# Date 2008-01-16 Time 01:55:52 PST -0800 (1200477352.24 s)
#phil __OFF__

Command line arguments: "../613.param" "adp.set_b_iso=10" "sites.shake=0.5" "main.number_of_macro_cycles=5" "--overwrite"

HOST = firebird.lbl.gov
HOSTTYPE = x86_64-linux
USER = phzwart
PID = 9168
JOB_ID = 5158
SGE_ARCH = lx24-amd64
SGE_TASK_FIRST = 1
SGE_TASK_LAST = 1330
SGE_TASK_ID = 613

-------------------------------------------------------------------------------
  PHENIX: Python-based Hierarchical ENvironment for Integrated Xtallography
  User: phzwart
-------------------------------------------------------------------------------

              phenix.refine: Macromolecular Structure Refinement

-------------------------------------------------------------------------------
Phenix developers include:
  Paul Adams, Pavel Afonine, Vicent Chen, Ian Davis, Kreshna Gopal,
  Ralf Grosse-Kunstleve, Li-Wei Hung, Robert Immormino, Tom Ioerger,
  Airlie McCoy, Erik McKee, Nigel Moriarty, Reetal Pai, Randy Read,
  Jane Richardson, David Richardson, Tod Romo, Jim Sacchettini,
  Nicholas Sauter, Jacob Smith, Laurent Storoni, Tom Terwilliger,
  Peter Zwart
Phenix home page:
  http://www.phenix-online.org/
-------------------------------------------------------------------------------

-------------------------------------------------------------------------------
Phenix components are copyrighted by:
  - Lawrence Berkeley National Laboratory
  - Los Alamos National Laboratory
  - University of Cambridge
  - Duke University
  - Texas Agricultural Experiment Station &
    Texas Engineering Experiment Station
-------------------------------------------------------------------------------

-------------------------------------------------------------------------------
Major third-party components of Phenix include:
    Python, wxwidgets, wxPython, Boost, SCons, Clipper,
    CCP4 Monomer Library, CCP4 I/O libraries, PyCifRW, FFTPACK, L-BFGS
  Enter phenix.acknowledgments for details.
-------------------------------------------------------------------------------

Processing inputs. This may take a minute or two.

Command line parameter definitions:
  refinement.modify_start_model.adp.set_b_iso = 10

  refinement.modify_start_model.sites.shake = 0.5

  refinement.main.number_of_macro_cycles = 5

Working crystal symmetry after inspecting all inputs:
  Unit cell: (70.25, 45.7567, 87.6859, 90, 90, 90)
  Space group: P 21 21 21 (No. 19)

/net/cci-filer1/vol1/tmp/phzwart/tassos/trial/model.pdb
  Monomer Library directory:
    "/net/rosie/scratch3/phzwart/CCTBX/Sources/mon_lib"
  Total number of atoms: 2823
  Number of models: 1
  Model: 0
    Number of conformers: 2
    Conformer: "A"
      Number of atoms: 2769
      Number of chains: 2
        Number of residues, atoms: 302, 2333
          Classifications: {'peptide': 302}
          Modifications used: {'COO': 1}
          Link IDs: {'PTRANS': 7, 'CIS': 1, 'TRANS': 293}
        Number of residues, atoms: 436, 436
          Classifications: {'water': 436}
          Link IDs: {None: 435}
    Conformer: "B"
      Number of atoms: 2771
      Common with "A": 2717
      Number of chains: 2
        Number of residues, atoms: 302, 2333
          Classifications: {'peptide': 302}
          Modifications used: {'COO': 1}
          Link IDs: {'PTRANS': 7, 'CIS': 1, 'TRANS': 293}
          bond proxies already assigned to first conformer: 2332
        Number of residues, atoms: 438, 438
          Classifications: {'water': 438}
          Link IDs: {None: 437}
  Time building chain proxies: 3.25, 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: (70.25, 45.7567, 87.6859, 90, 90, 90)
Space group: P 21 21 21 (No. 19)
Systematic absences: 0
Centric reflections: 2427
Resolution range: 15.054 1.95351
Completeness in resolution range: 0.929269
Completeness with d_max=infinity: 0.926588

Number of F-obs in resolution range:                   19589
Number of F-obs <= 0:                                  0
Refinement resolution range: d_max =  15.0540
                             d_min =   1.9535

Miller array info: /net/cci-filer1/vol1/tmp/phzwart/tassos/trial/1e0w.cns:TEST
Observation type: None
Type of data: int, size=19589
Type of sigmas: None
Number of Miller indices: 19589
Anomalous flag: False
Unit cell: (70.25, 45.7567, 87.6859, 90, 90, 90)
Space group: P 21 21 21 (No. 19)
Systematic absences: 0
Centric reflections: 2427
Resolution range: 15.054 1.95351
Completeness in resolution range: 0.929269
Completeness with d_max=infinity: 0.926588

Test (R-free flags) flag value: 1

Number of work/free reflections by resolution:
                                         work  free  %free
  bin  1: 15.0544 -  4.1815 [2213/2239]  1990   223  10.1%
  bin  2:  4.1815 -  3.3308 [2135/2155]  1925   210   9.8%
  bin  3:  3.3308 -  2.9132 [2091/2110]  1882   209  10.0%
  bin  4:  2.9132 -  2.6484 [2087/2117]  1869   218  10.4%
  bin  5:  2.6484 -  2.4595 [2068/2087]  1868   200   9.7%
  bin  6:  2.4595 -  2.3150 [2069/2094]  1859   210  10.1%
  bin  7:  2.3150 -  2.1994 [2023/2051]  1819   204  10.1%
  bin  8:  2.1994 -  2.1040 [2053/2089]  1846   207  10.1%
  bin  9:  2.1040 -  2.0232 [2032/2083]  1840   192   9.4%
  bin 10:  2.0232 -  1.9535 [ 818/2055]   732    86  10.5%
                                overall 17630  1959  10.0%
Writing MTZ file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/trial/run_613/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:
        1.68 -     2.32: 34
        2.32 -     2.97: 1778
        2.97 -     3.61: 4604
        3.61 -     4.26: 9215
        4.26 -     4.90: 12829
  Nonbonded interactions sorted by model distance:
             atom i - atom j             model   vdw sym.op. j
  " O   HOH Z  70 " - " O   HOH Z 302 "  1.680 3.040 -x+1/2,-y+1,z+1/2
  " OG1 THR A  29 " - " O   HOH Z 245 "  1.681 3.040 x,y+1,z
  " O   HOH Z  61 " - " O   HOH Z 246 "  1.742 3.040 x,y+1,z
  " OE1 GLN A  55 " - " O   HOH Z 403 "  1.759 3.040 -x+1,y-1/2,-z+1/2
  " N   ASN A 148 " - " O   HOH Z 138 "  1.794 3.120 x,y-1,z
  ... (remaining 28455 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_613/model_refine_001.eff

Writing geometry restraints to file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/trial/run_613/model_refine_001.geo

CPU time processing inputs: 9.05


============================ Non-default parameters ===========================

A complete record of all parameters was written to the .eff file above.
Below are only the non-defaults.

#phil __ON__
refinement {
  crystal_symmetry {
    unit_cell = 70.25 45.75675 87.68585 90 90 90
    space_group = "P 21 21 21"
  }
  input {
    pdb {
      file_name = "/net/cci-filer1/vol1/tmp/phzwart/tassos/trial/model.pdb"
    }
    xray_data {
      file_name = "/net/cci-filer1/vol1/tmp/phzwart/tassos/trial/1e0w.cns"
      labels = "FOBS,SIGMA"
      r_free_flags {
        file_name = "/net/cci-filer1/vol1/tmp/phzwart/tassos/trial/1e0w.cns"
        label = "TEST"
        test_flag_value = 1
      }
    }
  }
  output {
    prefix = "model_refine"
    serial = 1
  }
  main {
    number_of_macro_cycles = 5
  }
  modify_start_model {
    adp {
      set_b_iso = 10
    }
    sites {
      shake = 0.5
    }
  }
}
#phil __OFF__


