# Date 2008-01-16 Time 00:45:57 PST -0800 (1200473157.33 s)
#phil __OFF__

Command line arguments: "../152.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 = 20339
JOB_ID = 5158
SGE_ARCH = lx24-amd64
SGE_TASK_FIRST = 1
SGE_TASK_LAST = 1330
SGE_TASK_ID = 152

-------------------------------------------------------------------------------
  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: (68.845, 46.2261, 88.1178, 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: 3.25, per 1000 atoms: 1.15


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

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

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

Miller array info: /net/cci-filer1/vol1/tmp/phzwart/tassos/trial/1e0w.cns:FOBS,SIGMA
Observation type: xray.amplitude
Type of data: double, size=19589
Type of sigmas: double, size=19589
Number of Miller indices: 19589
Anomalous flag: False
Unit cell: (68.845, 46.2261, 88.1178, 90, 90, 90)
Space group: P 21 21 21 (No. 19)
Systematic absences: 0
Centric reflections: 2427
Resolution range: 14.855 1.96084
Completeness in resolution range: 0.944139
Completeness with d_max=infinity: 0.941281

Number of F-obs in resolution range:                   19589
Number of F-obs <= 0:                                  0
Refinement resolution range: d_max =  14.8550
                             d_min =   1.9608

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: (68.845, 46.2261, 88.1178, 90, 90, 90)
Space group: P 21 21 21 (No. 19)
Systematic absences: 0
Centric reflections: 2427
Resolution range: 14.855 1.96084
Completeness in resolution range: 0.944139
Completeness with d_max=infinity: 0.941281

Test (R-free flags) flag value: 1

Number of work/free reflections by resolution:
                                         work  free  %free
  bin  1: 14.8555 -  4.1957 [2182/2207]  1961   221  10.1%
  bin  2:  4.1957 -  3.3428 [2097/2116]  1887   210  10.0%
  bin  3:  3.3428 -  2.9239 [2066/2085]  1864   202   9.8%
  bin  4:  2.9239 -  2.6582 [2041/2071]  1827   214  10.5%
  bin  5:  2.6582 -  2.4686 [2031/2050]  1834   197   9.7%
  bin  6:  2.4686 -  2.3236 [2026/2051]  1819   207  10.2%
  bin  7:  2.3236 -  2.2077 [2011/2039]  1819   192   9.5%
  bin  8:  2.2077 -  2.1118 [2026/2062]  1819   207  10.2%
  bin  9:  2.1118 -  2.0308 [1986/2037]  1791   195   9.8%
  bin 10:  2.0308 -  1.9608 [1123/2030]  1009   114  10.2%
                                overall 17630  1959  10.0%
Writing MTZ file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/trial/run_152/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:
        1.21 -     1.95: 14
        1.95 -     2.68: 156
        2.68 -     3.42: 4525
        3.42 -     4.16: 9492
        4.16 -     4.90: 14471
  Nonbonded interactions sorted by model distance:
             atom i - atom j             model   vdw sym.op. j
  " OE1 GLN A  55 " - " O   HOH Z 403 "  1.207 3.040 -x+1,y-1/2,-z+1/2
  " O   HOH Z  43 " - " O   HOH Z 169 "  1.292 3.040 -x+1,y+1/2,-z+1/2
  " NH1 ARG A  24 " - " O   GLY A  91 "  1.313 3.120 -x+1,y+1/2,-z+1/2
  " O   HOH Z  42 " - " O   HOH Z 176 "  1.684 3.040 -x+1,y+1/2,-z+1/2
  " O   HOH Z  94 " - " NH1BARG A 145 "  1.776 3.120 -x+1,y+1/2,-z+1/2
  ... (remaining 28653 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_152/model_refine_001.eff

Writing geometry restraints to file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/trial/run_152/model_refine_001.geo

CPU time processing inputs: 9.06


============================ 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 = 68.845 46.22605 88.1178 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 - 14.86 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.5069   r_free= 0.4989   ksol= 0.00   Bsol= 0.00   scale= 0.780    |
|                                                                             |
| 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:   0.88 A                  |
| x-ray target function (ml) for work reflections: 6.301092                   |
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
| Bin     Resolution   Compl.  No. Refl.    R-factors          Targets        |
|number     range              work test   work   test        work        test|
|  1: 14.8555 -  4.6797 0.99   1416  156 0.4180 0.4024      6.6269      6.6099|
|  2:  4.6797 -  3.7339 0.99   1361  152 0.4282 0.4582      6.8106      6.8758|
|  3:  3.7339 -  3.2676 0.99   1335  151 0.4790 0.4221       6.716      6.6884|
|  4:  3.2676 -  2.9714 0.99   1326  141 0.5104 0.5190       6.565      6.5377|
|  5:  2.9714 -  2.7599 0.99   1317  149 0.5318 0.4893      6.3801      6.4182|
|  6:  2.7599 -  2.5981 0.99   1315  146 0.5402 0.5440      6.2985      6.2352|
|  7:  2.5981 -  2.4686 0.99   1303  149 0.5343 0.5269       6.252      6.1567|
|  8:  2.4686 -  2.3616 0.98   1313  144 0.5582 0.5483       6.198       6.214|
|  9:  2.3616 -  2.2710 0.98   1288  141 0.5365 0.5525      6.1149      6.2121|
| 10:  2.2710 -  2.1929 0.99   1311  139 0.5622 0.5636      6.1161      6.1048|
| 11:  2.1929 -  2.1245 0.98   1276  153 0.5447 0.5169       6.033      6.0399|
| 12:  2.1245 -  2.0640 0.97   1290  135 0.5390 0.5240      5.9713      6.0099|
| 13:  2.0640 -  2.0098 0.93   1213  135 0.5508 0.5107      5.9005        5.82|
| 14:  2.0098 -  1.9608 0.44    566   68 0.5515 0.5560      5.9048      5.8242|
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
|R-free likelihood based estimates for figures of merit, absolute phase error,|
|and distribution parameters alpha and beta (Acta Cryst. (1995). A51, 880-887)|
|                                                                             |
| Bin     Resolution      No. Refl.   FOM  Phase Scale    Alpha        Beta   |
|  #        range        work  test        error factor                       |
|  1: 14.8555 -  4.6797  1416   156  0.66  38.00   0.78     0.71      86899.72|
|  2:  4.6797 -  3.7339  1361   152  0.65  39.55   0.86     0.73     128173.62|
|  3:  3.7339 -  3.2676  1335   151  0.52  50.04   0.83     0.66     136870.13|
|  4:  3.2676 -  2.9714  1326   141  0.41  58.96   0.77     0.51     124602.23|
|  5:  2.9714 -  2.7599  1317   149  0.30  67.61   0.72     0.37      98664.33|
|  6:  2.7599 -  2.5981  1315   146  0.24  71.74   0.70     0.29      86376.26|
|  7:  2.5981 -  2.4686  1303   149  0.20  74.84   0.74     0.24      77763.14|
|  8:  2.4686 -  2.3616  1313   144  0.20  74.76   0.70     0.25      69649.29|
|  9:  2.3616 -  2.2710  1288   141  0.21  74.29   0.72     0.26      63841.89|
| 10:  2.2710 -  2.1929  1311   139  0.23  72.79   0.72     0.28      55116.42|
| 11:  2.1929 -  2.1245  1276   153  0.21  74.37   0.74     0.28      55304.48|
| 12:  2.1245 -  2.0640  1290   135  0.22  73.65   0.74     0.29      48560.35|
| 13:  2.0640 -  2.0098  1213   135  0.24  72.49   0.72     0.32      41704.39|
| 14:  2.0098 -  1.9608   566    68  0.33  65.70   0.73     0.36      30872.09|
|alpha:            min =        0.24 max =            0.73 mean =         0.40|
|beta:             min =    30872.09 max =       136870.13 mean =     81537.01|
|figures of merit: min =        0.00 max =            1.00 mean =         0.33|
|phase err.(work): min =        0.00 max =           89.99 mean =        64.54|
|phase err.(test): min =        0.00 max =           89.95 mean =        64.87|
|-----------------------------------------------------------------------------|

