# Date 2008-01-16 Time 02:14:01 PST -0800 (1200478441.36 s)
#phil __OFF__

Command line arguments: "../743.param" "adp.set_b_iso=10" "sites.shake=0.5" "main.number_of_macro_cycles=5" "--overwrite"

HOST = moonbird.lbl.gov
HOSTTYPE = x86_64-linux
USER = phzwart
PID = 31227
JOB_ID = 5158
SGE_ARCH = lx24-amd64
SGE_TASK_FIRST = 1
SGE_TASK_LAST = 1330
SGE_TASK_ID = 743

-------------------------------------------------------------------------------
  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, 45.9914, 86.822, 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: 3.28, per 1000 atoms: 1.16


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

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

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

Miller array info: /net/cci-filer1/vol1/tmp/phzwart/tassos/trial/1e0w.cns:FOBS,SIGMA
Observation type: xray.amplitude
Type of data: double, size=19589
Type of sigmas: double, size=19589
Number of Miller indices: 19589
Anomalous flag: False
Unit cell: (70.6012, 45.9914, 86.822, 90, 90, 90)
Space group: P 21 21 21 (No. 19)
Systematic absences: 0
Centric reflections: 2427
Resolution range: 15.0689 1.96328
Completeness in resolution range: 0.942776
Completeness with d_max=infinity: 0.939971

Number of F-obs in resolution range:                   19589
Number of F-obs <= 0:                                  0
Refinement resolution range: d_max =  15.0689
                             d_min =   1.9633

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, 45.9914, 86.822, 90, 90, 90)
Space group: P 21 21 21 (No. 19)
Systematic absences: 0
Centric reflections: 2427
Resolution range: 15.0689 1.96328
Completeness in resolution range: 0.942776
Completeness with d_max=infinity: 0.939971

Test (R-free flags) flag value: 1

Number of work/free reflections by resolution:
                                         work  free  %free
  bin  1: 15.0694 -  4.2021 [2185/2210]  1965   220  10.1%
  bin  2:  4.2021 -  3.3473 [2099/2119]  1892   207   9.9%
  bin  3:  3.3473 -  2.9277 [2073/2092]  1866   207  10.0%
  bin  4:  2.9277 -  2.6616 [2049/2079]  1840   209  10.2%
  bin  5:  2.6616 -  2.4718 [2034/2053]  1838   196   9.6%
  bin  6:  2.4718 -  2.3266 [2030/2055]  1819   211  10.4%
  bin  7:  2.3266 -  2.2104 [2022/2050]  1817   205  10.1%
  bin  8:  2.2104 -  2.1145 [2007/2043]  1809   198   9.9%
  bin  9:  2.1145 -  2.0333 [2007/2049]  1814   193   9.6%
  bin 10:  2.0333 -  1.9633 [1083/2028]   970   113  10.4%
                                overall 17630  1959  10.0%
Writing MTZ file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/trial/run_743/model_refine_data.mtz


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

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

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

  Number of disulfides: simple=3, symmetry=0
    Simple disulfide: " SG  CYS A 168 " - " SG ACYS A 201 " distance=2.08
    Simple disulfide: " SG  CYS A 168 " - " SG BCYS A 201 " distance=1.98
    Simple disulfide: " SG  CYS A 254 " - " SG  CYS A 260 " distance=2.05
  Time building geometry restraints manager: 0.14 seconds
  Histogram of bond lengths:
        1.21 -     1.38: 943
        1.38 -     1.56: 1465
        1.56 -     1.73: 7
        1.73 -     1.90: 21
        1.90 -     2.08: 3
  Bond restraints sorted by residual:
             atom i - atom j            ideal  model  delta   weight residual
  " SG  CYS A 168 " - " SG BCYS A 201 " 2.031  1.983  0.048 2.50e+03 5.87e+00
  " C   GLN A  88 " - " N   GLN A  89 " 1.329  1.360 -0.031 5.10e+03 4.97e+00
  " SG  CYS A 168 " - " SG ACYS A 201 " 2.031  2.075 -0.044 2.50e+03 4.89e+00
  " CB  CYS A 201 " - " SG ACYS A 201 " 1.808  1.738  0.070 9.18e+02 4.46e+00
  " C   PRO A 198 " - " N   ILE A 199 " 1.329  1.301  0.028 5.10e+03 4.10e+00
  ... (remaining 2434 not shown)
  Histogram of nonbonded interaction distances:
        1.81 -     2.42: 33
        2.42 -     3.04: 2210
        3.04 -     3.66: 4737
        3.66 -     4.28: 9079
        4.28 -     4.90: 12344
  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
  " OG1 THR A  29 " - " O   HOH Z 245 "  1.883 3.040 x,y+1,z
  " O   HOH Z 201 " - " O   HOH Z 349 "  1.923 3.040 -x+1/2,-y+1,z+1/2
  " O   HOH Z  70 " - " O   HOH Z 302 "  1.924 3.040 -x+1/2,-y+1,z+1/2
  " O   HOH Z  61 " - " O   HOH Z 246 "  1.941 3.040 x,y+1,z
  ... (remaining 28398 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_743/model_refine_001.eff

Writing geometry restraints to file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/trial/run_743/model_refine_001.geo

CPU time processing inputs: 9.15


============================ 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 45.9914 86.82195 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: 1.96 - 15.07 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.4766   r_free= 0.4700   ksol= 0.00   Bsol= 0.00   scale= 0.796    |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (0.00,0.00,0.00,0.00,0.00,0.00); trace/3= 0.00                              |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.73 A                  |
| x-ray target function (ml) for work reflections: 6.282205                   |
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
| Bin     Resolution   Compl.  No. Refl.    R-factors          Targets        |
|number     range              work test   work   test        work        test|
|  1: 15.0694 -  4.6873 0.99   1413  157 0.4071 0.3910      6.6064      6.6205|
|  2:  4.6873 -  3.7392 0.99   1365  154 0.3959 0.3617      6.8008      6.7284|
|  3:  3.7392 -  3.2720 0.99   1344  143 0.4189 0.3748      6.6533      6.6093|
|  4:  3.2720 -  2.9754 0.99   1326  151 0.4645 0.4523       6.531      6.5056|
|  5:  2.9754 -  2.7635 0.99   1325  149 0.5118 0.5092      6.3628      6.3873|
|  6:  2.7635 -  2.6014 0.99   1314  145 0.5062 0.5255      6.2735      6.2057|
|  7:  2.6014 -  2.4718 0.99   1314  140 0.5198 0.5105      6.2516      6.1907|
|  8:  2.4718 -  2.3646 0.98   1291  149 0.5202 0.4889      6.1684      6.1857|
|  9:  2.3646 -  2.2739 0.98   1294  146 0.5225 0.5388      6.1174      6.1875|
| 10:  2.2739 -  2.1957 1.00   1305  147 0.5201 0.5198      6.1007      6.0591|
| 11:  2.1957 -  2.1272 0.98   1311  140 0.5032 0.5036      6.0365      6.0198|
| 12:  2.1272 -  2.0665 0.98   1269  140 0.5192 0.5780      5.9516      6.0167|
| 13:  2.0665 -  2.0123 0.99   1288  142 0.5369 0.5445        5.88      5.7971|
| 14:  2.0123 -  1.9633 0.36    471   56 0.5624 0.4991      5.8725      5.8514|
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
|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: 15.0694 -  4.6873  1413   157  0.67  36.70   0.79     0.73      80441.49|
|  2:  4.6873 -  3.7392  1365   154  0.72  33.26   0.87     0.80      99382.35|
|  3:  3.7392 -  3.2720  1344   143  0.63  41.61   0.87     0.75     104354.19|
|  4:  3.2720 -  2.9754  1326   151  0.53  49.18   0.79     0.63      95826.55|
|  5:  2.9754 -  2.7635  1325   149  0.41  58.87   0.74     0.51      83154.20|
|  6:  2.7635 -  2.6014  1314   145  0.39  60.92   0.72     0.45      72583.83|
|  7:  2.6014 -  2.4718  1314   140  0.34  64.55   0.75     0.40      68344.38|
|  8:  2.4718 -  2.3646  1291   149  0.32  65.92   0.72     0.38      61484.07|
|  9:  2.3646 -  2.2739  1294   146  0.33  65.14   0.73     0.40      56121.08|
| 10:  2.2739 -  2.1957  1305   147  0.35  63.46   0.76     0.42      48322.73|
| 11:  2.1957 -  2.1272  1311   140  0.33  65.03   0.78     0.41      48124.68|
| 12:  2.1272 -  2.0665  1269   140  0.28  68.88   0.75     0.37      45518.85|
| 13:  2.0665 -  2.0123  1288   142  0.26  70.89   0.72     0.34      40308.90|
| 14:  2.0123 -  1.9633   471    56  0.33  65.62   0.69     0.37      30498.02|
|alpha:            min =        0.34 max =            0.80 mean =         0.51|
|beta:             min =    30498.02 max =       104354.19 mean =     68870.84|
|figures of merit: min =        0.00 max =            1.00 mean =         0.43|
|phase err.(work): min =        0.00 max =           89.95 mean =        57.19|
|phase err.(test): min =        0.00 max =           89.95 mean =        57.48|
|-----------------------------------------------------------------------------|