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


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


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

|--(resolution: 1.95 - 15.05 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.5041   r_free= 0.4939   ksol= 0.00   Bsol= 0.00   scale= 0.775    |
|                                                                             |
| 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:   0.83 A                  |
| x-ray target function (ml) for work reflections: 6.306876                   |
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
| Bin     Resolution   Compl.  No. Refl.    R-factors          Targets        |
|number     range              work test   work   test        work        test|
|  1: 15.0544 -  4.6645 0.99   1433  157 0.4360 0.4266      6.6608      6.6822|
|  2:  4.6645 -  3.7207 0.99   1384  158 0.4433 0.4128      6.8665      6.8121|
|  3:  3.7207 -  3.2558 0.99   1368  148 0.4680 0.4145      6.7059      6.6616|
|  4:  3.2558 -  2.9606 0.99   1337  154 0.4988 0.4855      6.5646      6.5118|
|  5:  2.9606 -  2.7498 0.99   1348  148 0.5455 0.5407      6.3784      6.4166|
|  6:  2.7498 -  2.5885 0.99   1327  146 0.5290 0.5469      6.2813       6.208|
|  7:  2.5885 -  2.4595 0.99   1337  149 0.5252 0.5067      6.2521      6.1993|
|  8:  2.4595 -  2.3528 0.98   1316  150 0.5547 0.5191      6.1791      6.1717|
|  9:  2.3528 -  2.2626 0.98   1305  143 0.5399 0.5746      6.1322       6.223|
| 10:  2.2626 -  2.1847 1.00   1343  148 0.5337 0.5435      6.0864      6.0826|
| 11:  2.1847 -  2.1166 0.98   1319  144 0.5160 0.5351      6.0349      6.0346|
| 12:  2.1166 -  2.0563 0.98   1293  139 0.5358 0.5590       5.939      5.9576|
| 13:  2.0563 -  2.0023 0.91   1205  136 0.5599 0.5544      5.8975       5.814|
| 14:  2.0023 -  1.9535 0.24    315   39 0.5406 0.3960       5.858       5.841|
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
|R-free likelihood based estimates for figures of merit, absolute phase error,|
|and distribution parameters alpha and beta (Acta Cryst. (1995). A51, 880-887)|
|                                                                             |
| Bin     Resolution      No. Refl.   FOM  Phase Scale    Alpha        Beta   |
|  #        range        work  test        error factor                       |
|  1: 15.0544 -  4.6645  1433   157  0.64  39.34   0.77     0.70      91448.35|
|  2:  4.6645 -  3.7207  1384   158  0.67  38.18   0.84     0.75     124723.78|
|  3:  3.7207 -  3.2558  1368   148  0.55  48.18   0.83     0.69     129509.80|
|  4:  3.2558 -  2.9606  1337   154  0.45  56.01   0.76     0.55     116287.42|
|  5:  2.9606 -  2.7498  1348   148  0.33  64.99   0.71     0.43      93848.50|
|  6:  2.7498 -  2.5885  1327   146  0.30  67.58   0.70     0.36      81408.61|
|  7:  2.5885 -  2.4595  1337   149  0.25  71.19   0.75     0.30      74596.20|
|  8:  2.4595 -  2.3528  1316   150  0.22  73.32   0.70     0.28      68062.27|
|  9:  2.3528 -  2.2626  1305   143  0.20  75.03   0.72     0.25      65279.92|
| 10:  2.2626 -  2.1847  1343   148  0.22  73.77   0.74     0.27      56368.22|
| 11:  2.1847 -  2.1166  1319   144  0.22  73.29   0.77     0.29      54086.02|
| 12:  2.1166 -  2.0563  1293   139  0.23  72.93   0.74     0.31      47081.35|
| 13:  2.0563 -  2.0023  1205   136  0.23  72.74   0.71     0.31      41544.82|
| 14:  2.0023 -  1.9535   315    39  0.28  68.89   0.72     0.32      32814.30|
|alpha:            min =        0.25 max =            0.75 mean =         0.42|
|beta:             min =    32814.30 max =       129509.80 mean =     80184.77|
|figures of merit: min =        0.00 max =            1.00 mean =         0.35|
|phase err.(work): min =        0.00 max =           89.99 mean =        63.32|
|phase err.(test): min =        0.00 max =           89.88 mean =        63.64|
|-----------------------------------------------------------------------------|

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

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

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 23.260903             wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 83.466   (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 1.912638              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 78.503   (deg)                 |
|-----------------------------------------------------------------------------|