============================== 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 = 21.810176             wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 83.935   (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 2.202140              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 78.205   (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:        6 |
| 0.140 - 0.280:   585 |   7.457 -  14.906:   711 |  1.566 -  1.937:       42 |
| 0.280 - 0.420:   441 |  14.906 -  22.354:   630 |  1.937 -  2.307:      178 |
| 0.420 - 0.560:   366 |  22.354 -  29.802:   474 |  2.307 -  2.677:      724 |
| 0.560 - 0.700:   237 |  29.802 -  37.251:   338 |  2.677 -  3.048:     1521 |
| 0.700 - 0.840:   127 |  37.251 -  44.699:   241 |  3.048 -  3.418:     2677 |
| 0.840 - 0.980:    59 |  44.699 -  52.147:   125 |  3.418 -  3.789:     3987 |
| 0.980 - 1.120:    17 |  52.147 -  59.595:    51 |  3.789 -  4.159:     5119 |
| 1.120 - 1.260:     9 |  59.595 -  67.044:    13 |  4.159 -  4.530:     6618 |
| 1.260 - 1.400:     1 |  67.044 -  74.492:     3 |  4.530 -  4.900:     7781 |
|-----------------------------------------------------------------------------|
|-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 |       53.288 |
| planarity |      436 |   0.145    0.405  0.000 |     250.485 |              |
|  dihedral |      870 |  33.790  144.062  0.019 |      20.704 |              |
| nonbonded |     2439 |   4.086    4.900  1.196 |       2.622 |              |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 11.581)------------------------------------------|
|    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 = 11.581)------------------------------------------|
|    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 - 14.86 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.5123   r_free= 0.5001   ksol= 0.00   Bsol= 0.00   scale= 0.750    |
|                                                                             |
| 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:   0.88 A                  |
| x-ray target function (ml) for work reflections: 6.301612                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.96 - 14.86 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.4984   r_free= 0.4869   ksol= 0.37   Bsol= 20.00   scale= 0.983   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (7.03,8.59,10.35,0.00,0.00,0.00); trace/3= 8.66                             |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.87 A                  |
| x-ray target function (ml) for work reflections: 6.294750                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 16.834363             wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 85.246   (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 1.959351              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 80.236   (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.4984      final r-factor (work) = 0.4362          |
| start r-factor (free) = 0.4869      final r-factor (free) = 0.4543          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 106.2877 = 16.83 * 0.50 * 6.2966 + 1.00 * 53.2878                           |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 52.7242 = 16.83 * 0.50 * 6.2464 + 1.00 * 0.1468                             |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 26     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.4362      final r-factor (work) = 0.3951          |
| start r-factor (free) = 0.4543      final r-factor (free) = 0.4582          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 12.2534 = 1.96 * 1.00 * 6.2464 + 1.00 * 0.0144                              |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 12.1450 = 1.96 * 1.00 * 6.1864 + 1.00 * 0.0236                              |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 29     |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 11.581)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.00    86.71   16.36    None  None   None       |
|    all(noH): 2823   0      0.00    86.71   16.36    None  None   None       |
|    Sol.    : 438    0      0.00    86.71   25.96    None  None   None       |
|    Mac.    : 2385   0      0.00    74.72   14.59    None  None   None       |
|    Hyd.    : 0      0      None    None    None     None  None   None       |
|    - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -      |
|       Distribution of isotropic (or equivalent) ADP for non-H atoms:        |
|    Bin#      value range     #atoms | Bin#      value range     #atoms      |
|      0:     0.000 -   8.671:  977   |   5:    43.354 -  52.025:   65        |
|      1:     8.671 -  17.342:  775   |   6:    52.025 -  60.696:   43        |
|      2:    17.342 -  26.013:  495   |   7:    60.696 -  69.367:   19        |
|      3:    26.013 -  34.684:  277   |   8:    69.367 -  78.038:    4        |
|      4:    34.684 -  43.354:  162   |   9:    78.038 -  86.709:    6        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.3951 r_free = 0.4582             target_work(ml) = 6.179         |
| occupancies: max = 1.00  min = 0.30   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.3952 r_free = 0.4586             target_work(ml) = 6.178         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:       10 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.96 - 14.86 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.3952   r_free= 0.4586   ksol= 0.37   Bsol= 20.00   scale= 1.131   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (7.03,8.59,10.35,0.00,0.00,0.00); trace/3= 8.66                             |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.68 A                  |
| x-ray target function (ml) for work reflections: 6.178184                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.96 - 14.86 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.3928   r_free= 0.4555   ksol= 0.35   Bsol= 38.39   scale= 1.038   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (3.92,4.66,6.76,0.00,0.00,0.00); trace/3= 5.11                              |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.69 A                  |
| x-ray target function (ml) for work reflections: 6.179163                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 14.080505             wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 99.841   (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 0.690027              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 135.086  (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.3928      final r-factor (work) = 0.3157          |
| start r-factor (free) = 0.4555      final r-factor (free) = 0.3829          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 43.6699 = 14.08 * 0.50 * 6.1820 + 1.00 * 0.1468                             |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 43.0477 = 14.08 * 0.50 * 6.0977 + 1.00 * 0.1182                             |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 27     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.3157      final r-factor (work) = 0.2861          |
| start r-factor (free) = 0.3829      final r-factor (free) = 0.3569          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 4.2310 = 0.69 * 1.00 * 6.0977 + 1.00 * 0.0234                               |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 4.1447 = 0.69 * 1.00 * 5.9715 + 1.00 * 0.0242                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 28     |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 11.581)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.00    87.22   15.05    None  None   None       |
|    all(noH): 2823   0      0.00    87.22   15.05    None  None   None       |
|    Sol.    : 438    0      0.00    87.22   31.97    None  None   None       |
|    Mac.    : 2385   0      0.00    62.36   11.94    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 -   8.722: 1107   |   5:    43.610 -  52.331:   79        |
|      1:     8.722 -  17.444:  848   |   6:    52.331 -  61.053:   33        |
|      2:    17.444 -  26.166:  408   |   7:    61.053 -  69.775:    9        |
|      3:    26.166 -  34.888:  223   |   8:    69.775 -  78.497:    4        |
|      4:    34.888 -  43.610:  110   |   9:    78.497 -  87.219:    2        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.2861 r_free = 0.3569             target_work(ml) = 5.937         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:       10 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.2857 r_free = 0.3573             target_work(ml) = 5.937         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:       12 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.96 - 14.86 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.2857   r_free= 0.3573   ksol= 0.35   Bsol= 38.39   scale= 1.086   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (3.92,4.66,6.76,0.00,0.00,0.00); trace/3= 5.11                              |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.42 A                  |
| x-ray target function (ml) for work reflections: 5.937313                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.96 - 14.86 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.2832   r_free= 0.3552   ksol= 0.33   Bsol= 45.91   scale= 1.020   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (1.47,2.39,4.10,0.00,0.00,0.00); trace/3= 2.65                              |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.43 A                  |
| x-ray target function (ml) for work reflections: 5.935409                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 3.900288              wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 100.476  (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 1.303892              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 93.996   (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.2832      final r-factor (work) = 0.2217          |
| start r-factor (free) = 0.3552      final r-factor (free) = 0.2822          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 11.7649 = 3.90 * 0.50 * 5.9723 + 1.00 * 0.1181                              |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 11.4704 = 3.90 * 0.50 * 5.8481 + 1.00 * 0.0658                              |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 27     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.2217      final r-factor (work) = 0.2005          |
| start r-factor (free) = 0.2822      final r-factor (free) = 0.2703          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 7.6391 = 1.30 * 1.00 * 5.8481 + 1.00 * 0.0138                               |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 7.4304 = 1.30 * 1.00 * 5.6852 + 1.00 * 0.0176                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 26     |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 11.581)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.00    101.65  16.17    None  None   None       |
|    all(noH): 2823   0      0.00    101.65  16.17    None  None   None       |
|    Sol.    : 438    0      0.67    101.65  41.58    None  None   None       |
|    Mac.    : 2385   0      0.00    90.92   11.50    None  None   None       |
|    Hyd.    : 0      0      None    None    None     None  None   None       |
|    - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -      |
|       Distribution of isotropic (or equivalent) ADP for non-H atoms:        |
|    Bin#      value range     #atoms | Bin#      value range     #atoms      |
|      0:     0.000 -  10.165: 1405   |   5:    50.824 -  60.989:   73        |
|      1:    10.165 -  20.330:  737   |   6:    60.989 -  71.153:   66        |
|      2:    20.330 -  30.494:  230   |   7:    71.153 -  81.318:   23        |
|      3:    30.494 -  40.659:  155   |   8:    81.318 -  91.483:    7        |
|      4:    40.659 -  50.824:  125   |   9:    91.483 - 101.647:    2        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.2005 r_free = 0.2703             target_work(ml) = 5.665         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:       12 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.2001 r_free = 0.2699             target_work(ml) = 5.664         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:       13 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.96 - 14.86 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.2001   r_free= 0.2699   ksol= 0.33   Bsol= 45.91   scale= 1.049   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (1.47,2.39,4.10,0.00,0.00,0.00); trace/3= 2.65                              |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.29 A                  |
| x-ray target function (ml) for work reflections: 5.663599                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.96 - 14.86 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1996   r_free= 0.2696   ksol= 0.31   Bsol= 49.71   scale= 1.019   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (0.41,1.27,3.14,0.00,0.00,0.00); trace/3= 1.61                              |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.29 A                  |
| x-ray target function (ml) for work reflections: 5.662611                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 5.605963              wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 96.884   (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 0.280622              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 119.471  (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1996      final r-factor (work) = 0.1543          |
| start r-factor (free) = 0.2696      final r-factor (free) = 0.2149          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 16.0063 = 5.61 * 0.50 * 5.6870 + 1.00 * 0.0658                              |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 15.6724 = 5.61 * 0.50 * 5.5640 + 1.00 * 0.0766                              |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 28     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1543      final r-factor (work) = 0.1436          |
