# Date 2008-01-16 Time 02:15:38 PST -0800 (1200478538.40 s)
#phil __OFF__

Command line arguments: "../756.param" "adp.set_b_iso=10" "sites.shake=0.5" "main.number_of_macro_cycles=5" "--overwrite"

HOST = idle.lbl.gov
HOSTTYPE = x86_64-linux
USER = phzwart
PID = 4080
JOB_ID = 5158
SGE_ARCH = lx24-amd64
SGE_TASK_FIRST = 1
SGE_TASK_LAST = 1330
SGE_TASK_ID = 756

-------------------------------------------------------------------------------
  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: (70.6012, 46.2261, 87.6859, 90, 90, 90)
  Space group: P 21 21 21 (No. 19)

/net/cci-filer1/vol1/tmp/phzwart/tassos/trial/model.pdb
  Monomer Library directory:
    "/net/rosie/scratch3/phzwart/CCTBX/Sources/mon_lib"
  Total number of atoms: 2823
  Number of models: 1
  Model: 0
    Number of conformers: 2
    Conformer: "A"
      Number of atoms: 2769
      Number of chains: 2
        Number of residues, atoms: 302, 2333
          Classifications: {'peptide': 302}
          Modifications used: {'COO': 1}
          Link IDs: {'PTRANS': 7, 'CIS': 1, 'TRANS': 293}
        Number of residues, atoms: 436, 436
          Classifications: {'water': 436}
          Link IDs: {None: 435}
    Conformer: "B"
      Number of atoms: 2771
      Common with "A": 2717
      Number of chains: 2
        Number of residues, atoms: 302, 2333
          Classifications: {'peptide': 302}
          Modifications used: {'COO': 1}
          Link IDs: {'PTRANS': 7, 'CIS': 1, 'TRANS': 293}
          bond proxies already assigned to first conformer: 2332
        Number of residues, atoms: 438, 438
          Classifications: {'water': 438}
          Link IDs: {None: 437}
  Time building chain proxies: 3.33, per 1000 atoms: 1.18


================================== 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: (70.6012, 46.2261, 87.6859, 90, 90, 90)
Space group: P 21 21 21 (No. 19)
Systematic absences: 0
Centric reflections: 2427
Resolution range: 15.1092 1.9731
Completeness in resolution range: 0.94264
Completeness with d_max=infinity: 0.939836

Number of F-obs in resolution range:                   19589
Number of F-obs <= 0:                                  0
Refinement resolution range: d_max =  15.1092
                             d_min =   1.9731

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: (70.6012, 46.2261, 87.6859, 90, 90, 90)
Space group: P 21 21 21 (No. 19)
Systematic absences: 0
Centric reflections: 2427
Resolution range: 15.1092 1.9731
Completeness in resolution range: 0.94264
Completeness with d_max=infinity: 0.939836

Test (R-free flags) flag value: 1

Number of work/free reflections by resolution:
                                         work  free  %free
  bin  1: 15.1096 -  4.2229 [2181/2206]  1961   220  10.1%
  bin  2:  4.2229 -  3.3640 [2100/2120]  1893   207   9.9%
  bin  3:  3.3640 -  2.9423 [2078/2097]  1871   207  10.0%
  bin  4:  2.9423 -  2.6749 [2042/2072]  1834   208  10.2%
  bin  5:  2.6749 -  2.4841 [2038/2057]  1841   197   9.7%
  bin  6:  2.4841 -  2.3382 [2035/2060]  1828   207  10.2%
  bin  7:  2.3382 -  2.2215 [2019/2047]  1812   207  10.3%
  bin  8:  2.2215 -  2.1251 [1998/2034]  1798   200  10.0%
  bin  9:  2.1251 -  2.0435 [2020/2062]  1823   197   9.8%
  bin 10:  2.0435 -  1.9731 [1078/2026]   969   109  10.1%
                                overall 17630  1959  10.0%
Writing MTZ file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/trial/run_756/model_refine_data.mtz


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

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

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

  Number of disulfides: simple=3, symmetry=0
    Simple disulfide: " SG  CYS A 168 " - " SG ACYS A 201 " distance=2.08
    Simple disulfide: " SG  CYS A 168 " - " SG BCYS A 201 " distance=1.98
    Simple disulfide: " SG  CYS A 254 " - " SG  CYS A 260 " distance=2.05
  Time building geometry restraints manager: 0.13 seconds
  Histogram of bond lengths:
        1.21 -     1.38: 943
        1.38 -     1.56: 1465
        1.56 -     1.73: 7
        1.73 -     1.90: 21
        1.90 -     2.08: 3
  Bond restraints sorted by residual:
             atom i - atom j            ideal  model  delta   weight residual
  " SG  CYS A 168 " - " SG BCYS A 201 " 2.031  1.983  0.048 2.50e+03 5.87e+00
  " C   GLN A  88 " - " N   GLN A  89 " 1.329  1.360 -0.031 5.10e+03 4.97e+00
  " SG  CYS A 168 " - " SG ACYS A 201 " 2.031  2.075 -0.044 2.50e+03 4.89e+00
  " CB  CYS A 201 " - " SG ACYS A 201 " 1.808  1.738  0.070 9.18e+02 4.46e+00
  " C   PRO A 198 " - " N   ILE A 199 " 1.329  1.301  0.028 5.10e+03 4.10e+00
  ... (remaining 2434 not shown)
  Histogram of nonbonded interaction distances:
        1.81 -     2.42: 33
        2.42 -     3.04: 2178
        3.04 -     3.66: 4693
        3.66 -     4.28: 9000
        4.28 -     4.90: 12345
  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  42 " - " O   HOH Z 183 "  2.016 3.040 -x+1,y+1/2,-z+1/2
  " OE1 GLN A  55 " - " O   HOH Z 403 "  2.064 3.040 -x+1,y-1/2,-z+1/2
  " OG1 THR A  29 " - " O   HOH Z 245 "  2.091 3.040 x,y+1,z
  " O   HOH Z  41 " - " O   HOH Z 182 "  2.092 3.040 -x+1,y+1/2,-z+1/2
  ... (remaining 28244 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_756/model_refine_001.eff

Writing geometry restraints to file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/trial/run_756/model_refine_001.geo

CPU time processing inputs: 8.94


============================ 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 = 70.60125 46.22605 87.68585 90 90 90
    space_group = "P 21 21 21"
  }
  input {
    pdb {
      file_name = "/net/cci-filer1/vol1/tmp/phzwart/tassos/trial/model.pdb"
    }
    xray_data {
      file_name = "/net/cci-filer1/vol1/tmp/phzwart/tassos/trial/1e0w.cns"
      labels = "FOBS,SIGMA"
      r_free_flags {
        file_name = "/net/cci-filer1/vol1/tmp/phzwart/tassos/trial/1e0w.cns"
        label = "TEST"
        test_flag_value = 1
      }
    }
  }
  output {
    prefix = "model_refine"
    serial = 1
  }
  main {
    number_of_macro_cycles = 5
  }
  modify_start_model {
    adp {
      set_b_iso = 10
    }
    sites {
      shake = 0.5
    }
  }
}
#phil __OFF__


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


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


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

|--(resolution: 1.97 - 15.11 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.4789   r_free= 0.4632   ksol= 0.00   Bsol= 0.00   scale= 0.793    |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (0.00,0.00,0.00,0.00,0.00,0.00); trace/3= 0.00                              |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.70 A                  |
| x-ray target function (ml) for work reflections: 6.280007                   |
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
| Bin     Resolution   Compl.  No. Refl.    R-factors          Targets        |
|number     range              work test   work   test        work        test|
|  1: 15.1096 -  4.7104 0.99   1416  156 0.4017 0.3767      6.6067      6.5652|
|  2:  4.7104 -  3.7577 0.99   1370  155 0.3912 0.3830      6.7777      6.7573|
|  3:  3.7577 -  3.2883 0.99   1332  145 0.4230 0.3730      6.6485      6.5803|
|  4:  3.2883 -  2.9902 0.99   1340  150 0.4702 0.4441      6.5352      6.4872|
|  5:  2.9902 -  2.7773 0.99   1318  149 0.5107 0.4763      6.3556      6.3712|
|  6:  2.7773 -  2.6144 0.99   1318  144 0.5095 0.5269       6.269       6.205|
|  7:  2.6144 -  2.4841 0.99   1306  140 0.5252 0.5034      6.2455      6.1926|
|  8:  2.4841 -  2.3764 0.98   1297  151 0.5297 0.4889      6.1726      6.1888|
|  9:  2.3764 -  2.2852 0.98   1290  142 0.5223 0.5308       6.124      6.1692|
| 10:  2.2852 -  2.2066 1.00   1297  148 0.5263 0.5125      6.0999      6.0682|
| 11:  2.2066 -  2.1378 0.98   1309  142 0.5180 0.5281       6.035       6.051|
| 12:  2.1378 -  2.0769 0.98   1275  141 0.5336 0.5424      5.9579      5.9972|
| 13:  2.0769 -  2.0223 0.98   1274  139 0.5329 0.5147       5.874      5.7843|
| 14:  2.0223 -  1.9731 0.37    488   57 0.5414 0.5024      5.8812      5.8389|
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
|R-free likelihood based estimates for figures of merit, absolute phase error,|
|and distribution parameters alpha and beta (Acta Cryst. (1995). A51, 880-887)|
|                                                                             |
| Bin     Resolution      No. Refl.   FOM  Phase Scale    Alpha        Beta   |
|  #        range        work  test        error factor                       |
|  1: 15.1096 -  4.7104  1416   156  0.71  33.57   0.79     0.76      69028.83|
|  2:  4.7104 -  3.7577  1370   155  0.74  32.03   0.87     0.81      93580.03|
|  3:  3.7577 -  3.2883  1332   145  0.64  40.57   0.86     0.76      99183.94|
|  4:  3.2883 -  2.9902  1340   150  0.56  47.36   0.78     0.65      90324.57|
|  5:  2.9902 -  2.7773  1318   149  0.45  55.72   0.74     0.54      76813.66|
|  6:  2.7773 -  2.6144  1318   144  0.41  59.16   0.72     0.47      69301.07|
|  7:  2.6144 -  2.4841  1306   140  0.35  63.39   0.74     0.41      67066.74|
|  8:  2.4841 -  2.3764  1297   151  0.32  65.73   0.71     0.38      61509.74|
|  9:  2.3764 -  2.2852  1290   142  0.33  65.16   0.73     0.39      56533.01|
| 10:  2.2852 -  2.2066  1297   148  0.35  63.76   0.75     0.41      48769.57|
| 11:  2.2066 -  2.1378  1309   142  0.34  64.80   0.77     0.42      47043.76|
| 12:  2.1378 -  2.0769  1275   141  0.32  66.31   0.73     0.41      43674.84|
| 13:  2.0769 -  2.0223  1274   139  0.30  67.51   0.72     0.39      38407.25|
| 14:  2.0223 -  1.9731   488    57  0.36  63.31   0.72     0.39      30048.16|
|alpha:            min =        0.38 max =            0.81 mean =         0.52|
|beta:             min =    30048.16 max =        99183.94 mean =     65574.91|
|figures of merit: min =        0.00 max =            1.00 mean =         0.45|
|phase err.(work): min =        0.00 max =           89.99 mean =        55.67|
|phase err.(test): min =        0.00 max =           89.74 mean =        55.91|
|-----------------------------------------------------------------------------|

