  ARG A  79 " =    0.871
peak=    3.330 closest distance to " OG1 THR A 294 " =    2.382
peak=    3.321 closest distance to " CG  GLN A  77 " =    2.224
peak=    3.320 closest distance to " O   HOH Z 251 " =    1.681
peak=    3.320 closest distance to " CB  GLU A  46 " =    1.065
peak=    3.317 closest distance to " NH1AARG A 145 " =    1.040
peak=    3.310 closest distance to " O   HOH Z 134 " =    1.378
peak=    3.308 closest distance to " O   HOH Z 171 " =    2.373
peak=    3.307 closest distance to " O   HOH Z 175 " =    2.155
peak=    3.304 closest distance to " OE1 GLU A   2 " =    2.142
peak=    3.304 closest distance to " O   HOH Z 337 " =    3.617
peak=    3.302 closest distance to " N   ARG A 190 " =    1.039
peak=    3.302 closest distance to " O   HOH Z 227 " =    1.647
peak=    3.299 closest distance to " CG  MET A 185 " =    1.099
peak=    3.298 closest distance to " O   HOH Z  21 " =    1.735
peak=    3.294 closest distance to " O   HOH Z  85 " =    1.402
peak=    3.293 closest distance to " CG1 ILE A 151 " =    0.996
peak=    3.291 closest distance to " O   HOH Z 133 " =    1.544
peak=    3.291 closest distance to " CB  ALA A 295 " =    1.242
peak=    3.290 closest distance to " O   HOH Z 374 " =    2.579
peak=    3.285 closest distance to " O   HOH Z 305 " =    3.601
peak=    3.284 closest distance to " O   HOH Z 180 " =    2.115
peak=    3.282 closest distance to " CA  ASP A 162 " =    1.052
peak=    3.279 closest distance to " CB  ILE A  20 " =    1.449
peak=    3.275 closest distance to " O   HOH Z  80 " =    1.598
peak=    3.273 closest distance to " CB  ALA A 114 " =    1.345
peak=    3.271 closest distance to " CG  GLN A  88 " =    1.023
peak=    3.270 closest distance to " CA  VAL A 126 " =    0.879
peak=    3.268 closest distance to " CB  ASN A 224 " =    1.082
peak=    3.268 closest distance to " O   HOH Z  44 " =    1.704
peak=    3.266 closest distance to " O   HOH Z 227 " =    1.578
peak=    3.265 closest distance to " O   HOH Z 313 " =    1.736
peak=    3.263 closest distance to " O   HOH Z 417 " =    2.131
peak=    3.262 closest distance to " O   HOH Z 130 " =    2.241
peak=    3.258 closest distance to " O   HOH Z 435 " =    1.991
peak=    3.255 closest distance to " O  BHOH Z 338 " =    2.457
peak=    3.250 closest distance to " NZ  LYS A  76 " =    1.277
peak=    3.248 closest distance to " O   HOH Z  19 " =    2.299
peak=    3.248 closest distance to " NH2BARG A 145 " =    1.942
peak=    3.248 closest distance to " O   HOH Z 422 " =    2.687
peak=    3.247 closest distance to " O   HOH Z 222 " =    2.495
peak=    3.242 closest distance to " CA  LYS A 290 " =    1.232
peak=    3.241 closest distance to " O   HOH Z 166 " =    3.665
peak=    3.240 closest distance to " OG BSER A 134 " =    2.989
peak=    3.236 closest distance to " O   HOH Z 290 " =    1.063
peak=    3.234 closest distance to " CG BARG A 102 " =    1.789
peak=    3.232 closest distance to " C   ALA A 299 " =    0.945
peak=    3.231 closest distance to " CB  ASN A 110 " =    1.142
peak=    3.230 closest distance to " O   HOH Z 250 " =    1.344
peak=    3.227 closest distance to " CZ2 TRP A 274 " =    1.548
peak=    3.225 closest distance to " N   ARG A 156 " =    1.346
peak=    3.222 closest distance to " NH2 ARG A  79 " =    1.348
peak=    3.219 closest distance to " CB  VAL A 268 " =    0.835
peak=    3.217 closest distance to " CA  LEU A 282 " =    1.094
peak=    3.216 closest distance to " CB  LEU A 255 " =    0.793
peak=    3.214 closest distance to " O   HOH Z 411 " =    1.724
peak=    3.212 closest distance to " OG  SER A  22 " =    2.787
peak=    3.209 closest distance to " CA  SER A 146 " =    1.788
peak=    3.206 closest distance to " O   HOH Z   1 " =    1.894
peak=    3.205 closest distance to " O   ALA A 165 " =    1.405
peak=    3.201 closest distance to " OE2 GLU A  53 " =    1.994
peak=    3.199 closest distance to " CD2 TYR A  30 " =    0.913
peak=    3.198 closest distance to " O   SER A 164 " =    1.145
peak=    3.197 closest distance to " O   HOH Z 313 " =    1.778