| start r-factor (free) = 0.2149      final r-factor (free) = 0.1959          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 1.5817 = 0.28 * 1.00 * 5.5640 + 1.00 * 0.0204                               |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 1.5453 = 0.28 * 1.00 * 5.4058 + 1.00 * 0.0283                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 28     |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 11.581)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.00    98.24   14.95    None  None   None       |
|    all(noH): 2823   0      0.00    98.24   14.95    None  None   None       |
|    Sol.    : 438    0      2.45    98.24   40.03    None  None   None       |
|    Mac.    : 2385   0      0.00    95.13   10.35    None  None   None       |
|    Hyd.    : 0      0      None    None    None     None  None   None       |
|    - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -      |
|       Distribution of isotropic (or equivalent) ADP for non-H atoms:        |
|    Bin#      value range     #atoms | Bin#      value range     #atoms      |
|      0:     0.000 -   9.824: 1536   |   5:    49.119 -  58.942:   79        |
|      1:     9.824 -  19.648:  703   |   6:    58.942 -  68.766:   50        |
|      2:    19.648 -  29.471:  166   |   7:    68.766 -  78.590:   20        |
|      3:    29.471 -  39.295:  139   |   8:    78.590 -  88.414:    4        |
|      4:    39.295 -  49.119:  122   |   9:    88.414 -  98.237:    4        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.1436 r_free = 0.1959             target_work(ml) = 5.352         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:       13 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.1431 r_free = 0.1953             target_work(ml) = 5.349         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:       11 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.96 - 14.86 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1431   r_free= 0.1953   ksol= 0.31   Bsol= 49.71   scale= 1.024   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (0.41,1.27,3.14,0.00,0.00,0.00); trace/3= 1.61                              |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.18 A                  |
| x-ray target function (ml) for work reflections: 5.349286                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.96 - 14.86 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1432   r_free= 0.1956   ksol= 0.31   Bsol= 47.12   scale= 1.009   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-0.02,0.66,2.60,0.00,0.00,0.00); trace/3= 1.08                             |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.19 A                  |
| x-ray target function (ml) for work reflections: 5.349741                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 2.858940              wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 118.229  (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 0.631404              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 94.377   (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1432      final r-factor (work) = 0.1278          |
| start r-factor (free) = 0.1956      final r-factor (free) = 0.1753          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 7.8052 = 2.86 * 0.50 * 5.4067 + 1.00 * 0.0766                               |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 7.6480 = 2.86 * 0.50 * 5.3061 + 1.00 * 0.0631                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 28     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1278      final r-factor (work) = 0.1238          |
| start r-factor (free) = 0.1753      final r-factor (free) = 0.1724          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 3.3628 = 0.63 * 1.00 * 5.3061 + 1.00 * 0.0125                               |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 3.3198 = 0.63 * 1.00 * 5.2391 + 1.00 * 0.0118                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 32     |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 11.581)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.00    98.03   14.84    None  None   None       |
|    all(noH): 2823   0      0.00    98.03   14.84    None  None   None       |
|    Sol.    : 438    0      2.91    97.72   40.38    None  None   None       |
|    Mac.    : 2385   0      0.00    98.03   10.15    None  None   None       |
|    Hyd.    : 0      0      None    None    None     None  None   None       |
|    - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -      |
|       Distribution of isotropic (or equivalent) ADP for non-H atoms:        |
|    Bin#      value range     #atoms | Bin#      value range     #atoms      |
|      0:     0.000 -   9.803: 1579   |   5:    49.017 -  58.820:   88        |
|      1:     9.803 -  19.607:  669   |   6:    58.820 -  68.623:   57        |
|      2:    19.607 -  29.410:  167   |   7:    68.623 -  78.427:   22        |
|      3:    29.410 -  39.213:  122   |   8:    78.427 -  88.230:    6        |
|      4:    39.213 -  49.017:  110   |   9:    88.230 -  98.033:    3        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.1238 r_free = 0.1724             target_work(ml) = 5.231         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:       11 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.1236 r_free = 0.1724             target_work(ml) = 5.230         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:       11 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.96 - 14.86 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1236   r_free= 0.1724   ksol= 0.31   Bsol= 47.12   scale= 1.009   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-0.02,0.66,2.60,0.00,0.00,0.00); trace/3= 1.08                             |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.17 A                  |
| x-ray target function (ml) for work reflections: 5.230314                   |
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
| Bin     Resolution   Compl.  No. Refl.    R-factors          Targets        |
|number     range              work test   work   test        work        test|
|  1: 14.8555 -  4.6797 0.99   1416  156 0.1033 0.1310      5.4217      5.5926|
|  2:  4.6797 -  3.7339 0.99   1361  152 0.0928 0.1222      5.5147       5.712|
|  3:  3.7339 -  3.2676 0.99   1335  151 0.1193 0.1682      5.5841      5.9382|
|  4:  3.2676 -  2.9714 0.99   1326  141 0.1372 0.1899      5.5415      5.7344|
|  5:  2.9714 -  2.7599 0.99   1317  149 0.1461 0.1675      5.4345      5.5621|
|  6:  2.7599 -  2.5981 0.99   1315  146 0.1380 0.2369      5.2967      5.6274|
|  7:  2.5981 -  2.4686 0.99   1303  149 0.1415 0.1742       5.272      5.4029|
|  8:  2.4686 -  2.3616 0.98   1313  144 0.1344 0.1855      5.1823      5.4202|
|  9:  2.3616 -  2.2710 0.98   1288  141 0.1337 0.1978      5.1196      5.4325|
| 10:  2.2710 -  2.1929 0.99   1311  139 0.1244 0.1697      5.0324      5.1912|
| 11:  2.1929 -  2.1245 0.98   1276  153 0.1226 0.2165      5.0024      5.3998|
| 12:  2.1245 -  2.0640 0.97   1290  135 0.1270 0.1700      4.9659      5.2156|
| 13:  2.0640 -  2.0098 0.93   1213  135 0.1096 0.1844       4.793      5.0294|
| 14:  2.0098 -  1.9608 0.44    566   68 0.1007 0.1530      4.6543      4.8726|
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
|R-free likelihood based estimates for figures of merit, absolute phase error,|
|and distribution parameters alpha and beta (Acta Cryst. (1995). A51, 880-887)|
|                                                                             |
| Bin     Resolution      No. Refl.   FOM  Phase Scale    Alpha        Beta   |
|  #        range        work  test        error factor                       |
|  1: 14.8555 -  4.6797  1416   156  0.93   9.86   0.98     0.95       7947.64|
|  2:  4.6797 -  3.7339  1361   152  0.95   8.99   1.02     1.01      10461.93|
|  3:  3.7339 -  3.2676  1335   151  0.92  13.31   1.04     1.03      12925.93|
|  4:  3.2676 -  2.9714  1326   141  0.90  15.62   1.03     1.02      12335.52|
|  5:  2.9714 -  2.7599  1317   149  0.88  18.07   1.01     0.97      10646.01|
|  6:  2.7599 -  2.5981  1315   146  0.88  18.20   0.98     0.95       8385.62|
|  7:  2.5981 -  2.4686  1303   149  0.88  17.98   1.00     0.95       7573.17|
|  8:  2.4686 -  2.3616  1313   144  0.89  17.25   1.01     0.99       6631.69|
|  9:  2.3616 -  2.2710  1288   141  0.89  17.36   1.00     0.96       5792.02|
| 10:  2.2710 -  2.1929  1311   139  0.89  17.65   1.01     0.97       5156.19|
| 11:  2.1929 -  2.1245  1276   153  0.88  18.11   1.01     0.97       5228.94|
| 12:  2.1245 -  2.0640  1290   135  0.88  18.09   1.01     1.00       4787.79|
| 13:  2.0640 -  2.0098  1213   135  0.90  16.54   1.00     0.97       3513.15|
| 14:  2.0098 -  1.9608   566    68  0.93  12.93   0.99     0.97       2380.13|
|alpha:            min =        0.95 max =            1.03 mean =         0.98|
|beta:             min =     2380.13 max =        12925.93 mean =      7680.41|
|figures of merit: min =        0.00 max =            1.00 mean =         0.90|
|phase err.(work): min =        0.00 max =           89.97 mean =        15.76|
|phase err.(test): min =        0.00 max =           89.47 mean =        15.09|
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.96 - 14.86 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1235   r_free= 0.1724   ksol= 0.32   Bsol= 48.20   scale= 1.010   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-1.10,-0.42,1.52,0.00,0.00,0.00); trace/3= 0.00                            |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.17 A                  |
| x-ray target function (ml) for work reflections: 5.230281                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.96 - 14.86 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1235   r_free= 0.1724   ksol= 0.32   Bsol= 48.20   scale= 1.010   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-1.10,-0.42,1.52,0.00,0.00,0.00); trace/3= 0.00                            |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.17 A                  |
| x-ray target function (ml) for work reflections: 5.230281                   |
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
| Bin     Resolution   Compl.  No. Refl.    R-factors          Targets        |
|number     range              work test   work   test        work        test|
|  1: 14.8555 -  4.6797 0.99   1416  156 0.1032 0.1312      5.4223      5.5916|
|  2:  4.6797 -  3.7339 0.99   1361  152 0.0928 0.1219      5.5137      5.7103|
|  3:  3.7339 -  3.2676 0.99   1335  151 0.1192 0.1682      5.5834       5.938|
|  4:  3.2676 -  2.9714 0.99   1326  141 0.1372 0.1899      5.5415      5.7344|
|  5:  2.9714 -  2.7599 0.99   1317  149 0.1461 0.1675      5.4346      5.5624|
|  6:  2.7599 -  2.5981 0.99   1315  146 0.1380 0.2370      5.2969      5.6276|
|  7:  2.5981 -  2.4686 0.99   1303  149 0.1415 0.1742      5.2722       5.403|
|  8:  2.4686 -  2.3616 0.98   1313  144 0.1344 0.1855      5.1824      5.4203|
|  9:  2.3616 -  2.2710 0.98   1288  141 0.1337 0.1978      5.1197      5.4324|
| 10:  2.2710 -  2.1929 0.99   1311  139 0.1244 0.1698      5.0325      5.1913|
| 11:  2.1929 -  2.1245 0.98   1276  153 0.1226 0.2166      5.0024      5.3998|
| 12:  2.1245 -  2.0640 0.97   1290  135 0.1270 0.1700      4.9659      5.2156|
| 13:  2.0640 -  2.0098 0.93   1213  135 0.1096 0.1844       4.793      5.0295|
| 14:  2.0098 -  1.9608 0.44    566   68 0.1007 0.1530      4.6543      4.8726|
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
|R-free likelihood based estimates for figures of merit, absolute phase error,|
|and distribution parameters alpha and beta (Acta Cryst. (1995). A51, 880-887)|
|                                                                             |
| Bin     Resolution      No. Refl.   FOM  Phase Scale    Alpha        Beta   |
|  #        range        work  test        error factor                       |
|  1: 14.8555 -  4.6797  1416   156  0.93   9.85   0.98     0.95       7941.77|
|  2:  4.6797 -  3.7339  1361   152  0.95   8.98   1.02     1.01      10438.66|
|  3:  3.7339 -  3.2676  1335   151  0.92  13.29   1.04     1.03      12900.53|
|  4:  3.2676 -  2.9714  1326   141  0.90  15.62   1.03     1.01      12331.69|
|  5:  2.9714 -  2.7599  1317   149  0.88  18.07   1.01     0.97      10649.44|
|  6:  2.7599 -  2.5981  1315   146  0.88  18.21   0.98     0.95       8388.80|
|  7:  2.5981 -  2.4686  1303   149  0.88  17.98   1.00     0.95       7575.75|
|  8:  2.4686 -  2.3616  1313   144  0.89  17.25   1.01     0.99       6632.98|
|  9:  2.3616 -  2.2710  1288   141  0.89  17.36   1.00     0.96       5793.13|
| 10:  2.2710 -  2.1929  1311   139  0.89  17.65   1.01     0.97       5156.46|
| 11:  2.1929 -  2.1245  1276   153  0.88  18.11   1.01     0.97       5229.55|
| 12:  2.1245 -  2.0640  1290   135  0.88  18.09   1.01     1.00       4787.82|
| 13:  2.0640 -  2.0098  1213   135  0.90  16.54   1.00     0.97       3513.38|
| 14:  2.0098 -  1.9608   566    68  0.93  12.93   0.99     0.97       2380.55|
|alpha:            min =        0.95 max =            1.03 mean =         0.98|
|beta:             min =     2380.55 max =        12900.53 mean =      7676.88|
|figures of merit: min =        0.00 max =            1.00 mean =         0.90|
|phase err.(work): min =        0.00 max =           89.96 mean =        15.76|
|phase err.(test): min =        0.00 max =           89.93 mean =        15.09|
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 11.581)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      1.08    99.12   15.92    None  None   None       |
|    all(noH): 2823   0      1.08    99.12   15.92    None  None   None       |
|    Sol.    : 438    0      4.00    98.80   41.46    None  None   None       |
|    Mac.    : 2385   0      1.08    99.12   11.23    None  None   None       |
|    Hyd.    : 0      0      None    None    None     None  None   None       |
|    - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -      |
|       Distribution of isotropic (or equivalent) ADP for non-H atoms:        |
|    Bin#      value range     #atoms | Bin#      value range     #atoms      |
|      0:     1.082 -  10.885: 1579   |   5:    50.098 -  59.902:   88        |
|      1:    10.885 -  20.689:  669   |   6:    59.902 -  69.705:   57        |
|      2:    20.689 -  30.492:  167   |   7:    69.705 -  79.508:   22        |
|      3:    30.492 -  40.295:  122   |   8:    79.508 -  89.312:    6        |
|      4:    40.295 -  50.098:  110   |   9:    89.312 -  99.115:    3        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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