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

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

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 13.166370             wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 80.504   (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 1.163278              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 78.368   (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:       29 |
| 0.280 - 0.420:   441 |  14.906 -  22.354:   630 |  1.937 -  2.307:      173 |
| 0.420 - 0.560:   366 |  22.354 -  29.802:   474 |  2.307 -  2.677:      685 |
| 0.560 - 0.700:   237 |  29.802 -  37.251:   338 |  2.677 -  3.048:     1500 |
| 0.700 - 0.840:   127 |  37.251 -  44.699:   241 |  3.048 -  3.418:     2620 |
| 0.840 - 0.980:    59 |  44.699 -  52.147:   125 |  3.418 -  3.789:     3919 |
| 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:     6536 |
| 1.260 - 1.400:     1 |  67.044 -  74.492:     3 |  4.530 -  4.900:     7665 |
|-----------------------------------------------------------------------------|
|-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 |       53.894 |
| planarity |      436 |   0.145    0.405  0.000 |     250.485 |              |
|  dihedral |      870 |  33.790  144.062  0.019 |      20.704 |              |
| nonbonded |     2439 |   4.090    4.900  1.196 |       1.834 |              |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 11.922)------------------------------------------|
|    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 = 11.922)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.01    19.99   9.86     None  None   None       |
|    all(noH): 2823   0      0.01    19.99   9.86     None  None   None       |
|    Sol.    : 438    0      0.06    19.99   10.10    None  None   None       |
|    Mac.    : 2385   0      0.01    19.98   9.82     None  None   None       |
|    Hyd.    : 0      0      None    None    None     None  None   None       |
|    - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -      |
|       Distribution of isotropic (or equivalent) ADP for non-H atoms:        |
|    Bin#      value range     #atoms | Bin#      value range     #atoms      |
|      0:     0.008 -   2.007:  301   |   5:    10.002 -  12.000:  285        |
|      1:     2.007 -   4.006:  276   |   6:    12.000 -  13.999:  292        |
|      2:     4.006 -   6.004:  309   |   7:    13.999 -  15.998:  289        |
|      3:     6.004 -   8.003:  285   |   8:    15.998 -  17.996:  266        |
|      4:     8.003 -  10.002:  251   |   9:    17.996 -  19.995:  269        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.97 - 15.11 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.4852   r_free= 0.4634   ksol= 0.00   Bsol= 0.00   scale= 0.762    |
|                                                                             |
| 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:   0.69 A                  |
| x-ray target function (ml) for work reflections: 6.282385                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.97 - 15.11 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.4709   r_free= 0.4470   ksol= 0.36   Bsol= 20.00   scale= 0.999   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (6.84,9.20,10.04,0.00,0.00,0.00); trace/3= 8.69                             |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.70 A                  |
| x-ray target function (ml) for work reflections: 6.275125                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 10.917450             wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 81.896   (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 1.049793              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 76.108   (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.4709      final r-factor (work) = 0.3820          |
| start r-factor (free) = 0.4470      final r-factor (free) = 0.4021          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 88.1475 = 10.92 * 0.50 * 6.2750 + 1.00 * 53.8939                            |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 33.8794 = 10.92 * 0.50 * 6.1808 + 1.00 * 0.1400                             |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 26     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.3820      final r-factor (work) = 0.3359          |
| start r-factor (free) = 0.4021      final r-factor (free) = 0.3906          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 6.5030 = 1.05 * 1.00 * 6.1808 + 1.00 * 0.0144                               |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 6.4073 = 1.05 * 1.00 * 6.0880 + 1.00 * 0.0161                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 26     |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 11.922)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.00    81.36   13.57    None  None   None       |
|    all(noH): 2823   0      0.00    81.36   13.57    None  None   None       |
|    Sol.    : 438    0      0.00    81.36   26.77    None  None   None       |
|    Mac.    : 2385   0      0.00    65.13   11.14    None  None   None       |
|    Hyd.    : 0      0      None    None    None     None  None   None       |
|    - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -      |
|       Distribution of isotropic (or equivalent) ADP for non-H atoms:        |
|    Bin#      value range     #atoms | Bin#      value range     #atoms      |
|      0:     0.000 -   8.136: 1142   |   5:    40.678 -  48.814:   66        |
|      1:     8.136 -  16.271:  832   |   6:    48.814 -  56.950:   29        |
|      2:    16.271 -  24.407:  404   |   7:    56.950 -  65.085:   13        |
|      3:    24.407 -  32.543:  220   |   8:    65.085 -  73.221:    5        |
|      4:    32.543 -  40.678:  111   |   9:    73.221 -  81.356:    1        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.3359 r_free = 0.3906             target_work(ml) = 6.070         |
| occupancies: max = 1.00  min = 0.30   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.3354 r_free = 0.3909             target_work(ml) = 6.069         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        1 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.97 - 15.11 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.3354   r_free= 0.3909   ksol= 0.36   Bsol= 20.00   scale= 1.119   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (6.84,9.20,10.04,0.00,0.00,0.00); trace/3= 8.69                             |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.50 A                  |
| x-ray target function (ml) for work reflections: 6.069196                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.97 - 15.11 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.3316   r_free= 0.3857   ksol= 0.35   Bsol= 43.88   scale= 1.015   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (3.37,4.80,5.98,0.00,0.00,0.00); trace/3= 4.71                              |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.51 A                  |
| x-ray target function (ml) for work reflections: 6.069845                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 7.279115              wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 98.701   (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 0.481879              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 139.956  (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.3316      final r-factor (work) = 0.2415          |
| start r-factor (free) = 0.3857      final r-factor (free) = 0.2987          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 22.2869 = 7.28 * 0.50 * 6.0850 + 1.00 * 0.1400                              |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 21.6979 = 7.28 * 0.50 * 5.9384 + 1.00 * 0.0847                              |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 29     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.2415      final r-factor (work) = 0.2140          |
| start r-factor (free) = 0.2987      final r-factor (free) = 0.2754          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 2.8777 = 0.48 * 1.00 * 5.9384 + 1.00 * 0.0160                               |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 2.7811 = 0.48 * 1.00 * 5.7468 + 1.00 * 0.0119                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 29     |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 11.922)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.00    89.00   13.21    None  None   None       |
|    all(noH): 2823   0      0.00    89.00   13.21    None  None   None       |
|    Sol.    : 438    0      0.00    89.00   33.45    None  None   None       |
|    Mac.    : 2385   0      0.00    70.04   9.50     None  None   None       |
|    Hyd.    : 0      0      None    None    None     None  None   None       |
|    - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -      |
|       Distribution of isotropic (or equivalent) ADP for non-H atoms:        |
|    Bin#      value range     #atoms | Bin#      value range     #atoms      |
|      0:     0.000 -   8.900: 1429   |   5:    44.499 -  53.399:   65        |
|      1:     8.900 -  17.800:  762   |   6:    53.399 -  62.298:   30        |
|      2:    17.800 -  26.699:  243   |   7:    62.298 -  71.198:   10        |
|      3:    26.699 -  35.599:  157   |   8:    71.198 -  80.098:    2        |
|      4:    35.599 -  44.499:  124   |   9:    80.098 -  88.998:    1        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.2140 r_free = 0.2754             target_work(ml) = 5.708         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        1 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.2139 r_free = 0.2751             target_work(ml) = 5.707         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        4 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.97 - 15.11 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.2139   r_free= 0.2751   ksol= 0.35   Bsol= 43.88   scale= 1.056   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (3.37,4.80,5.98,0.00,0.00,0.00); trace/3= 4.71                              |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.30 A                  |
| x-ray target function (ml) for work reflections: 5.707466                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.97 - 15.11 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.2121   r_free= 0.2736   ksol= 0.32   Bsol= 52.74   scale= 1.004   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (2.01,2.51,3.92,0.00,0.00,0.00); trace/3= 2.81                              |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.31 A                  |
| x-ray target function (ml) for work reflections: 5.707824                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 4.842956              wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 103.497  (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 0.833267              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 147.065  (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.2121      final r-factor (work) = 0.1533          |
| start r-factor (free) = 0.2736      final r-factor (free) = 0.2048          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 14.0159 = 4.84 * 0.50 * 5.7532 + 1.00 * 0.0847                              |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 13.5817 = 4.84 * 0.50 * 5.5791 + 1.00 * 0.0721                              |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 27     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1533      final r-factor (work) = 0.1388          |
| start r-factor (free) = 0.2048      final r-factor (free) = 0.1901          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 4.6607 = 0.83 * 1.00 * 5.5791 + 1.00 * 0.0119                               |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 4.4895 = 0.83 * 1.00 * 5.3720 + 1.00 * 0.0132                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 27     |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 11.922)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.00    89.37   13.71    None  None   None       |
|    all(noH): 2823   0      0.00    89.37   13.71    None  None   None       |
|    Sol.    : 438    0      1.74    89.37   38.56    None  None   None       |
|    Mac.    : 2385   0      0.00    76.86   9.15     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 -   8.937: 1567   |   5:    44.684 -  53.621:  103        |
|      1:     8.937 -  17.874:  638   |   6:    53.621 -  62.558:   69        |
|      2:    17.874 -  26.811:  202   |   7:    62.558 -  71.495:   27        |
|      3:    26.811 -  35.748:  107   |   8:    71.495 -  80.432:    7        |
|      4:    35.748 -  44.684:  102   |   9:    80.432 -  89.369:    1        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.1388 r_free = 0.1901             target_work(ml) = 5.335         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        4 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.1386 r_free = 0.1901             target_work(ml) = 5.334         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        5 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.97 - 15.11 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1386   r_free= 0.1901   ksol= 0.32   Bsol= 52.74   scale= 1.019   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (2.01,2.51,3.92,0.00,0.00,0.00); trace/3= 2.81                              |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.18 A                  |
| x-ray target function (ml) for work reflections: 5.334221                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.97 - 15.11 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1385   r_free= 0.1895   ksol= 0.32   Bsol= 56.85   scale= 1.004   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (1.65,1.73,3.45,0.00,0.00,0.00); trace/3= 2.27                              |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.19 A                  |
| x-ray target function (ml) for work reflections: 5.332453                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 3.833582              wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 116.580  (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 0.875067              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 139.829  (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1385      final r-factor (work) = 0.1212          |
| start r-factor (free) = 0.1895      final r-factor (free) = 0.1723          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 10.3731 = 3.83 * 0.50 * 5.3740 + 1.00 * 0.0723                              |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 10.1960 = 3.83 * 0.50 * 5.2818 + 1.00 * 0.0719                              |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 28     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1212      final r-factor (work) = 0.1177          |