============================== 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 = 15.111619             wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 80.374   (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 1.308148              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 78.729   (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:       35 |
| 0.280 - 0.420:   441 |  14.906 -  22.354:   630 |  1.937 -  2.307:      168 |
| 0.420 - 0.560:   366 |  22.354 -  29.802:   474 |  2.307 -  2.677:      694 |
| 0.560 - 0.700:   237 |  29.802 -  37.251:   338 |  2.677 -  3.048:     1522 |
| 0.700 - 0.840:   127 |  37.251 -  44.699:   241 |  3.048 -  3.418:     2643 |
| 0.840 - 0.980:    59 |  44.699 -  52.147:   125 |  3.418 -  3.789:     3950 |
| 0.980 - 1.120:    17 |  52.147 -  59.595:    51 |  3.789 -  4.159:     5113 |
| 1.120 - 1.260:     9 |  59.595 -  67.044:    13 |  4.159 -  4.530:     6565 |
| 1.260 - 1.400:     1 |  67.044 -  74.492:     3 |  4.530 -  4.900:     7729 |
|-----------------------------------------------------------------------------|
|-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 |       53.591 |
| planarity |      436 |   0.145    0.405  0.000 |     250.485 |              |
|  dihedral |      870 |  33.790  144.062  0.019 |      20.704 |              |
| nonbonded |     2439 |   4.088    4.900  1.196 |       2.004 |              |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 11.760)------------------------------------------|
|    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 = 11.760)------------------------------------------|
|    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: 1.96 - 15.07 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.4835   r_free= 0.4723   ksol= 0.00   Bsol= 0.00   scale= 0.766    |
|                                                                             |
| 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:   0.71 A                  |
| x-ray target function (ml) for work reflections: 6.284330                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.96 - 15.07 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.4686   r_free= 0.4558   ksol= 0.35   Bsol= 0.00   scale= 1.004    |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (7.38,10.42,8.52,0.00,0.00,0.00); trace/3= 8.77                             |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.72 A                  |
| x-ray target function (ml) for work reflections: 6.276396                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 12.656715             wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 81.757   (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 1.231134              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 76.611   (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.4686      final r-factor (work) = 0.3878          |
| start r-factor (free) = 0.4558      final r-factor (free) = 0.4107          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 93.3254 = 12.66 * 0.50 * 6.2788 + 1.00 * 53.5910                            |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 39.3556 = 12.66 * 0.50 * 6.1969 + 1.00 * 0.1394                             |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 26     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.3878      final r-factor (work) = 0.3437          |
| start r-factor (free) = 0.4107      final r-factor (free) = 0.4032          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 7.6436 = 1.23 * 1.00 * 6.1969 + 1.00 * 0.0144                               |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 7.5509 = 1.23 * 1.00 * 6.1197 + 1.00 * 0.0167                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 30     |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 11.760)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.00    77.97   13.55    None  None   None       |
|    all(noH): 2823   0      0.00    77.97   13.55    None  None   None       |
|    Sol.    : 438    0      0.00    77.97   24.26    None  None   None       |
|    Mac.    : 2385   0      0.00    68.24   11.58    None  None   None       |
|    Hyd.    : 0      0      None    None    None     None  None   None       |
|    - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -      |
|       Distribution of isotropic (or equivalent) ADP for non-H atoms:        |
|    Bin#      value range     #atoms | Bin#      value range     #atoms      |
|      0:     0.000 -   7.797: 1079   |   5:    38.985 -  46.781:   54        |
|      1:     7.797 -  15.594:  812   |   6:    46.781 -  54.578:   35        |
|      2:    15.594 -  23.391:  449   |   7:    54.578 -  62.375:   14        |
|      3:    23.391 -  31.188:  235   |   8:    62.375 -  70.172:    6        |
|      4:    31.188 -  38.985:  138   |   9:    70.172 -  77.969:    1        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.3437 r_free = 0.4032             target_work(ml) = 6.106         |
| occupancies: max = 1.00  min = 0.30   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.3436 r_free = 0.4027             target_work(ml) = 6.106         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        4 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.96 - 15.07 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.3436   r_free= 0.4027   ksol= 0.35   Bsol= 0.00   scale= 1.117    |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (7.38,10.42,8.52,0.00,0.00,0.00); trace/3= 8.77                             |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.56 A                  |
| x-ray target function (ml) for work reflections: 6.105851                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.96 - 15.07 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.3399   r_free= 0.3953   ksol= 0.35   Bsol= 37.82   scale= 1.015   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (3.77,5.87,4.68,0.00,0.00,0.00); trace/3= 4.77                              |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.56 A                  |
| x-ray target function (ml) for work reflections: 6.104709                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 6.660542              wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 100.339  (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 0.633049              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 135.206  (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.3399      final r-factor (work) = 0.2776          |
| start r-factor (free) = 0.3953      final r-factor (free) = 0.3379          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 20.5093 = 6.66 * 0.50 * 6.1166 + 1.00 * 0.1394                              |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 20.1209 = 6.66 * 0.50 * 6.0173 + 1.00 * 0.0816                              |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 29     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.2776      final r-factor (work) = 0.2568          |
| start r-factor (free) = 0.3379      final r-factor (free) = 0.3243          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 3.8264 = 0.63 * 1.00 * 6.0173 + 1.00 * 0.0171                               |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 3.7505 = 0.63 * 1.00 * 5.8997 + 1.00 * 0.0157                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 28     |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 11.760)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.00    86.04   13.55    None  None   None       |
|    all(noH): 2823   0      0.00    86.04   13.55    None  None   None       |
|    Sol.    : 438    0      0.00    86.04   30.80    None  None   None       |
|    Mac.    : 2385   0      0.00    70.65   10.38    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 -   8.604: 1287   |   5:    43.021 -  51.625:   52        |
|      1:     8.604 -  17.208:  787   |   6:    51.625 -  60.229:   26        |
|      2:    17.208 -  25.812:  332   |   7:    60.229 -  68.833:   12        |
|      3:    25.812 -  34.416:  203   |   8:    68.833 -  77.437:    4        |
|      4:    34.416 -  43.021:  118   |   9:    77.437 -  86.041:    2        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.2568 r_free = 0.3243             target_work(ml) = 5.881         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        4 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.2566 r_free = 0.3246             target_work(ml) = 5.881         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        6 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.96 - 15.07 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.2566   r_free= 0.3246   ksol= 0.35   Bsol= 37.82   scale= 1.055   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (3.77,5.87,4.68,0.00,0.00,0.00); trace/3= 4.77                              |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.39 A                  |
| x-ray target function (ml) for work reflections: 5.880941                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.96 - 15.07 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.2554   r_free= 0.3224   ksol= 0.34   Bsol= 49.04   scale= 1.010   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (2.46,3.31,3.55,0.00,0.00,0.00); trace/3= 3.10                              |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.39 A                  |
| x-ray target function (ml) for work reflections: 5.880476                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 4.991189              wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 103.636  (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 0.579776              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 112.006  (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.2554      final r-factor (work) = 0.1918          |
| start r-factor (free) = 0.3224      final r-factor (free) = 0.2512          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 14.8062 = 4.99 * 0.50 * 5.9003 + 1.00 * 0.0816                              |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 14.4564 = 4.99 * 0.50 * 5.7617 + 1.00 * 0.0776                              |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 27     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1918      final r-factor (work) = 0.1739          |
| start r-factor (free) = 0.2512      final r-factor (free) = 0.2350          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 3.3565 = 0.58 * 1.00 * 5.7617 + 1.00 * 0.0160                               |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 3.2684 = 0.58 * 1.00 * 5.5687 + 1.00 * 0.0398                               |
|-----------------------------------------------------------------------------|
| number of iterations = 9       |    number of function evaluations = 18     |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 11.760)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.00    86.19   13.51    None  None   None       |
|    all(noH): 2823   0      0.00    86.19   13.51    None  None   None       |
|    Sol.    : 438    0      2.23    86.19   33.96    None  None   None       |
|    Mac.    : 2385   0      0.00    73.26   9.76     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 -   8.619: 1382   |   5:    43.094 -  51.712:   60        |
|      1:     8.619 -  17.238:  745   |   6:    51.712 -  60.331:   37        |
|      2:    17.238 -  25.856:  235   |   7:    60.331 -  68.950:   11        |
|      3:    25.856 -  34.475:  187   |   8:    68.950 -  77.569:    6        |
|      4:    34.475 -  43.094:  158   |   9:    77.569 -  86.187:    2        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.1739 r_free = 0.2350             target_work(ml) = 5.534         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        6 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.1738 r_free = 0.2345             target_work(ml) = 5.533         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        4 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.96 - 15.07 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1738   r_free= 0.2345   ksol= 0.34   Bsol= 49.04   scale= 1.034   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (2.46,3.31,3.55,0.00,0.00,0.00); trace/3= 3.10                              |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.22 A                  |
| x-ray target function (ml) for work reflections: 5.533315                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.96 - 15.07 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1734   r_free= 0.2339   ksol= 0.33   Bsol= 46.00   scale= 1.009   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (1.63,1.84,3.01,0.00,0.00,0.00); trace/3= 2.16                              |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.22 A                  |
| x-ray target function (ml) for work reflections: 5.532216                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 4.375499              wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 102.969  (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 0.704198              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 91.160   (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1734      final r-factor (work) = 0.1401          |