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

Number of peaks found at mFobs-DFmodel map (map cutoff=3.00 sigma)= 308         
Filter by distance & map next to the model:
   mapped sites are within: 0.306 - 4.573
   number of sites selected in [dist_min= 0.70, dist_max= 6.00]: 303 from: 308
   mapped sites are within: 0.722 - 4.573

peak=   10.296 closest distance to " CB  VAL A 230 " =    1.481
peak=    9.558 closest distance to " CB  VAL A 296 " =    1.563
peak=    7.803 closest distance to " O   HOH Z 130 " =    1.819
peak=    6.336 closest distance to " CD2 LEU A   5 " =    1.260
peak=    6.108 closest distance to " O   HOH Z 375 " =    1.607
peak=    5.891 closest distance to " CG  PRO A  54 " =    1.468
peak=    5.673 closest distance to " O   HOH Z 222 " =    1.404
peak=    5.613 closest distance to " O   HOH Z 255 " =    0.778
peak=    5.511 closest distance to " O   HOH Z 236 " =    1.607
peak=    5.441 closest distance to " NE2 GLN A  11 " =    1.131
peak=    5.282 closest distance to " O   HOH Z  65 " =    1.337
peak=    5.214 closest distance to " CD1AILE A 234 " =    0.943
peak=    5.209 closest distance to " O   HOH Z 142 " =    1.865
peak=    5.100 closest distance to " O   HOH Z   9 " =    2.270
peak=    4.992 closest distance to " CB  GLN A 223 " =    1.520
peak=    4.981 closest distance to " CB  ARG A 275 " =    1.023
peak=    4.924 closest distance to " O   HOH Z 403 " =    1.761
peak=    4.862 closest distance to " O   HOH Z 232 " =    2.312
peak=    4.831 closest distance to " O   HOH Z 124 " =    1.387
peak=    4.818 closest distance to " O   HOH Z 425 " =    1.564
peak=    4.817 closest distance to " CB  VAL A 230 " =    1.224
peak=    4.788 closest distance to " O   HOH Z  39 " =    1.444
peak=    4.781 closest distance to " CG  LEU A 228 " =    1.209
peak=    4.771 closest distance to " O   HOH Z 427 " =    2.760
peak=    4.653 closest distance to " O   HOH Z 369 " =    2.364
peak=    4.619 closest distance to " O   HOH Z 258 " =    1.191
peak=    4.601 closest distance to " O   HOH Z 417 " =    1.617
peak=    4.599 closest distance to " O   HOH Z 143 " =    1.689
peak=    4.580 closest distance to " NH2AARG A 145 " =    1.134
peak=    4.569 closest distance to " CB  PRO A  54 " =    1.026
peak=    4.556 closest distance to " CG  LEU A   5 " =    1.164
peak=    4.550 closest distance to " NH2 ARG A  56 " =    2.020
peak=    4.533 closest distance to " O   HOH Z 402 " =    1.415
peak=    4.516 closest distance to " O   HOH Z 147 " =    1.170
peak=    4.511 closest distance to " NH2AARG A 190 " =    1.965
peak=    4.509 closest distance to " CD  LYS A  76 " =    1.726
peak=    4.507 closest distance to " O   HOH Z  69 " =    1.273
peak=    4.504 closest distance to " O   HOH Z 126 " =    1.972
peak=    4.497 closest distance to " O   HOH Z  78 " =    1.705
peak=    4.486 closest distance to " O   HOH Z  91 " =    2.412
peak=    4.467 closest distance to " O   HOH Z  49 " =    1.224
peak=    4.462 closest distance to " O   HOH Z 112 " =    1.259
peak=    4.423 closest distance to " O   HOH Z  11 " =    1.388
peak=    4.412 closest distance to " CG2 ILE A 234 " =    0.925
peak=    4.412 closest distance to " O   HOH Z 249 " =    1.197
peak=    4.406 closest distance to " CG  GLN A  11 " =    2.247
peak=    4.395 closest distance to " NH1 ARG A 138 " =    0.999
peak=    4.381 closest distance to " CG  GLN A  58 " =    1.067
peak=    4.379 closest distance to " CB  VAL A 265 " =    1.354
peak=    4.364 closest distance to " CB  ASN A 142 " =    1.050
peak=    4.341 closest distance to " CB  ASN A 148 " =    1.317
peak=    4.305 closest distance to " O   HOH Z 423 " =    1.733
peak=    4.292 closest distance to " O   HOH Z 346 " =    1.576
peak=    4.283 closest distance to " CG2 VAL A 257 " =    0.897
peak=    4.247 closest distance to " O   HOH Z 123 " =    1.381
peak=    4.238 closest distance to " O   HOH Z   7 " =    1.343
peak=    4.184 closest distance to " O   HOH Z 272 " =    1.830
peak=    4.176 closest distance to " O   HOH Z 251 " =    1.722
peak=    4.118 closest distance to " CA  PHE A 283 " =    1.186
peak=    4.061 closest distance to " O   HOH Z 418 " =    1.121
peak=    4.054 closest distance to " CB  SER A  26 " =    1.740
peak=    4.051 closest distance to " O   HOH Z 248 " =    1.265
peak=    4.044 closest distance to " CB  GLN A 183 " =    1.228
peak=    4.042 closest distance to " O   HOH Z  61 " =    1.763
peak=    4.034 closest distance to " O   HOH Z 406 " =    1.400
peak=    4.033 closest distance to " O   HOH Z 423 " =    1.752
peak=    4.025 closest distance to " O   HOH Z 188 " =    1.473
peak=    4.023 closest distance to " O   HOH Z 303 " =    2.160
peak=    4.021 closest distance to " O   HOH Z 389 " =    1.631
peak=    4.020 closest distance to " CG AARG A 275 " =    1.177
peak=    4.010 closest distance to " O   HOH Z 362 " =    2.196
peak=    4.008 closest distance to " O   HOH Z 116 " =    1.181
peak=    3.976 closest distance to " NZ  LYS A 117 " =    3.117
peak=    3.964 closest distance to " O   HOH Z 380 " =    2.019
peak=    3.959 closest distance to " CB  VAL A 202 " =    1.650
peak=    3.950 closest distance to " O   HOH Z 359 " =    1.533
peak=    3.944 closest distance to " O   HOH Z 193 " =    1.548
peak=    3.939 closest distance to " CD  ARG A 269 " =    1.039
peak=    3.938 closest distance to " O   HOH Z 234 " =    3.638
peak=    3.933 closest distance to " O   HOH Z  24 " =    1.771
peak=    3.925 closest distance to " CE3 TRP A 150 " =    1.160
peak=    3.923 closest distance to " CB BVAL A  41 " =    1.020
peak=    3.921 closest distance to " O   HOH Z  40 " =    1.655
peak=    3.895 closest distance to " O   HOH Z 422 " =    2.279
peak=    3.888 closest distance to " O   HOH Z  83 " =    1.051
peak=    3.880 closest distance to " OG ASER A 258 " =    3.049
peak=    3.874 closest distance to " CG  PRO A 243 " =    1.111
peak=    3.864 closest distance to " CB  GLU A 277 " =    3.512
peak=    3.832 closest distance to " CB  ARG A  79 " =    1.377
peak=    3.830 closest distance to " O   HOH Z  85 " =    1.476
peak=    3.825 closest distance to " O   HOH Z 287 " =    1.781
peak=    3.823 closest distance to " CB  SER A  63 " =    1.223
peak=    3.823 closest distance to " CD2 TRP A 179 " =    1.317
peak=    3.814 closest distance to " CD2 LEU A 228 " =    1.222
peak=    3.811 closest distance to " N   ASP A 162 " =    1.137
peak=    3.811 closest distance to " O   HOH Z 213 " =    1.934
peak=    3.809 closest distance to " CH2 TRP A 266 " =    1.081
peak=    3.808 closest distance to " O   HOH Z 238 " =    1.194
peak=    3.799 closest distance to " O   HOH Z  26 " =    1.447
peak=    3.793 closest distance to " O   HOH Z 392 " =    0.973
peak=    3.784 closest distance to " CA  ARG A 195 " =    1.230
peak=    3.772 closest distance to " O   HOH Z 211 " =    1.016
peak=    3.769 closest distance to " O   HOH Z 265 " =    2.044
peak=    3.768 closest distance to " O   HOH Z 103 " =    1.064
peak=    3.746 closest distance to " O   HOH Z  43 " =    1.101
peak=    3.745 closest distance to " CB  SER A   3 " =    1.240
peak=    3.743 closest distance to " CB  ALA A  43 " =    1.040
peak=    3.737 closest distance to " CG2 ILE A  20 " =    1.659
peak=    3.725 closest distance to " CB  ASN A 215 " =    1.169
peak=    3.724 closest distance to " O   HOH Z 365 " =    2.769
peak=    3.718 closest distance to " O   HOH Z 188 " =    2.459
peak=    3.717 closest distance to " O   HOH Z  76 " =    1.204
peak=    3.716 closest distance to " O   HOH Z 147 " =    1.367
peak=    3.710 closest distance to " CG  LEU A 167 " =    1.272
peak=    3.695 closest distance to " O   HOH Z 182 " =    1.043
peak=    3.691 closest distance to " O   HOH Z  22 " =    2.039
peak=    3.691 closest distance to " O   HOH Z 298 " =    1.683
peak=    3.680 closest distance to " O   PRO A 198 " =    1.529
peak=    3.654 closest distance to " CE  LYS A 119 " =    1.204
peak=    3.651 closest distance to " CG  PRO A 198 " =    1.303
peak=    3.647 closest distance to " CB  HIS A 108 " =    0.880
peak=    3.639 closest distance to " O   HOH Z 117 " =    1.199
peak=    3.639 closest distance to " NE AARG A 145 " =    1.016
peak=    3.638 closest distance to " CB  TYR A  30 " =    1.616
peak=    3.638 closest distance to " CG1 ILE A 120 " =    1.378
peak=    3.633 closest distance to " O   HOH Z 158 " =    2.960
peak=    3.624 closest distance to " CB  GLN A  88 " =    1.303
peak=    3.618 closest distance to " O   HOH Z 193 " =    1.565
peak=    3.613 closest distance to " CD1 ILE A 199 " =    1.320
peak=    3.595 closest distance to " O   HOH Z  59 " =    1.617
peak=    3.595 closest distance to " O   HOH Z 130 " =    2.041
peak=    3.594 closest distance to " O   HOH Z 261 " =    1.889
peak=    3.591 closest distance to " ND2 ASN A 187 " =    1.706
peak=    3.588 closest distance to " CA  ASN A 215 " =    1.023
peak=    3.587 closest distance to " O   HOH Z 128 " =    2.065
peak=    3.583 closest distance to " O   HOH Z 246 " =    1.059
peak=    3.569 closest distance to " CA  TYR A  30 " =    0.945
peak=    3.568 closest distance to " CB  TYR A 169 " =    0.830
peak=    3.562 closest distance to " O   HOH Z 411 " =    3.856
peak=    3.560 closest distance to " CA  ALA A  51 " =    0.958
peak=    3.559 closest distance to " CZ  PHE A  38 " =    1.083
peak=    3.559 closest distance to " CA  ASN A 127 " =    1.148
peak=    3.557 closest distance to " CD2 TYR A 186 " =    1.059
peak=    3.551 closest distance to " CB  THR A  52 " =    0.932
peak=    3.541 closest distance to " O   HOH Z  80 " =    1.589
peak=    3.538 closest distance to " ND2BASN A 224 " =    0.774
peak=    3.536 closest distance to " O   HOH Z 368 " =    3.422
peak=    3.536 closest distance to " CB  ARG A  79 " =    0.922
peak=    3.534 closest distance to " O   HOH Z 425 " =    2.049