| start r-factor (free) = 0.1723      final r-factor (free) = 0.1686          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 4.6349 = 0.88 * 1.00 * 5.2818 + 1.00 * 0.0130                               |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 4.5763 = 0.88 * 1.00 * 5.2147 + 1.00 * 0.0131                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 29     |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 11.922)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.00    88.52   13.57    None  None   None       |
|    all(noH): 2823   0      0.00    88.52   13.57    None  None   None       |
|    Sol.    : 438    0      2.62    88.52   38.70    None  None   None       |
|    Mac.    : 2385   0      0.00    85.42   8.95     None  None   None       |
|    Hyd.    : 0      0      None    None    None     None  None   None       |
|    - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -      |
|       Distribution of isotropic (or equivalent) ADP for non-H atoms:        |
|    Bin#      value range     #atoms | Bin#      value range     #atoms      |
|      0:     0.000 -   8.852: 1592   |   5:    44.261 -  53.114:   96        |
|      1:     8.852 -  17.705:  636   |   6:    53.114 -  61.966:   64        |
|      2:    17.705 -  26.557:  176   |   7:    61.966 -  70.818:   34        |
|      3:    26.557 -  35.409:  115   |   8:    70.818 -  79.670:   17        |
|      4:    35.409 -  44.261:   90   |   9:    79.670 -  88.522:    3        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.1177 r_free = 0.1686             target_work(ml) = 5.203         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        5 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.1176 r_free = 0.1685             target_work(ml) = 5.202         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        4 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.97 - 15.11 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1176   r_free= 0.1685   ksol= 0.32   Bsol= 56.85   scale= 1.004   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (1.65,1.73,3.45,0.00,0.00,0.00); trace/3= 2.27                              |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.17 A                  |
| x-ray target function (ml) for work reflections: 5.202392                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.97 - 15.11 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1176   r_free= 0.1684   ksol= 0.32   Bsol= 56.85   scale= 1.005   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (1.74,1.66,3.48,0.00,0.00,0.00); trace/3= 2.29                              |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.17 A                  |
| x-ray target function (ml) for work reflections: 5.202270                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 3.147388              wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 139.176  (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 0.389128              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 136.955  (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1176      final r-factor (work) = 0.1137          |
| start r-factor (free) = 0.1684      final r-factor (free) = 0.1643          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 8.2780 = 3.15 * 0.50 * 5.2145 + 1.00 * 0.0719                               |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 8.2378 = 3.15 * 0.50 * 5.1900 + 1.00 * 0.0704                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 29     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1137      final r-factor (work) = 0.1134          |
| start r-factor (free) = 0.1643      final r-factor (free) = 0.1623          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 2.0326 = 0.39 * 1.00 * 5.1900 + 1.00 * 0.0131                               |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 2.0265 = 0.39 * 1.00 * 5.1771 + 1.00 * 0.0120                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 30     |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 11.922)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.00    87.65   13.29    None  None   None       |
|    all(noH): 2823   0      0.00    87.65   13.29    None  None   None       |
|    Sol.    : 438    0      2.55    87.65   37.94    None  None   None       |
|    Mac.    : 2385   0      0.00    85.62   8.76     None  None   None       |
|    Hyd.    : 0      0      None    None    None     None  None   None       |
|    - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -      |
|       Distribution of isotropic (or equivalent) ADP for non-H atoms:        |
|    Bin#      value range     #atoms | Bin#      value range     #atoms      |
|      0:     0.000 -   8.765: 1624   |   5:    43.825 -  52.590:   93        |
|      1:     8.765 -  17.530:  620   |   6:    52.590 -  61.355:   63        |
|      2:    17.530 -  26.295:  161   |   7:    61.355 -  70.120:   30        |
|      3:    26.295 -  35.060:  117   |   8:    70.120 -  78.885:   18        |
|      4:    35.060 -  43.825:   93   |   9:    78.885 -  87.650:    4        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.1134 r_free = 0.1623             target_work(ml) = 5.171         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        4 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.1133 r_free = 0.1622             target_work(ml) = 5.170         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        4 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.97 - 15.11 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1133   r_free= 0.1622   ksol= 0.32   Bsol= 56.85   scale= 1.001   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (1.74,1.66,3.48,0.00,0.00,0.00); trace/3= 2.29                              |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.16 A                  |
| x-ray target function (ml) for work reflections: 5.170070                   |
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
| Bin     Resolution   Compl.  No. Refl.    R-factors          Targets        |
|number     range              work test   work   test        work        test|
|  1: 15.1096 -  4.7104 0.99   1416  156 0.0966 0.1302      5.3743      5.5761|
|  2:  4.7104 -  3.7577 0.99   1370  155 0.0846 0.1194      5.4443      5.6637|
|  3:  3.7577 -  3.2883 0.99   1332  145 0.1073 0.1530      5.4916      5.8386|
|  4:  3.2883 -  2.9902 0.99   1340  150 0.1228 0.1738      5.4558      5.6296|
|  5:  2.9902 -  2.7773 0.99   1318  149 0.1326 0.1735      5.3449      5.5856|
|  6:  2.7773 -  2.6144 0.99   1318  144 0.1245 0.2015      5.2167      5.5154|
|  7:  2.6144 -  2.4841 0.99   1306  140 0.1297 0.1660      5.2006      5.3374|
|  8:  2.4841 -  2.3764 0.98   1297  151 0.1206 0.1648      5.0912      5.3397|
|  9:  2.3764 -  2.2852 0.98   1290  142 0.1240 0.1881      5.0783      5.3452|
| 10:  2.2852 -  2.2066 1.00   1297  148 0.1146 0.1780      4.9741      5.2392|
| 11:  2.2066 -  2.1378 0.98   1309  142 0.1166 0.1903      4.9746      5.3569|
| 12:  2.1378 -  2.0769 0.98   1275  141 0.1171 0.1739      4.8855      5.1564|
| 13:  2.0769 -  2.0223 0.98   1274  139 0.1128 0.1648      4.7892      5.0048|
| 14:  2.0223 -  1.9731 0.37    488   57 0.1050 0.1472      4.7011      4.8588|
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
|R-free likelihood based estimates for figures of merit, absolute phase error,|
|and distribution parameters alpha and beta (Acta Cryst. (1995). A51, 880-887)|
|                                                                             |
| Bin     Resolution      No. Refl.   FOM  Phase Scale    Alpha        Beta   |
|  #        range        work  test        error factor                       |
|  1: 15.1096 -  4.7104  1416   156  0.94   9.43   0.98     0.95       7324.22|
|  2:  4.7104 -  3.7577  1370   155  0.95   8.17   1.01     1.00       9507.94|
|  3:  3.7577 -  3.2883  1332   145  0.93  11.86   1.03     1.02      11050.38|
|  4:  3.2883 -  2.9902  1340   150  0.91  14.20   1.01     0.99      10584.38|
|  5:  2.9902 -  2.7773  1318   149  0.90  16.20   1.00     0.98       8869.32|
|  6:  2.7773 -  2.6144  1318   144  0.89  16.74   0.98     0.95       7281.47|
|  7:  2.6144 -  2.4841  1306   140  0.90  16.16   0.99     0.95       6581.44|
|  8:  2.4841 -  2.3764  1297   151  0.90  16.10   0.99     0.97       5645.11|
|  9:  2.3764 -  2.2852  1290   142  0.90  16.50   1.00     0.96       5540.76|
| 10:  2.2852 -  2.2066  1297   148  0.90  16.19   1.00     0.96       4613.94|
| 11:  2.2066 -  2.1378  1309   142  0.89  16.94   0.99     0.94       4642.54|
| 12:  2.1378 -  2.0769  1275   141  0.90  15.96   1.01     1.01       4010.00|
| 13:  2.0769 -  2.0223  1274   139  0.89  17.02   1.00     0.98       3470.34|
| 14:  2.0223 -  1.9731   488    57  0.92  14.28   0.98     0.96       2767.56|
|alpha:            min =        0.94 max =            1.02 mean =         0.97|
|beta:             min =     2767.56 max =        11050.38 mean =      6783.69|
|figures of merit: min =        0.00 max =            1.00 mean =         0.91|
|phase err.(work): min =        0.00 max =           89.89 mean =        14.65|
|phase err.(test): min =        0.00 max =           89.14 mean =        13.98|
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.97 - 15.11 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1133   r_free= 0.1615   ksol= 0.33   Bsol= 59.13   scale= 1.001   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-0.53,-0.68,1.21,0.00,0.00,0.00); trace/3= 0.00                            |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.16 A                  |
| x-ray target function (ml) for work reflections: 5.168143                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.97 - 15.11 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1133   r_free= 0.1615   ksol= 0.33   Bsol= 59.13   scale= 1.001   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-0.53,-0.68,1.21,0.00,0.00,0.00); trace/3= 0.00                            |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.16 A                  |
| x-ray target function (ml) for work reflections: 5.168143                   |
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
| Bin     Resolution   Compl.  No. Refl.    R-factors          Targets        |
|number     range              work test   work   test        work        test|
|  1: 15.1096 -  4.7104 0.99   1416  156 0.0964 0.1258      5.3617      5.5442|
|  2:  4.7104 -  3.7577 0.99   1370  155 0.0845 0.1172      5.4368      5.6505|
|  3:  3.7577 -  3.2883 0.99   1332  145 0.1074 0.1531      5.4879      5.8405|
|  4:  3.2883 -  2.9902 0.99   1340  150 0.1229 0.1756      5.4569      5.6363|
|  5:  2.9902 -  2.7773 0.99   1318  149 0.1325 0.1733      5.3448      5.5829|
|  6:  2.7773 -  2.6144 0.99   1318  144 0.1244 0.2006      5.2167      5.5133|
|  7:  2.6144 -  2.4841 0.99   1306  140 0.1297 0.1666      5.2002      5.3394|
|  8:  2.4841 -  2.3764 0.98   1297  151 0.1206 0.1646      5.0907      5.3393|
|  9:  2.3764 -  2.2852 0.98   1290  142 0.1239 0.1875      5.0773      5.3439|
| 10:  2.2852 -  2.2066 1.00   1297  148 0.1144 0.1782      4.9738      5.2411|
| 11:  2.2066 -  2.1378 0.98   1309  142 0.1166 0.1903       4.975      5.3574|
| 12:  2.1378 -  2.0769 0.98   1275  141 0.1170 0.1735       4.886      5.1564|
| 13:  2.0769 -  2.0223 0.98   1274  139 0.1127 0.1645      4.7889      5.0041|
| 14:  2.0223 -  1.9731 0.37    488   57 0.1051 0.1470      4.7005      4.8578|
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
|R-free likelihood based estimates for figures of merit, absolute phase error,|
|and distribution parameters alpha and beta (Acta Cryst. (1995). A51, 880-887)|
|                                                                             |
| Bin     Resolution      No. Refl.   FOM  Phase Scale    Alpha        Beta   |
|  #        range        work  test        error factor                       |
|  1: 15.1096 -  4.7104  1416   156  0.94   9.17   0.97     0.95       7048.56|
|  2:  4.7104 -  3.7577  1370   155  0.95   7.99   1.01     1.00       9182.99|
|  3:  3.7577 -  3.2883  1332   145  0.93  11.73   1.03     1.02      10852.47|
|  4:  3.2883 -  2.9902  1340   150  0.91  14.26   1.01     0.99      10640.74|
|  5:  2.9902 -  2.7773  1318   149  0.90  16.22   1.00     0.98       8885.96|
|  6:  2.7773 -  2.6144  1318   144  0.89  16.74   0.98     0.95       7288.79|
|  7:  2.6144 -  2.4841  1306   140  0.90  16.14   0.99     0.95       6574.20|
|  8:  2.4841 -  2.3764  1297   151  0.90  16.09   0.99     0.97       5642.79|
|  9:  2.3764 -  2.2852  1290   142  0.90  16.49   1.00     0.96       5531.38|
| 10:  2.2852 -  2.2066  1297   148  0.90  16.19   1.00     0.96       4616.30|
| 11:  2.2066 -  2.1378  1309   142  0.89  16.96   0.99     0.94       4650.10|
| 12:  2.1378 -  2.0769  1275   141  0.90  15.97   1.01     1.01       4016.67|
| 13:  2.0769 -  2.0223  1274   139  0.89  17.01   1.00     0.98       3468.16|
| 14:  2.0223 -  1.9731   488    57  0.92  14.26   0.98     0.96       2761.63|
|alpha:            min =        0.94 max =            1.02 mean =         0.97|
|beta:             min =     2761.63 max =        10852.47 mean =      6726.92|
|figures of merit: min =        0.00 max =            1.00 mean =         0.91|
|phase err.(work): min =        0.00 max =           89.96 mean =        14.61|
|phase err.(test): min =        0.00 max =           89.14 mean =        13.97|
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 11.922)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      2.28    89.93   15.57    None  None   None       |
|    all(noH): 2823   0      2.28    89.93   15.57    None  None   None       |
|    Sol.    : 438    0      4.83    89.93   40.23    None  None   None       |
|    Mac.    : 2385   0      2.28    87.90   11.05    None  None   None       |
|    Hyd.    : 0      0      None    None    None     None  None   None       |
|    - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -      |
|       Distribution of isotropic (or equivalent) ADP for non-H atoms:        |
|    Bin#      value range     #atoms | Bin#      value range     #atoms      |
|      0:     2.282 -  11.047: 1624   |   5:    46.107 -  54.872:   93        |
|      1:    11.047 -  19.812:  620   |   6:    54.872 -  63.637:   63        |
|      2:    19.812 -  28.577:  161   |   7:    63.637 -  72.402:   30        |
|      3:    28.577 -  37.342:  117   |   8:    72.402 -  81.167:   18        |
|      4:    37.342 -  46.107:   93   |   9:    81.167 -  89.932:    4        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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