peak=    3.196 closest distance to " CD2 HIS A  81 " =    1.122
peak=    3.195 closest distance to " O   HOH Z  40 " =    2.495
peak=    3.193 closest distance to " O   HOH Z 132 " =    3.235
peak=    3.193 closest distance to " CB  MET A  40 " =    0.819
peak=    3.192 closest distance to " CB  MET A  47 " =    1.131
peak=    3.189 closest distance to " O   HOH Z 357 " =    1.771
peak=    3.189 closest distance to " O   HOH Z 359 " =    3.712
peak=    3.189 closest distance to " CB  LYS A 290 " =    1.062
peak=    3.187 closest distance to " O   HOH Z 199 " =    1.574
peak=    3.186 closest distance to " O   HOH Z 261 " =    1.529
peak=    3.184 closest distance to " O   HOH Z 359 " =    1.847
peak=    3.184 closest distance to " O   HOH Z 341 " =    2.079
peak=    3.183 closest distance to " CB  SER A  62 " =    1.259
peak=    3.182 closest distance to " O   HOH Z  49 " =    2.477
peak=    3.182 closest distance to " CG2 THR A 294 " =    1.727
peak=    3.176 closest distance to " ND1 HIS A  81 " =    1.660
peak=    3.175 closest distance to " O   HOH Z 353 " =    2.634
peak=    3.174 closest distance to " O   HOH Z 409 " =    3.342
peak=    3.173 closest distance to " O   HOH Z 285 " =    3.041
peak=    3.173 closest distance to " O   HOH Z 151 " =    1.767
peak=    3.172 closest distance to " CA  ILE A 106 " =    0.764
peak=    3.168 closest distance to " O   ALA A   1 " =    1.527
peak=    3.165 closest distance to " O   HOH Z 367 " =    3.472
peak=    3.160 closest distance to " CD1 LEU A 228 " =    1.917
peak=    3.158 closest distance to " O   HOH Z 406 " =    1.616
peak=    3.158 closest distance to " O   HOH Z  61 " =    1.558
peak=    3.155 closest distance to " CD2 LEU A 255 " =    1.559
peak=    3.154 closest distance to " O   HOH Z 392 " =    1.417
peak=    3.152 closest distance to " CB  ILE A 120 " =    1.323
peak=    3.149 closest distance to " CZ  PHE A 192 " =    1.014
peak=    3.148 closest distance to " CE1 HIS A 108 " =    1.115
peak=    3.140 closest distance to " CA  ALA A  84 " =    1.458
peak=    3.137 closest distance to " O   HOH Z 350 " =    1.590
peak=    3.136 closest distance to " ND1 HIS A  86 " =    1.633
peak=    3.134 closest distance to " N   GLN A 278 " =    1.063
peak=    3.131 closest distance to " CG1 ILE A 120 " =    1.137
peak=    3.130 closest distance to " CG2 VAL A 202 " =    1.164
peak=    3.130 closest distance to " O   ALA A   1 " =    1.749
peak=    3.128 closest distance to " CA  ASP A 191 " =    0.894
peak=    3.126 closest distance to " CA  ASN A 217 " =    1.294
peak=    3.111 closest distance to " CA  GLN A 194 " =    1.317
peak=    3.108 closest distance to " CB  ASN A 215 " =    1.138
peak=    3.105 closest distance to " O   HOH Z 164 " =    2.021
peak=    3.103 closest distance to " CD1 LEU A 261 " =    1.188
peak=    3.101 closest distance to " O   HOH Z 163 " =    1.839
peak=    3.090 closest distance to " O   HOH Z 303 " =    1.686
peak=    3.084 closest distance to " CD2 LEU A   5 " =    0.727
peak=    3.082 closest distance to " N   ASP A 162 " =    1.295
peak=    3.071 closest distance to " CG  GLN A  89 " =    1.531
peak=    3.066 closest distance to " O   HOH Z 141 " =    1.555
peak=    3.063 closest distance to " CD1AILE A 234 " =    0.974
peak=    3.056 closest distance to " CG  LYS A  76 " =    0.982
peak=    3.056 closest distance to " CA  ASN A 176 " =    1.059
peak=    3.009 closest distance to " CZ3 TRP A  85 " =    0.951

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

Number of peaks found at mFobs-DFmodel map (map cutoff=3.00 sigma)= 204         
Filter by distance & map next to the model:
   mapped sites are within: 0.555 - 5.438
   number of sites selected in [dist_min= 0.70, dist_max= 6.00]: 201 from: 204
   mapped sites are within: 0.756 - 5.438

peak=   -5.675 closest distance to " CG2 VAL A 230 " =    0.756
peak=   -4.608 closest distance to " CD  ARG A 156 " =    2.033
peak=   -4.596 closest distance to " SG  CYS A 254 " =    3.205
peak=   -4.399 closest distance to " O   HOH Z 266 " =    4.823