peak=    3.528 closest distance to " CB  GLU A 152 " =    1.255
peak=    3.521 closest distance to " CA  TRP A 150 " =    0.972
peak=    3.516 closest distance to " CB  THR A  31 " =    1.542
peak=    3.510 closest distance to " O   HOH Z 145 " =    1.530
peak=    3.500 closest distance to " O   HOH Z  30 " =    1.555
peak=    3.498 closest distance to " CB  LEU A 300 " =    1.012
peak=    3.495 closest distance to " O   HOH Z  69 " =    1.672
peak=    3.494 closest distance to " O   HOH Z 214 " =    2.546
peak=    3.492 closest distance to " O   HOH Z 419 " =    1.957
peak=    3.479 closest distance to " NZ  LYS A 117 " =    1.164
peak=    3.478 closest distance to " O   HOH Z 148 " =    2.278
peak=    3.476 closest distance to " CB  ARG A 219 " =    0.996
peak=    3.475 closest distance to " CB  SER A 216 " =    0.874
peak=    3.467 closest distance to " O   HOH Z 415 " =    3.371
peak=    3.467 closest distance to " CB  PHE A 204 " =    0.940
peak=    3.467 closest distance to " CB  ASN A 110 " =    1.101
peak=    3.462 closest distance to " O   HOH Z 392 " =    1.733
peak=    3.462 closest distance to " O   HOH Z  44 " =    1.827
peak=    3.451 closest distance to " O   ARG A 275 " =    1.395
peak=    3.450 closest distance to " O   HOH Z 107 " =    0.804
peak=    3.445 closest distance to " O  BHOH Z  74 " =    1.232
peak=    3.444 closest distance to " O   HOH Z   1 " =    1.784
peak=    3.441 closest distance to " CB  ASP A 124 " =    0.945
peak=    3.441 closest distance to " N   ASN A 127 " =    1.302
peak=    3.439 closest distance to " CA  ILE A 234 " =    1.073
peak=    3.438 closest distance to " CB  ALA A 114 " =    0.842
peak=    3.435 closest distance to " CA  ASN A 217 " =    1.049
peak=    3.434 closest distance to " CA  ALA A 129 " =    1.262
peak=    3.429 closest distance to " CB  ALA A   9 " =    1.564
peak=    3.419 closest distance to " O   HOH Z 146 " =    1.475
peak=    3.416 closest distance to " O   HOH Z  68 " =    2.196
peak=    3.414 closest distance to " NE2 GLN A  73 " =    1.470
peak=    3.410 closest distance to " O   HOH Z   1 " =    1.607
peak=    3.407 closest distance to " O   HOH Z 323 " =    1.573
peak=    3.406 closest distance to " N   PHE A 130 " =    1.290
peak=    3.402 closest distance to " OG BSER A 212 " =    2.776
peak=    3.401 closest distance to " CB  SER A 212 " =    1.402
peak=    3.396 closest distance to " O   HOH Z 128 " =    2.016
peak=    3.392 closest distance to " O   HOH Z  10 " =    1.679
peak=    3.390 closest distance to " CB  ASN A  39 " =    0.955
peak=    3.389 closest distance to " O   HOH Z 331 " =    1.014
peak=    3.387 closest distance to " O   HOH Z 106 " =    3.282
peak=    3.383 closest distance to " O   THR A 182 " =    1.460
peak=    3.379 closest distance to " CG  LYS A 119 " =    1.019
peak=    3.375 closest distance to " N   ALA A 256 " =    0.989
peak=    3.374 closest distance to " CB  LYS A 117 " =    1.212
peak=    3.373 closest distance to " N   ASN A  39 " =    1.133
peak=    3.371 closest distance to " O   HOH Z  47 " =    1.714
peak=    3.369 closest distance to " O   HOH Z 414 " =    1.009
peak=    3.367 closest distance to " OG  SER A  62 " =    2.843
peak=    3.366 closest distance to " O   ASP A 191 " =    1.625
peak=    3.360 closest distance to " NH1 ARG A  14 " =    1.124
peak=    3.355 closest distance to " CB  ARG A 190 " =    1.465
peak=    3.347 closest distance to " O  BHOH Z 338 " =    2.492
peak=    3.345 closest distance to " CZ  PHE A 218 " =    1.186
peak=    3.333 closest distance to " CA  ALA A 233 " =    1.368
peak=    3.332 closest distance to " O   HOH Z 170 " =    2.145
peak=    3.329 closest distance to " O   HOH Z 344 " =    1.290
peak=    3.328 closest distance to " N   ARG A 156 " =    1.338
peak=    3.328 closest distance to " NE  ARG A  56 " =    3.529
peak=    3.327 closest distance to " CB  MET A  47 " =    1.047
peak=    3.323 closest distance to " O   HOH Z 213 " =    2.069
peak=    3.320 closest distance to " CA  LYS A 117 " =    1.129
peak=    3.319 closest distance to " O   HOH Z 218 " =    2.048
peak=    3.318 closest distance to " CB  SER A 273 " =    0.912
peak=    3.316 closest distance to " CB  TRP A 179 " =    1.283
peak=    3.311 closest distance to " O   HOH Z 132 " =    2.277
peak=    3.311 closest distance to " O   HOH Z 172 " =    2.946
peak=    3.308 closest distance to " O   HOH Z 371 " =    1.829
peak=    3.302 closest distance to " O   HOH Z   6 " =    1.565
peak=    3.300 closest distance to " CE AMET A  47 " =    1.327
peak=    3.297 closest distance to " CE3 TRP A 274 " =    1.284
peak=    3.297 closest distance to " O   HOH Z 385 " =    3.871
peak=    3.295 closest distance to " CB  ASP A 191 " =    1.216
peak=    3.294 closest distance to " N   CYS A 260 " =    0.899
peak=    3.292 closest distance to " CA  SER A  87 " =    1.056
peak=    3.289 closest distance to " CG2 ILE A 120 " =    1.153
peak=    3.289 closest distance to " O   HOH Z 153 " =    3.680
peak=    3.288 closest distance to " CA  ALA A 160 " =    1.142
peak=    3.284 closest distance to " OG BSER A  99 " =    2.307
peak=    3.282 closest distance to " O   HOH Z  88 " =    3.250
peak=    3.280 closest distance to " OG BSER A 164 " =    2.205
peak=    3.276 closest distance to " O   HOH Z 427 " =    1.284
peak=    3.272 closest distance to " O   HOH Z 281 " =    2.224
peak=    3.267 closest distance to " CB  SER A 276 " =    1.197
peak=    3.258 closest distance to " O   HOH Z 193 " =    1.361
peak=    3.258 closest distance to " O   HOH Z 252 " =    2.376
peak=    3.254 closest distance to " O   HOH Z 284 " =    2.839
peak=    3.250 closest distance to " CG BARG A 102 " =    1.875
peak=    3.239 closest distance to " O   HOH Z 379 " =    1.313
peak=    3.238 closest distance to " CG  PRO A  90 " =    1.448
peak=    3.234 closest distance to " O   HOH Z 299 " =    4.296
peak=    3.230 closest distance to " O   HOH Z 272 " =    2.057
peak=    3.227 closest distance to " ND2 ASN A 249 " =    0.906
peak=    3.219 closest distance to " O   LYS A 119 " =    1.679
peak=    3.216 closest distance to " CA  ASP A 162 " =    0.895
peak=    3.210 closest distance to " CB  SER A  62 " =    0.982
peak=    3.208 closest distance to " O   HOH Z 421 " =    2.110
peak=    3.208 closest distance to " O   HOH Z  71 " =    1.401
peak=    3.204 closest distance to " CB  ASP A 107 " =    1.173
peak=    3.204 closest distance to " CZ3 TRP A 177 " =    1.124
peak=    3.201 closest distance to " O   HOH Z 222 " =    1.717
peak=    3.200 closest distance to " CD1 LEU A  96 " =    0.722
peak=    3.198 closest distance to " CG1 ILE A  49 " =    1.417
peak=    3.198 closest distance to " O   HOH Z 109 " =    2.365
peak=    3.194 closest distance to " NE1 TRP A  85 " =    1.088
peak=    3.192 closest distance to " NE1 TRP A 274 " =    0.939
peak=    3.190 closest distance to " O   HOH Z 368 " =    2.104
peak=    3.188 closest distance to " O   HOH Z 132 " =    2.779
peak=    3.187 closest distance to " O   HOH Z 305 " =    3.517
peak=    3.187 closest distance to " CG  LEU A 281 " =    0.976
peak=    3.183 closest distance to " O   HOH Z 128 " =    1.883
peak=    3.178 closest distance to " O   HOH Z 227 " =    2.036
peak=    3.178 closest distance to " CA  SER A 210 " =    1.502
peak=    3.176 closest distance to " O   HOH Z  85 " =    1.795
peak=    3.174 closest distance to " OD1 ASN A  45 " =    1.294
peak=    3.170 closest distance to " O   HOH Z 357 " =    1.949
peak=    3.170 closest distance to " O   HOH Z 189 " =    2.887
peak=    3.169 closest distance to " O   HOH Z  41 " =    2.549
peak=    3.167 closest distance to " O   HOH Z  61 " =    1.506
peak=    3.163 closest distance to " NH2BARG A 190 " =    1.376
peak=    3.163 closest distance to " O   HOH Z 183 " =    1.849
peak=    3.159 closest distance to " O   HOH Z 337 " =    2.127
peak=    3.157 closest distance to " O   HOH Z 216 " =    3.511
peak=    3.151 closest distance to " O   HOH Z 327 " =    2.131
peak=    3.150 closest distance to " O   HOH Z 203 " =    1.676
peak=    3.148 closest distance to " CB  ALA A 114 " =    0.941
peak=    3.147 closest distance to " CG2 THR A 221 " =    1.313
peak=    3.145 closest distance to " CD  LYS A 119 " =    1.699
peak=    3.143 closest distance to " O   HOH Z  51 " =    1.516
peak=    3.142 closest distance to " NE2 GLN A  58 " =    4.573
peak=    3.141 closest distance to " O   HOH Z 407 " =    1.373
peak=    3.132 closest distance to " CB  ASN A 187 " =    1.194
peak=    3.127 closest distance to " O   GLN A 194 " =    1.536
peak=    3.125 closest distance to " CB  ALA A 248 " =    1.071
peak=    3.123 closest distance to " CG  LYS A 289 " =    1.396
peak=    3.121 closest distance to " CB  ALA A 248 " =    1.318
peak=    3.119 closest distance to " OE1 GLU A   2 " =    1.386
peak=    3.117 closest distance to " O   HOH Z 191 " =    3.149
peak=    3.112 closest distance to " O   HOH Z  99 " =    1.816
peak=    3.112 closest distance to " O   HOH Z 422 " =    0.852
peak=    3.106 closest distance to " OG1 THR A 221 " =    1.211
peak=    3.104 closest distance to " O   HOH Z 260 " =    2.407
peak=    3.100 closest distance to " CB  TRP A 266 " =    1.195
peak=    3.098 closest distance to " OE2 GLU A   2 " =    1.934
peak=    3.093 closest distance to " CG  PRO A 213 " =    1.273
peak=    3.086 closest distance to " O   HOH Z 178 " =    1.473
peak=    3.080 closest distance to " O   HOH Z  43 " =    1.894
peak=    3.066 closest distance to " O   HOH Z 117 " =    1.793
peak=    3.060 closest distance to " CD  LYS A 119 " =    1.830
peak=    3.059 closest distance to " O   HOH Z 184 " =    1.475
peak=    3.041 closest distance to " O   HOH Z 371 " =    2.646
peak=    3.030 closest distance to " O   HOH Z 421 " =    3.580
peak=    3.017 closest distance to " O   HOH Z 438 " =    2.272