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

Number of peaks found at mFobs-DFmodel map (map cutoff=3.00 sigma)= 322         
Filter by distance & map next to the model:
   mapped sites are within: 0.357 - 4.806
   number of sites selected in [dist_min= 0.70, dist_max= 6.00]: 321 from: 322
   mapped sites are within: 0.715 - 4.806

peak=   10.887 closest distance to " CB  VAL A 230 " =    1.447
peak=    8.492 closest distance to " CG2 VAL A 296 " =    1.304
peak=    6.464 closest distance to " CD2 LEU A   5 " =    1.256
peak=    6.397 closest distance to " O   HOH Z 130 " =    1.150
peak=    6.080 closest distance to " NE2 GLN A  11 " =    1.199
peak=    5.737 closest distance to " O   HOH Z 142 " =    2.090
peak=    5.731 closest distance to " CG  LEU A 228 " =    1.202
peak=    5.713 closest distance to " CG  LEU A   5 " =    1.165
peak=    5.708 closest distance to " NH2 ARG A  56 " =    2.086
peak=    5.604 closest distance to " CG  PRO A  54 " =    1.357
peak=    5.475 closest distance to " O   HOH Z   9 " =    2.073
peak=    5.337 closest distance to " O   HOH Z 232 " =    2.245
peak=    5.007 closest distance to " O   HOH Z   7 " =    1.364
peak=    4.887 closest distance to " O   HOH Z 427 " =    2.541
peak=    4.864 closest distance to " CB  PRO A  54 " =    1.018
peak=    4.788 closest distance to " CB  GLN A 223 " =    1.510
peak=    4.627 closest distance to " O   PRO A 198 " =    1.629
peak=    4.625 closest distance to " O   HOH Z 425 " =    1.496
peak=    4.576 closest distance to " CB  GLN A 183 " =    1.241
peak=    4.568 closest distance to " CB  SER A  63 " =    1.235
peak=    4.501 closest distance to " O   HOH Z 369 " =    2.147
peak=    4.490 closest distance to " O   HOH Z 287 " =    1.931
peak=    4.395 closest distance to " CG  PRO A 213 " =    1.228
peak=    4.368 closest distance to " ND2 ASN A 187 " =    1.669
peak=    4.363 closest distance to " O   HOH Z  65 " =    0.952
peak=    4.352 closest distance to " O   HOH Z 126 " =    1.559
peak=    4.342 closest distance to " O   HOH Z 209 " =    2.311
peak=    4.293 closest distance to " CG  PRO A 198 " =    1.278
peak=    4.277 closest distance to " CB  ASN A 148 " =    1.353
peak=    4.254 closest distance to " O   HOH Z  30 " =    1.761
peak=    4.243 closest distance to " CB  VAL A 230 " =    1.169
peak=    4.235 closest distance to " O   HOH Z  78 " =    1.613
peak=    4.224 closest distance to " O   HOH Z 346 " =    1.592
peak=    4.212 closest distance to " O   SER A  87 " =    2.336
peak=    4.195 closest distance to " CG  LEU A 167 " =    1.257
peak=    4.188 closest distance to " O   HOH Z  68 " =    2.082
peak=    4.176 closest distance to " O   HOH Z 362 " =    2.407
peak=    4.154 closest distance to " CB  SER A   3 " =    1.446
peak=    4.141 closest distance to " CG  PRO A 243 " =    1.120
peak=    4.140 closest distance to " CB  ARG A  79 " =    1.455
peak=    4.137 closest distance to " O   HOH Z 298 " =    1.690
peak=    4.103 closest distance to " O   HOH Z 380 " =    1.839
peak=    4.102 closest distance to " CB  ARG A 275 " =    0.927
peak=    4.089 closest distance to " O   HOH Z 423 " =    1.508
peak=    4.063 closest distance to " CB  TRP A 266 " =    1.027
peak=    4.058 closest distance to " CD2 LEU A 228 " =    1.235
peak=    4.054 closest distance to " CB  VAL A 265 " =    1.351
peak=    4.039 closest distance to " O   HOH Z   2 " =    1.610
peak=    4.021 closest distance to " CB AVAL A  41 " =    1.228
peak=    4.020 closest distance to " CB  ASN A 142 " =    1.000
peak=    4.010 closest distance to " O   HOH Z 214 " =    2.196
peak=    3.991 closest distance to " O   HOH Z  63 " =    1.333
peak=    3.989 closest distance to " CD  ARG A  66 " =    2.386
peak=    3.977 closest distance to " CB  SER A 216 " =    0.900
peak=    3.976 closest distance to " CB  ARG A 190 " =    1.452
peak=    3.974 closest distance to " CB  ASP A 124 " =    0.801
peak=    3.968 closest distance to " O   HOH Z 303 " =    2.202
peak=    3.960 closest distance to " NH2AARG A 190 " =    1.780
peak=    3.950 closest distance to " O   HOH Z 359 " =    1.431
peak=    3.937 closest distance to " CB  GLU A 277 " =    3.572
peak=    3.932 closest distance to " OG  SER A  97 " =    2.907
peak=    3.927 closest distance to " O   HOH Z 126 " =    1.992
peak=    3.926 closest distance to " O   HOH Z 272 " =    1.801
peak=    3.923 closest distance to " NH1AARG A 145 " =    1.175
peak=    3.909 closest distance to " CB  ASN A  39 " =    0.977
peak=    3.901 closest distance to " O   HOH Z 234 " =    3.709
peak=    3.899 closest distance to " CH2 TRP A 266 " =    1.160
peak=    3.889 closest distance to " O   HOH Z 368 " =    2.066
peak=    3.883 closest distance to " O   HOH Z 248 " =    1.653
peak=    3.876 closest distance to " CA  VAL A 296 " =    1.077
peak=    3.869 closest distance to " O   HOH Z 265 " =    1.913
peak=    3.869 closest distance to " CB  VAL A 202 " =    1.642
peak=    3.860 closest distance to " O   HOH Z  61 " =    1.612
peak=    3.849 closest distance to " OD1 ASN A  69 " =    2.531
peak=    3.839 closest distance to " O   HOH Z 180 " =    2.098
peak=    3.833 closest distance to " CZ  PHE A 218 " =    1.101
peak=    3.824 closest distance to " O   HOH Z  88 " =    3.028
peak=    3.820 closest distance to " OG ASER A 258 " =    3.070
peak=    3.810 closest distance to " CB  GLU A 128 " =    1.060
peak=    3.805 closest distance to " O   HOH Z   1 " =    1.887
peak=    3.800 closest distance to " O   HOH Z  10 " =    1.739
peak=    3.787 closest distance to " O   HOH Z 258 " =    2.112
peak=    3.779 closest distance to " CA  TYR A  30 " =    0.987
peak=    3.745 closest distance to " O   HOH Z 128 " =    1.825
peak=    3.741 closest distance to " CA  ALA A  51 " =    0.999
peak=    3.738 closest distance to " OG BSER A 164 " =    2.215
peak=    3.736 closest distance to " O   HOH Z  43 " =    1.789
peak=    3.726 closest distance to " O   HOH Z 261 " =    2.141
peak=    3.722 closest distance to " CB  GLU A 152 " =    1.163
peak=    3.700 closest distance to " NZ  LYS A 117 " =    2.953
peak=    3.690 closest distance to " N   PHE A 130 " =    1.271
peak=    3.689 closest distance to " CB  LYS A 117 " =    1.232
peak=    3.685 closest distance to " CA  SER A  87 " =    0.920
peak=    3.684 closest distance to " O   HOH Z 193 " =    1.952
peak=    3.675 closest distance to " ND1 HIS A  86 " =    1.796
peak=    3.672 closest distance to " CB  GLN A  88 " =    1.287
peak=    3.665 closest distance to " CD  LYS A 166 " =    1.321
peak=    3.663 closest distance to " O   HOH Z 365 " =    3.035
peak=    3.660 closest distance to " O   HOH Z 286 " =    2.259
peak=    3.658 closest distance to " CB  ARG A  79 " =    0.914
peak=    3.658 closest distance to " O   HOH Z 158 " =    3.257
peak=    3.650 closest distance to " CG2 VAL A 257 " =    0.853
peak=    3.647 closest distance to " O   HOH Z 437 " =    1.998
peak=    3.639 closest distance to " O   HOH Z 184 " =    1.420
peak=    3.639 closest distance to " CA  ALA A 158 " =    1.256
peak=    3.629 closest distance to " OG  SER A  62 " =    2.908
peak=    3.629 closest distance to " CB  TRP A 179 " =    1.431
peak=    3.626 closest distance to " OG  SER A  62 " =    2.979
peak=    3.624 closest distance to " O   HOH Z 368 " =    3.544
peak=    3.624 closest distance to " O   HOH Z 427 " =    1.042
peak=    3.623 closest distance to " O   HOH Z 218 " =    1.550
peak=    3.616 closest distance to " CE  LYS A  76 " =    0.889
peak=    3.614 closest distance to " O   HOH Z 411 " =    3.626
peak=    3.612 closest distance to " O   HOH Z 128 " =    2.171
peak=    3.610 closest distance to " O   HOH Z 203 " =    1.752
peak=    3.605 closest distance to " CD  ARG A 159 " =    0.715
peak=    3.605 closest distance to " CG2 THR A 221 " =    1.096
peak=    3.596 closest distance to " O   HOH Z 422 " =    2.671
peak=    3.596 closest distance to " CB  SER A 212 " =    1.256
peak=    3.591 closest distance to " CD1 ILE A  33 " =    1.769
peak=    3.587 closest distance to " O   HOH Z 193 " =    1.661
peak=    3.585 closest distance to " O   HOH Z 406 " =    1.556
peak=    3.581 closest distance to " O   HOH Z 195 " =    1.272
peak=    3.562 closest distance to " NH1 ARG A 138 " =    1.100
peak=    3.558 closest distance to " CE3 TRP A 150 " =    1.042
peak=    3.558 closest distance to " O   HOH Z  97 " =    2.022
peak=    3.548 closest distance to " CD  LYS A  76 " =    1.710
peak=    3.548 closest distance to " O   HOH Z 419 " =    2.010
peak=    3.545 closest distance to " CB  TYR A 169 " =    0.728
peak=    3.532 closest distance to " O   HOH Z 371 " =    2.847
peak=    3.530 closest distance to " CD2 TRP A 179 " =    1.268
peak=    3.522 closest distance to " CA  TYR A 116 " =    1.434
peak=    3.516 closest distance to " NE2 HIS A 207 " =    1.196
peak=    3.516 closest distance to " O   HOH Z  20 " =    1.511
peak=    3.515 closest distance to " O  BHOH Z 338 " =    2.392
peak=    3.510 closest distance to " CA  ASN A 215 " =    1.110
peak=    3.508 closest distance to " CD  ARG A 269 " =    0.937
peak=    3.506 closest distance to " O   HOH Z 343 " =    3.240
peak=    3.505 closest distance to " O   HOH Z 417 " =    1.176
peak=    3.501 closest distance to " CG2 ILE A  20 " =    1.626
peak=    3.496 closest distance to " CG1 ILE A  49 " =    1.501
peak=    3.495 closest distance to " O   HOH Z   3 " =    2.012
peak=    3.495 closest distance to " CA  THR A 264 " =    0.768
peak=    3.492 closest distance to " CA  LYS A 117 " =    1.190
peak=    3.486 closest distance to " CB  LEU A 143 " =    1.150
peak=    3.483 closest distance to " CB  GLN A  89 " =    1.308
peak=    3.482 closest distance to " O   HOH Z 133 " =    2.541
peak=    3.481 closest distance to " O   HOH Z 147 " =    1.718
peak=    3.477 closest distance to " N   SER A 135 " =    1.354
peak=    3.474 closest distance to " CA  ALA A 160 " =    0.960
peak=    3.473 closest distance to " O   HOH Z 392 " =    1.188
peak=    3.462 closest distance to " CB  TRP A 150 " =    1.308
peak=    3.460 closest distance to " CB  ALA A 104 " =    0.715
peak=    3.458 closest distance to " CG BARG A 102 " =    1.880
peak=    3.457 closest distance to " CA  VAL A 125 " =    1.126
peak=    3.456 closest distance to " CB  THR A  52 " =    1.034
peak=    3.451 closest distance to " CG1 ILE A 151 " =    1.209
peak=    3.449 closest distance to " CD1 LEU A 300 " =    1.121