peak=   -4.341 closest distance to " O   HOH Z 290 " =    1.103
peak=   -4.317 closest distance to " CB  PRO A 243 " =    2.610
peak=   -4.156 closest distance to " C   HIS A 108 " =    1.211
peak=   -4.139 closest distance to " O   ILE A 109 " =    2.576
peak=   -4.123 closest distance to " CG2 VAL A 296 " =    1.213
peak=   -4.111 closest distance to " OG BSER A 134 " =    1.174
peak=   -4.095 closest distance to " N   GLN A  58 " =    1.703
peak=   -4.077 closest distance to " CG  ASP A 231 " =    0.804
peak=   -4.062 closest distance to " CG  GLN A 223 " =    1.998
peak=   -4.024 closest distance to " CG2BVAL A  41 " =    2.648
peak=   -3.975 closest distance to " CE2 TYR A  30 " =    2.799
peak=   -3.924 closest distance to " O   HOH Z 351 " =    1.517
peak=   -3.910 closest distance to " O   VAL A  67 " =    2.800
peak=   -3.906 closest distance to " CD2 LEU A 300 " =    2.763
peak=   -3.891 closest distance to " O   PRO A 163 " =    2.096
peak=   -3.881 closest distance to " O   HOH Z 231 " =    1.917
peak=   -3.816 closest distance to " OXT GLY A 302 " =    2.826
peak=   -3.804 closest distance to " CZ3 TRP A 179 " =    1.262
peak=   -3.799 closest distance to " CD  GLN A  58 " =    1.113
peak=   -3.790 closest distance to " O   HOH Z 389 " =    1.819
peak=   -3.788 closest distance to " CG1 VAL A 112 " =    2.775
peak=   -3.780 closest distance to " CB  ALA A 248 " =    2.064
peak=   -3.771 closest distance to " O   HOH Z  11 " =    1.898
peak=   -3.763 closest distance to " N   ALA A 226 " =    2.025
peak=   -3.750 closest distance to " CD  ARG A 139 " =    1.580
peak=   -3.731 closest distance to " OD1 ASN A 187 " =    1.700
peak=   -3.726 closest distance to " NH2AARG A 275 " =    5.113
peak=   -3.721 closest distance to " CB  PHE A 192 " =    1.859
peak=   -3.714 closest distance to " ND2 ASN A  45 " =    1.046
peak=   -3.704 closest distance to " O   HOH Z 196 " =    2.086
peak=   -3.697 closest distance to " CE  MET A 105 " =    2.094
peak=   -3.688 closest distance to " CD1 LEU A 101 " =    2.413
peak=   -3.684 closest distance to " CD  LYS A 289 " =    2.551
peak=   -3.665 closest distance to " N   THR A 157 " =    1.503
peak=   -3.659 closest distance to " O   HOH Z 114 " =    3.059
peak=   -3.647 closest distance to " CG  PHE A 283 " =    2.807
peak=   -3.643 closest distance to " ND2 ASN A 187 " =    1.556
peak=   -3.635 closest distance to " O   HOH Z 435 " =    2.786
peak=   -3.622 closest distance to " O   PRO A 198 " =    1.215
peak=   -3.617 closest distance to " CB  PRO A 163 " =    2.569
peak=   -3.611 closest distance to " O   HOH Z 198 " =    2.413
peak=   -3.603 closest distance to " O   HOH Z 211 " =    1.631
peak=   -3.598 closest distance to " CE2 PHE A 218 " =    2.612
peak=   -3.593 closest distance to " O   HOH Z 394 " =    1.509
peak=   -3.586 closest distance to " CZ  TYR A 169 " =    1.692
peak=   -3.578 closest distance to " OG  SER A  97 " =    2.217
peak=   -3.577 closest distance to " CB  PRO A 280 " =    2.085
peak=   -3.565 closest distance to " CG  LEU A 228 " =    0.971
peak=   -3.560 closest distance to " CD1 LEU A 101 " =    2.742
peak=   -3.550 closest distance to " CG1 VAL A 250 " =    2.750
peak=   -3.546 closest distance to " NE2 GLN A  88 " =    1.993
peak=   -3.530 closest distance to " O   HOH Z 103 " =    1.748
peak=   -3.530 closest distance to " O   HOH Z 185 " =    2.317
peak=   -3.526 closest distance to " O   HOH Z  47 " =    1.585
peak=   -3.518 closest distance to " NH2 ARG A  79 " =    1.940
peak=   -3.513 closest distance to " CA  ASP A 298 " =    1.054
peak=   -3.511 closest distance to " O   HOH Z 166 " =    1.985
peak=   -3.510 closest distance to " CZ  PHE A  59 " =    1.541
peak=   -3.506 closest distance to " C   MET A 188 " =    1.436
peak=   -3.502 closest distance to " O   HOH Z 407 " =    3.012
peak=   -3.500 closest distance to " O   HOH Z 166 " =    1.414
peak=   -3.486 closest distance to " C   ALA A 158 " =    1.318
peak=   -3.480 closest distance to " CG2 ILE A 263 " =    2.344