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

|-Geometry statistics: start--------------------------------------------------|
|            Histogram of deviations from ideal values for                    |
| Bonds                | Angles                   |  Nonbonded contacts       |
| 0.000 - 0.140:   597 |   0.009 -   7.457:   713 |  1.196 -  1.566:        4 |
| 0.140 - 0.280:   585 |   7.457 -  14.906:   711 |  1.566 -  1.937:       37 |
| 0.280 - 0.420:   441 |  14.906 -  22.354:   630 |  1.937 -  2.307:      177 |
| 0.420 - 0.560:   366 |  22.354 -  29.802:   474 |  2.307 -  2.677:      715 |
| 0.560 - 0.700:   237 |  29.802 -  37.251:   338 |  2.677 -  3.048:     1504 |
| 0.700 - 0.840:   127 |  37.251 -  44.699:   241 |  3.048 -  3.418:     2649 |
| 0.840 - 0.980:    59 |  44.699 -  52.147:   125 |  3.418 -  3.789:     3963 |
| 0.980 - 1.120:    17 |  52.147 -  59.595:    51 |  3.789 -  4.159:     5112 |
| 1.120 - 1.260:     9 |  59.595 -  67.044:    13 |  4.159 -  4.530:     6563 |
| 1.260 - 1.400:     1 |  67.044 -  74.492:     3 |  4.530 -  4.900:     7786 |
|-----------------------------------------------------------------------------|
|-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 |       53.482 |
| planarity |      436 |   0.145    0.405  0.000 |     250.485 |              |
|  dihedral |      870 |  33.790  144.062  0.019 |      20.704 |              |
| nonbonded |     2439 |   4.089    4.900  1.196 |       2.360 |              |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 11.695)------------------------------------------|
|    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 = 11.695)------------------------------------------|
|    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: 1.95 - 15.05 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.5081   r_free= 0.4924   ksol= 0.00   Bsol= 0.00   scale= 0.747    |
|                                                                             |
| 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:   0.81 A                  |
| x-ray target function (ml) for work reflections: 6.307467                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.95 - 15.05 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.4959   r_free= 0.4812   ksol= 0.37   Bsol= 20.00   scale= 0.960   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (5.86,8.89,9.11,0.00,0.00,0.00); trace/3= 7.96                              |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.82 A                  |
| x-ray target function (ml) for work reflections: 6.303588                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 17.992224             wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 84.571   (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 1.779353              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 76.650   (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.4959      final r-factor (work) = 0.4308          |
| start r-factor (free) = 0.4812      final r-factor (free) = 0.4577          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 110.1531 = 17.99 * 0.50 * 6.2995 + 1.00 * 53.4823                           |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 56.3948 = 17.99 * 0.50 * 6.2516 + 1.00 * 0.1545                             |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 26     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.4308      final r-factor (work) = 0.3942          |
| start r-factor (free) = 0.4577      final r-factor (free) = 0.4612          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 11.1383 = 1.78 * 1.00 * 6.2516 + 1.00 * 0.0144                              |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 11.0599 = 1.78 * 1.00 * 6.2039 + 1.00 * 0.0210                              |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 30     |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 11.695)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.00    88.55   16.18    None  None   None       |
|    all(noH): 2823   0      0.00    88.55   16.18    None  None   None       |
|    Sol.    : 438    0      0.00    88.55   24.35    None  None   None       |
|    Mac.    : 2385   0      0.00    82.56   14.68    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 -   8.855:  915   |   5:    44.276 -  53.131:   70        |
|      1:     8.855 -  17.710:  905   |   6:    53.131 -  61.986:   29        |
|      2:    17.710 -  26.566:  516   |   7:    61.986 -  70.841:   11        |
|      3:    26.566 -  35.421:  235   |   8:    70.841 -  79.696:    7        |
|      4:    35.421 -  44.276:  132   |   9:    79.696 -  88.552:    3        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.3942 r_free = 0.4612             target_work(ml) = 6.199         |
| occupancies: max = 1.00  min = 0.30   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.3940 r_free = 0.4609             target_work(ml) = 6.199         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        7 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.95 - 15.05 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.3940   r_free= 0.4609   ksol= 0.37   Bsol= 20.00   scale= 1.112   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (5.86,8.89,9.11,0.00,0.00,0.00); trace/3= 7.96                              |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.72 A                  |
| x-ray target function (ml) for work reflections: 6.198898                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.95 - 15.05 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.3926   r_free= 0.4577   ksol= 0.36   Bsol= 46.01   scale= 1.021   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (2.98,5.04,5.30,0.00,0.00,0.00); trace/3= 4.44                              |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.72 A                  |
| x-ray target function (ml) for work reflections: 6.200949                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 14.178036             wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 103.056  (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 0.785596              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 148.493  (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.3926      final r-factor (work) = 0.3424          |
| start r-factor (free) = 0.4577      final r-factor (free) = 0.4269          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 44.1110 = 14.18 * 0.50 * 6.2007 + 1.00 * 0.1545                             |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 43.6793 = 14.18 * 0.50 * 6.1465 + 1.00 * 0.1068                             |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 29     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.3424      final r-factor (work) = 0.3276          |
| start r-factor (free) = 0.4269      final r-factor (free) = 0.4134          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 4.8502 = 0.79 * 1.00 * 6.1465 + 1.00 * 0.0215                               |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 4.8020 = 0.79 * 1.00 * 6.0935 + 1.00 * 0.0149                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 29     |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 11.695)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.00    82.18   15.47    None  None   None       |
|    all(noH): 2823   0      0.00    82.18   15.47    None  None   None       |
|    Sol.    : 438    0      0.00    82.18   26.53    None  None   None       |
|    Mac.    : 2385   0      0.00    71.69   13.44    None  None   None       |
|    Hyd.    : 0      0      None    None    None     None  None   None       |
|    - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -      |
|       Distribution of isotropic (or equivalent) ADP for non-H atoms:        |
|    Bin#      value range     #atoms | Bin#      value range     #atoms      |
|      0:     0.000 -   8.218:  855   |   5:    41.089 -  49.307:   59        |
|      1:     8.218 -  16.436:  893   |   6:    49.307 -  57.525:   21        |
|      2:    16.436 -  24.654:  564   |   7:    57.525 -  65.743:   15        |
|      3:    24.654 -  32.871:  266   |   8:    65.743 -  73.961:    6        |
|      4:    32.871 -  41.089:  143   |   9:    73.961 -  82.178:    1        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.3276 r_free = 0.4134             target_work(ml) = 6.079         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        7 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.3275 r_free = 0.4135             target_work(ml) = 6.079         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        8 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.95 - 15.05 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.3275   r_free= 0.4135   ksol= 0.36   Bsol= 46.01   scale= 1.061   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (2.98,5.04,5.30,0.00,0.00,0.00); trace/3= 4.44                              |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.57 A                  |
| x-ray target function (ml) for work reflections: 6.079465                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.95 - 15.05 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.3274   r_free= 0.4115   ksol= 0.33   Bsol= 50.85   scale= 1.013   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (1.71,2.77,3.39,0.00,0.00,0.00); trace/3= 2.62                              |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.57 A                  |
| x-ray target function (ml) for work reflections: 6.078960                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 11.928088             wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 112.340  (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 4.146377              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 107.893  (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.3274      final r-factor (work) = 0.2646          |
| start r-factor (free) = 0.4115      final r-factor (free) = 0.3357          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 36.4448 = 11.93 * 0.50 * 6.0929 + 1.00 * 0.1067                             |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 35.9296 = 11.93 * 0.50 * 6.0065 + 1.00 * 0.1066                             |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 27     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.2646      final r-factor (work) = 0.2338          |
| start r-factor (free) = 0.3357      final r-factor (free) = 0.3216          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 24.9204 = 4.15 * 1.00 * 6.0065 + 1.00 * 0.0152                              |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 24.2418 = 4.15 * 1.00 * 5.8407 + 1.00 * 0.0238                              |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 27     |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 11.695)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.00    99.29   17.35    None  None   None       |
|    all(noH): 2823   0      0.00    99.29   17.35    None  None   None       |
|    Sol.    : 438    0      0.00    99.29   40.83    None  None   None       |
|    Mac.    : 2385   0      0.00    93.64   13.04    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 -   9.929: 1221   |   5:    49.645 -  59.574:   88        |
|      1:     9.929 -  19.858:  748   |   6:    59.574 -  69.503:   62        |
|      2:    19.858 -  29.787:  336   |   7:    69.503 -  79.432:   27        |
|      3:    29.787 -  39.716:  203   |   8:    79.432 -  89.361:   11        |
|      4:    39.716 -  49.645:  123   |   9:    89.361 -  99.290:    4        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.2338 r_free = 0.3216             target_work(ml) = 5.813         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        8 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.2336 r_free = 0.3219             target_work(ml) = 5.812         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        9 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.95 - 15.05 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.2336   r_free= 0.3219   ksol= 0.33   Bsol= 50.85   scale= 1.048   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (1.71,2.77,3.39,0.00,0.00,0.00); trace/3= 2.62                              |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.36 A                  |
| x-ray target function (ml) for work reflections: 5.812354                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.95 - 15.05 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.2329   r_free= 0.3216   ksol= 0.31   Bsol= 54.71   scale= 1.023   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (1.04,1.45,2.66,0.00,0.00,0.00); trace/3= 1.72                              |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.36 A                  |
| x-ray target function (ml) for work reflections: 5.810978                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 5.875793              wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 101.509  (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 1.011631              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 134.543  (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.2329      final r-factor (work) = 0.1910          |
| start r-factor (free) = 0.3216      final r-factor (free) = 0.2650          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 17.2643 = 5.88 * 0.50 * 5.8401 + 1.00 * 0.1066                              |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 16.9327 = 5.88 * 0.50 * 5.7393 + 1.00 * 0.0714                              |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 27     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1910      final r-factor (work) = 0.1718          |