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

Number of peaks found at mFobs-DFmodel map (map cutoff=3.00 sigma)= 197         
Filter by distance & map next to the model:
   mapped sites are within: 0.690 - 5.837
   number of sites selected in [dist_min= 0.70, dist_max= 6.00]: 196 from: 197
   mapped sites are within: 0.720 - 5.837

peak=   -4.826 closest distance to " O   HOH Z 211 " =    0.802
peak=   -4.712 closest distance to " O   HOH Z  69 " =    1.599
peak=   -4.551 closest distance to " O   PRO A 198 " =    1.222
peak=   -4.542 closest distance to " O   HOH Z 193 " =    0.821
peak=   -4.459 closest distance to " C   HIS A 108 " =    1.186
peak=   -4.252 closest distance to " O   HOH Z 147 " =    1.960
peak=   -4.243 closest distance to " CD1 LEU A 255 " =    2.766
peak=   -4.184 closest distance to " O   HOH Z 131 " =    4.182
peak=   -4.121 closest distance to " CG  GLN A  58 " =    1.012
peak=   -4.100 closest distance to " CB  ALA A  43 " =    2.458
peak=   -4.060 closest distance to " O   HOH Z 231 " =    1.097
peak=   -4.050 closest distance to " CB  VAL A 230 " =    1.000
peak=   -4.007 closest distance to " CD  ARG A 156 " =    1.959
peak=   -3.994 closest distance to " OG BSER A 134 " =    1.408
peak=   -3.976 closest distance to " O   HOH Z 147 " =    1.073
peak=   -3.958 closest distance to " CG2 ILE A  20 " =    2.839
peak=   -3.957 closest distance to " CZ2 TRP A  92 " =    2.768
peak=   -3.918 closest distance to " NE2 GLN A  55 " =    1.072
peak=   -3.897 closest distance to " O   HOH Z 134 " =    4.238
peak=   -3.859 closest distance to " CB  GLN A  55 " =    1.275
peak=   -3.835 closest distance to " O   SER A 135 " =    1.516
peak=   -3.818 closest distance to " CG2 VAL A 202 " =    2.748
peak=   -3.818 closest distance to " O   HOH Z 295 " =    1.731
peak=   -3.795 closest distance to " CD1 LEU A 101 " =    2.292
peak=   -3.795 closest distance to " O   VAL A  67 " =    2.499
peak=   -3.785 closest distance to " CD  PRO A 213 " =    1.995
peak=   -3.769 closest distance to " CD  ARG A  14 " =    3.180
peak=   -3.751 closest distance to " CB  ALA A 114 " =    2.513
peak=   -3.748 closest distance to " N   ALA A 244 " =    1.301
peak=   -3.746 closest distance to " CE2 TYR A  30 " =    2.745
peak=   -3.736 closest distance to " OG  SER A  97 " =    2.229
peak=   -3.718 closest distance to " OE1 GLN A 183 " =    1.622
peak=   -3.715 closest distance to " CB  SER A 210 " =    1.087
peak=   -3.711 closest distance to " O   PRO A 163 " =    1.899
peak=   -3.711 closest distance to " CD2 TYR A 293 " =    1.876
peak=   -3.700 closest distance to " O   HOH Z 100 " =    0.923
peak=   -3.694 closest distance to " CB  ALA A 248 " =    2.100
peak=   -3.666 closest distance to " O   SER A 276 " =    1.593
peak=   -3.666 closest distance to " O   HOH Z  40 " =    1.499
peak=   -3.656 closest distance to " O   HOH Z 208 " =    2.241
peak=   -3.648 closest distance to " O   HOH Z 281 " =    2.909
peak=   -3.647 closest distance to " O   HOH Z 266 " =    5.445
peak=   -3.645 closest distance to " OG  SER A  87 " =    1.388
peak=   -3.639 closest distance to " O   ALA A 227 " =    1.445
peak=   -3.632 closest distance to " O   HOH Z 286 " =    1.609
peak=   -3.620 closest distance to " CE1 TYR A 247 " =    2.562
peak=   -3.609 closest distance to " OE1 GLN A 223 " =    2.353
peak=   -3.603 closest distance to " O   HOH Z 423 " =    2.425
peak=   -3.595 closest distance to " CD2 HIS A 207 " =    2.083
peak=   -3.585 closest distance to " C   ASN A 285 " =    2.071
peak=   -3.575 closest distance to " CA  GLN A  58 " =    1.232
peak=   -3.551 closest distance to " CG  TRP A 266 " =    1.869
peak=   -3.547 closest distance to " O   HOH Z 231 " =    2.082
peak=   -3.539 closest distance to " O   HOH Z 116 " =    1.635
peak=   -3.530 closest distance to " CD2 TYR A 247 " =    2.532
peak=   -3.507 closest distance to " SG BCYS A 201 " =    2.244
peak=   -3.502 closest distance to " CB  ASP A 132 " =    2.428
peak=   -3.499 closest distance to " CD  GLN A  88 " =    1.271
peak=   -3.496 closest distance to " O   HOH Z 236 " =    1.514
peak=   -3.489 closest distance to " OG  SER A  62 " =    4.085
peak=   -3.486 closest distance to " O   HOH Z 352 " =    1.466
peak=   -3.481 closest distance to " O   HOH Z  26 " =    0.731
peak=   -3.479 closest distance to " CA  GLY A 241 " =    2.355
peak=   -3.472 closest distance to " O   ALA A 292 " =    2.193
peak=   -3.467 closest distance to " O   HOH Z 404 " =    1.432
peak=   -3.456 closest distance to " CZ  PHE A  38 " =    2.386
peak=   -3.455 closest distance to " O   HOH Z  60 " =    1.749
peak=   -3.453 closest distance to " O   HOH Z 427 " =    1.825
peak=   -3.448 closest distance to " CD2 LEU A   5 " =    1.103
peak=   -3.440 closest distance to " O   HOH Z 359 " =    3.218
peak=   -3.434 closest distance to " O   HOH Z 183 " =    1.701
peak=   -3.433 closest distance to " OD2 ASP A 191 " =    1.268
peak=   -3.424 closest distance to " O   HOH Z 394 " =    1.510
peak=   -3.420 closest distance to " CD  PRO A 243 " =    1.905
peak=   -3.419 closest distance to " O   HOH Z 111 " =    1.603
peak=   -3.414 closest distance to " CG1 VAL A 250 " =    2.743
peak=   -3.411 closest distance to " O   HOH Z 185 " =    1.755
peak=   -3.407 closest distance to " OE2 GLU A 152 " =    1.328
peak=   -3.407 closest distance to " NZ  LYS A 119 " =    0.931
peak=   -3.390 closest distance to " ND2 ASN A 249 " =    2.032
peak=   -3.390 closest distance to " O   HOH Z 235 " =    1.151
peak=   -3.390 closest distance to " CG2 THR A   4 " =    1.862
peak=   -3.388 closest distance to " OXT GLY A 302 " =    3.091
peak=   -3.387 closest distance to " O   HOH Z  64 " =    1.318
peak=   -3.386 closest distance to " O   HOH Z 162 " =    2.734
peak=   -3.384 closest distance to " CG  PHE A 283 " =    2.694
peak=   -3.384 closest distance to " O   HOH Z 111 " =    4.783
peak=   -3.384 closest distance to " O   ILE A  49 " =    1.714
peak=   -3.382 closest distance to " CA  ASP A  27 " =    2.386
peak=   -3.379 closest distance to " O   HOH Z 107 " =    1.001
peak=   -3.376 closest distance to " CZ2 TRP A 274 " =    0.927
peak=   -3.366 closest distance to " ND2 ASN A  45 " =    2.208
peak=   -3.365 closest distance to " O   HOH Z 290 " =    1.049
peak=   -3.354 closest distance to " N   ALA A 248 " =    1.571
peak=   -3.353 closest distance to " CG2 THR A 221 " =    2.134
peak=   -3.353 closest distance to " O   HOH Z 164 " =    5.837
peak=   -3.352 closest distance to " CG1 VAL A 112 " =    3.040
peak=   -3.344 closest distance to " O   HOH Z 126 " =    1.639
peak=   -3.344 closest distance to " O   VAL A 189 " =    2.487
peak=   -3.343 closest distance to " O   SER A  95 " =    1.510
peak=   -3.342 closest distance to " NH2 ARG A  79 " =    2.130
peak=   -3.337 closest distance to " CZ3 TRP A 179 " =    1.299
peak=   -3.337 closest distance to " O   LEU A 297 " =    0.775
peak=   -3.337 closest distance to " O   ARG A 219 " =    1.812
peak=   -3.329 closest distance to " O   HOH Z 191 " =    5.739
peak=   -3.324 closest distance to " OG  SER A  63 " =    1.192
peak=   -3.322 closest distance to " OE1 GLN A  88 " =    1.058
peak=   -3.316 closest distance to " OE1 GLU A 277 " =    2.246
peak=   -3.315 closest distance to " CB  TRP A  85 " =    2.530
peak=   -3.312 closest distance to " O   HOH Z 158 " =    1.753
peak=   -3.311 closest distance to " C   GLN A 205 " =    1.884
peak=   -3.310 closest distance to " O   HOH Z 238 " =    0.720
peak=   -3.304 closest distance to " O   HOH Z 177 " =    1.159
peak=   -3.297 closest distance to " O   HOH Z 276 " =    1.472
peak=   -3.296 closest distance to " O   HOH Z 149 " =    1.722
peak=   -3.286 closest distance to " CB  TYR A  68 " =    1.493
peak=   -3.276 closest distance to " O   HOH Z  73 " =    2.441
peak=   -3.275 closest distance to " ND2 ASN A 252 " =    2.019
peak=   -3.274 closest distance to " O   HOH Z 359 " =    1.716
peak=   -3.272 closest distance to " O   HOH Z 165 " =    2.131
peak=   -3.266 closest distance to " CZ  TYR A 169 " =    1.695
peak=   -3.263 closest distance to " O   HOH Z 252 " =    3.934
peak=   -3.260 closest distance to " ND2 ASN A 187 " =    1.513
peak=   -3.259 closest distance to " O   HOH Z 374 " =    1.701
peak=   -3.257 closest distance to " CG2 THR A  18 " =    2.832
peak=   -3.257 closest distance to " CB  ALA A   7 " =    2.143
peak=   -3.256 closest distance to " O   HOH Z 201 " =    2.179
peak=   -3.255 closest distance to " C   ARG A 269 " =    1.192
peak=   -3.254 closest distance to " CD1 TRP A 274 " =    1.210
peak=   -3.253 closest distance to " CG2 VAL A 189 " =    1.942
peak=   -3.250 closest distance to " OH  TYR A 172 " =    1.760
peak=   -3.247 closest distance to " O   HOH Z 398 " =    1.320
peak=   -3.241 closest distance to " CG2 ILE A 151 " =    2.442
peak=   -3.240 closest distance to " CG  TYR A 169 " =    2.065
peak=   -3.240 closest distance to " O   HOH Z 331 " =    1.061
peak=   -3.237 closest distance to " NE2 GLN A  11 " =    1.808
peak=   -3.232 closest distance to " O   HOH Z 351 " =    1.695
peak=   -3.232 closest distance to " O   HOH Z 385 " =    1.492
peak=   -3.230 closest distance to " O   HOH Z 377 " =    1.128
peak=   -3.227 closest distance to " O   HOH Z 140 " =    1.107
peak=   -3.224 closest distance to " O   HOH Z 346 " =    1.730
peak=   -3.218 closest distance to " CA  GLY A 203 " =    2.490
peak=   -3.210 closest distance to " CA  ASP A 298 " =    1.048
peak=   -3.210 closest distance to " O   PRO A 163 " =    1.320
peak=   -3.209 closest distance to " CD  LYS A 289 " =    2.282
peak=   -3.208 closest distance to " C   LEU A 222 " =    1.391
peak=   -3.205 closest distance to " O   SER A 271 " =    2.180
peak=   -3.204 closest distance to " O   HOH Z 293 " =    1.628
peak=   -3.201 closest distance to " O   LEU A  83 " =    2.777
peak=   -3.191 closest distance to " CB  TYR A  68 " =    1.077
peak=   -3.190 closest distance to " C   GLN A  58 " =    2.075
peak=   -3.190 closest distance to " O   HOH Z 312 " =    1.526
peak=   -3.189 closest distance to " O   HOH Z 244 " =    1.715
peak=   -3.188 closest distance to " N   ALA A 226 " =    1.888
peak=   -3.188 closest distance to " O   HOH Z 166 " =    1.824
peak=   -3.187 closest distance to " O   HOH Z 117 " =    1.806
peak=   -3.183 closest distance to " O   SER A  22 " =    2.482
peak=   -3.180 closest distance to " O   HOH Z 313 " =    1.489
peak=   -3.173 closest distance to " O   HOH Z  28 " =    2.515
peak=   -3.173 closest distance to " CE2 PHE A 218 " =    2.428
peak=   -3.172 closest distance to " O   HOH Z  53 " =    1.479
peak=   -3.167 closest distance to " CZ  PHE A  16 " =    2.062
peak=   -3.166 closest distance to " OD1 ASN A 301 " =    2.021
peak=   -3.165 closest distance to " O   PRO A 243 " =    1.963
peak=   -3.162 closest distance to " O   ALA A 180 " =    1.346
peak=   -3.161 closest distance to " NH2 ARG A 219 " =    1.528
peak=   -3.160 closest distance to " CD2 LEU A 237 " =    2.534
peak=   -3.156 closest distance to " O   HOH Z 216 " =    1.477
peak=   -3.151 closest distance to " O   HOH Z 203 " =    1.796
peak=   -3.146 closest distance to " CB  ASN A  45 " =    1.985
peak=   -3.134 closest distance to " NH2 ARG A  36 " =    2.567
peak=   -3.131 closest distance to " OG BSER A 210 " =    1.727
peak=   -3.128 closest distance to " CA  GLY A 133 " =    1.929
peak=   -3.126 closest distance to " O   HOH Z  68 " =    1.273
peak=   -3.126 closest distance to " CD1 ILE A 199 " =    2.360
peak=   -3.123 closest distance to " CA  GLY A  23 " =    1.762
peak=   -3.120 closest distance to " O   HOH Z 215 " =    1.509
peak=   -3.120 closest distance to " OG  SER A 271 " =    1.210
peak=   -3.120 closest distance to " CG2BVAL A  72 " =    1.909
peak=   -3.112 closest distance to " O   ASP A  27 " =    1.892
peak=   -3.107 closest distance to " CE1 TYR A 186 " =    2.101
peak=   -3.102 closest distance to " O   ALA A  10 " =    1.730
peak=   -3.101 closest distance to " CG  MET A 105 " =    0.987
peak=   -3.093 closest distance to " C   MET A 188 " =    1.503
peak=   -3.092 closest distance to " O   HOH Z 166 " =    2.101
peak=   -3.091 closest distance to " CG  ASP A 231 " =    0.873
peak=   -3.087 closest distance to " O   HOH Z  51 " =    0.779
peak=   -3.084 closest distance to " CG  GLN A 103 " =    2.346
peak=   -3.082 closest distance to " CA  HIS A 207 " =    1.260
peak=   -3.075 closest distance to " OG  SER A 245 " =    1.465
peak=   -3.071 closest distance to " O   HOH Z 437 " =    1.658
peak=   -3.055 closest distance to " NE2 GLN A 278 " =    1.678
peak=   -3.047 closest distance to " CG  LEU A 228 " =    1.045
peak=   -3.035 closest distance to " O   HOH Z 389 " =    1.407
peak=   -3.033 closest distance to " O   HOH Z 392 " =    0.959
peak=   -3.024 closest distance to " CD  GLN A 183 " =    1.739