peak=   -3.471 closest distance to " CB  ASP A 132 " =    2.278
peak=   -3.471 closest distance to " O   HOH Z 102 " =    1.634
peak=   -3.470 closest distance to " OG BSER A 134 " =    1.721
peak=   -3.469 closest distance to " N   MET A 188 " =    1.865
peak=   -3.463 closest distance to " N   SER A 212 " =    1.984
peak=   -3.463 closest distance to " CB  ASP A 132 " =    2.327
peak=   -3.457 closest distance to " CG  ASP A  50 " =    2.336
peak=   -3.453 closest distance to " N   ALA A  43 " =    2.482
peak=   -3.453 closest distance to " O   HOH Z  13 " =    1.389
peak=   -3.445 closest distance to " CB  ALA A 291 " =    2.296
peak=   -3.440 closest distance to " O   HOH Z 198 " =    1.371
peak=   -3.439 closest distance to " O   HOH Z  44 " =    2.175
peak=   -3.433 closest distance to " CD1 LEU A 228 " =    2.200
peak=   -3.432 closest distance to " N   PHE A  59 " =    2.204
peak=   -3.428 closest distance to " CG  TRP A 266 " =    1.867
peak=   -3.428 closest distance to " O   HOH Z 353 " =    2.035
peak=   -3.425 closest distance to " O   HOH Z  43 " =    1.775
peak=   -3.425 closest distance to " CG1 VAL A 112 " =    2.594
peak=   -3.419 closest distance to " CG1 VAL A 296 " =    1.327
peak=   -3.418 closest distance to " N   THR A 235 " =    1.265
peak=   -3.416 closest distance to " O   HOH Z 339 " =    1.837
peak=   -3.411 closest distance to " N   ALA A 248 " =    1.592
peak=   -3.404 closest distance to " CD1 PHE A  59 " =    1.931
peak=   -3.402 closest distance to " NZ  LYS A 119 " =    3.451
peak=   -3.400 closest distance to " CB  ASN A  69 " =    1.156
peak=   -3.391 closest distance to " CB  ALA A 248 " =    2.415
peak=   -3.389 closest distance to " CA  GLY A  98 " =    1.899
peak=   -3.387 closest distance to " C   ASP A 231 " =    2.581
peak=   -3.387 closest distance to " O   SER A  95 " =    1.591
peak=   -3.384 closest distance to " O   VAL A 189 " =    2.588
peak=   -3.384 closest distance to " O   GLY A 196 " =    1.072
peak=   -3.380 closest distance to " O   HOH Z 311 " =    3.631
peak=   -3.375 closest distance to " OG  SER A  62 " =    1.588
peak=   -3.370 closest distance to " OG ASER A 134 " =    1.204
peak=   -3.369 closest distance to " CG  GLU A 277 " =    1.132
peak=   -3.367 closest distance to " OG  SER A 206 " =    1.640
peak=   -3.366 closest distance to " CG1 VAL A 230 " =    1.849
peak=   -3.364 closest distance to " O   HOH Z 389 " =    4.554
peak=   -3.359 closest distance to " CB  TYR A  15 " =    2.201
peak=   -3.356 closest distance to " O   HOH Z 165 " =    1.922
peak=   -3.350 closest distance to " OD2 ASP A 171 " =    2.291
peak=   -3.343 closest distance to " CG  ARG A 269 " =    2.362
peak=   -3.340 closest distance to " CE3 TRP A 150 " =    1.998
peak=   -3.331 closest distance to " O   HOH Z  60 " =    2.057
peak=   -3.329 closest distance to " CB  ASN A  39 " =    2.141
peak=   -3.325 closest distance to " CA  GLY A 133 " =    2.224
peak=   -3.324 closest distance to " CD2 LEU A 237 " =    2.687
peak=   -3.324 closest distance to " OD1 ASN A 148 " =    1.506
peak=   -3.316 closest distance to " O   HOH Z 134 " =    2.724
peak=   -3.315 closest distance to " OG  SER A  87 " =    1.365
peak=   -3.313 closest distance to " O   MET A  40 " =    2.648
peak=   -3.312 closest distance to " CB  ALA A 291 " =    2.153
peak=   -3.310 closest distance to " CD1 TYR A 247 " =    2.628
peak=   -3.303 closest distance to " O   HOH Z 417 " =    2.693
peak=   -3.301 closest distance to " C   LEU A 222 " =    0.820
peak=   -3.300 closest distance to " N   VAL A 230 " =    1.185
peak=   -3.297 closest distance to " O   HOH Z 234 " =    4.083
peak=   -3.293 closest distance to " NH2 ARG A  66 " =    1.871
peak=   -3.288 closest distance to " O   ALA A 161 " =    1.615
peak=   -3.287 closest distance to " C   ASN A 285 " =    2.423
peak=   -3.287 closest distance to " CD2 LEU A 167 " =    1.767
peak=   -3.284 closest distance to " O   GLY A  80 " =    2.498
peak=   -3.284 closest distance to " O   HOH Z 191 " =    5.438