peak=    3.445 closest distance to " OE2 GLU A  53 " =    1.934
peak=    3.444 closest distance to " CG AARG A 275 " =    1.208
peak=    3.443 closest distance to " OE2 GLU A   2 " =    1.914
peak=    3.442 closest distance to " O   HOH Z  21 " =    1.712
peak=    3.442 closest distance to " O   HOH Z 153 " =    3.681
peak=    3.436 closest distance to " O   HOH Z  59 " =    1.744
peak=    3.432 closest distance to " CB  LEU A 228 " =    1.216
peak=    3.425 closest distance to " O   HOH Z 403 " =    1.559
peak=    3.423 closest distance to " CB  THR A 157 " =    1.164
peak=    3.407 closest distance to " O   HOH Z  44 " =    1.631
peak=    3.406 closest distance to " O   TYR A 116 " =    1.267
peak=    3.399 closest distance to " CG2AVAL A  72 " =    1.614
peak=    3.397 closest distance to " O   HOH Z 273 " =    2.897
peak=    3.392 closest distance to " CA  ALA A 291 " =    0.847
peak=    3.385 closest distance to " CA  ALA A  21 " =    1.199
peak=    3.382 closest distance to " CA  ALA A 299 " =    0.960
peak=    3.381 closest distance to " CB  MET A  47 " =    1.148
peak=    3.375 closest distance to " O   HOH Z 280 " =    3.036
peak=    3.374 closest distance to " CG  GLN A  88 " =    1.102
peak=    3.374 closest distance to " CA  ALA A 295 " =    0.991
peak=    3.372 closest distance to " CB  ASN A 110 " =    1.061
peak=    3.370 closest distance to " CA  PHE A 283 " =    1.258
peak=    3.367 closest distance to " CE1 TYR A 186 " =    1.335
peak=    3.365 closest distance to " O   HOH Z 410 " =    1.360
peak=    3.364 closest distance to " O   HOH Z 119 " =    1.738
peak=    3.358 closest distance to " O   HOH Z 148 " =    2.206
peak=    3.358 closest distance to " CB  VAL A 250 " =    1.086
peak=    3.353 closest distance to " O   HOH Z 145 " =    1.715
peak=    3.350 closest distance to " O   HOH Z   1 " =    1.780
peak=    3.349 closest distance to " CB  SER A  62 " =    1.077
peak=    3.349 closest distance to " O   HOH Z 405 " =    1.375
peak=    3.348 closest distance to " CG  MET A 185 " =    1.217
peak=    3.346 closest distance to " NZ  LYS A  48 " =    1.258
peak=    3.344 closest distance to " CB  LEU A  83 " =    0.752
peak=    3.340 closest distance to " CA  ARG A 159 " =    1.173
peak=    3.340 closest distance to " O   HOH Z 263 " =    1.755
peak=    3.340 closest distance to " O   HOH Z 357 " =    2.044
peak=    3.338 closest distance to " O   HOH Z 116 " =    3.061
peak=    3.337 closest distance to " CB  ALA A   9 " =    1.588
peak=    3.333 closest distance to " CD2 TYR A 186 " =    1.129
peak=    3.331 closest distance to " ND2 ASN A 249 " =    0.824
peak=    3.331 closest distance to " O   HOH Z 285 " =    2.271
peak=    3.329 closest distance to " CA  THR A 221 " =    1.042
peak=    3.329 closest distance to " CB  SER A 210 " =    0.783
peak=    3.327 closest distance to " O   HOH Z 389 " =    1.764
peak=    3.323 closest distance to " CD1 ILE A 263 " =    1.215
peak=    3.323 closest distance to " CA  ALA A 154 " =    1.041
peak=    3.322 closest distance to " O   HOH Z 329 " =    4.022
peak=    3.321 closest distance to " CA  ASN A 127 " =    1.032
peak=    3.320 closest distance to " O   HOH Z 290 " =    1.043
peak=    3.320 closest distance to " CA  ARG A 195 " =    1.151
peak=    3.316 closest distance to " O   HOH Z 294 " =    1.515
peak=    3.314 closest distance to " O   HOH Z 145 " =    1.758
peak=    3.312 closest distance to " CG  GLN A 278 " =    1.300
peak=    3.311 closest distance to " NH2BARG A 190 " =    1.503
peak=    3.310 closest distance to " CB  ASP A 140 " =    0.938
peak=    3.308 closest distance to " CB  ASN A 187 " =    1.104
peak=    3.303 closest distance to " CB  ASN A 215 " =    1.149
peak=    3.303 closest distance to " O   HOH Z  80 " =    1.426
peak=    3.301 closest distance to " CB  ALA A   1 " =    4.806
peak=    3.300 closest distance to " O   HOH Z 209 " =    2.512
peak=    3.300 closest distance to " O   HOH Z  76 " =    1.032
peak=    3.299 closest distance to " CA  ILE A 106 " =    0.767
peak=    3.299 closest distance to " O   HOH Z 325 " =    2.245
peak=    3.297 closest distance to " O   HOH Z 305 " =    3.400
peak=    3.293 closest distance to " N   SER A 146 " =    1.755
peak=    3.293 closest distance to " O   HOH Z 373 " =    1.508
peak=    3.293 closest distance to " O   HOH Z 310 " =    2.260
peak=    3.289 closest distance to " O   HOH Z 109 " =    2.482
peak=    3.289 closest distance to " CB  ALA A 248 " =    1.031
peak=    3.284 closest distance to " O   HOH Z 148 " =    3.448
peak=    3.283 closest distance to " CD  LYS A 193 " =    2.029
peak=    3.283 closest distance to " O   HOH Z 222 " =    2.338
peak=    3.279 closest distance to " O   HOH Z 299 " =    4.184
peak=    3.278 closest distance to " O   HOH Z 222 " =    1.170
peak=    3.277 closest distance to " O   HOH Z  58 " =    1.832
peak=    3.276 closest distance to " CA  TYR A  30 " =    1.069
peak=    3.276 closest distance to " CA  MET A 105 " =    0.927
peak=    3.273 closest distance to " O   HOH Z 143 " =    1.358
peak=    3.272 closest distance to " CE  LYS A  48 " =    1.160
peak=    3.272 closest distance to " O   HOH Z 409 " =    2.545
peak=    3.271 closest distance to " CB  GLU A  46 " =    0.982
peak=    3.270 closest distance to " NE2 GLN A  73 " =    3.907
peak=    3.270 closest distance to " CA  ALA A 233 " =    1.148
peak=    3.270 closest distance to " CB  SER A  26 " =    1.671
peak=    3.267 closest distance to " O   HOH Z 403 " =    1.387
peak=    3.264 closest distance to " CD1AILE A 234 " =    0.917
peak=    3.262 closest distance to " O   HOH Z  90 " =    2.065
peak=    3.259 closest distance to " O   HOH Z 193 " =    1.762
peak=    3.259 closest distance to " O   HOH Z 189 " =    2.925
peak=    3.257 closest distance to " CA  ARG A  36 " =    1.063
peak=    3.256 closest distance to " CG  GLN A  89 " =    1.470
peak=    3.255 closest distance to " CA  ILE A 234 " =    0.997
peak=    3.254 closest distance to " O   HOH Z  88 " =    3.003
peak=    3.253 closest distance to " CA  ASP A 162 " =    0.917
peak=    3.251 closest distance to " O   HOH Z 424 " =    2.693
peak=    3.247 closest distance to " N   GLN A 278 " =    1.221
peak=    3.245 closest distance to " O   HOH Z 251 " =    1.564
peak=    3.237 closest distance to " CD BLYS A 290 " =    1.154
peak=    3.237 closest distance to " CB  ARG A 139 " =    1.033
peak=    3.236 closest distance to " O   HOH Z  61 " =    1.632
peak=    3.235 closest distance to " O   HOH Z  85 " =    2.184
peak=    3.234 closest distance to " CB  MET A  40 " =    0.791
peak=    3.228 closest distance to " CB  PRO A  90 " =    1.213
peak=    3.227 closest distance to " CG2 ILE A 234 " =    1.086
peak=    3.226 closest distance to " O   HOH Z 291 " =    1.547
peak=    3.221 closest distance to " O   HOH Z 197 " =    3.156
peak=    3.221 closest distance to " CD  ARG A  24 " =    1.093
peak=    3.220 closest distance to " CB  ARG A 138 " =    0.958
peak=    3.218 closest distance to " N   ALA A 256 " =    1.044
peak=    3.216 closest distance to " O   HOH Z  94 " =    2.091
peak=    3.215 closest distance to " CG1 ILE A  33 " =    1.298
peak=    3.215 closest distance to " CA  ARG A 102 " =    1.135
peak=    3.214 closest distance to " O   HOH Z 213 " =    2.097
peak=    3.213 closest distance to " CE3 TRP A  85 " =    1.167
peak=    3.211 closest distance to " CD1 LEU A   5 " =    1.459
peak=    3.207 closest distance to " OG BSER A 212 " =    2.866
peak=    3.204 closest distance to " CA  GLY A 267 " =    1.065
peak=    3.201 closest distance to " O   HOH Z 218 " =    2.038
peak=    3.201 closest distance to " O   MET A 105 " =    1.739
peak=    3.197 closest distance to " O   HOH Z 135 " =    1.942
peak=    3.195 closest distance to " N   ASN A 127 " =    1.361
peak=    3.193 closest distance to " O   HOH Z 122 " =    1.884
peak=    3.192 closest distance to " O   HOH Z 340 " =    2.071
peak=    3.191 closest distance to " O   PRO A 198 " =    1.252
peak=    3.190 closest distance to " O   HOH Z 303 " =    2.936
peak=    3.189 closest distance to " NH2BARG A 145 " =    1.996
peak=    3.187 closest distance to " O   HOH Z 132 " =    2.507
peak=    3.186 closest distance to " OD2 ASP A 286 " =    2.727
peak=    3.186 closest distance to " O   GLN A 278 " =    1.275
peak=    3.180 closest distance to " O   ALA A 291 " =    1.545
peak=    3.176 closest distance to " CB  ALA A  34 " =    1.137
peak=    3.172 closest distance to " CZ3 TRP A  92 " =    1.363
peak=    3.171 closest distance to " CD1 LEU A 261 " =    1.243
peak=    3.171 closest distance to " NH1AARG A 145 " =    0.829
peak=    3.169 closest distance to " O   PHE A 192 " =    1.373
peak=    3.165 closest distance to " N   CYS A 260 " =    0.757
peak=    3.163 closest distance to " CB  LEU A 300 " =    0.865
peak=    3.163 closest distance to " O   HOH Z 172 " =    2.917
peak=    3.162 closest distance to " O   HOH Z 394 " =    3.799
peak=    3.161 closest distance to " CG1 ILE A 120 " =    1.333
peak=    3.155 closest distance to " O   HOH Z 323 " =    1.601
peak=    3.149 closest distance to " O   HOH Z 233 " =    1.569
peak=    3.139 closest distance to " CB  HIS A 108 " =    0.814
peak=    3.139 closest distance to " O   HOH Z 359 " =    4.219
peak=    3.135 closest distance to " CB  TYR A 116 " =    0.939
peak=    3.134 closest distance to " CA  ASN A 217 " =    1.239
peak=    3.133 closest distance to " O   HOH Z 329 " =    2.925
peak=    3.119 closest distance to " O   ASP A 200 " =    1.535
peak=    3.118 closest distance to " O   HOH Z  51 " =    1.507
peak=    3.114 closest distance to " O   HOH Z 128 " =    2.116
peak=    3.110 closest distance to " O   HOH Z 261 " =    1.452
peak=    3.107 closest distance to " O   HOH Z 425 " =    2.107
peak=    3.104 closest distance to " CB  ASN A 173 " =    1.000
peak=    3.103 closest distance to " CG  ARG A 159 " =    0.874
peak=    3.102 closest distance to " O   HOH Z 188 " =    2.655
peak=    3.101 closest distance to " CG  MET A 113 " =    1.220
peak=    3.095 closest distance to " O   HOH Z 175 " =    2.192
peak=    3.075 closest distance to " CA  LYS A 290 " =    1.200
peak=    3.072 closest distance to " O   HOH Z 371 " =    3.307
peak=    3.065 closest distance to " O   HOH Z 260 " =    1.523
peak=    3.031 closest distance to " O   HOH Z 133 " =    1.492
peak=    3.027 closest distance to " CB  TRP A 150 " =    1.149