| start r-factor (free) = 0.2650      final r-factor (free) = 0.2370          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 5.8296 = 1.01 * 1.00 * 5.7393 + 1.00 * 0.0235                               |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 5.6739 = 1.01 * 1.00 * 5.5908 + 1.00 * 0.0181                               |
|-----------------------------------------------------------------------------|
| number of iterations = 17      |    number of function evaluations = 19     |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 11.695)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.00    99.23   16.35    None  None   None       |
|    all(noH): 2823   0      0.00    99.23   16.35    None  None   None       |
|    Sol.    : 438    0      2.16    96.34   43.83    None  None   None       |
|    Mac.    : 2385   0      0.00    99.23   11.30    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 -   9.923: 1448   |   5:    49.614 -  59.536:   95        |
|      1:     9.923 -  19.846:  707   |   6:    59.536 -  69.459:   63        |
|      2:    19.846 -  29.768:  198   |   7:    69.459 -  79.382:   30        |
|      3:    29.768 -  39.691:  138   |   8:    79.382 -  89.305:   14        |
|      4:    39.691 -  49.614:  125   |   9:    89.305 -  99.227:    5        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.1718 r_free = 0.2370             target_work(ml) = 5.530         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        9 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.1715 r_free = 0.2367             target_work(ml) = 5.528         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        8 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.95 - 15.05 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1715   r_free= 0.2367   ksol= 0.31   Bsol= 54.71   scale= 1.029   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (1.04,1.45,2.66,0.00,0.00,0.00); trace/3= 1.72                              |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.24 A                  |
| x-ray target function (ml) for work reflections: 5.528378                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.95 - 15.05 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1716   r_free= 0.2366   ksol= 0.32   Bsol= 52.59   scale= 1.017   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (0.75,0.64,2.46,0.00,0.00,0.00); trace/3= 1.28                              |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.24 A                  |
| x-ray target function (ml) for work reflections: 5.526532                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 2.569168              wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 107.459  (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 0.485374              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 102.264  (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1716      final r-factor (work) = 0.1504          |
| start r-factor (free) = 0.2366      final r-factor (free) = 0.2107          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 7.2528 = 2.57 * 0.50 * 5.5905 + 1.00 * 0.0714                               |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 7.0905 = 2.57 * 0.50 * 5.4751 + 1.00 * 0.0573                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 29     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1504      final r-factor (work) = 0.1438          |
| start r-factor (free) = 0.2107      final r-factor (free) = 0.1986          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 2.6826 = 0.49 * 1.00 * 5.4751 + 1.00 * 0.0251                               |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 2.7086 = 0.49 * 1.00 * 5.4002 + 1.00 * 0.0875                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 31     |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 11.695)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.00    125.37  15.59    None  None   None       |
|    all(noH): 2823   0      0.00    125.37  15.59    None  None   None       |
|    Sol.    : 438    0      3.32    97.06   43.09    None  None   None       |
|    Mac.    : 2385   0      0.00    125.37  10.54    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 -  12.537: 1860   |   5:    62.684 -  75.221:   53        |
|      1:    12.537 -  25.074:  467   |   6:    75.221 -  87.758:   20        |
|      2:    25.074 -  37.611:  164   |   7:    87.758 - 100.295:    6        |
|      3:    37.611 -  50.148:  132   |   8:   100.295 - 112.832:    0        |
|      4:    50.148 -  62.684:  120   |   9:   112.832 - 125.369:    1        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.1438 r_free = 0.1986             target_work(ml) = 5.370         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        8 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.1436 r_free = 0.1982             target_work(ml) = 5.368         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        8 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.95 - 15.05 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1436   r_free= 0.1982   ksol= 0.32   Bsol= 52.59   scale= 1.014   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (0.75,0.64,2.46,0.00,0.00,0.00); trace/3= 1.28                              |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.19 A                  |
| x-ray target function (ml) for work reflections: 5.368271                   |
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
| Bin     Resolution   Compl.  No. Refl.    R-factors          Targets        |
|number     range              work test   work   test        work        test|
|  1: 15.0544 -  4.6645 0.99   1433  157 0.1038 0.1402      5.4472       5.663|
|  2:  4.6645 -  3.7207 0.99   1384  158 0.0991 0.1407      5.5845       5.865|
|  3:  3.7207 -  3.2558 0.99   1368  148 0.1353 0.1867      5.6845      5.9753|
|  4:  3.2558 -  2.9606 0.99   1337  154 0.1644 0.2131      5.6924       5.841|
|  5:  2.9606 -  2.7498 0.99   1348  148 0.1761 0.2288      5.5746        5.82|
|  6:  2.7498 -  2.5885 0.99   1327  146 0.1630 0.2504      5.4416      5.6649|
|  7:  2.5885 -  2.4595 0.99   1337  149 0.1611 0.2082      5.3891      5.5578|
|  8:  2.4595 -  2.3528 0.98   1316  150 0.1636 0.2215      5.3298      5.5568|
|  9:  2.3528 -  2.2626 0.98   1305  143 0.1580 0.2222      5.2686      5.5149|
| 10:  2.2626 -  2.1847 1.00   1343  148 0.1446 0.2155      5.1542      5.3917|
| 11:  2.1847 -  2.1166 0.98   1319  144 0.1458 0.2258      5.1512      5.5247|
| 12:  2.1166 -  2.0563 0.98   1293  139 0.1562 0.2329      5.1009      5.3778|
| 13:  2.0563 -  2.0023 0.91   1205  136 0.1486 0.1902       5.005      5.1431|
| 14:  2.0023 -  1.9535 0.24    315   39 0.1403 0.2052      4.9125      5.1729|
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
|R-free likelihood based estimates for figures of merit, absolute phase error,|
|and distribution parameters alpha and beta (Acta Cryst. (1995). A51, 880-887)|
|                                                                             |
| Bin     Resolution      No. Refl.   FOM  Phase Scale    Alpha        Beta   |
|  #        range        work  test        error factor                       |
|  1: 15.0544 -  4.6645  1433   157  0.93  10.58   0.97     0.95       8844.91|
|  2:  4.6645 -  3.7207  1384   158  0.94  10.28   1.03     1.02      12502.01|
|  3:  3.7207 -  3.2558  1368   148  0.90  15.57   1.05     1.05      16375.75|
|  4:  3.2558 -  2.9606  1337   154  0.87  19.46   1.03     0.99      17236.08|
|  5:  2.9606 -  2.7498  1348   148  0.85  21.32   1.00     0.98      14020.64|
|  6:  2.7498 -  2.5885  1327   146  0.84  22.09   0.99     0.93      11578.93|
|  7:  2.5885 -  2.4595  1337   149  0.86  20.91   1.01     0.96      10084.88|
|  8:  2.4595 -  2.3528  1316   150  0.84  22.17   1.02     0.98       9387.43|
|  9:  2.3528 -  2.2626  1305   143  0.86  20.93   1.00     0.94       8028.96|
| 10:  2.2626 -  2.1847  1343   148  0.86  20.52   1.02     0.98       6795.89|
| 11:  2.1847 -  2.1166  1319   144  0.85  21.21   1.01     0.95       6871.96|
| 12:  2.1166 -  2.0563  1293   139  0.86  21.29   1.01     1.00       6333.83|
| 13:  2.0563 -  2.0023  1205   136  0.84  22.32   1.01     0.96       5367.02|
| 14:  2.0023 -  1.9535   315    39  0.90  16.94   1.00     0.97       3893.38|
|alpha:            min =        0.93 max =            1.05 mean =         0.98|
|beta:             min =     3893.38 max =        17236.08 mean =     10214.33|
|figures of merit: min =        0.00 max =            1.00 mean =         0.87|
|phase err.(work): min =        0.00 max =           89.96 mean =        18.97|
|phase err.(test): min =        0.00 max =           89.81 mean =        18.07|
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.95 - 15.05 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1440   r_free= 0.1981   ksol= 0.32   Bsol= 53.68   scale= 1.008   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-0.50,-0.74,1.24,0.00,0.00,0.00); trace/3= 0.00                            |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.19 A                  |
| x-ray target function (ml) for work reflections: 5.368002                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.95 - 15.05 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1440   r_free= 0.1981   ksol= 0.32   Bsol= 53.68   scale= 1.008   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-0.50,-0.74,1.24,0.00,0.00,0.00); trace/3= 0.00                            |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.19 A                  |
| x-ray target function (ml) for work reflections: 5.368002                   |
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
| Bin     Resolution   Compl.  No. Refl.    R-factors          Targets        |
|number     range              work test   work   test        work        test|
|  1: 15.0544 -  4.6645 0.99   1433  157 0.1049 0.1398      5.4463      5.6635|
|  2:  4.6645 -  3.7207 0.99   1384  158 0.0993 0.1400      5.5857      5.8617|
|  3:  3.7207 -  3.2558 0.99   1368  148 0.1357 0.1875      5.6865      5.9797|
|  4:  3.2558 -  2.9606 0.99   1337  154 0.1649 0.2122      5.6933      5.8371|
|  5:  2.9606 -  2.7498 0.99   1348  148 0.1763 0.2286      5.5746      5.8209|
|  6:  2.7498 -  2.5885 0.99   1327  146 0.1631 0.2505      5.4402       5.664|
|  7:  2.5885 -  2.4595 0.99   1337  149 0.1611 0.2076      5.3881      5.5557|
|  8:  2.4595 -  2.3528 0.98   1316  150 0.1633 0.2212      5.3284      5.5558|
|  9:  2.3528 -  2.2626 0.98   1305  143 0.1579 0.2218      5.2683      5.5134|
| 10:  2.2626 -  2.1847 1.00   1343  148 0.1444 0.2160      5.1533      5.3933|
| 11:  2.1847 -  2.1166 0.98   1319  144 0.1456 0.2257      5.1505      5.5256|
| 12:  2.1166 -  2.0563 0.98   1293  139 0.1562 0.2328      5.1005      5.3776|
| 13:  2.0563 -  2.0023 0.91   1205  136 0.1487 0.1897      5.0044      5.1416|
| 14:  2.0023 -  1.9535 0.24    315   39 0.1404 0.2047      4.9111      5.1702|
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
|R-free likelihood based estimates for figures of merit, absolute phase error,|
|and distribution parameters alpha and beta (Acta Cryst. (1995). A51, 880-887)|
|                                                                             |
| Bin     Resolution      No. Refl.   FOM  Phase Scale    Alpha        Beta   |
|  #        range        work  test        error factor                       |
|  1: 15.0544 -  4.6645  1433   157  0.93  10.53   0.97     0.94       8691.88|
|  2:  4.6645 -  3.7207  1384   158  0.94  10.27   1.03     1.02      12457.74|
|  3:  3.7207 -  3.2558  1368   148  0.90  15.59   1.05     1.05      16408.82|
|  4:  3.2558 -  2.9606  1337   154  0.87  19.48   1.02     0.98      17222.54|
|  5:  2.9606 -  2.7498  1348   148  0.85  21.26   1.00     0.97      13974.87|
|  6:  2.7498 -  2.5885  1327   146  0.84  22.04   0.98     0.93      11531.58|
|  7:  2.5885 -  2.4595  1337   149  0.86  20.87   1.00     0.95      10062.24|
|  8:  2.4595 -  2.3528  1316   150  0.84  22.13   1.01     0.97       9359.12|
|  9:  2.3528 -  2.2626  1305   143  0.86  20.93   0.99     0.93       8021.45|
| 10:  2.2626 -  2.1847  1343   148  0.86  20.51   1.01     0.97       6787.61|
| 11:  2.1847 -  2.1166  1319   144  0.85  21.21   1.00     0.94       6874.47|
| 12:  2.1166 -  2.0563  1293   139  0.86  21.27   1.00     0.99       6327.90|
| 13:  2.0563 -  2.0023  1205   136  0.84  22.29   0.99     0.95       5358.12|
| 14:  2.0023 -  1.9535   315    39  0.90  16.86   0.99     0.96       3873.53|
|alpha:            min =        0.93 max =            1.05 mean =         0.97|
|beta:             min =     3873.53 max =        17222.54 mean =     10186.67|
|figures of merit: min =        0.00 max =            1.00 mean =         0.87|
|phase err.(work): min =        0.00 max =           90.00 mean =        18.95|
|phase err.(test): min =        0.00 max =           89.86 mean =        18.05|
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 11.695)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      1.09    126.46  16.69    None  None   None       |
|    all(noH): 2823   0      1.09    126.46  16.69    None  None   None       |
|    Sol.    : 438    0      4.41    98.15   44.18    None  None   None       |
|    Mac.    : 2385   0      1.09    126.46  11.64    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:     1.092 -  13.629: 1860   |   5:    63.777 -  76.314:   53        |
|      1:    13.629 -  26.166:  467   |   6:    76.314 -  88.851:   20        |
|      2:    26.166 -  38.703:  164   |   7:    88.851 - 101.387:    6        |
|      3:    38.703 -  51.240:  132   |   8:   101.387 - 113.924:    0        |
|      4:    51.240 -  63.777:  120   |   9:   113.924 - 126.461:    1        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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