peak=   -3.283 closest distance to " O   HOH Z 313 " =    1.780
peak=   -3.283 closest distance to " O   HOH Z 426 " =    1.622
peak=   -3.282 closest distance to " O   HOH Z  38 " =    1.680
peak=   -3.282 closest distance to " O   PRO A 198 " =    1.296
peak=   -3.277 closest distance to " C   GLN A 205 " =    1.957
peak=   -3.277 closest distance to " O   HOH Z 388 " =    2.164
peak=   -3.275 closest distance to " O   SER A  22 " =    2.250
peak=   -3.266 closest distance to " OG  SER A  26 " =    1.192
peak=   -3.263 closest distance to " O   HOH Z  22 " =    2.481
peak=   -3.263 closest distance to " N   ASP A 171 " =    2.356
peak=   -3.257 closest distance to " OXT GLY A 302 " =    3.469
peak=   -3.256 closest distance to " CG  ARG A  66 " =    2.462
peak=   -3.254 closest distance to " O   LYS A 117 " =    1.665
peak=   -3.254 closest distance to " CE BMET A  47 " =    1.774
peak=   -3.250 closest distance to " O   HOH Z 372 " =    2.390
peak=   -3.249 closest distance to " N   HIS A 115 " =    2.045
peak=   -3.246 closest distance to " CB  GLN A  11 " =    1.778
peak=   -3.240 closest distance to " N   SER A 276 " =    1.284
peak=   -3.238 closest distance to " CA  GLY A 241 " =    3.013
peak=   -3.238 closest distance to " O   HOH Z 350 " =    1.812
peak=   -3.234 closest distance to " O   PHE A 218 " =    1.705
peak=   -3.234 closest distance to " O   HOH Z  52 " =    1.482
peak=   -3.228 closest distance to " NH1 ARG A  36 " =    2.049
peak=   -3.227 closest distance to " N   MET A 105 " =    2.634
peak=   -3.226 closest distance to " O   HOH Z 222 " =    1.504
peak=   -3.211 closest distance to " O   HOH Z  19 " =    2.342
peak=   -3.211 closest distance to " O   HOH Z 210 " =    1.133
peak=   -3.207 closest distance to " CD1 ILE A 199 " =    2.516
peak=   -3.204 closest distance to " O   HOH Z 359 " =    3.206
peak=   -3.200 closest distance to " OG1 THR A 178 " =    1.254
peak=   -3.200 closest distance to " O   HOH Z 411 " =    3.836
peak=   -3.198 closest distance to " O   GLY A  80 " =    2.362
peak=   -3.192 closest distance to " O   HOH Z 262 " =    2.781
peak=   -3.187 closest distance to " CG  GLU A  53 " =    1.501
peak=   -3.182 closest distance to " ND2 ASN A 249 " =    2.444
peak=   -3.179 closest distance to " CG  MET A 105 " =    0.925
peak=   -3.175 closest distance to " CA  GLY A 133 " =    1.966
peak=   -3.170 closest distance to " N   GLN A  77 " =    1.500
peak=   -3.166 closest distance to " O   HOH Z 193 " =    1.811
peak=   -3.165 closest distance to " NH1 ARG A 195 " =    2.556
peak=   -3.162 closest distance to " CG2 THR A 221 " =    2.037
peak=   -3.156 closest distance to " NE2 GLN A 278 " =    1.986
peak=   -3.151 closest distance to " N   LYS A 289 " =    1.540
peak=   -3.145 closest distance to " NH1 ARG A  56 " =    2.548
peak=   -3.144 closest distance to " O   HOH Z  10 " =    1.464
peak=   -3.144 closest distance to " O   HOH Z 423 " =    2.084
peak=   -3.140 closest distance to " O   HOH Z 436 " =    1.561
peak=   -3.136 closest distance to " O   HOH Z 281 " =    2.688
peak=   -3.135 closest distance to " O   HOH Z 139 " =    3.067
peak=   -3.135 closest distance to " O   ASP A 200 " =    1.116
peak=   -3.131 closest distance to " CB  VAL A 296 " =    1.202
peak=   -3.122 closest distance to " O   HOH Z 123 " =    2.330
peak=   -3.107 closest distance to " O   ALA A  51 " =    1.341
peak=   -3.104 closest distance to " O   HOH Z 241 " =    1.405
peak=   -3.103 closest distance to " O   LEU A 167 " =    1.512
peak=   -3.102 closest distance to " CG1 VAL A 197 " =    2.223
peak=   -3.101 closest distance to " O   HOH Z 148 " =    3.190
peak=   -3.096 closest distance to " O   HOH Z 175 " =    4.308
peak=   -3.095 closest distance to " NH2 ARG A  79 " =    1.580
peak=   -3.093 closest distance to " O   HOH Z 283 " =    2.068
peak=   -3.091 closest distance to " OD1 ASP A 200 " =    1.345
peak=   -3.085 closest distance to " N   ALA A 248 " =    1.880
peak=   -3.072 closest distance to " O   HOH Z 417 " =    2.649
peak=   -3.064 closest distance to " CD2 TYR A 293 " =    2.123