| start r-factor (free) = 0.2339      final r-factor (free) = 0.1968          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 12.2664 = 4.38 * 0.50 * 5.5714 + 1.00 * 0.0776                              |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 11.9772 = 4.38 * 0.50 * 5.4440 + 1.00 * 0.0672                              |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 29     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1401      final r-factor (work) = 0.1298          |
| start r-factor (free) = 0.1968      final r-factor (free) = 0.1827          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 3.8619 = 0.70 * 1.00 * 5.4440 + 1.00 * 0.0282                               |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 3.7633 = 0.70 * 1.00 * 5.3268 + 1.00 * 0.0122                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 26     |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 11.760)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.00    84.26   13.67    None  None   None       |
|    all(noH): 2823   0      0.00    84.26   13.67    None  None   None       |
|    Sol.    : 438    0      2.61    84.25   38.01    None  None   None       |
|    Mac.    : 2385   0      0.00    84.26   9.21     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 -   8.426: 1478   |   5:    42.128 -  50.553:   95        |
|      1:     8.426 -  16.851:  699   |   6:    50.553 -  58.979:   72        |
|      2:    16.851 -  25.277:  198   |   7:    58.979 -  67.404:   38        |
|      3:    25.277 -  33.702:  122   |   8:    67.404 -  75.830:    9        |
|      4:    33.702 -  42.128:  105   |   9:    75.830 -  84.255:    7        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.1298 r_free = 0.1827             target_work(ml) = 5.284         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        4 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.1297 r_free = 0.1825             target_work(ml) = 5.283         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        6 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.96 - 15.07 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1297   r_free= 0.1825   ksol= 0.33   Bsol= 46.00   scale= 1.012   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (1.63,1.84,3.01,0.00,0.00,0.00); trace/3= 2.16                              |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.17 A                  |
| x-ray target function (ml) for work reflections: 5.283277                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.96 - 15.07 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1301   r_free= 0.1819   ksol= 0.32   Bsol= 48.59   scale= 1.007   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (1.59,1.46,2.97,0.00,0.00,0.00); trace/3= 2.01                              |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.17 A                  |
| x-ray target function (ml) for work reflections: 5.281865                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 2.270555              wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 131.539  (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 0.566181              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 141.587  (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1301      final r-factor (work) = 0.1220          |
| start r-factor (free) = 0.1819      final r-factor (free) = 0.1723          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 6.1148 = 2.27 * 0.50 * 5.3270 + 1.00 * 0.0671                               |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 6.0287 = 2.27 * 0.50 * 5.2593 + 1.00 * 0.0579                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 28     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1220      final r-factor (work) = 0.1197          |
| start r-factor (free) = 0.1723      final r-factor (free) = 0.1697          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 2.9898 = 0.57 * 1.00 * 5.2593 + 1.00 * 0.0121                               |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 2.9724 = 0.57 * 1.00 * 5.2233 + 1.00 * 0.0151                               |
|-----------------------------------------------------------------------------|
| number of iterations = 16      |    number of function evaluations = 22     |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 11.760)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.00    86.21   13.41    None  None   None       |
|    all(noH): 2823   0      0.00    86.21   13.41    None  None   None       |
|    Sol.    : 438    0      2.26    83.86   37.82    None  None   None       |
|    Mac.    : 2385   0      0.00    86.21   8.93     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 -   8.621: 1573   |   5:    43.106 -  51.727:   94        |
|      1:     8.621 -  17.242:  649   |   6:    51.727 -  60.348:   68        |
|      2:    17.242 -  25.864:  175   |   7:    60.348 -  68.970:   31        |
|      3:    25.864 -  34.485:  118   |   8:    68.970 -  77.591:   10        |
|      4:    34.485 -  43.106:   99   |   9:    77.591 -  86.212:    6        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.1197 r_free = 0.1697             target_work(ml) = 5.215         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        6 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.1196 r_free = 0.1695             target_work(ml) = 5.215         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        5 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.96 - 15.07 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1196   r_free= 0.1695   ksol= 0.32   Bsol= 48.59   scale= 1.004   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (1.59,1.46,2.97,0.00,0.00,0.00); trace/3= 2.01                              |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.16 A                  |
| x-ray target function (ml) for work reflections: 5.214597                   |
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
| Bin     Resolution   Compl.  No. Refl.    R-factors          Targets        |
|number     range              work test   work   test        work        test|
|  1: 15.0694 -  4.6873 0.99   1413  157 0.0999 0.1287      5.3892      5.5774|
|  2:  4.6873 -  3.7392 0.99   1365  154 0.0898 0.1232      5.4788      5.7076|
|  3:  3.7392 -  3.2720 0.99   1344  143 0.1133 0.1515      5.5355      5.8408|
|  4:  3.2720 -  2.9754 0.99   1326  151 0.1318 0.1844      5.5102      5.6744|
|  5:  2.9754 -  2.7635 0.99   1325  149 0.1421 0.1858      5.3861      5.6182|
|  6:  2.7635 -  2.6014 0.99   1314  145 0.1288 0.1982      5.2513      5.5279|
|  7:  2.6014 -  2.4718 0.99   1314  140 0.1339 0.1743      5.2283      5.3728|
|  8:  2.4718 -  2.3646 0.98   1291  149 0.1295 0.1859      5.1512      5.4105|
|  9:  2.3646 -  2.2739 0.98   1294  146 0.1302 0.1989      5.1211      5.4123|
| 10:  2.2739 -  2.1957 1.00   1305  147 0.1226 0.1812      5.0278      5.2477|
| 11:  2.1957 -  2.1272 0.98   1311  140 0.1209 0.2096      5.0227      5.4036|
| 12:  2.1272 -  2.0665 0.98   1269  140 0.1249 0.1790      4.9501      5.2084|
| 13:  2.0665 -  2.0123 0.99   1288  142 0.1198 0.1817      4.8565      5.0807|
| 14:  2.0123 -  1.9633 0.36    471   56 0.1090 0.1501      4.7286      4.9336|
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
|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: 15.0694 -  4.6873  1413   157  0.94   9.45   0.98     0.95       7377.96|
|  2:  4.6873 -  3.7392  1365   154  0.95   8.41   1.02     1.00       9788.75|
|  3:  3.7392 -  3.2720  1344   143  0.93  12.41   1.03     1.03      11836.29|
|  4:  3.2720 -  2.9754  1326   151  0.91  15.14   1.02     0.99      11660.92|
|  5:  2.9754 -  2.7635  1325   149  0.89  17.12   1.00     0.98       9362.13|
|  6:  2.7635 -  2.6014  1314   145  0.89  17.17   0.98     0.95       7735.98|
|  7:  2.6014 -  2.4718  1314   140  0.90  16.67   1.00     0.96       7031.02|
|  8:  2.4718 -  2.3646  1291   149  0.89  17.21   0.99     0.97       6366.78|
|  9:  2.3646 -  2.2739  1294   146  0.89  17.62   0.99     0.95       6039.06|
| 10:  2.2739 -  2.1957  1305   147  0.89  17.34   1.00     0.96       5178.33|
| 11:  2.1957 -  2.1272  1311   140  0.89  17.60   0.99     0.94       5137.07|
| 12:  2.1272 -  2.0665  1269   140  0.89  17.79   1.01     1.00       4714.78|
| 13:  2.0665 -  2.0123  1288   142  0.88  18.54   1.00     0.98       4024.03|
| 14:  2.0123 -  1.9633   471    56  0.91  15.54   0.99     0.95       3024.32|
|alpha:            min =        0.94 max =            1.03 mean =         0.97|
|beta:             min =     3024.32 max =        11836.29 mean =      7321.76|
|figures of merit: min =        0.00 max =            1.00 mean =         0.90|
|phase err.(work): min =        0.00 max =           89.94 mean =        15.50|
|phase err.(test): min =        0.00 max =           89.71 mean =        14.87|
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.96 - 15.07 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1195   r_free= 0.1694   ksol= 0.32   Bsol= 50.68   scale= 1.006   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-0.37,-0.62,0.99,0.00,0.00,0.00); trace/3= 0.00                            |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.16 A                  |
| x-ray target function (ml) for work reflections: 5.214563                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.96 - 15.07 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1195   r_free= 0.1694   ksol= 0.32   Bsol= 50.68   scale= 1.006   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-0.37,-0.62,0.99,0.00,0.00,0.00); trace/3= 0.00                            |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.16 A                  |
| x-ray target function (ml) for work reflections: 5.214563                   |
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
| Bin     Resolution   Compl.  No. Refl.    R-factors          Targets        |
|number     range              work test   work   test        work        test|
|  1: 15.0694 -  4.6873 0.99   1413  157 0.1000 0.1287      5.3897      5.5782|
|  2:  4.6873 -  3.7392 0.99   1365  154 0.0898 0.1232      5.4792      5.7075|
|  3:  3.7392 -  3.2720 0.99   1344  143 0.1133 0.1515      5.5356      5.8412|
|  4:  3.2720 -  2.9754 0.99   1326  151 0.1317 0.1844      5.5101      5.6742|
|  5:  2.9754 -  2.7635 0.99   1325  149 0.1421 0.1857      5.3858      5.6178|
|  6:  2.7635 -  2.6014 0.99   1314  145 0.1287 0.1981      5.2509      5.5275|
|  7:  2.6014 -  2.4718 0.99   1314  140 0.1339 0.1745      5.2283      5.3733|
|  8:  2.4718 -  2.3646 0.98   1291  149 0.1295 0.1858      5.1512      5.4103|
|  9:  2.3646 -  2.2739 0.98   1294  146 0.1302 0.1985       5.121      5.4116|
| 10:  2.2739 -  2.1957 1.00   1305  147 0.1225 0.1813      5.0279      5.2487|
| 11:  2.1957 -  2.1272 0.98   1311  140 0.1208 0.2096      5.0228      5.4041|
| 12:  2.1272 -  2.0665 0.98   1269  140 0.1249 0.1789        4.95      5.2085|
| 13:  2.0665 -  2.0123 0.99   1288  142 0.1198 0.1813       4.856      5.0791|
| 14:  2.0123 -  1.9633 0.36    471   56 0.1090 0.1500      4.7273      4.9329|
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
|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: 15.0694 -  4.6873  1413   157  0.94   9.46   0.98     0.95       7385.91|
|  2:  4.6873 -  3.7392  1365   154  0.95   8.41   1.02     1.00       9797.39|
|  3:  3.7392 -  3.2720  1344   143  0.93  12.41   1.03     1.03      11844.41|
|  4:  3.2720 -  2.9754  1326   151  0.91  15.14   1.02     0.99      11656.19|
|  5:  2.9754 -  2.7635  1325   149  0.89  17.11   1.00     0.98       9353.46|
|  6:  2.7635 -  2.6014  1314   145  0.89  17.16   0.99     0.95       7730.50|
|  7:  2.6014 -  2.4718  1314   140  0.90  16.67   1.00     0.96       7029.96|
|  8:  2.4718 -  2.3646  1291   149  0.89  17.21   0.99     0.97       6365.99|
|  9:  2.3646 -  2.2739  1294   146  0.89  17.62   1.00     0.95       6039.37|
| 10:  2.2739 -  2.1957  1305   147  0.89  17.35   1.00     0.96       5182.48|
| 11:  2.1957 -  2.1272  1311   140  0.89  17.61   1.00     0.95       5143.64|
| 12:  2.1272 -  2.0665  1269   140  0.89  17.79   1.01     1.00       4716.19|
| 13:  2.0665 -  2.0123  1288   142  0.88  18.53   1.01     0.98       4019.22|
| 14:  2.0123 -  1.9633   471    56  0.91  15.51   0.99     0.96       3015.35|
|alpha:            min =        0.95 max =            1.03 mean =         0.98|
|beta:             min =     3015.35 max =        11844.41 mean =      7322.46|
|figures of merit: min =        0.00 max =            1.00 mean =         0.90|
|phase err.(work): min =        0.00 max =           89.94 mean =        15.50|
|phase err.(test): min =        0.00 max =           89.71 mean =        14.87|
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 11.760)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      2.09    88.30   15.50    None  None   None       |
|    all(noH): 2823   0      2.09    88.30   15.50    None  None   None       |
|    Sol.    : 438    0      4.35    85.95   39.91    None  None   None       |
|    Mac.    : 2385   0      2.09    88.30   11.02    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:     2.091 -  10.712: 1573   |   5:    45.197 -  53.818:   94        |
|      1:    10.712 -  19.333:  649   |   6:    53.818 -  62.439:   68        |
|      2:    19.333 -  27.955:  175   |   7:    62.439 -  71.060:   31        |
|      3:    27.955 -  36.576:  118   |   8:    71.060 -  79.682:   10        |
|      4:    36.576 -  45.197:   99   |   9:    79.682 -  88.303:    6        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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