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

Number of peaks found at mFobs-DFmodel map (map cutoff=3.00 sigma)= 221         
Filter by distance & map next to the model:
   mapped sites are within: 0.756 - 5.466
   number of sites selected in [dist_min= 0.70, dist_max= 6.00]: 220 from: 221
   mapped sites are within: 0.756 - 5.466

peak=   -4.939 closest distance to " CG2 VAL A 230 " =    0.768
peak=   -4.375 closest distance to " CD  ARG A  14 " =    3.193
peak=   -4.331 closest distance to " CD  ARG A 156 " =    2.073
peak=   -4.273 closest distance to " OG BSER A 134 " =    1.366
peak=   -4.235 closest distance to " CB  PRO A 243 " =    2.690
peak=   -4.161 closest distance to " O   VAL A  67 " =    2.563
peak=   -4.070 closest distance to " O   HOH Z 266 " =    5.333
peak=   -4.013 closest distance to " O   HOH Z 211 " =    1.214
peak=   -3.947 closest distance to " CB  ALA A  43 " =    2.567
peak=   -3.920 closest distance to " O   HOH Z 111 " =    1.588
peak=   -3.917 closest distance to " CA  GLY A 241 " =    2.344
peak=   -3.909 closest distance to " CG2 VAL A 202 " =    2.698
peak=   -3.890 closest distance to " N   THR A 157 " =    1.484
peak=   -3.854 closest distance to " CB  ALA A 248 " =    2.090
peak=   -3.841 closest distance to " CG1 VAL A 112 " =    2.659
peak=   -3.837 closest distance to " CD2 LEU A 237 " =    2.814
peak=   -3.834 closest distance to " O   HOH Z 231 " =    1.943
peak=   -3.830 closest distance to " ND2 ASN A 249 " =    2.411
peak=   -3.827 closest distance to " C   HIS A 108 " =    1.283
peak=   -3.807 closest distance to " CE2 TYR A  30 " =    2.621
peak=   -3.793 closest distance to " CD1 LEU A 255 " =    2.896
peak=   -3.783 closest distance to " O   HOH Z 351 " =    1.512
peak=   -3.774 closest distance to " CG2 VAL A 296 " =    1.499
peak=   -3.771 closest distance to " O   HOH Z 131 " =    4.124
peak=   -3.771 closest distance to " O   PRO A 198 " =    1.211
peak=   -3.760 closest distance to " NH2 ARG A  79 " =    2.049
peak=   -3.748 closest distance to " O   HOH Z 389 " =    1.569
peak=   -3.745 closest distance to " O   HOH Z 185 " =    2.218
peak=   -3.730 closest distance to " CG  GLN A 223 " =    2.357
peak=   -3.724 closest distance to " O   HOH Z 290 " =    1.222
peak=   -3.724 closest distance to " OG  SER A  97 " =    2.224
peak=   -3.711 closest distance to " O   HOH Z 394 " =    1.508
peak=   -3.710 closest distance to " CD2 LEU A   5 " =    1.060
peak=   -3.709 closest distance to " CG2 VAL A 296 " =    1.011
peak=   -3.698 closest distance to " O   HOH Z 359 " =    3.194
peak=   -3.694 closest distance to " O   HOH Z 100 " =    1.154
peak=   -3.689 closest distance to " CD  GLN A  58 " =    0.962
peak=   -3.672 closest distance to " O   HOH Z  52 " =    1.269
peak=   -3.667 closest distance to " O   PRO A 163 " =    2.019
peak=   -3.664 closest distance to " O   HOH Z 377 " =    2.102
peak=   -3.656 closest distance to " CB  ALA A 161 " =    2.531
peak=   -3.652 closest distance to " CE BMET A  47 " =    1.458
peak=   -3.651 closest distance to " O   HOH Z 191 " =    5.466
peak=   -3.630 closest distance to " O   HOH Z  73 " =    2.245
peak=   -3.630 closest distance to " O   HOH Z 140 " =    1.395
peak=   -3.621 closest distance to " CD1 LEU A 101 " =    2.305
peak=   -3.621 closest distance to " CG1 VAL A 250 " =    2.754
peak=   -3.612 closest distance to " O   HOH Z 231 " =    0.909
peak=   -3.611 closest distance to " O   SER A 135 " =    1.431
peak=   -3.609 closest distance to " O   HOH Z  43 " =    1.788
peak=   -3.604 closest distance to " CB  VAL A 230 " =    1.086
peak=   -3.599 closest distance to " CA  GLY A  98 " =    1.881
peak=   -3.598 closest distance to " O   HOH Z  51 " =    0.903
peak=   -3.590 closest distance to " O   HOH Z 198 " =    2.220
peak=   -3.589 closest distance to " O   HOH Z 427 " =    1.696
peak=   -3.588 closest distance to " O   SER A  22 " =    2.448
peak=   -3.577 closest distance to " O   HOH Z 389 " =    2.125
peak=   -3.564 closest distance to " CD2 TYR A 293 " =    1.917
peak=   -3.558 closest distance to " CB  TRP A  85 " =    2.516
peak=   -3.555 closest distance to " CZ3 TRP A 179 " =    1.270
peak=   -3.551 closest distance to " CB  ASP A 132 " =    2.351
peak=   -3.546 closest distance to " ND2 ASN A 187 " =    1.420
peak=   -3.534 closest distance to " OXT GLY A 302 " =    3.205
peak=   -3.528 closest distance to " O   VAL A 189 " =    2.577
peak=   -3.514 closest distance to " CB  PHE A 192 " =    1.881
peak=   -3.513 closest distance to " OG  SER A  62 " =    4.508
peak=   -3.509 closest distance to " OE1 GLN A  88 " =    1.109
peak=   -3.496 closest distance to " CB  PRO A 163 " =    2.375
peak=   -3.494 closest distance to " O   HOH Z  44 " =    2.300
peak=   -3.494 closest distance to " C   MET A 188 " =    1.465
peak=   -3.492 closest distance to " O   PRO A 198 " =    1.389
peak=   -3.492 closest distance to " O   HOH Z  11 " =    1.924
peak=   -3.486 closest distance to " OG  SER A  87 " =    1.377
peak=   -3.484 closest distance to " CD1 LEU A 228 " =    2.332
peak=   -3.481 closest distance to " O   HOH Z 134 " =    3.943
peak=   -3.468 closest distance to " O   HOH Z 166 " =    2.086
peak=   -3.463 closest distance to " OH  TYR A 172 " =    1.755
peak=   -3.458 closest distance to " CA  ASP A  27 " =    2.440
peak=   -3.455 closest distance to " CA  ASP A 298 " =    1.075
peak=   -3.454 closest distance to " O   HOH Z  22 " =    2.336
peak=   -3.448 closest distance to " O   HOH Z 103 " =    1.831
peak=   -3.448 closest distance to " CG2 THR A  18 " =    2.867
peak=   -3.447 closest distance to " N   ALA A 226 " =    2.098
peak=   -3.441 closest distance to " N   ALA A  43 " =    2.668
peak=   -3.429 closest distance to " ND2 ASN A  45 " =    1.249
peak=   -3.421 closest distance to " O   GLY A 203 " =    2.536
peak=   -3.420 closest distance to " CD  LYS A 289 " =    2.380
peak=   -3.414 closest distance to " CG  GLN A  88 " =    0.851
peak=   -3.409 closest distance to " NH2AARG A 275 " =    5.331
peak=   -3.409 closest distance to " O   HOH Z 166 " =    2.072
peak=   -3.404 closest distance to " O   HOH Z 147 " =    2.052
peak=   -3.401 closest distance to " OG BSER A 134 " =    1.833
peak=   -3.401 closest distance to " CD2 TYR A 247 " =    2.532
peak=   -3.401 closest distance to " O   GLY A 229 " =    1.846
peak=   -3.399 closest distance to " O   ALA A 161 " =    1.726
peak=   -3.396 closest distance to " CE  MET A 105 " =    2.435
peak=   -3.392 closest distance to " O   HOH Z 350 " =    2.260
peak=   -3.388 closest distance to " O   ASP A  27 " =    1.802
peak=   -3.387 closest distance to " CG  TRP A 266 " =    1.810
peak=   -3.386 closest distance to " C   LEU A 222 " =    0.816
peak=   -3.381 closest distance to " CB  TYR A  15 " =    2.234
peak=   -3.379 closest distance to " O   HOH Z 412 " =    4.298
peak=   -3.372 closest distance to " O   HOH Z 176 " =    0.756
peak=   -3.367 closest distance to " CA  GLY A 203 " =    2.447
peak=   -3.364 closest distance to " CZ2 TRP A 274 " =    0.995
peak=   -3.361 closest distance to " CA  VAL A  67 " =    3.002
peak=   -3.355 closest distance to " ND2 ASN A  45 " =    2.059
peak=   -3.352 closest distance to " CE1 PHE A  59 " =    1.949
peak=   -3.343 closest distance to " O   HOH Z  60 " =    2.286
peak=   -3.343 closest distance to " O   HOH Z 353 " =    1.963
peak=   -3.343 closest distance to " CG  LEU A   5 " =    0.925
peak=   -3.340 closest distance to " O   GLN A 240 " =    2.492
peak=   -3.336 closest distance to " N   ALA A 248 " =    1.549
peak=   -3.334 closest distance to " O   HOH Z  65 " =    1.273
peak=   -3.331 closest distance to " CE3 TRP A 150 " =    2.284
peak=   -3.330 closest distance to " O   HOH Z 359 " =    1.564
peak=   -3.328 closest distance to " O   ARG A 145 " =    1.414
peak=   -3.321 closest distance to " CA  GLY A 133 " =    1.948
peak=   -3.319 closest distance to " CB  ALA A 129 " =    2.511
peak=   -3.316 closest distance to " O   HOH Z 292 " =    1.589
peak=   -3.313 closest distance to " CE  LYS A  76 " =    2.772
peak=   -3.310 closest distance to " O   PHE A 218 " =    1.471
peak=   -3.301 closest distance to " CZ  TYR A 186 " =    2.418
peak=   -3.292 closest distance to " O   HOH Z 318 " =    2.012
peak=   -3.288 closest distance to " CE2 PHE A 218 " =    2.451
peak=   -3.286 closest distance to " CB  ALA A   7 " =    2.100
peak=   -3.281 closest distance to " CB  ALA A 248 " =    2.395
peak=   -3.279 closest distance to " O   GLY A  80 " =    2.532
peak=   -3.277 closest distance to " O   HOH Z  90 " =    2.721
peak=   -3.270 closest distance to " O   HOH Z 276 " =    1.784
peak=   -3.268 closest distance to " OG  SER A 206 " =    1.702
peak=   -3.264 closest distance to " O   ALA A   1 " =    1.672
peak=   -3.260 closest distance to " CD2 HIS A 207 " =    2.289
peak=   -3.257 closest distance to " CG2 THR A  42 " =    1.834
peak=   -3.254 closest distance to " C   ASN A 285 " =    2.301
peak=   -3.252 closest distance to " O   ILE A  49 " =    1.712
peak=   -3.247 closest distance to " O   HOH Z 377 " =    0.850
peak=   -3.247 closest distance to " CB  GLN A  55 " =    1.263
peak=   -3.247 closest distance to " NH2 ARG A 219 " =    1.729
peak=   -3.244 closest distance to " ND2 ASN A  69 " =    1.773
peak=   -3.244 closest distance to " CG2 ILE A 151 " =    2.549
peak=   -3.243 closest distance to " O   HOH Z  39 " =    1.308
peak=   -3.238 closest distance to " CG2 ILE A 263 " =    2.338
peak=   -3.230 closest distance to " O   HOH Z 357 " =    2.056
peak=   -3.229 closest distance to " O   HOH Z 313 " =    1.659
peak=   -3.229 closest distance to " CB  ALA A 227 " =    2.423
peak=   -3.226 closest distance to " OD1 ASN A 148 " =    1.486
peak=   -3.225 closest distance to " CG  LEU A 228 " =    0.889
peak=   -3.225 closest distance to " ND2 ASN A  60 " =    1.514
peak=   -3.220 closest distance to " O   HOH Z 216 " =    1.525
peak=   -3.218 closest distance to " O   HOH Z 189 " =    2.196
peak=   -3.216 closest distance to " O   HOH Z 253 " =    3.887
peak=   -3.214 closest distance to " O   GLY A 211 " =    1.240
peak=   -3.209 closest distance to " O   HOH Z 317 " =    1.362
peak=   -3.208 closest distance to " CG  ASP A 231 " =    0.762
peak=   -3.207 closest distance to " CE3 TRP A  70 " =    1.724
peak=   -3.202 closest distance to " C   VAL A 265 " =    0.794
peak=   -3.202 closest distance to " O   HOH Z 383 " =    2.109
peak=   -3.201 closest distance to " O   HOH Z 166 " =    1.490
peak=   -3.200 closest distance to " CZ2 TRP A  92 " =    2.869
peak=   -3.199 closest distance to " C   ARG A 269 " =    1.450
peak=   -3.198 closest distance to " O   SER A 210 " =    1.928
peak=   -3.197 closest distance to " OE2 GLU A 152 " =    1.190
peak=   -3.196 closest distance to " O   LEU A 101 " =    2.801
peak=   -3.196 closest distance to " O   HOH Z  38 " =    1.853
peak=   -3.192 closest distance to " CG  GLU A 277 " =    1.274
peak=   -3.192 closest distance to " O   LYS A 289 " =    3.035
peak=   -3.187 closest distance to " O   SER A 271 " =    2.208
peak=   -3.184 closest distance to " CB  PRO A  54 " =    2.474
peak=   -3.183 closest distance to " O   HOH Z 143 " =    1.667
peak=   -3.177 closest distance to " ND2 ASN A  45 " =    1.467
peak=   -3.175 closest distance to " CD  PRO A 243 " =    2.084
peak=   -3.175 closest distance to " CD2 PHE A  61 " =    1.914
peak=   -3.166 closest distance to " CB  ALA A 291 " =    2.176
peak=   -3.161 closest distance to " CA  GLY A 241 " =    3.145
peak=   -3.160 closest distance to " OD1 ASP A 191 " =    1.759
peak=   -3.160 closest distance to " O   HOH Z 282 " =    5.105
peak=   -3.157 closest distance to " CD  LYS A 166 " =    2.477
peak=   -3.153 closest distance to " O   HOH Z 390 " =    2.297
peak=   -3.153 closest distance to " O   HOH Z 384 " =    2.408
peak=   -3.152 closest distance to " CG  GLU A 152 " =    1.479
peak=   -3.151 closest distance to " O   ALA A  10 " =    1.780
peak=   -3.148 closest distance to " CB  ASN A  39 " =    2.232
peak=   -3.147 closest distance to " CG2 VAL A 189 " =    1.856
peak=   -3.145 closest distance to " O   HOH Z  60 " =    1.960
peak=   -3.141 closest distance to " O   HOH Z 210 " =    1.066
peak=   -3.139 closest distance to " CG1 VAL A 296 " =    1.558
peak=   -3.136 closest distance to " N   SER A 276 " =    1.404
peak=   -3.136 closest distance to " N   VAL A  72 " =    1.578
peak=   -3.135 closest distance to " N   VAL A 232 " =    2.200
peak=   -3.133 closest distance to " CB  PRO A 213 " =    2.182
peak=   -3.133 closest distance to " CG1 VAL A 112 " =    3.052
peak=   -3.129 closest distance to " O   HOH Z 174 " =    3.070
peak=   -3.127 closest distance to " NE2 GLN A 240 " =    1.725
peak=   -3.125 closest distance to " O   HOH Z 298 " =    2.919
peak=   -3.121 closest distance to " O   HOH Z 407 " =    3.123
peak=   -3.121 closest distance to " O   HOH Z 286 " =    1.929
peak=   -3.121 closest distance to " CB  ALA A 114 " =    2.401
peak=   -3.117 closest distance to " CB  PHE A 130 " =    1.269
peak=   -3.114 closest distance to " CB  SER A 210 " =    1.074
peak=   -3.103 closest distance to " CB  PRO A  90 " =    1.787
peak=   -3.102 closest distance to " CG1 VAL A 197 " =    2.326
peak=   -3.101 closest distance to " O   HOH Z 281 " =    2.547
peak=   -3.098 closest distance to " CG  PHE A 283 " =    2.628
peak=   -3.094 closest distance to " O   HOH Z 323 " =    1.773
peak=   -3.093 closest distance to " CG2 VAL A 296 " =    1.938
peak=   -3.086 closest distance to " O   HOH Z  99 " =    1.575
peak=   -3.085 closest distance to " CG  PRO A 163 " =    2.568
peak=   -3.084 closest distance to " O   HOH Z 380 " =    1.198
peak=   -3.078 closest distance to " O   HOH Z   9 " =    3.246
peak=   -3.075 closest distance to " O   HOH Z 368 " =    1.633
peak=   -3.066 closest distance to " O   HOH Z 134 " =    3.582
peak=   -3.060 closest distance to " OD1 ASP A 171 " =    1.670
peak=   -3.059 closest distance to " O   HOH Z  24 " =    1.440
peak=   -3.058 closest distance to " OH  TYR A 247 " =    1.835
peak=   -3.045 closest distance to " CB  ASP A 286 " =    2.221
peak=   -3.036 closest distance to " OD1 ASN A 301 " =    2.000
peak=   -3.029 closest distance to " O   HOH Z 410 " =    2.213
peak=   -3.029 closest distance to " CD2 LEU A 297 " =    2.066
peak=   -3.025 closest distance to " NE2 GLN A 278 " =    1.922