peak=   -3.061 closest distance to " O   VAL A 125 " =    2.330
peak=   -3.061 closest distance to " O   HOH Z 298 " =    2.605
peak=   -3.059 closest distance to " CG  GLU A   2 " =    1.804
peak=   -3.057 closest distance to " CB  ASP A 286 " =    2.240
peak=   -3.044 closest distance to " O   HOH Z   6 " =    1.722
peak=   -3.039 closest distance to " CD2 TYR A 247 " =    2.435
peak=   -3.034 closest distance to " O   HOH Z 353 " =    2.037

================= 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    :  0.4153 0.4047   6.201892e+00   6.180957e+00
   1_bss:  0.4068 0.3963   6.198234e+00   6.165794e+00
   1_xyz:  0.2960 0.3203   5.958352e+00   6.011943e+00
   1_adp:  0.2241 0.2590   5.708474e+00   5.836434e+00
   1_occ:  0.2236 0.2593   5.707081e+00   5.836324e+00
   2_bss:  0.2172 0.2517   5.702366e+00   5.828295e+00
   2_xyz:  0.1540 0.1908   5.395121e+00   5.577056e+00
   2_adp:  0.1426 0.1802   5.328437e+00   5.521179e+00
   2_occ:  0.1425 0.1802   5.327984e+00   5.520789e+00
   3_bss:  0.1421 0.1796   5.327409e+00   5.519197e+00
   3_xyz:  0.1214 0.1591   5.188771e+00   5.404615e+00
   3_adp:  0.1169 0.1570   5.166250e+00   5.392734e+00
   3_occ:  0.1169 0.1570   5.166108e+00   5.392647e+00
   4_bss:  0.1169 0.1570   5.165930e+00   5.392521e+00
   4_xyz:  0.1124 0.1553   5.142728e+00   5.381998e+00
   4_adp:  0.1130 0.1547   5.141827e+00   5.375267e+00
   4_occ:  0.1130 0.1546   5.141637e+00   5.375060e+00
   5_bss:  0.1133 0.1545   5.142607e+00   5.374519e+00
   5_xyz:  0.1104 0.1540   5.129136e+00   5.372391e+00
   5_adp:  0.1097 0.1549   5.130007e+00   5.378513e+00
   5_occ:  0.1097 0.1550   5.129988e+00   5.378560e+00
   5_bss:  0.1097 0.1550   5.129998e+00   5.378570e+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:  0.343  10.358   7.479   8.372   8.719   0.000   0.000   0.000
   1_xyz:  0.343  10.358   7.479   8.372   8.719   0.000   0.000   0.000
   1_adp:  0.343  10.358   7.479   8.372   8.719   0.000   0.000   0.000
   1_occ:  0.343  10.358   7.479   8.372   8.719   0.000   0.000   0.000
   2_bss:  0.334  33.643   3.975   4.445   5.610   0.000   0.000   0.000
   2_xyz:  0.334  33.643   3.975   4.445   5.610   0.000   0.000   0.000
   2_adp:  0.334  33.643   3.975   4.445   5.610   0.000   0.000   0.000
   2_occ:  0.334  33.643   3.975   4.445   5.610   0.000   0.000   0.000
   3_bss:  0.322  39.749   3.168   3.594   4.497   0.000   0.000   0.000
   3_xyz:  0.322  39.749   3.168   3.594   4.497   0.000   0.000   0.000
   3_adp:  0.322  39.749   3.168   3.594   4.497   0.000   0.000   0.000
   3_occ:  0.322  39.749   3.168   3.594   4.497   0.000   0.000   0.000
   4_bss:  0.322  39.749   3.090   3.482   4.236   0.000   0.000   0.000
   4_xyz:  0.322  39.749   3.090   3.482   4.236   0.000   0.000   0.000
   4_adp:  0.322  39.749   3.090   3.482   4.236   0.000   0.000   0.000
   4_occ:  0.322  39.749   3.090   3.482   4.236   0.000   0.000   0.000
   5_bss:  0.323  39.749   3.026   3.412   4.146   0.000   0.000   0.000
   5_xyz:  0.323  39.749   3.026   3.412   4.146   0.000   0.000   0.000
   5_adp:  0.323  39.749   3.026   3.412   4.146   0.000   0.000   0.000
   5_occ:  0.323  39.749   3.026   3.412   4.146   0.000   0.000   0.000
   5_bss:  0.323  43.328  -0.486  -0.126   0.612  -0.000   0.000   0.000
------------------------------------------------------------------------
 stage     <pher>    fom   alpha         beta
   0    :  44.570 0.5895  0.6575    47257.967
   1_bss:  44.414 0.5887  0.8365    44470.046
   1_xyz:  33.939 0.7124  0.9860    27402.622
   1_adp:  25.355 0.8084  1.0772    16835.522
   1_occ:  25.357 0.8083  1.0769    16803.842
   2_bss:  25.065 0.8112  0.9519    16458.736
   2_xyz:  18.047 0.8800  1.0010     9235.392
   2_adp:  16.640 0.8932  1.0120     8288.659
   2_occ:  16.636 0.8933  1.0118     8279.100
   3_bss:  16.596 0.8935  0.9782     8251.240
   3_xyz:  14.273 0.9128  0.9862     6524.669
   3_adp:  14.019 0.9151  0.9871     6380.962
   3_occ:  14.015 0.9151  0.9871     6380.188