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

Number of peaks found at mFobs-DFmodel map (map cutoff=3.00 sigma)= 346         
Filter by distance & map next to the model:
   mapped sites are within: 0.323 - 5.734
   number of sites selected in [dist_min= 0.70, dist_max= 6.00]: 344 from: 346
   mapped sites are within: 0.707 - 5.734

peak=    7.713 closest distance to " CB  VAL A 230 " =    1.465
peak=    7.204 closest distance to " O   HOH Z 268 " =    1.251
peak=    6.980 closest distance to " O   HOH Z 130 " =    2.180
peak=    6.944 closest distance to " CG2 VAL A 296 " =    1.467
peak=    6.509 closest distance to " CD2 LEU A   5 " =    1.539
peak=    6.193 closest distance to " CG  ARG A 138 " =    1.228
peak=    6.055 closest distance to " O   HOH Z 390 " =    1.151
peak=    5.977 closest distance to " NH1 ARG A 138 " =    0.987
peak=    5.839 closest distance to " O   HOH Z 385 " =    1.654
peak=    5.790 closest distance to " O   HOH Z 105 " =    1.279
peak=    5.680 closest distance to " CD1AILE A 234 " =    1.051
peak=    5.661 closest distance to " O   HOH Z 415 " =    1.593
peak=    5.616 closest distance to " O   HOH Z 245 " =    1.125
peak=    5.303 closest distance to " O   HOH Z  46 " =    1.431
peak=    5.247 closest distance to " O   HOH Z 127 " =    1.389
peak=    5.145 closest distance to " O   HOH Z  65 " =    1.923
peak=    5.124 closest distance to " O   HOH Z  77 " =    1.225
peak=    5.095 closest distance to " CG2 ILE A 120 " =    1.016
peak=    5.042 closest distance to " O   PRO A 198 " =    1.433
peak=    5.039 closest distance to " O   HOH Z 330 " =    1.186
peak=    5.035 closest distance to " O   HOH Z 403 " =    1.766
peak=    5.016 closest distance to " O   HOH Z  63 " =    1.598
peak=    5.013 closest distance to " NE2 GLN A  11 " =    1.235
peak=    5.004 closest distance to " O   HOH Z 350 " =    1.727
peak=    4.998 closest distance to " O   HOH Z 293 " =    1.481
peak=    4.979 closest distance to " O   HOH Z  66 " =    1.364
peak=    4.962 closest distance to " O   HOH Z 360 " =    1.234
peak=    4.937 closest distance to " O   HOH Z 425 " =    1.514
peak=    4.851 closest distance to " O   VAL A  72 " =    1.007
peak=    4.836 closest distance to " O   HOH Z 359 " =    1.508
peak=    4.818 closest distance to " CB  VAL A 230 " =    1.281
peak=    4.811 closest distance to " O   HOH Z 124 " =    1.713
peak=    4.773 closest distance to " O   HOH Z 428 " =    1.429
peak=    4.751 closest distance to " O   HOH Z 222 " =    1.661
peak=    4.717 closest distance to " O   HOH Z 139 " =    1.622
peak=    4.708 closest distance to " O   HOH Z 258 " =    1.393
peak=    4.687 closest distance to " O   HOH Z 417 " =    2.213
peak=    4.679 closest distance to " CB  PRO A  54 " =    1.256
peak=    4.678 closest distance to " O   HOH Z  24 " =    1.918
peak=    4.664 closest distance to " NH2 ARG A  56 " =    2.120
peak=    4.650 closest distance to " O   HOH Z 418 " =    1.501
peak=    4.574 closest distance to " O   HOH Z 410 " =    1.518
peak=    4.556 closest distance to " O   HOH Z 427 " =    2.114
peak=    4.544 closest distance to " O   HOH Z 214 " =    1.158
peak=    4.541 closest distance to " O   HOH Z 375 " =    1.098
peak=    4.531 closest distance to " O   HOH Z 422 " =    1.106
peak=    4.531 closest distance to " CG  PRO A  54 " =    1.540
peak=    4.516 closest distance to " O   HOH Z  59 " =    1.766
peak=    4.477 closest distance to " C   GLN A  73 " =    1.035
peak=    4.470 closest distance to " OD1 ASN A  69 " =    1.119
peak=    4.456 closest distance to " O   HOH Z  69 " =    1.853
peak=    4.451 closest distance to " NZ BLYS A 290 " =    0.989
peak=    4.442 closest distance to " O   HOH Z   7 " =    2.065
peak=    4.421 closest distance to " O   HOH Z  43 " =    1.562
peak=    4.413 closest distance to " O   HOH Z 331 " =    1.310
peak=    4.376 closest distance to " O   HOH Z 103 " =    1.144
peak=    4.356 closest distance to " O   HOH Z 316 " =    3.030
peak=    4.354 closest distance to " CG  LEU A   5 " =    1.251
peak=    4.317 closest distance to " O   HOH Z 287 " =    1.757
peak=    4.310 closest distance to " CA  ILE A 234 " =    1.079
peak=    4.308 closest distance to " O   HOH Z   9 " =    2.394
peak=    4.291 closest distance to " O   HOH Z 126 " =    2.069
peak=    4.288 closest distance to " O   HOH Z 419 " =    2.211
peak=    4.277 closest distance to " O   HOH Z 142 " =    1.928
peak=    4.276 closest distance to " CB  ASP A 124 " =    0.998
peak=    4.276 closest distance to " O   HOH Z 424 " =    1.606
peak=    4.268 closest distance to " CB  ARG A 275 " =    1.122
peak=    4.263 closest distance to " O   HOH Z 427 " =    1.143
peak=    4.253 closest distance to " CB  SER A   3 " =    1.540
peak=    4.249 closest distance to " CG2AVAL A  72 " =    0.774
peak=    4.238 closest distance to " N   GLN A 278 " =    0.970
peak=    4.228 closest distance to " O   HOH Z 146 " =    1.772
peak=    4.189 closest distance to " O   HOH Z 358 " =    1.346
peak=    4.161 closest distance to " O   HOH Z 232 " =    2.216
peak=    4.160 closest distance to " CD2 LEU A 228 " =    1.274
peak=    4.154 closest distance to " CG  LEU A 228 " =    1.152
peak=    4.122 closest distance to " O   HOH Z 225 " =    1.870
peak=    4.112 closest distance to " O  BHOH Z  74 " =    1.206
peak=    4.107 closest distance to " O   HOH Z 416 " =    1.374
peak=    4.097 closest distance to " O   HOH Z 342 " =    1.085
peak=    4.087 closest distance to " CG  PRO A 243 " =    1.107
peak=    4.073 closest distance to " CB  ALA A 114 " =    1.087
peak=    4.036 closest distance to " O   HOH Z 246 " =    1.133
peak=    4.006 closest distance to " CB  GLN A 223 " =    1.601
peak=    3.999 closest distance to " CB  SER A 216 " =    1.005
peak=    3.992 closest distance to " CG2 THR A 221 " =    1.216
peak=    3.989 closest distance to " O   HOH Z 112 " =    1.160
peak=    3.985 closest distance to " O   HOH Z  49 " =    1.264
peak=    3.975 closest distance to " OG  SER A 276 " =    0.956
peak=    3.973 closest distance to " O   HOH Z  88 " =    3.363
peak=    3.970 closest distance to " O   HOH Z 361 " =    1.682
peak=    3.954 closest distance to " CG2 ILE A 234 " =    0.868
peak=    3.934 closest distance to " O   HOH Z 353 " =    2.084
peak=    3.931 closest distance to " CB  SER A  63 " =    1.361
peak=    3.930 closest distance to " O   HOH Z 414 " =    1.755
peak=    3.911 closest distance to " O   HOH Z 369 " =    2.101
peak=    3.889 closest distance to " O   HOH Z  92 " =    1.308
peak=    3.878 closest distance to " O   HOH Z 153 " =    3.454
peak=    3.878 closest distance to " CD  ARG A 138 " =    0.940
peak=    3.876 closest distance to " O   HOH Z 148 " =    1.771
peak=    3.876 closest distance to " O   HOH Z  39 " =    1.474
peak=    3.872 closest distance to " O   HOH Z 133 " =    1.684
peak=    3.832 closest distance to " CB  ASN A 148 " =    1.486
peak=    3.829 closest distance to " CD1 LEU A   5 " =    1.347
peak=    3.823 closest distance to " O   HOH Z 189 " =    2.205
peak=    3.802 closest distance to " N   CYS A 260 " =    1.056
peak=    3.802 closest distance to " CB  ASN A  39 " =    0.828
peak=    3.794 closest distance to " O   ASN A 142 " =    1.126
peak=    3.785 closest distance to " O   HOH Z 400 " =    0.810
peak=    3.785 closest distance to " O   HOH Z 123 " =    1.224
peak=    3.778 closest distance to " CZ3 TRP A 266 " =    1.183