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

Number of peaks found at mFobs-DFmodel map (map cutoff=3.00 sigma)= 339         
Filter by distance & map next to the model:
   mapped sites are within: 0.284 - 5.791
   number of sites selected in [dist_min= 0.70, dist_max= 6.00]: 336 from: 339
   mapped sites are within: 0.715 - 5.791

peak=   10.145 closest distance to " CB  VAL A 230 " =    1.454
peak=    8.209 closest distance to " O   HOH Z 130 " =    1.748
peak=    7.835 closest distance to " CG2 VAL A 296 " =    1.242
peak=    7.176 closest distance to " CG  ARG A 138 " =    1.156
peak=    6.677 closest distance to " CD2 LEU A   5 " =    1.269
peak=    6.067 closest distance to " O   HOH Z  65 " =    1.475
peak=    5.996 closest distance to " NE2 GLN A  11 " =    1.156
peak=    5.454 closest distance to " CG  LEU A   5 " =    1.213
peak=    5.431 closest distance to " CD1AILE A 234 " =    1.072
peak=    5.375 closest distance to " O   HOH Z 142 " =    2.027
peak=    5.356 closest distance to " CG  PRO A  54 " =    1.426
peak=    5.349 closest distance to " NH2 ARG A  56 " =    2.050
peak=    5.332 closest distance to " O   HOH Z 222 " =    1.301
peak=    5.311 closest distance to " O   HOH Z   9 " =    1.805
peak=    5.192 closest distance to " NH1 ARG A 138 " =    1.019
peak=    5.038 closest distance to " CG  LEU A 228 " =    1.207
peak=    4.988 closest distance to " O   HOH Z 232 " =    2.199
peak=    4.961 closest distance to " O   HOH Z   7 " =    1.677
peak=    4.956 closest distance to " CB  PRO A  54 " =    1.083
peak=    4.822 closest distance to " O   HOH Z 425 " =    1.707
peak=    4.810 closest distance to " O   HOH Z 427 " =    2.364
peak=    4.752 closest distance to " O   HOH Z 424 " =    1.118
peak=    4.683 closest distance to " O   HOH Z 126 " =    2.049
peak=    4.624 closest distance to " CB  VAL A 230 " =    1.177
peak=    4.613 closest distance to " O   HOH Z 225 " =    1.578
peak=    4.603 closest distance to " CB  SER A   3 " =    1.426
peak=    4.557 closest distance to " O   HOH Z 417 " =    1.546
peak=    4.528 closest distance to " CG  PRO A 280 " =    0.835
peak=    4.508 closest distance to " CG  PRO A 198 " =    1.265
peak=    4.503 closest distance to " O   HOH Z 369 " =    2.037
peak=    4.492 closest distance to " O   HOH Z 139 " =    1.270
peak=    4.465 closest distance to " O   HOH Z 127 " =    1.064
peak=    4.464 closest distance to " O   HOH Z 287 " =    1.948
peak=    4.463 closest distance to " CB  GLN A 183 " =    1.239
peak=    4.462 closest distance to " CB  ASN A 148 " =    1.400
peak=    4.458 closest distance to " CB  ARG A 275 " =    0.957
peak=    4.452 closest distance to " O   HOH Z  63 " =    1.540
peak=    4.400 closest distance to " O   HOH Z 316 " =    3.033
peak=    4.392 closest distance to " CB  GLN A 223 " =    1.482
peak=    4.378 closest distance to " O   HOH Z 380 " =    1.881
peak=    4.360 closest distance to " O   HOH Z  78 " =    1.612
peak=    4.346 closest distance to " CG  LEU A 167 " =    1.259
peak=    4.343 closest distance to " CB  VAL A 296 " =    1.141
peak=    4.338 closest distance to " O   HOH Z 418 " =    1.032
peak=    4.316 closest distance to " O   HOH Z   2 " =    1.910
peak=    4.314 closest distance to " O   HOH Z 375 " =    1.039
peak=    4.300 closest distance to " O   HOH Z 124 " =    1.389
peak=    4.293 closest distance to " O   HOH Z 298 " =    1.834
peak=    4.216 closest distance to " CB  ASP A 124 " =    0.791
peak=    4.203 closest distance to " O   HOH Z 427 " =    1.158
peak=    4.183 closest distance to " CB  SER A  63 " =    1.296
peak=    4.159 closest distance to " O   HOH Z 361 " =    1.399
peak=    4.134 closest distance to " O   HOH Z   1 " =    1.856
peak=    4.133 closest distance to " CD  ARG A 138 " =    1.058
peak=    4.132 closest distance to " CB  SER A 216 " =    0.924
peak=    4.128 closest distance to " CG  PRO A 213 " =    1.254
peak=    4.107 closest distance to " CB  VAL A 202 " =    1.664
peak=    4.096 closest distance to " CB  ASN A  39 " =    0.938
peak=    4.089 closest distance to " O   HOH Z 423 " =    1.628
peak=    4.082 closest distance to " O   HOH Z 133 " =    1.459
peak=    4.081 closest distance to " O   HOH Z 410 " =    1.461
peak=    4.067 closest distance to " O   HOH Z 392 " =    1.369
peak=    4.060 closest distance to " O   HOH Z 209 " =    2.392
peak=    4.057 closest distance to " CD  ARG A  66 " =    2.515
peak=    4.046 closest distance to " O   HOH Z  24 " =    1.973
peak=    4.033 closest distance to " O   HOH Z 272 " =    1.838
peak=    3.995 closest distance to " O   HOH Z 422 " =    2.618
peak=    3.994 closest distance to " OG  SER A  62 " =    2.715
peak=    3.993 closest distance to " O   HOH Z 214 " =    2.152
peak=    3.985 closest distance to " CB BVAL A  41 " =    1.118
peak=    3.982 closest distance to " O   HOH Z 193 " =    1.745
peak=    3.980 closest distance to " NH1AARG A 145 " =    1.137
peak=    3.972 closest distance to " CD2 LEU A 228 " =    1.204
peak=    3.969 closest distance to " O   HOH Z 371 " =    2.730
peak=    3.954 closest distance to " O   HOH Z 419 " =    2.038
peak=    3.954 closest distance to " O   SER A  87 " =    2.393
peak=    3.944 closest distance to " O   PRO A 198 " =    1.296
peak=    3.911 closest distance to " O   HOH Z  59 " =    1.622
peak=    3.911 closest distance to " CA  ASN A 127 " =    1.095
peak=    3.886 closest distance to " O   HOH Z  61 " =    1.593
peak=    3.880 closest distance to " CG  TRP A 179 " =    2.243
peak=    3.878 closest distance to " O   ASN A 209 " =    1.535
peak=    3.853 closest distance to " O   HOH Z  55 " =    1.892
peak=    3.845 closest distance to " O   HOH Z 158 " =    3.012
peak=    3.843 closest distance to " O   HOH Z  59 " =    2.047
peak=    3.827 closest distance to " CB  TRP A 266 " =    1.029
peak=    3.826 closest distance to " CB  GLU A 128 " =    1.070
peak=    3.808 closest distance to " CG  PRO A 243 " =    1.107
peak=    3.800 closest distance to " CB  ASN A 142 " =    0.933
peak=    3.792 closest distance to " O   HOH Z 365 " =    3.098
peak=    3.791 closest distance to " CB  LEU A 228 " =    1.297
peak=    3.787 closest distance to " O   HOH Z 112 " =    0.999
peak=    3.785 closest distance to " O   HOH Z 236 " =    1.612
peak=    3.780 closest distance to " O   HOH Z 414 " =    1.262
peak=    3.771 closest distance to " O   HOH Z 234 " =    3.761
peak=    3.738 closest distance to " N   GLN A 278 " =    1.222
peak=    3.723 closest distance to " O   HOH Z  68 " =    2.155
peak=    3.722 closest distance to " CE3 TRP A 150 " =    1.033
peak=    3.715 closest distance to " O   HOH Z 359 " =    1.323
peak=    3.713 closest distance to " O   HOH Z 352 " =    1.650
peak=    3.695 closest distance to " CB  GLU A 277 " =    3.562
peak=    3.692 closest distance to " O   HOH Z 195 " =    1.534
peak=    3.689 closest distance to " CG  LYS A  76 " =    1.682
peak=    3.683 closest distance to " CG  GLN A  11 " =    2.248
peak=    3.678 closest distance to " O   HOH Z 362 " =    2.077
peak=    3.676 closest distance to " N   SER A 271 " =    0.987
peak=    3.671 closest distance to " OG BSER A 212 " =    2.813
peak=    3.656 closest distance to " O   HOH Z 258 " =    2.149
peak=    3.654 closest distance to " O   HOH Z 167 " =    1.854
peak=    3.646 closest distance to " CG  LEU A 281 " =    1.069
peak=    3.643 closest distance to " NH2AARG A 190 " =    1.690
peak=    3.643 closest distance to " O   HOH Z 222 " =    2.085
peak=    3.642 closest distance to " CB  VAL A 265 " =    1.338
peak=    3.628 closest distance to " O   HOH Z 375 " =    2.450
peak=    3.623 closest distance to " CB  MET A  40 " =    0.877
peak=    3.611 closest distance to " CA  ILE A 234 " =    0.969
peak=    3.610 closest distance to " N   PHE A 130 " =    1.220
peak=    3.609 closest distance to " CB  GLU A 152 " =    1.399
peak=    3.608 closest distance to " O   HOH Z 146 " =    1.627
peak=    3.605 closest distance to " O   HOH Z 425 " =    1.864
peak=    3.598 closest distance to " CA  SER A  87 " =    0.955
peak=    3.595 closest distance to " OG  SER A  62 " =    3.110
peak=    3.592 closest distance to " CB  GLN A  88 " =    1.332
peak=    3.592 closest distance to " CB  TRP A 179 " =    1.432
peak=    3.589 closest distance to " CH2 TRP A 266 " =    1.103
peak=    3.587 closest distance to " O   HOH Z 128 " =    1.964
peak=    3.583 closest distance to " CB  LEU A 237 " =    0.879
peak=    3.582 closest distance to " CD  ARG A 159 " =    0.734
peak=    3.578 closest distance to " N   ARG A 156 " =    1.266
peak=    3.577 closest distance to " O   HOH Z 189 " =    2.754
peak=    3.573 closest distance to " CA  GLY A 267 " =    1.123
peak=    3.573 closest distance to " O   HOH Z 175 " =    2.132
peak=    3.571 closest distance to " CG1 ILE A 151 " =    1.077
peak=    3.563 closest distance to " NH2BARG A 145 " =    1.976
peak=    3.554 closest distance to " CB  LYS A 117 " =    1.238
peak=    3.553 closest distance to " O   HOH Z 193 " =    1.948
peak=    3.552 closest distance to " O   HOH Z 424 " =    2.438
peak=    3.549 closest distance to " CA  LYS A 117 " =    1.120
peak=    3.546 closest distance to " O   HOH Z 405 " =    1.528
peak=    3.544 closest distance to " O   HOH Z 153 " =    3.719
peak=    3.541 closest distance to " ND2 ASN A 187 " =    1.741
peak=    3.540 closest distance to " CB  SER A 276 " =    1.187
peak=    3.534 closest distance to " O   HOH Z  88 " =    3.568
peak=    3.533 closest distance to " OD2 ASP A 286 " =    2.670
peak=    3.531 closest distance to " CA  PHE A 283 " =    1.280
peak=    3.527 closest distance to " CG BARG A 102 " =    1.932
peak=    3.524 closest distance to " CZ  PHE A 218 " =    1.125
peak=    3.523 closest distance to " O   HOH Z 184 " =    1.406
peak=    3.521 closest distance to " CG2 VAL A 257 " =    0.839
peak=    3.516 closest distance to " O   HOH Z 389 " =    1.273
peak=    3.516 closest distance to " O   HOH Z 289 " =    1.660
peak=    3.511 closest distance to " O   HOH Z  10 " =    1.753
peak=    3.510 closest distance to " O   HOH Z 144 " =    2.486
peak=    3.509 closest distance to " O   HOH Z 329 " =    3.933
peak=    3.504 closest distance to " O   HOH Z 217 " =    3.243
peak=    3.498 closest distance to " CB  ASN A 187 " =    1.088
peak=    3.495 closest distance to " CB  HIS A 108 " =    0.832
peak=    3.492 closest distance to " O   HOH Z 368 " =    1.935
peak=    3.487 closest distance to " O   HOH Z 425 " =    2.117
peak=    3.483 closest distance to " CB  SER A 212 " =    1.441
peak=    3.479 closest distance to " O   HOH Z 411 " =    3.540
peak=    3.478 closest distance to " CD  LYS A 166 " =    1.405
peak=    3.478 closest distance to " CA  ALA A 299 " =    0.943
peak=    3.475 closest distance to " CA  ALA A  51 " =    1.094
peak=    3.473 closest distance to " O   HOH Z  39 " =    1.280