================= 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    :  0.4789 0.4632   6.280007e+00   6.257715e+00
   1_bss:  0.4709 0.4470   6.275125e+00   6.249341e+00
   1_xyz:  0.3820 0.4021   6.153437e+00   6.178017e+00
   1_adp:  0.3359 0.3906   6.069999e+00   6.158099e+00
   1_occ:  0.3354 0.3909   6.069196e+00   6.158483e+00
   2_bss:  0.3316 0.3857   6.069845e+00   6.157064e+00
   2_xyz:  0.2415 0.2987   5.801650e+00   5.954083e+00
   2_adp:  0.2140 0.2754   5.707993e+00   5.883535e+00
   2_occ:  0.2139 0.2751   5.707466e+00   5.883405e+00
   3_bss:  0.2121 0.2736   5.707824e+00   5.883516e+00
   3_xyz:  0.1533 0.2048   5.415962e+00   5.634402e+00
   3_adp:  0.1388 0.1901   5.334708e+00   5.563482e+00
   3_occ:  0.1386 0.1901   5.334221e+00   5.563150e+00
   4_bss:  0.1385 0.1895   5.332453e+00   5.560284e+00
   4_xyz:  0.1212 0.1723   5.225191e+00   5.470219e+00
   4_adp:  0.1177 0.1686   5.202736e+00   5.447927e+00
   4_occ:  0.1176 0.1685   5.202392e+00   5.447463e+00
   5_bss:  0.1176 0.1684   5.202270e+00   5.447339e+00
   5_xyz:  0.1137 0.1643   5.177696e+00   5.429482e+00
   5_adp:  0.1134 0.1623   5.170802e+00   5.418878e+00
   5_occ:  0.1133 0.1622   5.170070e+00   5.417835e+00
   5_bss:  0.1133 0.1615   5.168143e+00   5.414673e+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:  0.359  20.001   6.838   9.197  10.039   0.000   0.000   0.000
   1_xyz:  0.359  20.001   6.838   9.197  10.039   0.000   0.000   0.000
   1_adp:  0.359  20.001   6.838   9.197  10.039   0.000   0.000   0.000
   1_occ:  0.359  20.001   6.838   9.197  10.039   0.000   0.000   0.000
   2_bss:  0.345  43.881   3.366   4.798   5.975   0.000   0.000   0.000
   2_xyz:  0.345  43.881   3.366   4.798   5.975   0.000   0.000   0.000
   2_adp:  0.345  43.881   3.366   4.798   5.975   0.000   0.000   0.000
   2_occ:  0.345  43.881   3.366   4.798   5.975   0.000   0.000   0.000
   3_bss:  0.320  52.736   2.013   2.510   3.921   0.000   0.000   0.000
   3_xyz:  0.320  52.736   2.013   2.510   3.921   0.000   0.000   0.000
   3_adp:  0.320  52.736   2.013   2.510   3.921   0.000   0.000   0.000
   3_occ:  0.320  52.736   2.013   2.510   3.921   0.000   0.000   0.000
   4_bss:  0.324  56.846   1.647   1.727   3.446   0.000   0.000   0.000
   4_xyz:  0.324  56.846   1.647   1.727   3.446   0.000   0.000   0.000
   4_adp:  0.324  56.846   1.647   1.727   3.446   0.000   0.000   0.000
   4_occ:  0.324  56.846   1.647   1.727   3.446   0.000   0.000   0.000
   5_bss:  0.324  56.846   1.743   1.662   3.478   0.000   0.000   0.000
   5_xyz:  0.324  56.846   1.743   1.662   3.478   0.000   0.000   0.000
   5_adp:  0.324  56.846   1.743   1.662   3.478   0.000   0.000   0.000
   5_occ:  0.324  56.846   1.743   1.662   3.478   0.000   0.000   0.000
   5_bss:  0.326  59.128  -0.528  -0.679   1.206   0.000   0.000   0.000
------------------------------------------------------------------------
 stage     <pher>    fom   alpha         beta
   0    :  55.690 0.4486  0.5239    65573.874
   1_bss:  55.320 0.4521  0.6814    63509.613
   1_xyz:  46.267 0.5650  0.8262    46882.803
   1_adp:  43.209 0.6029  0.9371    43144.110
   1_occ:  43.268 0.6022  0.9344    43196.286
   2_bss:  42.889 0.6067  0.8195    42666.926
   2_xyz:  30.915 0.7461  0.9710    23291.473
   2_adp:  27.473 0.7849  0.9945    19352.601
   2_occ:  27.459 0.7851  0.9941    19314.984
   3_bss:  27.427 0.7855  0.9299    19372.670
   3_xyz:  19.859 0.8626  0.9874    10761.711
   3_adp:  18.067 0.8797  0.9890     9321.808
   3_occ:  18.060 0.8798  0.9889     9309.075
   4_bss:  17.984 0.8804  0.9700     9222.403
   4_xyz:  15.891 0.8988  0.9793     7517.573
   4_adp:  15.358 0.9037  0.9750     7200.328
   4_occ:  15.350 0.9037  0.9749     7188.839
   5_bss:  15.349 0.9038  0.9757     7188.744
   5_xyz:  14.861 0.9081  0.9771     6920.162
   5_adp:  14.598 0.9104  0.9741     6800.621
   5_occ:  14.582 0.9106  0.9741     6783.450
   5_bss:  14.541 0.9108  0.9737     6726.691
------------------------------------------------------------------------
 stage       angl   bond   chir   dihe   plan   repu  geom_target
   0    :  24.226  0.414  2.119 33.790  0.145  4.090   5.3894e+01
   1_bss:  24.226  0.414  2.119 33.790  0.145  4.090   5.3894e+01
   1_xyz:   1.689  0.013  0.107 18.253  0.006  4.109   1.4005e-01
   1_adp:   1.689  0.013  0.107 18.253  0.006  4.109   1.4005e-01
   1_occ:   1.689  0.013  0.107 18.253  0.006  4.109   1.4005e-01
   2_bss:   1.689  0.013  0.107 18.253  0.006  4.109   1.4005e-01
   2_xyz:   1.160  0.009  0.086 16.327  0.005  4.110   8.4701e-02
   2_adp:   1.160  0.009  0.086 16.327  0.005  4.110   8.4701e-02
   2_occ:   1.160  0.009  0.086 16.327  0.005  4.110   8.4701e-02
   3_bss:   1.160  0.009  0.086 16.327  0.005  4.110   8.4701e-02
   3_xyz:   1.102  0.008  0.084 16.074  0.004  4.124   7.2135e-02
   3_adp:   1.102  0.008  0.084 16.074  0.004  4.124   7.2135e-02
   3_occ:   1.102  0.008  0.084 16.074  0.004  4.124   7.2135e-02
   4_bss:   1.102  0.008  0.084 16.074  0.004  4.124   7.2135e-02
   4_xyz:   1.079  0.009  0.083 15.786  0.004  4.120   7.1865e-02
   4_adp:   1.079  0.009  0.083 15.786  0.004  4.120   7.1865e-02
   4_occ:   1.079  0.009  0.083 15.786  0.004  4.120   7.1865e-02
   5_bss:   1.079  0.009  0.083 15.786  0.004  4.120   7.1865e-02
   5_xyz:   1.077  0.009  0.084 15.524  0.004  4.123   7.0404e-02
   5_adp:   1.077  0.009  0.084 15.524  0.004  4.123   7.0404e-02
   5_occ:   1.077  0.009  0.084 15.524  0.004  4.123   7.0404e-02
   5_bss:   1.077  0.009  0.084 15.524  0.004  4.123   7.0404e-02
------------------------------------------------------------------------
                      Maximal deviations:
 stage       angl   bond   chir   dihe   plan   repu       |grad|
   0    :  74.492  1.400  6.404144.062  0.405  1.196   6.9867e+00
   1_bss:  74.492  1.400  6.404144.062  0.405  1.196   6.9867e+00
   1_xyz:  13.578  0.186  0.412 84.934  0.031  2.179   1.0002e-01
   1_adp:  13.578  0.186  0.412 84.934  0.031  2.179   1.0002e-01
   1_occ:  13.578  0.186  0.412 84.934  0.031  2.179   1.0002e-01
   2_bss:  13.578  0.186  0.412 84.934  0.031  2.179   1.0002e-01
   2_xyz:   6.797  0.078  0.287 86.324  0.029  2.261   6.7526e-02
   2_adp:   6.797  0.078  0.287 86.324  0.029  2.261   6.7526e-02
   2_occ:   6.797  0.078  0.287 86.324  0.029  2.261   6.7526e-02
   3_bss:   6.797  0.078  0.287 86.324  0.029  2.261   6.7526e-02
   3_xyz:   9.865  0.055  0.418 83.577  0.032  2.260   5.5966e-02
   3_adp:   9.865  0.055  0.418 83.577  0.032  2.260   5.5966e-02
   3_occ:   9.865  0.055  0.418 83.577  0.032  2.260   5.5966e-02
   4_bss:   9.865  0.055  0.418 83.577  0.032  2.260   5.5966e-02
   4_xyz:   6.938  0.048  0.473 85.379  0.040  2.296   5.8373e-02
   4_adp:   6.938  0.048  0.473 85.379  0.040  2.296   5.8373e-02
   4_occ:   6.938  0.048  0.473 85.379  0.040  2.296   5.8373e-02
   5_bss:   6.938  0.048  0.473 85.379  0.040  2.296   5.8373e-02
   5_xyz:   7.301  0.049  0.460 83.511  0.044  2.327   5.3068e-02
   5_adp:   7.301  0.049  0.460 83.511  0.044  2.327   5.3068e-02
   5_occ:   7.301  0.049  0.460 83.511  0.044  2.327   5.3068e-02
   5_bss:   7.301  0.049  0.460 83.511  0.044  2.327   5.3068e-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:  81.36   0.00  13.57  65.13   0.00  11.14  81.36   0.00  26.77
   1_occ:  81.36   0.00  13.57  65.13   0.00  11.14  81.36   0.00  26.77
   2_bss:  81.36   0.00  13.57  65.13   0.00  11.14  81.36   0.00  26.77
   2_xyz:  81.36   0.00  13.57  65.13   0.00  11.14  81.36   0.00  26.77
   2_adp:  89.00   0.00  13.21  70.04   0.00   9.50  89.00   0.00  33.45
   2_occ:  89.00   0.00  13.21  70.04   0.00   9.50  89.00   0.00  33.45
   3_bss:  89.00   0.00  13.21  70.04   0.00   9.50  89.00   0.00  33.45
   3_xyz:  89.00   0.00  13.21  70.04   0.00   9.50  89.00   0.00  33.45
   3_adp:  89.37   0.00  13.71  76.86   0.00   9.15  89.37   1.74  38.56
   3_occ:  89.37   0.00  13.71  76.86   0.00   9.15  89.37   1.74  38.56
   4_bss:  89.37   0.00  13.71  76.86   0.00   9.15  89.37   1.74  38.56
   4_xyz:  89.37   0.00  13.71  76.86   0.00   9.15  89.37   1.74  38.56
   4_adp:  88.52   0.00  13.57  85.42   0.00   8.95  88.52   2.62  38.70
   4_occ:  88.52   0.00  13.57  85.42   0.00   8.95  88.52   2.62  38.70
   5_bss:  88.52   0.00  13.57  85.42   0.00   8.95  88.52   2.62  38.70
   5_xyz:  88.52   0.00  13.57  85.42   0.00   8.95  88.52   2.62  38.70
   5_adp:  87.65   0.00  13.29  85.62   0.00   8.76  87.65   2.55  37.94
   5_occ:  87.65   0.00  13.29  85.62   0.00   8.76  87.65   2.55  37.94
   5_bss:  89.93   2.28  15.57  87.90   2.28  11.05  89.93   4.83  40.23
------------------------------------------------------------------------
 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:    1.264    0.023    0.410
   1_adp:    1.264    0.023    0.410
   1_occ:    1.264    0.023    0.410
   2_bss:    1.264    0.023    0.410
   2_xyz:    1.538    0.017    0.584
   2_adp:    1.538    0.017    0.584
   2_occ:    1.538    0.017    0.584
   3_bss:    1.538    0.017    0.584
   3_xyz:    1.585    0.033    0.669
   3_adp:    1.585    0.033    0.669
   3_occ:    1.585    0.033    0.669
   4_bss:    1.585    0.033    0.669
   4_xyz:    1.693    0.038    0.701
   4_adp:    1.693    0.038    0.701
   4_occ:    1.693    0.038    0.701
   5_bss:    1.693    0.038    0.701
   5_xyz:    1.743    0.042    0.712
   5_adp:    1.743    0.042    0.712
   5_occ:    1.743    0.042    0.712
   5_bss:    1.743    0.042    0.712
------------------------------------------------------------------------