================= 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    :  0.5069 0.4989   6.301092e+00   6.293265e+00
   1_bss:  0.4984 0.4869   6.294750e+00   6.286022e+00
   1_xyz:  0.4362 0.4543   6.227835e+00   6.250862e+00
   1_adp:  0.3951 0.4582   6.179154e+00   6.249822e+00
   1_occ:  0.3952 0.4586   6.178184e+00   6.250468e+00
   2_bss:  0.3928 0.4555   6.179163e+00   6.251342e+00
   2_xyz:  0.3157 0.3829   6.006490e+00   6.143911e+00
   2_adp:  0.2861 0.3569   5.937319e+00   6.085002e+00
   2_occ:  0.2857 0.3573   5.937313e+00   6.084618e+00
   3_bss:  0.2832 0.3552   5.935409e+00   6.083174e+00
   3_xyz:  0.2217 0.2822   5.730652e+00   5.911119e+00
   3_adp:  0.2005 0.2703   5.664942e+00   5.871141e+00
   3_occ:  0.2001 0.2699   5.663599e+00   5.870306e+00
   4_bss:  0.1996 0.2696   5.662611e+00   5.869744e+00
   4_xyz:  0.1543 0.2149   5.433189e+00   5.667784e+00
   4_adp:  0.1436 0.1959   5.351868e+00   5.573774e+00
   4_occ:  0.1431 0.1953   5.349286e+00   5.570869e+00
   5_bss:  0.1432 0.1956   5.349741e+00   5.570982e+00
   5_xyz:  0.1278 0.1753   5.254119e+00   5.484877e+00
   5_adp:  0.1238 0.1724   5.230834e+00   5.467486e+00
   5_occ:  0.1236 0.1724   5.230314e+00   5.467037e+00
   5_bss:  0.1235 0.1724   5.230281e+00   5.466870e+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:  0.374  20.000   7.030   8.594  10.353   0.000   0.000   0.000
   1_xyz:  0.374  20.000   7.030   8.594  10.353   0.000   0.000   0.000
   1_adp:  0.374  20.000   7.030   8.594  10.353   0.000   0.000   0.000
   1_occ:  0.374  20.000   7.030   8.594  10.353   0.000   0.000   0.000
   2_bss:  0.349  38.385   3.921   4.659   6.757   0.000   0.000   0.000
   2_xyz:  0.349  38.385   3.921   4.659   6.757   0.000   0.000   0.000
   2_adp:  0.349  38.385   3.921   4.659   6.757   0.000   0.000   0.000
   2_occ:  0.349  38.385   3.921   4.659   6.757   0.000   0.000   0.000
   3_bss:  0.329  45.911   1.468   2.387   4.096   0.000   0.000   0.000
   3_xyz:  0.329  45.911   1.468   2.387   4.096   0.000   0.000   0.000
   3_adp:  0.329  45.911   1.468   2.387   4.096   0.000   0.000   0.000
   3_occ:  0.329  45.911   1.468   2.387   4.096   0.000   0.000   0.000
   4_bss:  0.313  49.705   0.408   1.270   3.144   0.000   0.000   0.000
   4_xyz:  0.313  49.705   0.408   1.270   3.144   0.000   0.000   0.000
   4_adp:  0.313  49.705   0.408   1.270   3.144   0.000   0.000   0.000
   4_occ:  0.313  49.705   0.408   1.270   3.144   0.000   0.000   0.000
   5_bss:  0.308  47.118  -0.017   0.660   2.603   0.000   0.000   0.000
   5_xyz:  0.308  47.118  -0.017   0.660   2.603   0.000   0.000   0.000
   5_adp:  0.308  47.118  -0.017   0.660   2.603   0.000   0.000   0.000
   5_occ:  0.308  47.118  -0.017   0.660   2.603   0.000   0.000   0.000
   5_bss:  0.315  48.199  -1.099  -0.422   1.521   0.000   0.000   0.000
------------------------------------------------------------------------
 stage     <pher>    fom   alpha         beta
   0    :  64.572 0.3340  0.4023    81530.968
   1_bss:  64.648 0.3318  0.5087    79731.876
   1_xyz:  55.067 0.4553  0.6899    64080.969
   1_adp:  53.807 0.4714  0.7884    63461.942
   1_occ:  53.810 0.4714  0.7859    63493.708
   2_bss:  53.576 0.4742  0.7008    63009.215
   2_xyz:  42.118 0.6159  0.9001    40827.392
   2_adp:  37.760 0.6686  0.9582    34322.070
   2_occ:  37.799 0.6682  0.9572    34330.722
   3_bss:  37.597 0.6703  0.8788    34003.299
   3_xyz:  28.345 0.7755  0.9789    20695.332
   3_adp:  26.710 0.7936  0.9848    18953.602
   3_occ:  26.704 0.7936  0.9845    18905.429
   4_bss:  26.647 0.7942  0.9480    18840.132
   4_xyz:  20.910 0.8521  0.9881    11841.436
   4_adp:  18.328 0.8775  0.9938     9785.791
   4_occ:  18.270 0.8780  0.9940     9719.411
   5_bss:  18.251 0.8782  0.9752     9717.866
   5_xyz:  16.104 0.8974  0.9846     7951.129
   5_adp:  15.695 0.9012  0.9794     7693.069
   5_occ:  15.692 0.9011  0.9792     7679.645
   5_bss:  15.689 0.9012  0.9793     7676.121
------------------------------------------------------------------------
 stage       angl   bond   chir   dihe   plan   repu  geom_target
   0    :  24.226  0.414  2.119 33.790  0.145  4.086   5.3288e+01
   1_bss:  24.226  0.414  2.119 33.790  0.145  4.086   5.3288e+01
   1_xyz:   1.730  0.013  0.106 18.334  0.006  4.104   1.4685e-01
   1_adp:   1.730  0.013  0.106 18.334  0.006  4.104   1.4685e-01
   1_occ:   1.730  0.013  0.106 18.334  0.006  4.104   1.4685e-01
   2_bss:   1.730  0.013  0.106 18.334  0.006  4.104   1.4685e-01
   2_xyz:   1.388  0.011  0.091 16.637  0.006  4.104   1.1821e-01
   2_adp:   1.388  0.011  0.091 16.637  0.006  4.104   1.1821e-01
   2_occ:   1.388  0.011  0.091 16.637  0.006  4.104   1.1821e-01
   3_bss:   1.388  0.011  0.091 16.637  0.006  4.104   1.1821e-01
   3_xyz:   1.045  0.007  0.072 15.362  0.004  4.120   6.5756e-02
   3_adp:   1.045  0.007  0.072 15.362  0.004  4.120   6.5756e-02
   3_occ:   1.045  0.007  0.072 15.362  0.004  4.120   6.5756e-02
   4_bss:   1.045  0.007  0.072 15.362  0.004  4.120   6.5756e-02
   4_xyz:   1.158  0.008  0.081 15.659  0.005  4.130   7.6555e-02
   4_adp:   1.158  0.008  0.081 15.659  0.005  4.130   7.6555e-02
   4_occ:   1.158  0.008  0.081 15.659  0.005  4.130   7.6555e-02
   5_bss:   1.158  0.008  0.081 15.659  0.005  4.130   7.6555e-02
   5_xyz:   1.021  0.007  0.075 15.377  0.004  4.113   6.3090e-02
   5_adp:   1.021  0.007  0.075 15.377  0.004  4.113   6.3090e-02
   5_occ:   1.021  0.007  0.075 15.377  0.004  4.113   6.3090e-02
   5_bss:   1.021  0.007  0.075 15.377  0.004  4.113   6.3090e-02
------------------------------------------------------------------------
                      Maximal deviations:
 stage       angl   bond   chir   dihe   plan   repu       |grad|
   0    :  74.492  1.400  6.404144.062  0.405  1.196   6.9019e+00
   1_bss:  74.492  1.400  6.404144.062  0.405  1.196   6.9019e+00
   1_xyz:  13.774  0.172  0.415 84.951  0.035  2.139   9.8573e-02
   1_adp:  13.774  0.172  0.415 84.951  0.035  2.139   9.8573e-02
   1_occ:  13.774  0.172  0.415 84.951  0.035  2.139   9.8573e-02
   2_bss:  13.774  0.172  0.415 84.951  0.035  2.139   9.8573e-02
   2_xyz:  10.378  0.151  0.360 86.289  0.052  1.987   1.0054e-01
   2_adp:  10.378  0.151  0.360 86.289  0.052  1.987   1.0054e-01
   2_occ:  10.378  0.151  0.360 86.289  0.052  1.987   1.0054e-01
   3_bss:  10.378  0.151  0.360 86.289  0.052  1.987   1.0054e-01
   3_xyz:   6.359  0.046  0.224 83.604  0.033  2.383   9.2167e-02
   3_adp:   6.359  0.046  0.224 83.604  0.033  2.383   9.2167e-02
   3_occ:   6.359  0.046  0.224 83.604  0.033  2.383   9.2167e-02
   4_bss:   6.359  0.046  0.224 83.604  0.033  2.383   9.2167e-02
   4_xyz:   8.797  0.056  0.293 88.124  0.043  2.203   6.0545e-02
   4_adp:   8.797  0.056  0.293 88.124  0.043  2.203   6.0545e-02
   4_occ:   8.797  0.056  0.293 88.124  0.043  2.203   6.0545e-02
   5_bss:   8.797  0.056  0.293 88.124  0.043  2.203   6.0545e-02
   5_xyz:   6.718  0.048  0.243 82.479  0.044  2.351   4.6318e-02
   5_adp:   6.718  0.048  0.243 82.479  0.044  2.351   4.6318e-02
   5_occ:   6.718  0.048  0.243 82.479  0.044  2.351   4.6318e-02
   5_bss:   6.718  0.048  0.243 82.479  0.044  2.351   4.6318e-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:  86.71   0.00  16.36  74.72   0.00  14.59  86.71   0.00  25.96
   1_occ:  86.71   0.00  16.36  74.72   0.00  14.59  86.71   0.00  25.96
   2_bss:  86.71   0.00  16.36  74.72   0.00  14.59  86.71   0.00  25.96
   2_xyz:  86.71   0.00  16.36  74.72   0.00  14.59  86.71   0.00  25.96
   2_adp:  87.22   0.00  15.05  62.36   0.00  11.94  87.22   0.00  31.97
   2_occ:  87.22   0.00  15.05  62.36   0.00  11.94  87.22   0.00  31.97
   3_bss:  87.22   0.00  15.05  62.36   0.00  11.94  87.22   0.00  31.97
   3_xyz:  87.22   0.00  15.05  62.36   0.00  11.94  87.22   0.00  31.97
   3_adp: 101.65   0.00  16.17  90.92   0.00  11.50 101.65   0.67  41.58
   3_occ: 101.65   0.00  16.17  90.92   0.00  11.50 101.65   0.67  41.58
   4_bss: 101.65   0.00  16.17  90.92   0.00  11.50 101.65   0.67  41.58
   4_xyz: 101.65   0.00  16.17  90.92   0.00  11.50 101.65   0.67  41.58
   4_adp:  98.24   0.00  14.95  95.13   0.00  10.35  98.24   2.45  40.03
   4_occ:  98.24   0.00  14.95  95.13   0.00  10.35  98.24   2.45  40.03
   5_bss:  98.24   0.00  14.95  95.13   0.00  10.35  98.24   2.45  40.03
   5_xyz:  98.24   0.00  14.95  95.13   0.00  10.35  98.24   2.45  40.03
   5_adp:  98.03   0.00  14.84  98.03   0.00  10.15  97.72   2.91  40.38
   5_occ:  98.03   0.00  14.84  98.03   0.00  10.15  97.72   2.91  40.38
   5_bss:  99.12   1.08  15.92  99.12   1.08  11.23  98.80   4.00  41.46
------------------------------------------------------------------------
 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:    1.284    0.031    0.410
   1_adp:    1.284    0.031    0.410
   1_occ:    1.284    0.031    0.410
   2_bss:    1.284    0.031    0.410
   2_xyz:    1.822    0.028    0.614
   2_adp:    1.822    0.028    0.614
   2_occ:    1.822    0.028    0.614
   3_bss:    1.822    0.028    0.614
   3_xyz:    1.604    0.024    0.701
   3_adp:    1.604    0.024    0.701
   3_occ:    1.604    0.024    0.701
   4_bss:    1.604    0.024    0.701
   4_xyz:    1.649    0.035    0.793
   4_adp:    1.649    0.035    0.793
   4_occ:    1.649    0.035    0.793
   5_bss:    1.649    0.035    0.793
   5_xyz:    1.907    0.046    0.821
   5_adp:    1.907    0.046    0.821
   5_occ:    1.907    0.046    0.821
   5_bss:    1.907    0.046    0.821
------------------------------------------------------------------------