peak=    3.469 closest distance to " OE2 GLU A   2 " =    2.005
peak=    3.460 closest distance to " O   HOH Z 181 " =    2.315
peak=    3.457 closest distance to " O   HOH Z 327 " =    1.582
peak=    3.453 closest distance to " CD1 LEU A 300 " =    1.220
peak=    3.453 closest distance to " CB  SER A 210 " =    0.936
peak=    3.451 closest distance to " O   HOH Z  51 " =    1.476
peak=    3.450 closest distance to " CD  GLN A 240 " =    1.608
peak=    3.449 closest distance to " CG  GLN A  88 " =    1.152
peak=    3.448 closest distance to " O   HOH Z 438 " =    2.213
peak=    3.443 closest distance to " O   HOH Z 233 " =    1.629
peak=    3.443 closest distance to " ND2 ASN A 110 " =    1.774
peak=    3.439 closest distance to " ND2 ASN A 249 " =    0.831
peak=    3.438 closest distance to " O   HOH Z 207 " =    2.375
peak=    3.436 closest distance to " CG2 THR A 221 " =    1.232
peak=    3.435 closest distance to " CD  ARG A 269 " =    0.966
peak=    3.430 closest distance to " O   HOH Z  88 " =    3.001
peak=    3.428 closest distance to " CB  THR A 157 " =    1.081
peak=    3.425 closest distance to " N   TYR A  15 " =    0.992
peak=    3.421 closest distance to " O   HOH Z 193 " =    1.765
peak=    3.420 closest distance to " O   HOH Z 373 " =    1.485
peak=    3.420 closest distance to " O   PRO A 198 " =    1.525
peak=    3.418 closest distance to " OE2 GLU A  53 " =    1.841
peak=    3.414 closest distance to " O   HOH Z  44 " =    1.960
peak=    3.411 closest distance to " NZ BLYS A 290 " =    0.984
peak=    3.411 closest distance to " O   HOH Z   9 " =    1.615
peak=    3.408 closest distance to " CB  LEU A 143 " =    1.075
peak=    3.405 closest distance to " O   HOH Z 250 " =    1.363
peak=    3.402 closest distance to " CA  THR A 264 " =    0.715
peak=    3.402 closest distance to " CE  MET A  93 " =    1.536
peak=    3.401 closest distance to " O   HOH Z 145 " =    1.871
peak=    3.400 closest distance to " CB  ILE A 234 " =    1.029
peak=    3.399 closest distance to " O   HOH Z 389 " =    1.669
peak=    3.394 closest distance to " O   HOH Z 128 " =    2.168
peak=    3.391 closest distance to " NZ  LYS A 117 " =    1.251
peak=    3.390 closest distance to " O   HOH Z 273 " =    2.830
peak=    3.388 closest distance to " N   GLU A   2 " =    1.348
peak=    3.380 closest distance to " CA  TYR A  30 " =    0.919
peak=    3.379 closest distance to " O   HOH Z  97 " =    1.994
peak=    3.378 closest distance to " CB  ASN A 110 " =    1.029
peak=    3.375 closest distance to " O   HOH Z  58 " =    1.905
peak=    3.374 closest distance to " CB  GLN A  89 " =    1.171
peak=    3.372 closest distance to " O   HOH Z 109 " =    2.266
peak=    3.366 closest distance to " O   HOH Z  44 " =    2.618
peak=    3.363 closest distance to " ND2BASN A 224 " =    0.848
peak=    3.362 closest distance to " CA  ASN A 215 " =    1.130
peak=    3.362 closest distance to " NH1 ARG A  14 " =    0.987
peak=    3.360 closest distance to " CG1 ILE A 263 " =    1.267
peak=    3.358 closest distance to " NH2BARG A 190 " =    1.453
peak=    3.357 closest distance to " CB  VAL A 250 " =    1.049
peak=    3.355 closest distance to " CB  ARG A 138 " =    1.088
peak=    3.355 closest distance to " CA  THR A 221 " =    0.915
peak=    3.354 closest distance to " CE3 TRP A 274 " =    1.296
peak=    3.351 closest distance to " CD1 ILE A  33 " =    1.810
peak=    3.347 closest distance to " NE AARG A 275 " =    1.402
peak=    3.346 closest distance to " NE2 GLN A  58 " =    3.768
peak=    3.345 closest distance to " O   HOH Z 371 " =    1.913
peak=    3.343 closest distance to " N   ASN A 127 " =    1.384
peak=    3.340 closest distance to " O   HOH Z 154 " =    1.873
peak=    3.339 closest distance to " CD1 LEU A   5 " =    1.382
peak=    3.337 closest distance to " CB  ARG A 190 " =    1.740
peak=    3.336 closest distance to " CG1 ILE A  33 " =    1.354
peak=    3.333 closest distance to " O   HOH Z 119 " =    1.531
peak=    3.329 closest distance to " O   HOH Z 133 " =    2.566
peak=    3.328 closest distance to " CG2 ILE A 234 " =    0.804
peak=    3.327 closest distance to " O   HOH Z  22 " =    2.084
peak=    3.324 closest distance to " CB  SER A 273 " =    0.894
peak=    3.324 closest distance to " O   HOH Z 368 " =    3.594
peak=    3.323 closest distance to " O   HOH Z 305 " =    3.430
peak=    3.312 closest distance to " O   HOH Z 409 " =    2.337
peak=    3.310 closest distance to " O   HOH Z 290 " =    1.010
peak=    3.307 closest distance to " CE3 TRP A  85 " =    1.233
peak=    3.305 closest distance to " O   HOH Z 145 " =    2.042
peak=    3.301 closest distance to " CA  ILE A 106 " =    0.751
peak=    3.300 closest distance to " O   MET A 105 " =    1.695
peak=    3.294 closest distance to " O   HOH Z 145 " =    3.742
peak=    3.292 closest distance to " CA  LEU A 101 " =    1.435
peak=    3.291 closest distance to " OG BSER A  99 " =    2.170
peak=    3.286 closest distance to " CA  LEU A 282 " =    1.062
peak=    3.285 closest distance to " CE1 TYR A 186 " =    1.303
peak=    3.285 closest distance to " CB  ALA A 104 " =    0.720
peak=    3.280 closest distance to " O   GLY A 302 " =    2.110
peak=    3.275 closest distance to " O   HOH Z 423 " =    1.558
peak=    3.273 closest distance to " N   ALA A 256 " =    0.928
peak=    3.272 closest distance to " CG  GLN A  89 " =    1.476
peak=    3.271 closest distance to " O   HOH Z 133 " =    2.558
peak=    3.263 closest distance to " CB  ARG A  79 " =    1.273
peak=    3.260 closest distance to " O   HOH Z 353 " =    1.783
peak=    3.258 closest distance to " O   HOH Z 180 " =    2.133
peak=    3.256 closest distance to " O   HOH Z 148 " =    2.276
peak=    3.249 closest distance to " O   HOH Z   1 " =    1.783
peak=    3.248 closest distance to " CB  ARG A 139 " =    1.022
peak=    3.247 closest distance to " CB  ALA A 114 " =    1.507
peak=    3.245 closest distance to " O   HOH Z 213 " =    2.235
peak=    3.243 closest distance to " NH1BARG A 145 " =    1.312
peak=    3.243 closest distance to " O   HOH Z 403 " =    1.511
peak=    3.241 closest distance to " O   HOH Z 356 " =    1.344
peak=    3.239 closest distance to " CG1 ILE A  49 " =    1.379
peak=    3.238 closest distance to " O   HOH Z 303 " =    2.838
peak=    3.238 closest distance to " CZ  PHE A 192 " =    0.929
peak=    3.236 closest distance to " CB  ASN A 215 " =    1.160
peak=    3.235 closest distance to " O   HOH Z 172 " =    2.527
peak=    3.232 closest distance to " O   HOH Z 209 " =    2.388
peak=    3.227 closest distance to " O  BHOH Z  74 " =    1.359
peak=    3.226 closest distance to " O   HOH Z 344 " =    2.892
peak=    3.225 closest distance to " CG  ARG A 159 " =    0.961
peak=    3.224 closest distance to " OH  TYR A 116 " =    1.065
peak=    3.224 closest distance to " CZ  PHE A  38 " =    1.201
peak=    3.220 closest distance to " O   CYS A 168 " =    1.284
peak=    3.214 closest distance to " CA  ALA A 248 " =    1.216
peak=    3.211 closest distance to " N   SER A  97 " =    0.854
peak=    3.210 closest distance to " CG  GLN A 278 " =    3.716
peak=    3.208 closest distance to " CB  SER A  26 " =    1.601
peak=    3.208 closest distance to " NZ  LYS A  48 " =    1.375
peak=    3.207 closest distance to " CG2 ILE A  20 " =    1.727
peak=    3.205 closest distance to " CG BARG A 190 " =    1.155
peak=    3.200 closest distance to " O   HOH Z 412 " =    5.185
peak=    3.197 closest distance to " OE1 GLU A   2 " =    1.918
peak=    3.197 closest distance to " O   HOH Z  40 " =    2.066
peak=    3.195 closest distance to " CA  ARG A 195 " =    1.308
peak=    3.192 closest distance to " CZ3 TRP A  92 " =    1.245
peak=    3.190 closest distance to " CA  ALA A 160 " =    0.994
peak=    3.188 closest distance to " O   HOH Z 384 " =    1.322
peak=    3.188 closest distance to " CB  GLU A 152 " =    1.455
peak=    3.188 closest distance to " O   HOH Z  88 " =    3.527
peak=    3.187 closest distance to " O   HOH Z 130 " =    2.677
peak=    3.180 closest distance to " OD1 ASN A 217 " =    1.645
peak=    3.175 closest distance to " O   HOH Z 438 " =    2.801
peak=    3.173 closest distance to " CB  ALA A 291 " =    1.374
peak=    3.167 closest distance to " O   HOH Z 343 " =    3.262
peak=    3.162 closest distance to " OG BSER A 164 " =    2.237
peak=    3.162 closest distance to " CD  ARG A  24 " =    1.053
peak=    3.159 closest distance to " CA  ALA A 158 " =    1.154
peak=    3.154 closest distance to " O   HOH Z 263 " =    1.657
peak=    3.145 closest distance to " CA  MET A 105 " =    0.863
peak=    3.141 closest distance to " O   HOH Z 113 " =    2.024
peak=    3.138 closest distance to " O   HOH Z 132 " =    2.427
peak=    3.136 closest distance to " O   HOH Z 110 " =    1.728
peak=    3.133 closest distance to " CB  GLU A 175 " =    0.945
peak=    3.130 closest distance to " OG BSER A 258 " =    0.831
peak=    3.128 closest distance to " O   HOH Z 323 " =    1.651
peak=    3.127 closest distance to " O   HOH Z 414 " =    3.240
peak=    3.126 closest distance to " CG1 VAL A 153 " =    0.870
peak=    3.126 closest distance to " OE1 GLN A  11 " =    2.440
peak=    3.123 closest distance to " O   HOH Z 403 " =    1.451
peak=    3.121 closest distance to " CB  ALA A   1 " =    4.722
peak=    3.119 closest distance to " CG AARG A 275 " =    1.175
peak=    3.114 closest distance to " O   HOH Z 357 " =    2.128
peak=    3.110 closest distance to " CA  TYR A 116 " =    1.455
peak=    3.109 closest distance to " O   TYR A 116 " =    1.259
peak=    3.108 closest distance to " CA  ARG A 102 " =    1.129
peak=    3.105 closest distance to " O   HOH Z  20 " =    1.658
peak=    3.105 closest distance to " ND1 HIS A  81 " =    1.720
peak=    3.101 closest distance to " O   HOH Z 209 " =    2.180
peak=    3.101 closest distance to " O   HOH Z 406 " =    1.566
peak=    3.101 closest distance to " O   HOH Z 389 " =    3.022
peak=    3.096 closest distance to " CB  SER A  62 " =    1.158
peak=    3.095 closest distance to " O   HOH Z 334 " =    1.357
peak=    3.085 closest distance to " O   HOH Z 438 " =    2.116
peak=    3.085 closest distance to " CA  GLY A 136 " =    1.005
peak=    3.074 closest distance to " NE2 GLN A  58 " =    5.791
peak=    3.073 closest distance to " CA  ARG A 139 " =    0.908
peak=    3.072 closest distance to " CA  ASP A 149 " =    1.216
peak=    3.072 closest distance to " O   HOH Z  21 " =    1.634
peak=    3.065 closest distance to " O   HOH Z 368 " =    2.704
peak=    3.063 closest distance to " O   HOH Z 272 " =    2.178
peak=    3.059 closest distance to " O   HOH Z 426 " =    2.105
peak=    3.057 closest distance to " O   HOH Z  50 " =    1.615
peak=    3.049 closest distance to " CB  LEU A 300 " =    0.879
peak=    3.045 closest distance to " O   HOH Z 340 " =    1.798
peak=    3.036 closest distance to " N   SER A 135 " =    1.202
peak=    3.015 closest distance to " O   HOH Z 299 " =    4.332