peak=    3.778 closest distance to " O   HOH Z 211 " =    1.394
peak=    3.775 closest distance to " CG2 THR A 178 " =    1.250
peak=    3.764 closest distance to " CB  SER A 276 " =    1.213
peak=    3.762 closest distance to " O   HOH Z 298 " =    1.900
peak=    3.760 closest distance to " O   HOH Z  78 " =    1.886
peak=    3.746 closest distance to " O   HOH Z 371 " =    3.100
peak=    3.743 closest distance to " CD  ARG A  66 " =    2.190
peak=    3.738 closest distance to " O   HOH Z 125 " =    1.829
peak=    3.737 closest distance to " N   GLN A  73 " =    1.088
peak=    3.731 closest distance to " CB  TRP A 266 " =    0.937
peak=    3.728 closest distance to " CG BASN A 224 " =    1.046
peak=    3.716 closest distance to " O   HOH Z 357 " =    1.345
peak=    3.703 closest distance to " O   HOH Z 214 " =    2.057
peak=    3.698 closest distance to " N   ARG A 156 " =    1.309
peak=    3.694 closest distance to " O   HOH Z  91 " =    2.299
peak=    3.694 closest distance to " O   HOH Z  58 " =    1.941
peak=    3.692 closest distance to " O   HOH Z  49 " =    2.614
peak=    3.679 closest distance to " CB  LYS A 290 " =    0.901
peak=    3.677 closest distance to " CG  PRO A 198 " =    1.324
peak=    3.667 closest distance to " O   HOH Z  69 " =    1.118
peak=    3.664 closest distance to " O   HOH Z 422 " =    2.448
peak=    3.657 closest distance to " O   HOH Z  68 " =    2.090
peak=    3.648 closest distance to " O   HOH Z 303 " =    2.019
peak=    3.645 closest distance to " O   HOH Z  30 " =    1.184
peak=    3.642 closest distance to " NZ  LYS A 119 " =    2.659
peak=    3.639 closest distance to " CB  ASN A 215 " =    1.437
peak=    3.638 closest distance to " O   HOH Z 366 " =    2.866
peak=    3.634 closest distance to " O   HOH Z 238 " =    1.256
peak=    3.633 closest distance to " CB  ALA A  43 " =    0.929
peak=    3.632 closest distance to " N   TYR A  15 " =    1.019
peak=    3.632 closest distance to " NE AARG A 275 " =    1.611
peak=    3.631 closest distance to " N   SER A  97 " =    0.853
peak=    3.629 closest distance to " O   HOH Z 380 " =    1.781
peak=    3.617 closest distance to " O   HOH Z  57 " =    1.429
peak=    3.616 closest distance to " CG  LEU A 167 " =    1.370
peak=    3.616 closest distance to " O   HOH Z   1 " =    1.938
peak=    3.614 closest distance to " CG1 ILE A  33 " =    1.295
peak=    3.614 closest distance to " CG  ARG A 156 " =    1.192
peak=    3.609 closest distance to " O   HOH Z 378 " =    1.169
peak=    3.602 closest distance to " CE  MET A  93 " =    1.430
peak=    3.598 closest distance to " CE3 TRP A 274 " =    1.370
peak=    3.595 closest distance to " NH2 ARG A 269 " =    1.020
peak=    3.594 closest distance to " O   HOH Z 233 " =    1.503
peak=    3.583 closest distance to " NZ  LYS A 117 " =    1.113
peak=    3.575 closest distance to " CA  ALA A  21 " =    0.954
peak=    3.574 closest distance to " O   HOH Z 218 " =    2.190
peak=    3.573 closest distance to " CA  ALA A  51 " =    1.067
peak=    3.565 closest distance to " O   HOH Z  11 " =    1.213
peak=    3.562 closest distance to " O   HOH Z 172 " =    1.785
peak=    3.554 closest distance to " CG1AVAL A 121 " =    0.819
peak=    3.552 closest distance to " CB  GLN A  73 " =    1.073
peak=    3.552 closest distance to " NE1 TRP A 274 " =    1.077
peak=    3.547 closest distance to " OD2 ASP A 286 " =    2.232
peak=    3.542 closest distance to " CG BARG A 102 " =    2.011
peak=    3.541 closest distance to " NH2AARG A 145 " =    2.291
peak=    3.538 closest distance to " OD1 ASP A  27 " =    0.987
peak=    3.538 closest distance to " O   HOH Z 158 " =    2.226
peak=    3.535 closest distance to " O   HOH Z 389 " =    1.459
peak=    3.533 closest distance to " OD1 ASP A 200 " =    1.490
peak=    3.531 closest distance to " C   VAL A 153 " =    1.110
peak=    3.527 closest distance to " O   HOH Z  52 " =    1.083
peak=    3.527 closest distance to " O   HOH Z 423 " =    2.008
peak=    3.527 closest distance to " CB  TRP A 150 " =    1.183
peak=    3.526 closest distance to " NH2AARG A 145 " =    1.053
peak=    3.517 closest distance to " O   HOH Z 119 " =    1.532
peak=    3.515 closest distance to " O   HOH Z 426 " =    1.091
peak=    3.514 closest distance to " NZ  LYS A 117 " =    3.243
peak=    3.510 closest distance to " CE1 PHE A  38 " =    1.241
peak=    3.509 closest distance to " O   HOH Z   7 " =    2.992
peak=    3.501 closest distance to " O   HOH Z 381 " =    1.150
peak=    3.500 closest distance to " CB  GLU A 128 " =    0.981
peak=    3.500 closest distance to " O   HOH Z  26 " =    1.723
peak=    3.499 closest distance to " CD1 ILE A  33 " =    1.861
peak=    3.498 closest distance to " CB  LEU A 300 " =    1.023
peak=    3.492 closest distance to " OE1 GLU A   2 " =    1.878
peak=    3.483 closest distance to " CB  ARG A 138 " =    0.938
peak=    3.481 closest distance to " O   HOH Z 272 " =    1.851
peak=    3.479 closest distance to " CB  GLN A 183 " =    1.099
peak=    3.477 closest distance to " O   HOH Z 219 " =    1.876
peak=    3.472 closest distance to " CB  SER A 210 " =    1.023
peak=    3.471 closest distance to " CA  ARG A  36 " =    1.031
peak=    3.470 closest distance to " O   HOH Z 158 " =    1.324
peak=    3.462 closest distance to " CA  PHE A 283 " =    1.235
peak=    3.455 closest distance to " CA  ALA A 160 " =    1.152
peak=    3.454 closest distance to " CE2 PHE A  16 " =    0.978
peak=    3.450 closest distance to " O   HOH Z  78 " =    2.210
peak=    3.449 closest distance to " N   ASN A  74 " =    0.875
peak=    3.446 closest distance to " O   HOH Z 423 " =    1.939
peak=    3.440 closest distance to " CB  GLU A 277 " =    3.605
peak=    3.437 closest distance to " O   HOH Z 279 " =    2.604
peak=    3.434 closest distance to " ND2 ASN A 249 " =    0.779
peak=    3.434 closest distance to " CB  VAL A 202 " =    1.734
peak=    3.427 closest distance to " O   HOH Z 371 " =    2.376
peak=    3.427 closest distance to " O   HOH Z 213 " =    1.603
peak=    3.424 closest distance to " CD1 LEU A 228 " =    1.717
peak=    3.421 closest distance to " O   HOH Z 290 " =    1.124
peak=    3.418 closest distance to " CB  ARG A  79 " =    0.877
peak=    3.414 closest distance to " O   HOH Z 332 " =    1.527
peak=    3.401 closest distance to " O   HOH Z 425 " =    2.085
peak=    3.397 closest distance to " O   HOH Z  61 " =    1.942
peak=    3.393 closest distance to " O   HOH Z  51 " =    2.216
peak=    3.387 closest distance to " CB  ASN A 187 " =    1.061
peak=    3.385 closest distance to " CD  PRO A 243 " =    1.533
peak=    3.381 closest distance to " CA  ASP A 162 " =    0.987
peak=    3.379 closest distance to " O   HOH Z 357 " =    1.661
peak=    3.377 closest distance to " O   HOH Z 132 " =    1.179
peak=    3.376 closest distance to " O   THR A 294 " =    1.231
peak=    3.373 closest distance to " O   HOH Z 220 " =    1.404
peak=    3.368 closest distance to " CA  ARG A 102 " =    1.066
peak=    3.367 closest distance to " CB  PRO A  90 " =    1.184
peak=    3.366 closest distance to " O   TYR A 116 " =    1.174
peak=    3.364 closest distance to " O   HOH Z 356 " =    1.984
peak=    3.359 closest distance to " OD1 ASP A  50 " =    0.879
peak=    3.359 closest distance to " OE1 GLN A 240 " =    1.714
peak=    3.352 closest distance to " CB  LEU A  83 " =    0.707
peak=    3.345 closest distance to " N   VAL A  72 " =    0.843
peak=    3.344 closest distance to " O   HOH Z 430 " =    1.762