CPU time actual refinement: 338.81


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

Writing refined structure to PDB file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/trial/run_152/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_152/model_refine_001_2mFobs-DFmodel.map
Writing mFobs-DFmodel XPLOR map to file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/trial/run_152/model_refine_001_mFobs-DFmodel.map
Writing map coefficients to MTZ file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/trial/run_152/model_refine_001_map_coeffs.mtz

Writing default parameters for subsequent refinement:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/trial/run_152/model_refine_002.def


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

Pure refinement (no I/O, processing, etc)= 338.66 
  Macro-tasks:
    bulk solvent and scale       = 40.44  
    individual site refinement   = 140.07 
    weights calculation          = 32.44  
    collect and process          = 6.51   
    model show statistics        = 0.12   
    TOTAL for macro-tasks        = 219.58 
  Micro-tasks:
    mask                            = 2.35   
    f_calc                          = 106.11 
    alpha_beta                      = 8.43   
    target                          = 1.17   
    gradients_wrt_atomic_parameters = 115.25 
    fmodel                         = 7.18   
    r_factors                      = 0.19   
    phase_errors                   = 10.14  
    foms                           = 0.25   
    TOTAL for micro-tasks          = 251.07 
NUMBER OF MASK CALCS=  5
Time per interpreted Python bytecode instruction: 4.830 micro seconds
Total CPU time: 5.87 minutes
from_scatterers_fft:    629 calls, 105.76 s
gradients_fft:          575 calls, 102.61 s

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

# Date 2008-01-16 Time 00:51:49 PST -0800 (1200473509.37 s)
Start R-work = 0.5069, R-free = 0.4989 (no bulk solvent and anisotropic scale)
Final R-work = 0.1412, R-free = 0.1881 (no bulk solvent and anisotropic scale)

Start R-work = 0.4984, R-free = 0.4869
Final R-work = 0.1235, R-free = 0.1724