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

Number of peaks found at mFobs-DFmodel map (map cutoff=3.00 sigma)= 210         
Filter by distance & map next to the model:
   mapped sites are within: 0.678 - 5.989
   number of sites selected in [dist_min= 0.70, dist_max= 6.00]: 207 from: 210
   mapped sites are within: 0.759 - 5.989

peak=   -5.080 closest distance to " CG2 VAL A 230 " =    0.759
peak=   -4.485 closest distance to " OG BSER A 134 " =    1.513
peak=   -4.371 closest distance to " CG  ARG A 138 " =    0.973
peak=   -4.253 closest distance to " CD  ARG A 138 " =    1.267
peak=   -4.252 closest distance to " CD  ARG A  14 " =    3.104
peak=   -4.230 closest distance to " CE2 PHE A 218 " =    2.438
peak=   -4.217 closest distance to " CB  PRO A 243 " =    2.624
peak=   -4.150 closest distance to " O   HOH Z 266 " =    4.939
peak=   -4.120 closest distance to " O   PRO A 198 " =    1.147
peak=   -4.100 closest distance to " OG  SER A  87 " =    1.348
peak=   -4.088 closest distance to " O   SER A 135 " =    1.435
peak=   -4.051 closest distance to " O   HOH Z 185 " =    2.081
peak=   -4.008 closest distance to " CD  ARG A 156 " =    1.994
peak=   -3.995 closest distance to " O   HOH Z 131 " =    3.931
peak=   -3.956 closest distance to " CD1 LEU A 255 " =    2.947
peak=   -3.910 closest distance to " O   HOH Z 359 " =    1.614
peak=   -3.899 closest distance to " N   THR A 157 " =    1.447
peak=   -3.885 closest distance to " CA  ASP A  27 " =    2.385
peak=   -3.822 closest distance to " CB  ALA A  43 " =    2.378
peak=   -3.796 closest distance to " O   VAL A  67 " =    2.477
peak=   -3.778 closest distance to " CB  VAL A 230 " =    1.126
peak=   -3.758 closest distance to " NH2 ARG A  79 " =    2.058
peak=   -3.751 closest distance to " O   HOH Z  43 " =    1.827
peak=   -3.751 closest distance to " N   PRO A 163 " =    1.516
peak=   -3.732 closest distance to " CG2 VAL A 296 " =    1.449
peak=   -3.718 closest distance to " O   HOH Z 409 " =    5.989
peak=   -3.717 closest distance to " CB  ASP A 132 " =    2.382
peak=   -3.713 closest distance to " CZ2 TRP A 274 " =    0.921
peak=   -3.701 closest distance to " O   HOH Z 407 " =    3.123
peak=   -3.697 closest distance to " CA  GLY A  98 " =    1.872
peak=   -3.678 closest distance to " O   SER A  22 " =    2.511
peak=   -3.673 closest distance to " O   HOH Z 389 " =    1.392
peak=   -3.667 closest distance to " CB  ALA A 248 " =    2.096
peak=   -3.661 closest distance to " CG  PRO A 163 " =    2.574
peak=   -3.645 closest distance to " O   HOH Z  11 " =    1.863
peak=   -3.633 closest distance to " O   HOH Z 290 " =    1.141
peak=   -3.632 closest distance to " O   HOH Z 427 " =    1.780
peak=   -3.630 closest distance to " CB  TYR A  15 " =    2.109
peak=   -3.629 closest distance to " O   HOH Z 211 " =    1.331
peak=   -3.621 closest distance to " CD2 TYR A 293 " =    1.850
peak=   -3.616 closest distance to " ND2 ASN A 187 " =    1.538
peak=   -3.614 closest distance to " O   HOH Z 359 " =    3.444
peak=   -3.611 closest distance to " O   PRO A 243 " =    2.423
peak=   -3.607 closest distance to " O   HOH Z 377 " =    0.933
peak=   -3.602 closest distance to " CA  GLY A 241 " =    2.226
peak=   -3.580 closest distance to " CD2 LEU A   5 " =    0.993
peak=   -3.580 closest distance to " CD  LYS A 289 " =    2.421
peak=   -3.575 closest distance to " ND2 ASN A 249 " =    2.384
peak=   -3.575 closest distance to " O   HOH Z  52 " =    1.584
peak=   -3.575 closest distance to " CE2 TYR A 116 " =    3.154
peak=   -3.569 closest distance to " O   HOH Z 377 " =    1.704
peak=   -3.565 closest distance to " O   HOH Z  39 " =    1.173
peak=   -3.564 closest distance to " O   PRO A 163 " =    1.900
peak=   -3.563 closest distance to " O   GLY A  80 " =    2.472
peak=   -3.541 closest distance to " O   ALA A  84 " =    1.731
peak=   -3.539 closest distance to " CA  GLY A 203 " =    2.360
peak=   -3.525 closest distance to " CD  GLN A 223 " =    2.469
peak=   -3.517 closest distance to " O   HOH Z 231 " =    1.824
peak=   -3.516 closest distance to " N   ALA A  43 " =    2.585
peak=   -3.508 closest distance to " CE2 TYR A  30 " =    2.567
peak=   -3.498 closest distance to " CD1 LEU A 101 " =    2.251
peak=   -3.497 closest distance to " O   HOH Z 348 " =    1.774
peak=   -3.495 closest distance to " NH2 ARG A 219 " =    1.753
peak=   -3.493 closest distance to " CG  MET A 105 " =    0.967
peak=   -3.492 closest distance to " CD2 LEU A 237 " =    2.845
peak=   -3.489 closest distance to " O   HOH Z 368 " =    2.452
peak=   -3.489 closest distance to " CD  LYS A 166 " =    2.433
peak=   -3.478 closest distance to " C   HIS A 108 " =    1.215
peak=   -3.477 closest distance to " O   HOH Z 350 " =    1.770
peak=   -3.474 closest distance to " OG  SER A 245 " =    1.264
peak=   -3.468 closest distance to " OG  SER A  97 " =    2.148
peak=   -3.465 closest distance to " O   HOH Z 216 " =    1.551
peak=   -3.460 closest distance to " CB  ALA A 227 " =    2.400
peak=   -3.456 closest distance to " O   HOH Z 298 " =    1.045
peak=   -3.455 closest distance to " CB  ALA A   9 " =    2.391
peak=   -3.452 closest distance to " CG  TRP A 266 " =    1.775
peak=   -3.450 closest distance to " C   ARG A 269 " =    1.385
peak=   -3.450 closest distance to " O   HOH Z 351 " =    1.503
peak=   -3.446 closest distance to " OG  SER A  62 " =    4.379
peak=   -3.445 closest distance to " ND2 ASN A 285 " =    2.077
peak=   -3.440 closest distance to " O   ILE A  49 " =    1.724
peak=   -3.437 closest distance to " CB  PHE A 130 " =    1.319
peak=   -3.417 closest distance to " CB  TRP A  85 " =    2.635
peak=   -3.417 closest distance to " OE1 GLN A  88 " =    1.104
peak=   -3.415 closest distance to " CE2 TRP A  70 " =    2.324
peak=   -3.411 closest distance to " O   HOH Z 292 " =    1.597
peak=   -3.408 closest distance to " CD  GLN A  58 " =    0.997
peak=   -3.406 closest distance to " C   GLU A 236 " =    0.908
peak=   -3.406 closest distance to " OE1 GLU A 277 " =    2.234
peak=   -3.402 closest distance to " O   HOH Z 389 " =    2.091
peak=   -3.401 closest distance to " O   HOH Z 140 " =    1.319
peak=   -3.400 closest distance to " N   VAL A  72 " =    1.687
peak=   -3.399 closest distance to " CB  ALA A 161 " =    2.491
peak=   -3.395 closest distance to " O   HOH Z 134 " =    3.075
peak=   -3.385 closest distance to " OE2 GLU A 152 " =    1.143
peak=   -3.382 closest distance to " O   HOH Z 435 " =    2.274
peak=   -3.382 closest distance to " CB  PRO A  90 " =    1.678
peak=   -3.381 closest distance to " CB  ASN A  39 " =    2.153
peak=   -3.380 closest distance to " CZ  TYR A 169 " =    1.616
peak=   -3.379 closest distance to " CB  ALA A   7 " =    2.002
peak=   -3.367 closest distance to " CA  GLY A 133 " =    2.005
peak=   -3.366 closest distance to " O   ARG A 145 " =    1.417
peak=   -3.360 closest distance to " O   HOH Z 103 " =    1.425
peak=   -3.359 closest distance to " N   ALA A 226 " =    2.120
peak=   -3.354 closest distance to " C   MET A 188 " =    1.578
peak=   -3.350 closest distance to " O   HOH Z  60 " =    1.813
peak=   -3.349 closest distance to " O   HOH Z 134 " =    3.792
peak=   -3.346 closest distance to " CB  CYS A 201 " =    2.134
peak=   -3.345 closest distance to " O   HOH Z  60 " =    2.407
peak=   -3.344 closest distance to " CA  ASN A 127 " =    1.139
peak=   -3.342 closest distance to " O   HOH Z 353 " =    1.339
peak=   -3.338 closest distance to " O   HOH Z 298 " =    2.886
peak=   -3.337 closest distance to " O   HOH Z 166 " =    1.703
peak=   -3.336 closest distance to " O   HOH Z  67 " =    3.087
peak=   -3.333 closest distance to " CG2 VAL A 296 " =    0.822
peak=   -3.332 closest distance to " CB  CYS A 254 " =    1.873
peak=   -3.331 closest distance to " O   TYR A  30 " =    2.541
peak=   -3.326 closest distance to " O   HOH Z 352 " =    2.087
peak=   -3.317 closest distance to " OG  SER A  63 " =    1.334
peak=   -3.317 closest distance to " O   VAL A 189 " =    2.499
peak=   -3.313 closest distance to " C   ALA A 158 " =    1.363
peak=   -3.312 closest distance to " CE  MET A 105 " =    2.411
peak=   -3.306 closest distance to " CB  GLN A  55 " =    1.221
peak=   -3.304 closest distance to " CD1 PHE A  59 " =    2.057
peak=   -3.304 closest distance to " OD2 ASP A  27 " =    1.717
peak=   -3.304 closest distance to " O   SER A 141 " =    1.892
peak=   -3.303 closest distance to " CG1 VAL A 296 " =    1.384
peak=   -3.300 closest distance to " OG  SER A 206 " =    1.770
peak=   -3.298 closest distance to " ND2 ASN A 252 " =    2.019
peak=   -3.297 closest distance to " O   GLN A  11 " =    1.480
peak=   -3.294 closest distance to " CB  TYR A 172 " =    2.447
peak=   -3.287 closest distance to " O   HOH Z 100 " =    1.251
peak=   -3.280 closest distance to " CZ  PHE A 130 " =    0.959
peak=   -3.280 closest distance to " NH2AARG A 275 " =    5.373
peak=   -3.278 closest distance to " N   ARG A 138 " =    1.518
peak=   -3.277 closest distance to " N   ALA A   1 " =    1.713
peak=   -3.271 closest distance to " O   SER A 271 " =    2.099
peak=   -3.270 closest distance to " O   HOH Z 122 " =    2.098
peak=   -3.264 closest distance to " CG2 ILE A  20 " =    2.898
peak=   -3.258 closest distance to " CB  PRO A 213 " =    2.121
peak=   -3.257 closest distance to " CZ3 TRP A 179 " =    1.211
peak=   -3.255 closest distance to " CE3 TRP A 123 " =    1.319
peak=   -3.252 closest distance to " O   HOH Z 243 " =    1.958
peak=   -3.250 closest distance to " CB  PRO A 163 " =    2.407
peak=   -3.249 closest distance to " O   HOH Z 111 " =    2.007
peak=   -3.246 closest distance to " OG ASER A 134 " =    1.176
peak=   -3.244 closest distance to " O   HOH Z 282 " =    4.998
peak=   -3.242 closest distance to " O   HOH Z 238 " =    1.007
peak=   -3.242 closest distance to " O   HOH Z 414 " =    1.865
peak=   -3.240 closest distance to " O   HOH Z 191 " =    5.438
peak=   -3.238 closest distance to " OH  TYR A 172 " =    1.849
peak=   -3.236 closest distance to " OD2 ASP A  50 " =    1.635
peak=   -3.232 closest distance to " OD1 ASP A 191 " =    1.885
peak=   -3.232 closest distance to " CA  HIS A 207 " =    1.233
peak=   -3.231 closest distance to " O   HOH Z 426 " =    2.185
peak=   -3.228 closest distance to " O   HOH Z 394 " =    1.520
peak=   -3.227 closest distance to " N   SER A 276 " =    1.317
peak=   -3.223 closest distance to " O   GLY A 203 " =    2.500
peak=   -3.217 closest distance to " O   HOH Z 368 " =    1.387
peak=   -3.214 closest distance to " O   HOH Z 385 " =    1.912
peak=   -3.213 closest distance to " CG2 THR A 178 " =    2.167
peak=   -3.210 closest distance to " O   HOH Z 207 " =    2.005
peak=   -3.208 closest distance to " O   GLY A  80 " =    2.555
peak=   -3.204 closest distance to " O   ASP A 270 " =    1.568
peak=   -3.204 closest distance to " O   HOH Z 421 " =    3.324
peak=   -3.201 closest distance to " O   HOH Z 286 " =    1.776
peak=   -3.196 closest distance to " CD  PRO A 243 " =    2.060
peak=   -3.193 closest distance to " N   HIS A 115 " =    2.145
peak=   -3.193 closest distance to " CD1 PHE A  61 " =    2.933
peak=   -3.193 closest distance to " O   HOH Z 415 " =    1.189
peak=   -3.184 closest distance to " O   HOH Z 198 " =    2.183
peak=   -3.175 closest distance to " O   HOH Z 313 " =    1.293
peak=   -3.174 closest distance to " OD2 ASP A 191 " =    1.420
peak=   -3.172 closest distance to " O   GLY A 211 " =    1.181
peak=   -3.166 closest distance to " O   HOH Z 114 " =    1.627
peak=   -3.164 closest distance to " CB  ALA A 114 " =    2.382
peak=   -3.158 closest distance to " O   HOH Z 256 " =    1.328
peak=   -3.157 closest distance to " CD1 LEU A 228 " =    2.280
peak=   -3.157 closest distance to " O   ASN A 301 " =    1.473
peak=   -3.155 closest distance to " N   VAL A 232 " =    2.168
peak=   -3.152 closest distance to " CD2 LEU A 237 " =    2.724
peak=   -3.150 closest distance to " O   HOH Z 111 " =    1.118
peak=   -3.150 closest distance to " O   HOH Z  52 " =    2.062
peak=   -3.149 closest distance to " CB  ALA A 244 " =    2.102
peak=   -3.146 closest distance to " CG1 VAL A 112 " =    2.574
peak=   -3.145 closest distance to " O   HOH Z  65 " =    1.178
peak=   -3.143 closest distance to " O   HOH Z 166 " =    1.561
peak=   -3.141 closest distance to " N   ALA A 248 " =    1.510
peak=   -3.129 closest distance to " CG  ASN A 301 " =    1.984
peak=   -3.125 closest distance to " CB  TYR A  68 " =    1.526
peak=   -3.120 closest distance to " O   HOH Z 111 " =    4.548
peak=   -3.115 closest distance to " CG1 VAL A 197 " =    2.404
peak=   -3.114 closest distance to " N   GLN A  58 " =    1.906
peak=   -3.112 closest distance to " O   MET A  40 " =    2.852
peak=   -3.104 closest distance to " CG2 VAL A 202 " =    2.650
peak=   -3.098 closest distance to " CG  GLN A 240 " =    2.365
peak=   -3.097 closest distance to " CG  LEU A 281 " =    1.728
peak=   -3.096 closest distance to " CD2 PHE A  61 " =    2.024
peak=   -3.093 closest distance to " CZ2 TRP A  92 " =    2.828
peak=   -3.080 closest distance to " CD2 LEU A 297 " =    1.958
peak=   -3.077 closest distance to " O   HOH Z 193 " =    1.989
peak=   -3.074 closest distance to " O   HOH Z 357 " =    2.076
peak=   -3.074 closest distance to " CB  ASP A 132 " =    2.456
peak=   -3.068 closest distance to " O   ALA A   1 " =    1.363
peak=   -3.025 closest distance to " CG  PHE A 283 " =    2.550
peak=   -3.024 closest distance to " OG BSER A 134 " =    1.839
peak=   -3.017 closest distance to " CE  MET A 105 " =    2.327