   4_bss:  14.011 0.9152  0.9817     6380.055
   4_xyz:  13.747 0.9173  0.9821     6221.926
   4_adp:  13.574 0.9188  0.9827     6154.848
   4_occ:  13.570 0.9188  0.9826     6153.511
   5_bss:  13.585 0.9187  0.9792     6155.620
   5_xyz:  13.554 0.9188  0.9787     6130.468
   5_adp:  13.686 0.9178  0.9762     6197.725
   5_occ:  13.687 0.9178  0.9761     6199.984
   5_bss:  13.687 0.9178  0.9779     6200.554
------------------------------------------------------------------------
 stage       angl   bond   chir   dihe   plan   repu  geom_target
   0    :  24.226  0.414  2.119 33.790  0.145  4.091   5.3577e+01
   1_bss:  24.226  0.414  2.119 33.790  0.145  4.091   5.3577e+01
   1_xyz:   1.457  0.011  0.099 17.733  0.006  4.120   1.0996e-01
   1_adp:   1.457  0.011  0.099 17.733  0.006  4.120   1.0996e-01
   1_occ:   1.457  0.011  0.099 17.733  0.006  4.120   1.0996e-01
   2_bss:   1.457  0.011  0.099 17.733  0.006  4.120   1.0996e-01
   2_xyz:   0.903  0.005  0.069 15.810  0.003  4.119   5.4203e-02
   2_adp:   0.903  0.005  0.069 15.810  0.003  4.119   5.4203e-02
   2_occ:   0.903  0.005  0.069 15.810  0.003  4.119   5.4203e-02
   3_bss:   0.903  0.005  0.069 15.810  0.003  4.119   5.4203e-02
   3_xyz:   0.976  0.006  0.078 15.686  0.003  4.123   5.8127e-02
   3_adp:   0.976  0.006  0.078 15.686  0.003  4.123   5.8127e-02
   3_occ:   0.976  0.006  0.078 15.686  0.003  4.123   5.8127e-02
   4_bss:   0.976  0.006  0.078 15.686  0.003  4.123   5.8127e-02
   4_xyz:   0.954  0.006  0.079 15.507  0.003  4.115   5.6907e-02
   4_adp:   0.954  0.006  0.079 15.507  0.003  4.115   5.6907e-02
   4_occ:   0.954  0.006  0.079 15.507  0.003  4.115   5.6907e-02
   5_bss:   0.954  0.006  0.079 15.507  0.003  4.115   5.6907e-02
   5_xyz:   0.987  0.007  0.081 15.416  0.004  4.119   6.0099e-02
   5_adp:   0.987  0.007  0.081 15.416  0.004  4.119   6.0099e-02
   5_occ:   0.987  0.007  0.081 15.416  0.004  4.119   6.0099e-02
   5_bss:   0.987  0.007  0.081 15.416  0.004  4.119   6.0099e-02
------------------------------------------------------------------------
                      Maximal deviations:
 stage       angl   bond   chir   dihe   plan   repu       |grad|
   0    :  74.492  1.400  6.404144.062  0.405  1.196   6.9467e+00
   1_bss:  74.492  1.400  6.404144.062  0.405  1.196   6.9467e+00
   1_xyz:  11.964  0.129  0.406 88.137  0.041  2.231   8.1381e-02
   1_adp:  11.964  0.129  0.406 88.137  0.041  2.231   8.1381e-02
   1_occ:  11.964  0.129  0.406 88.137  0.041  2.231   8.1381e-02
   2_bss:  11.964  0.129  0.406 88.137  0.041  2.231   8.1381e-02
   2_xyz:   6.176  0.056  0.317 81.585  0.033  2.356   5.0099e-02
   2_adp:   6.176  0.056  0.317 81.585  0.033  2.356   5.0099e-02
   2_occ:   6.176  0.056  0.317 81.585  0.033  2.356   5.0099e-02
   3_bss:   6.176  0.056  0.317 81.585  0.033  2.356   5.0099e-02
   3_xyz:   6.826  0.042  0.524 83.172  0.036  2.363   4.0377e-02
   3_adp:   6.826  0.042  0.524 83.172  0.036  2.363   4.0377e-02
   3_occ:   6.826  0.042  0.524 83.172  0.036  2.363   4.0377e-02
   4_bss:   6.826  0.042  0.524 83.172  0.036  2.363   4.0377e-02
   4_xyz:   6.482  0.036  0.531 83.284  0.035  2.352   3.5732e-02
   4_adp:   6.482  0.036  0.531 83.284  0.035  2.352   3.5732e-02
   4_occ:   6.482  0.036  0.531 83.284  0.035  2.352   3.5732e-02
   5_bss:   6.482  0.036  0.531 83.284  0.035  2.352   3.5732e-02
   5_xyz:   6.615  0.045  0.567 82.867  0.037  2.298   4.3019e-02
   5_adp:   6.615  0.045  0.567 82.867  0.037  2.298   4.3019e-02
   5_occ:   6.615  0.045  0.567 82.867  0.037  2.298   4.3019e-02
   5_bss:   6.615  0.045  0.567 82.867  0.037  2.298   4.3019e-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:  61.26   0.00  10.33  60.46   0.00   7.10  61.26   0.00  27.89
   1_occ:  61.26   0.00  10.33  60.46   0.00   7.10  61.26   0.00  27.89
   2_bss:  61.26   0.00  10.33  60.46   0.00   7.10  61.26   0.00  27.89
   2_xyz:  61.26   0.00  10.33  60.46   0.00   7.10  61.26   0.00  27.89
   2_adp:  64.39   0.00  10.84  64.39   0.00   7.11  59.31   1.54  31.13