peak=    3.342 closest distance to " CZ  PHE A 218 " =    1.227
peak=    3.342 closest distance to " CB  PRO A 213 " =    1.238
peak=    3.342 closest distance to " O   HOH Z 424 " =    2.607
peak=    3.334 closest distance to " O   HOH Z 405 " =    1.884
peak=    3.332 closest distance to " CA  ASN A 127 " =    1.360
peak=    3.332 closest distance to " O   HOH Z  76 " =    1.293
peak=    3.332 closest distance to " CE3 TRP A 150 " =    1.087
peak=    3.332 closest distance to " O   HOH Z 334 " =    2.090
peak=    3.329 closest distance to " O   HOH Z 411 " =    3.167
peak=    3.328 closest distance to " O   HOH Z 329 " =    4.130
peak=    3.328 closest distance to " CB  ASN A 110 " =    0.989
peak=    3.325 closest distance to " CB  SER A  62 " =    1.158
peak=    3.324 closest distance to " CB  MET A  47 " =    1.030
peak=    3.322 closest distance to " O   HOH Z  47 " =    1.765
peak=    3.317 closest distance to " O   HOH Z  94 " =    2.485
peak=    3.317 closest distance to " N   GLU A   2 " =    1.394
peak=    3.309 closest distance to " OG  SER A  26 " =    1.527
peak=    3.308 closest distance to " O   ASN A 301 " =    2.018
peak=    3.307 closest distance to " O   HOH Z 434 " =    5.372
peak=    3.307 closest distance to " N   PHE A 130 " =    1.303
peak=    3.306 closest distance to " O   HOH Z 193 " =    1.723
peak=    3.305 closest distance to " CG2BVAL A  72 " =    1.440
peak=    3.301 closest distance to " OD2 ASP A  50 " =    1.095
peak=    3.301 closest distance to " CD  ARG A  56 " =    1.051
peak=    3.298 closest distance to " O   HOH Z 118 " =    2.139
peak=    3.298 closest distance to " O   HOH Z 412 " =    2.942
peak=    3.296 closest distance to " O   ILE A  20 " =    1.857
peak=    3.296 closest distance to " CA  ALA A 295 " =    0.873
peak=    3.294 closest distance to " ND2 ASN A 110 " =    1.718
peak=    3.292 closest distance to " CA  ALA A 299 " =    0.993
peak=    3.292 closest distance to " CB  ALA A 114 " =    1.836
peak=    3.291 closest distance to " O   HOH Z 392 " =    1.282
peak=    3.290 closest distance to " O   HOH Z 139 " =    2.947
peak=    3.290 closest distance to " CZ3 TRP A 123 " =    1.640
peak=    3.290 closest distance to " CB  SER A 273 " =    1.033
peak=    3.289 closest distance to " O   HOH Z 143 " =    1.590
peak=    3.286 closest distance to " O   HOH Z  94 " =    1.685
peak=    3.280 closest distance to " C   ASN A 301 " =    0.977
peak=    3.280 closest distance to " CA  GLY A 136 " =    1.079
peak=    3.277 closest distance to " CG2 THR A 279 " =    0.991
peak=    3.266 closest distance to " CA  LEU A 222 " =    1.111
peak=    3.266 closest distance to " N   ALA A   1 " =    1.452
peak=    3.265 closest distance to " O   HOH Z 154 " =    1.904
peak=    3.265 closest distance to " NE2 GLN A  73 " =    1.442
peak=    3.265 closest distance to " N   VAL A 296 " =    1.751
peak=    3.262 closest distance to " CA  ASN A 284 " =    0.911
peak=    3.261 closest distance to " CG  PRO A  90 " =    1.655
peak=    3.253 closest distance to " OG1 THR A 279 " =    1.392
peak=    3.249 closest distance to " CB  VAL A 296 " =    1.207
peak=    3.245 closest distance to " OE2 GLU A  53 " =    1.900
peak=    3.243 closest distance to " CG  GLN A 278 " =    4.015
peak=    3.239 closest distance to " O   HOH Z 201 " =    1.769
peak=    3.235 closest distance to " N   ARG A 275 " =    0.928
peak=    3.235 closest distance to " O   HOH Z 236 " =    1.853
peak=    3.233 closest distance to " O   HOH Z  21 " =    1.335
peak=    3.229 closest distance to " O   GLY A 302 " =    2.371
peak=    3.227 closest distance to " CG  LYS A  76 " =    1.923
peak=    3.227 closest distance to " CB  ASN A 142 " =    0.997
peak=    3.226 closest distance to " CB  TRP A 179 " =    1.479
peak=    3.224 closest distance to " OG  SER A  62 " =    3.108
peak=    3.221 closest distance to " O   HOH Z 110 " =    1.709
peak=    3.218 closest distance to " O   HOH Z 362 " =    1.632
peak=    3.218 closest distance to " O   HOH Z 323 " =    1.813
peak=    3.217 closest distance to " O   HOH Z  44 " =    1.908
peak=    3.216 closest distance to " O   HOH Z 145 " =    2.238
peak=    3.214 closest distance to " CD2 LEU A 297 " =    0.928
peak=    3.211 closest distance to " CA  SER A  12 " =    1.713
peak=    3.210 closest distance to " CG2 ILE A 239 " =    0.920
peak=    3.209 closest distance to " CZ3 TRP A  92 " =    1.267
peak=    3.208 closest distance to " CE AMET A  47 " =    1.260
peak=    3.207 closest distance to " O   HOH Z  95 " =    1.645
peak=    3.204 closest distance to " O   HOH Z 328 " =    1.602
peak=    3.203 closest distance to " CD  GLN A  77 " =    1.305
peak=    3.201 closest distance to " N   SER A 210 " =    0.869
peak=    3.196 closest distance to " O   HOH Z 248 " =    2.054
peak=    3.192 closest distance to " NH1AARG A 145 " =    1.124
peak=    3.179 closest distance to " CB  LEU A 237 " =    0.938
peak=    3.177 closest distance to " O   THR A 220 " =    1.863
peak=    3.173 closest distance to " CG1 VAL A 296 " =    1.234
peak=    3.173 closest distance to " O   HOH Z 389 " =    1.534
peak=    3.173 closest distance to " O   HOH Z 194 " =    2.442
peak=    3.172 closest distance to " O   HOH Z   3 " =    1.408
peak=    3.172 closest distance to " N   TYR A 116 " =    1.649
peak=    3.169 closest distance to " O   HOH Z   6 " =    1.431
peak=    3.168 closest distance to " CA  ARG A 195 " =    1.236
peak=    3.165 closest distance to " O   HOH Z  41 " =    2.474
peak=    3.162 closest distance to " CB  ARG A 139 " =    1.292
peak=    3.157 closest distance to " CG  GLU A 277 " =    1.960
peak=    3.155 closest distance to " CG2 ILE A  20 " =    1.616
peak=    3.151 closest distance to " CA  ARG A 159 " =    1.233
peak=    3.150 closest distance to " CG  GLN A  89 " =    1.672
peak=    3.148 closest distance to " O   HOH Z  59 " =    2.309
peak=    3.147 closest distance to " N   ARG A 139 " =    0.982
peak=    3.147 closest distance to " O   HOH Z 118 " =    2.458
peak=    3.146 closest distance to " O   HOH Z  97 " =    1.535
peak=    3.145 closest distance to " CG BARG A 275 " =    1.411
peak=    3.144 closest distance to " NE2 GLN A  58 " =    5.734
peak=    3.140 closest distance to " O   HOH Z 384 " =    1.548
peak=    3.135 closest distance to " CG2 VAL A 232 " =    1.633
peak=    3.135 closest distance to " C   PHE A 208 " =    0.900
peak=    3.133 closest distance to " CE AMET A  47 " =    1.643
peak=    3.131 closest distance to " OG BSER A  99 " =    2.091
peak=    3.129 closest distance to " OG ASER A 212 " =    1.652
peak=    3.128 closest distance to " O   ASN A  69 " =    1.254
peak=    3.120 closest distance to " O   HOH Z 368 " =    1.868
peak=    3.116 closest distance to " CG  GLN A  58 " =    1.184
peak=    3.114 closest distance to " CB  PHE A  16 " =    1.146
peak=    3.111 closest distance to " CA  LEU A 261 " =    1.580
peak=    3.098 closest distance to " O   HOH Z 244 " =    1.574
peak=    3.096 closest distance to " O   HOH Z  88 " =    3.316
peak=    3.094 closest distance to " CD1 LEU A   5 " =    0.797
peak=    3.088 closest distance to " O   HOH Z 388 " =    1.925
peak=    3.087 closest distance to " CA  LEU A 282 " =    1.077
peak=    3.081 closest distance to " CB  GLU A 175 " =    0.890
peak=    3.074 closest distance to " NH2AARG A 190 " =    2.022
peak=    3.006 closest distance to " O   HOH Z 425 " =    1.398