================= 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    :  0.4766 0.4700   6.282205e+00   6.264937e+00
   1_bss:  0.4686 0.4558   6.276396e+00   6.255642e+00
   1_xyz:  0.3878 0.4107   6.172235e+00   6.203473e+00
   1_adp:  0.3437 0.4032   6.106244e+00   6.194456e+00
   1_occ:  0.3436 0.4027   6.105851e+00   6.194819e+00
   2_bss:  0.3399 0.3953   6.104709e+00   6.191351e+00
   2_xyz:  0.2776 0.3379   5.930824e+00   6.063878e+00
   2_adp:  0.2568 0.3243   5.880866e+00   6.032397e+00
   2_occ:  0.2566 0.3246   5.880941e+00   6.033049e+00
   3_bss:  0.2554 0.3224   5.880476e+00   6.031478e+00
   3_xyz:  0.1918 0.2512   5.617204e+00   5.811290e+00
   3_adp:  0.1739 0.2350   5.534399e+00   5.752118e+00
   3_occ:  0.1738 0.2345   5.533315e+00   5.750585e+00
   4_bss:  0.1734 0.2339   5.532216e+00   5.748409e+00
   4_xyz:  0.1401 0.1968   5.356132e+00   5.601190e+00
   4_adp:  0.1298 0.1827   5.284057e+00   5.525662e+00
   4_occ:  0.1297 0.1825   5.283277e+00   5.524600e+00
   5_bss:  0.1301 0.1819   5.281865e+00   5.522616e+00
   5_xyz:  0.1220 0.1723   5.229776e+00   5.472045e+00
   5_adp:  0.1197 0.1697   5.215370e+00   5.457225e+00
   5_occ:  0.1196 0.1695   5.214597e+00   5.456213e+00
   5_bss:  0.1195 0.1694   5.214563e+00   5.456181e+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:  0.350   0.000   7.383  10.421   8.515   0.000   0.000   0.000
   1_xyz:  0.350   0.000   7.383  10.421   8.515   0.000   0.000   0.000
   1_adp:  0.350   0.000   7.383  10.421   8.515   0.000   0.000   0.000
   1_occ:  0.350   0.000   7.383  10.421   8.515   0.000   0.000   0.000
   2_bss:  0.351  37.825   3.771   5.865   4.682   0.000   0.000   0.000
   2_xyz:  0.351  37.825   3.771   5.865   4.682   0.000   0.000   0.000
   2_adp:  0.351  37.825   3.771   5.865   4.682   0.000   0.000   0.000
   2_occ:  0.351  37.825   3.771   5.865   4.682   0.000   0.000   0.000
   3_bss:  0.339  49.037   2.456   3.307   3.547   0.000   0.000   0.000
   3_xyz:  0.339  49.037   2.456   3.307   3.547   0.000   0.000   0.000
   3_adp:  0.339  49.037   2.456   3.307   3.547   0.000   0.000   0.000
   3_occ:  0.339  49.037   2.456   3.307   3.547   0.000   0.000   0.000
   4_bss:  0.328  45.997   1.633   1.843   3.015   0.000   0.000   0.000
   4_xyz:  0.328  45.997   1.633   1.843   3.015   0.000   0.000   0.000
   4_adp:  0.328  45.997   1.633   1.843   3.015   0.000   0.000   0.000
   4_occ:  0.328  45.997   1.633   1.843   3.015   0.000   0.000   0.000
   5_bss:  0.321  48.591   1.595   1.465   2.973   0.000   0.000   0.000
   5_xyz:  0.321  48.591   1.595   1.465   2.973   0.000   0.000   0.000
   5_adp:  0.321  48.591   1.595   1.465   2.973   0.000   0.000   0.000
   5_occ:  0.321  48.591   1.595   1.465   2.973   0.000   0.000   0.000
   5_bss:  0.321  50.682  -0.372  -0.620   0.992   0.000   0.000   0.000
------------------------------------------------------------------------
 stage     <pher>    fom   alpha         beta
   0    :  57.224 0.4292  0.5062    68865.303
   1_bss:  56.785 0.4336  0.6556    66523.534
   1_xyz:  49.252 0.5280  0.7806    52291.199
   1_adp:  46.812 0.5588  0.8768    49560.339
   1_occ:  46.881 0.5579  0.8749    49664.953
   2_bss:  46.177 0.5667  0.7786    48644.320
   2_xyz:  36.411 0.6839  0.9183    31908.196
   2_adp:  33.980 0.7128  0.9491    29071.623
   2_occ:  34.029 0.7122  0.9484    29143.488
   3_bss:  33.812 0.7147  0.8968    28920.064
   3_xyz:  24.822 0.8125  0.9846    16133.615
   3_adp:  22.650 0.8353  0.9965    13952.244
   3_occ:  22.621 0.8356  0.9965    13898.957
   4_bss:  22.552 0.8362  0.9637    13808.847
   4_xyz:  18.973 0.8709  0.9804     9980.608
   4_adp:  17.135 0.8882  0.9791     8543.113
   4_occ:  17.113 0.8883  0.9789     8517.274
   5_bss:  17.047 0.8888  0.9738     8447.091
   5_xyz:  15.840 0.8996  0.9780     7538.692
   5_adp:  15.452 0.9033  0.9725     7348.959
   5_occ:  15.435 0.9034  0.9724     7321.174
   5_bss:  15.436 0.9034  0.9752     7321.868
------------------------------------------------------------------------
 stage       angl   bond   chir   dihe   plan   repu  geom_target
   0    :  24.226  0.414  2.119 33.790  0.145  4.088   5.3591e+01
   1_bss:  24.226  0.414  2.119 33.790  0.145  4.088   5.3591e+01
   1_xyz:   1.668  0.013  0.105 18.324  0.006  4.107   1.3941e-01
   1_adp:   1.668  0.013  0.105 18.324  0.006  4.107   1.3941e-01
   1_occ:   1.668  0.013  0.105 18.324  0.006  4.107   1.3941e-01
   2_bss:   1.668  0.013  0.105 18.324  0.006  4.107   1.3941e-01
   2_xyz:   1.134  0.008  0.081 16.278  0.005  4.107   8.1573e-02
   2_adp:   1.134  0.008  0.081 16.278  0.005  4.107   8.1573e-02
   2_occ:   1.134  0.008  0.081 16.278  0.005  4.107   8.1573e-02
   3_bss:   1.134  0.008  0.081 16.278  0.005  4.107   8.1573e-02
   3_xyz:   1.163  0.008  0.084 16.044  0.004  4.120   7.7580e-02
   3_adp:   1.163  0.008  0.084 16.044  0.004  4.120   7.7580e-02
   3_occ:   1.163  0.008  0.084 16.044  0.004  4.120   7.7580e-02
   4_bss:   1.163  0.008  0.084 16.044  0.004  4.120   7.7580e-02
   4_xyz:   1.049  0.008  0.080 15.705  0.004  4.124   6.7187e-02
   4_adp:   1.049  0.008  0.080 15.705  0.004  4.124   6.7187e-02
   4_occ:   1.049  0.008  0.080 15.705  0.004  4.124   6.7187e-02
   5_bss:   1.049  0.008  0.080 15.705  0.004  4.124   6.7187e-02
   5_xyz:   0.964  0.006  0.075 15.472  0.003  4.113   5.7882e-02
   5_adp:   0.964  0.006  0.075 15.472  0.003  4.113   5.7882e-02
   5_occ:   0.964  0.006  0.075 15.472  0.003  4.113   5.7882e-02
   5_bss:   0.964  0.006  0.075 15.472  0.003  4.113   5.7882e-02
------------------------------------------------------------------------
                      Maximal deviations:
 stage       angl   bond   chir   dihe   plan   repu       |grad|
   0    :  74.492  1.400  6.404144.062  0.405  1.196   6.9462e+00
   1_bss:  74.492  1.400  6.404144.062  0.405  1.196   6.9462e+00
   1_xyz:  12.947  0.184  0.403 88.229  0.036  2.127   9.7627e-02
   1_adp:  12.947  0.184  0.403 88.229  0.036  2.127   9.7627e-02
   1_occ:  12.947  0.184  0.403 88.229  0.036  2.127   9.7627e-02
   2_bss:  12.947  0.184  0.403 88.229  0.036  2.127   9.7627e-02
   2_xyz:   6.888  0.093  0.303 87.372  0.045  2.172   6.1306e-02
   2_adp:   6.888  0.093  0.303 87.372  0.045  2.172   6.1306e-02
   2_occ:   6.888  0.093  0.303 87.372  0.045  2.172   6.1306e-02
   3_bss:   6.888  0.093  0.303 87.372  0.045  2.172   6.1306e-02
   3_xyz:   7.826  0.074  0.420 89.679  0.028  2.254   6.9692e-02
   3_adp:   7.826  0.074  0.420 89.679  0.028  2.254   6.9692e-02
   3_occ:   7.826  0.074  0.420 89.679  0.028  2.254   6.9692e-02
   4_bss:   7.826  0.074  0.420 89.679  0.028  2.254   6.9692e-02
   4_xyz:   7.421  0.063  0.419 81.460  0.023  2.279   4.8932e-02
   4_adp:   7.421  0.063  0.419 81.460  0.023  2.279   4.8932e-02
   4_occ:   7.421  0.063  0.419 81.460  0.023  2.279   4.8932e-02
   5_bss:   7.421  0.063  0.419 81.460  0.023  2.279   4.8932e-02
   5_xyz:   7.613  0.046  0.412 83.600  0.031  2.342   3.5083e-02
   5_adp:   7.613  0.046  0.412 83.600  0.031  2.342   3.5083e-02
   5_occ:   7.613  0.046  0.412 83.600  0.031  2.342   3.5083e-02
   5_bss:   7.613  0.046  0.412 83.600  0.031  2.342   3.5083e-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:  77.97   0.00  13.55  68.24   0.00  11.58  77.97   0.00  24.26
   1_occ:  77.97   0.00  13.55  68.24   0.00  11.58  77.97   0.00  24.26
   2_bss:  77.97   0.00  13.55  68.24   0.00  11.58  77.97   0.00  24.26
   2_xyz:  77.97   0.00  13.55  68.24   0.00  11.58  77.97   0.00  24.26
   2_adp:  86.04   0.00  13.55  70.65   0.00  10.38  86.04   0.00  30.80
   2_occ:  86.04   0.00  13.55  70.65   0.00  10.38  86.04   0.00  30.80
   3_bss:  86.04   0.00  13.55  70.65   0.00  10.38  86.04   0.00  30.80
   3_xyz:  86.04   0.00  13.55  70.65   0.00  10.38  86.04   0.00  30.80
   3_adp:  86.19   0.00  13.51  73.26   0.00   9.76  86.19   2.23  33.96
   3_occ:  86.19   0.00  13.51  73.26   0.00   9.76  86.19   2.23  33.96
   4_bss:  86.19   0.00  13.51  73.26   0.00   9.76  86.19   2.23  33.96
   4_xyz:  86.19   0.00  13.51  73.26   0.00   9.76  86.19   2.23  33.96
   4_adp:  84.26   0.00  13.67  84.26   0.00   9.21  84.25   2.61  38.01
   4_occ:  84.26   0.00  13.67  84.26   0.00   9.21  84.25   2.61  38.01
   5_bss:  84.26   0.00  13.67  84.26   0.00   9.21  84.25   2.61  38.01
   5_xyz:  84.26   0.00  13.67  84.26   0.00   9.21  84.25   2.61  38.01
   5_adp:  86.21   0.00  13.41  86.21   0.00   8.93  83.86   2.26  37.82
   5_occ:  86.21   0.00  13.41  86.21   0.00   8.93  83.86   2.26  37.82
   5_bss:  88.30   2.09  15.50  88.30   2.09  11.02  85.95   4.35  39.91
------------------------------------------------------------------------
 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:    1.245    0.015    0.409
   1_adp:    1.245    0.015    0.409
   1_occ:    1.245    0.015    0.409
   2_bss:    1.245    0.015    0.409
   2_xyz:    1.483    0.023    0.559
   2_adp:    1.483    0.023    0.559
   2_occ:    1.483    0.023    0.559
   3_bss:    1.483    0.023    0.559
   3_xyz:    1.671    0.018    0.668
   3_adp:    1.671    0.018    0.668
   3_occ:    1.671    0.018    0.668
   4_bss:    1.671    0.018    0.668
   4_xyz:    1.845    0.042    0.729
   4_adp:    1.845    0.042    0.729
   4_occ:    1.845    0.042    0.729
   5_bss:    1.845    0.042    0.729
   5_xyz:    1.929    0.042    0.749
   5_adp:    1.929    0.042    0.749
   5_occ:    1.929    0.042    0.749
   5_bss:    1.929    0.042    0.749
------------------------------------------------------------------------