   2_occ:  64.39   0.00  10.84  64.39   0.00   7.11  59.31   1.54  31.13
   3_bss:  64.39   0.00  10.84  64.39   0.00   7.11  59.31   1.54  31.13
   3_xyz:  64.39   0.00  10.84  64.39   0.00   7.11  59.31   1.54  31.13
   3_adp:  76.53   0.00  11.42  76.53   0.00   7.27  71.10   0.87  34.02
   3_occ:  76.53   0.00  11.42  76.53   0.00   7.27  71.10   0.87  34.02
   4_bss:  76.53   0.00  11.42  76.53   0.00   7.27  71.10   0.87  34.02
   4_xyz:  76.53   0.00  11.42  76.53   0.00   7.27  71.10   0.87  34.02
   4_adp:  76.80   0.00  11.07  76.80   0.00   7.16  65.82   0.89  32.34
   4_occ:  76.80   0.00  11.07  76.80   0.00   7.16  65.82   0.89  32.34
   5_bss:  76.80   0.00  11.07  76.80   0.00   7.16  65.82   0.89  32.34
   5_xyz:  76.80   0.00  11.07  76.80   0.00   7.16  65.82   0.89  32.34
   5_adp:  77.66   0.00  11.07  77.66   0.00   7.15  65.94   1.06  32.45
   5_occ:  77.66   0.00  11.07  77.66   0.00   7.15  65.94   1.06  32.45
   5_bss:  81.24   3.58  14.65  81.24   3.58  10.73  69.52   4.64  36.03
------------------------------------------------------------------------
 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:    1.158    0.017    0.399
   1_adp:    1.158    0.017    0.399
   1_occ:    1.158    0.017    0.399
   2_bss:    1.158    0.017    0.399
   2_xyz:    1.404    0.030    0.470
   2_adp:    1.404    0.030    0.470
   2_occ:    1.404    0.030    0.470
   3_bss:    1.404    0.030    0.470
   3_xyz:    1.434    0.048    0.497
   3_adp:    1.434    0.048    0.497
   3_occ:    1.434    0.048    0.497
   4_bss:    1.434    0.048    0.497
   4_xyz:    1.498    0.051    0.510
   4_adp:    1.498    0.051    0.510
   4_occ:    1.498    0.051    0.510
   5_bss:    1.498    0.051    0.510
   5_xyz:    1.499    0.041    0.522
   5_adp:    1.499    0.041    0.522
   5_occ:    1.499    0.041    0.522
   5_bss:    1.499    0.041    0.522
------------------------------------------------------------------------

CPU time actual refinement: 320.80


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

Writing refined structure to PDB file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/trial/run_663/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_663/model_refine_001_2mFobs-DFmodel.map
Writing mFobs-DFmodel XPLOR map to file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/trial/run_663/model_refine_001_mFobs-DFmodel.map
Writing map coefficients to MTZ file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/trial/run_663/model_refine_001_map_coeffs.mtz

Writing default parameters for subsequent refinement:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/trial/run_663/model_refine_002.def


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

Pure refinement (no I/O, processing, etc)= 320.64 
  Macro-tasks:
    bulk solvent and scale       = 40.44  
    individual site refinement   = 128.80 
    weights calculation          = 32.97  
    collect and process          = 6.57   
    model show statistics        = 0.10   
    TOTAL for macro-tasks        = 208.88 
  Micro-tasks:
    mask                            = 1.77   
    f_calc                          = 96.66  
    alpha_beta                      = 7.93   
    target                          = 1.15   
    gradients_wrt_atomic_parameters = 107.23 
    fmodel                         = 6.69   
    r_factors                      = 0.21   
    phase_errors                   = 11.08  
    foms                           = 0.28   
    TOTAL for micro-tasks          = 233.00 
NUMBER OF MASK CALCS=  4
Time per interpreted Python bytecode instruction: 4.523 micro seconds
Total CPU time: 5.57 minutes
from_scatterers_fft:    641 calls, 96.33 s
gradients_fft:          586 calls, 93.77 s

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

# Date 2008-01-16 Time 02:07:56 PST -0800 (1200478076.77 s)
Start R-work = 0.4153, R-free = 0.4047 (no bulk solvent and anisotropic scale)
Final R-work = 0.1272, R-free = 0.1710 (no bulk solvent and anisotropic scale)

Start R-work = 0.4068, R-free = 0.3963
Final R-work = 0.1097, R-free = 0.1550