CPU time actual refinement: 333.83


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

Writing refined structure to PDB file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/trial/run_756/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_756/model_refine_001_2mFobs-DFmodel.map
Writing mFobs-DFmodel XPLOR map to file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/trial/run_756/model_refine_001_mFobs-DFmodel.map
Writing map coefficients to MTZ file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/trial/run_756/model_refine_001_map_coeffs.mtz

Writing default parameters for subsequent refinement:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/trial/run_756/model_refine_002.def


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

Pure refinement (no I/O, processing, etc)= 333.68 
  Macro-tasks:
    bulk solvent and scale       = 44.46  
    individual site refinement   = 137.28 
    weights calculation          = 31.78  
    collect and process          = 6.54   
    model show statistics        = 0.09   
    TOTAL for macro-tasks        = 220.15 
  Micro-tasks:
    mask                            = 2.23   
    f_calc                          = 102.99 
    alpha_beta                      = 8.33   
    target                          = 1.21   
    gradients_wrt_atomic_parameters = 108.75 
    fmodel                         = 7.34   
    r_factors                      = 0.16   
    phase_errors                   = 11.26  
    foms                           = 0.20   
    TOTAL for micro-tasks          = 242.47 
NUMBER OF MASK CALCS=  5
Time per interpreted Python bytecode instruction: 4.662 micro seconds
Total CPU time: 5.78 minutes
from_scatterers_fft:    648 calls, 102.54 s
gradients_fft:          593 calls,  96.96 s

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

# Date 2008-01-16 Time 02:21:25 PST -0800 (1200478885.36 s)
Start R-work = 0.4789, R-free = 0.4632 (no bulk solvent and anisotropic scale)
Final R-work = 0.1302, R-free = 0.1784 (no bulk solvent and anisotropic scale)

Start R-work = 0.4709, R-free = 0.4470
Final R-work = 0.1133, R-free = 0.1615