CPU time actual refinement: 340.68


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

Writing refined structure to PDB file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/trial/run_743/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_743/model_refine_001_2mFobs-DFmodel.map
Writing mFobs-DFmodel XPLOR map to file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/trial/run_743/model_refine_001_mFobs-DFmodel.map
Writing map coefficients to MTZ file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/trial/run_743/model_refine_001_map_coeffs.mtz

Writing default parameters for subsequent refinement:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/trial/run_743/model_refine_002.def


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

Pure refinement (no I/O, processing, etc)= 340.53 
  Macro-tasks:
    bulk solvent and scale       = 41.97  
    individual site refinement   = 142.86 
    weights calculation          = 32.18  
    collect and process          = 6.44   
    model show statistics        = 0.13   
    TOTAL for macro-tasks        = 223.58 
  Micro-tasks:
    mask                            = 2.37   
    f_calc                          = 105.04 
    alpha_beta                      = 7.95   
    target                          = 1.10   
    gradients_wrt_atomic_parameters = 116.36 
    fmodel                         = 7.28   
    r_factors                      = 0.17   
    phase_errors                   = 10.34  
    foms                           = 0.31   
    TOTAL for micro-tasks          = 250.92 
NUMBER OF MASK CALCS=  5
Time per interpreted Python bytecode instruction: 4.739 micro seconds
Total CPU time: 5.90 minutes
from_scatterers_fft:    655 calls, 104.73 s
gradients_fft:          599 calls, 102.44 s

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

# Date 2008-01-16 Time 02:19:55 PST -0800 (1200478795.48 s)
Start R-work = 0.4766, R-free = 0.4700 (no bulk solvent and anisotropic scale)
Final R-work = 0.1361, R-free = 0.1843 (no bulk solvent and anisotropic scale)

Start R-work = 0.4686, R-free = 0.4558
Final R-work = 0.1195, R-free = 0.1694