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

Number of peaks found at mFobs-DFmodel map (map cutoff=3.00 sigma)= 211         
Filter by distance & map next to the model:
   mapped sites are within: 0.591 - 5.356
   number of sites selected in [dist_min= 0.70, dist_max= 6.00]: 207 from: 211
   mapped sites are within: 0.760 - 5.356

peak=   -5.756 closest distance to " CD  ARG A 138 " =    1.244
peak=   -4.820 closest distance to " O   PRO A 198 " =    1.098
peak=   -4.794 closest distance to " CG2 VAL A 230 " =    0.819
peak=   -4.491 closest distance to " O   HOH Z 242 " =    1.472
peak=   -4.410 closest distance to " OE1 GLU A 277 " =    2.348
peak=   -4.247 closest distance to " O   HOH Z 163 " =    1.852
peak=   -4.191 closest distance to " O   HOH Z 131 " =    3.685
peak=   -4.155 closest distance to " O   THR A 178 " =    0.872
peak=   -4.119 closest distance to " OG BSER A 134 " =    1.653
peak=   -4.116 closest distance to " N   THR A 157 " =    1.773
peak=   -4.082 closest distance to " CB  VAL A 230 " =    0.904
peak=   -4.018 closest distance to " OD1 ASP A  27 " =    0.764
peak=   -3.982 closest distance to " CG  MET A 105 " =    0.925
peak=   -3.946 closest distance to " O   HOH Z 268 " =    0.925
peak=   -3.927 closest distance to " CD1 TRP A 179 " =    1.156
peak=   -3.896 closest distance to " C   VAL A  72 " =    0.821
peak=   -3.890 closest distance to " CB  GLN A  55 " =    1.197
peak=   -3.859 closest distance to " O   HOH Z 300 " =    0.947
peak=   -3.841 closest distance to " CE2 TYR A  30 " =    2.588
peak=   -3.840 closest distance to " CA  GLY A 133 " =    2.019
peak=   -3.836 closest distance to " CD2 TYR A 293 " =    1.886
peak=   -3.829 closest distance to " O   HOH Z 415 " =    0.838
peak=   -3.826 closest distance to " O   ALA A  51 " =    1.239
peak=   -3.815 closest distance to " O   HOH Z 331 " =    0.760
peak=   -3.800 closest distance to " CD  ARG A  14 " =    2.948
peak=   -3.800 closest distance to " OG  SER A  97 " =    2.189
peak=   -3.747 closest distance to " CG2 ILE A 120 " =    1.290
peak=   -3.745 closest distance to " O   HOH Z  69 " =    1.788
peak=   -3.736 closest distance to " O   HOH Z 385 " =    1.115
peak=   -3.735 closest distance to " O   HOH Z 313 " =    0.857
peak=   -3.733 closest distance to " O   HOH Z  39 " =    0.834
peak=   -3.720 closest distance to " CB  ALA A 248 " =    2.040
peak=   -3.703 closest distance to " CD2 LEU A   5 " =    0.932
peak=   -3.702 closest distance to " O   ASP A 191 " =    1.868
peak=   -3.701 closest distance to " O   HOH Z  28 " =    1.052
peak=   -3.701 closest distance to " O   HOH Z  60 " =    1.677
peak=   -3.699 closest distance to " N   VAL A  72 " =    2.109
peak=   -3.696 closest distance to " CB  PHE A 130 " =    1.119
peak=   -3.694 closest distance to " O   HOH Z 105 " =    2.106
peak=   -3.684 closest distance to " CG2AVAL A  41 " =    2.716
peak=   -3.674 closest distance to " O   HOH Z 205 " =    1.235
peak=   -3.650 closest distance to " O   ALA A  10 " =    1.545
peak=   -3.648 closest distance to " CB  ASP A  27 " =    2.434
peak=   -3.644 closest distance to " C   GLU A   2 " =    1.888
peak=   -3.642 closest distance to " CG  ASP A  50 " =    1.073
peak=   -3.636 closest distance to " O   HOH Z 298 " =    2.701
peak=   -3.615 closest distance to " O   HOH Z  95 " =    1.387
peak=   -3.610 closest distance to " CA  GLY A  35 " =    2.032
peak=   -3.593 closest distance to " N   PRO A 163 " =    1.409
peak=   -3.556 closest distance to " O   HOH Z 235 " =    1.111
peak=   -3.554 closest distance to " O   HOH Z 275 " =    1.625
peak=   -3.538 closest distance to " CD2 LEU A 237 " =    2.206
peak=   -3.531 closest distance to " O   HOH Z  61 " =    1.390
peak=   -3.519 closest distance to " O   HOH Z 328 " =    0.907
peak=   -3.517 closest distance to " O   SER A 245 " =    1.385
peak=   -3.509 closest distance to " O   HOH Z 211 " =    0.827
peak=   -3.508 closest distance to " CA  HIS A  86 " =    2.085
peak=   -3.502 closest distance to " O   HOH Z 352 " =    1.537
peak=   -3.501 closest distance to " CD  LYS A 166 " =    2.545
peak=   -3.493 closest distance to " NE2 GLN A  55 " =    1.032
peak=   -3.491 closest distance to " O   HOH Z 428 " =    1.392
peak=   -3.480 closest distance to " O   HOH Z 216 " =    1.650
peak=   -3.477 closest distance to " CB  ALA A 114 " =    2.515
peak=   -3.476 closest distance to " O   HOH Z  54 " =    0.864
peak=   -3.475 closest distance to " O   ALA A  84 " =    1.644
peak=   -3.474 closest distance to " CA  GLY A 203 " =    2.620
peak=   -3.472 closest distance to " CE2 PHE A 218 " =    2.519
peak=   -3.465 closest distance to " O   HOH Z 186 " =    1.287
peak=   -3.456 closest distance to " NH2BARG A 102 " =    1.043
peak=   -3.445 closest distance to " O   ILE A  49 " =    1.527
peak=   -3.443 closest distance to " CG  PRO A 163 " =    2.642
peak=   -3.441 closest distance to " O   HOH Z 389 " =    2.397
peak=   -3.440 closest distance to " O   HOH Z 189 " =    3.797
peak=   -3.439 closest distance to " NE2 GLN A 223 " =    1.570
peak=   -3.418 closest distance to " O   HOH Z 286 " =    1.524
peak=   -3.414 closest distance to " CG  PHE A  59 " =    1.553
peak=   -3.407 closest distance to " O   SER A  22 " =    2.632
peak=   -3.398 closest distance to " NE2 GLN A 194 " =    1.950
peak=   -3.395 closest distance to " CE1 HIS A  81 " =    1.318
peak=   -3.393 closest distance to " CG  TRP A 266 " =    1.885
peak=   -3.392 closest distance to " CG2 ILE A 120 " =    0.911
peak=   -3.388 closest distance to " O   HOH Z 241 " =    1.061
peak=   -3.388 closest distance to " OD2 ASP A 272 " =    1.391
peak=   -3.385 closest distance to " O   CYS A 260 " =    1.382
peak=   -3.375 closest distance to " CA  GLY A  57 " =    2.112
peak=   -3.370 closest distance to " O   HOH Z 102 " =    1.620
peak=   -3.370 closest distance to " O   HOH Z 359 " =    1.533
peak=   -3.370 closest distance to " C   PHE A 155 " =    0.773
peak=   -3.368 closest distance to " O   HOH Z 404 " =    1.405
peak=   -3.365 closest distance to " O   HOH Z 177 " =    2.519
peak=   -3.365 closest distance to " OG  SER A  63 " =    1.377
peak=   -3.363 closest distance to " C   ASN A 285 " =    2.029
peak=   -3.359 closest distance to " CZ2 TRP A 274 " =    0.907
peak=   -3.358 closest distance to " O   HOH Z 411 " =    4.935
peak=   -3.357 closest distance to " OE1 GLU A  44 " =    1.055
peak=   -3.351 closest distance to " CG  PRO A 243 " =    1.753
peak=   -3.351 closest distance to " O   HOH Z 350 " =    2.355
peak=   -3.349 closest distance to " O   LYS A  76 " =    1.191
peak=   -3.345 closest distance to " C   HIS A 108 " =    1.332
peak=   -3.341 closest distance to " CG  GLN A  73 " =    1.354
peak=   -3.339 closest distance to " O   HOH Z 390 " =    2.383
peak=   -3.339 closest distance to " O   HOH Z  53 " =    1.693
peak=   -3.333 closest distance to " O   GLY A  80 " =    2.492
peak=   -3.326 closest distance to " CD2 LEU A 237 " =    2.586
peak=   -3.324 closest distance to " CG  LEU A 282 " =    2.498
peak=   -3.321 closest distance to " CB  ALA A   7 " =    2.000
peak=   -3.318 closest distance to " CD1 TRP A 274 " =    1.036
peak=   -3.318 closest distance to " CB  ASP A 132 " =    2.467
peak=   -3.311 closest distance to " O   HOH Z  67 " =    3.028
peak=   -3.310 closest distance to " O   HOH Z 128 " =    2.437
peak=   -3.304 closest distance to " O   SER A 271 " =    1.602
peak=   -3.298 closest distance to " NE2 GLN A  11 " =    1.569
peak=   -3.298 closest distance to " O   HOH Z 165 " =    2.135
peak=   -3.296 closest distance to " O   GLY A 136 " =    1.559
peak=   -3.295 closest distance to " OG  SER A 276 " =    0.928
peak=   -3.295 closest distance to " O   HOH Z 387 " =    1.247
peak=   -3.294 closest distance to " O   VAL A  72 " =    1.062
peak=   -3.292 closest distance to " O   HOH Z 351 " =    1.677
peak=   -3.281 closest distance to " CB  TYR A  68 " =    1.149
peak=   -3.279 closest distance to " CG1 VAL A 125 " =    2.382
peak=   -3.273 closest distance to " O   SER A   3 " =    2.342
peak=   -3.271 closest distance to " O   GLU A 277 " =    2.155
peak=   -3.269 closest distance to " O   HOH Z 111 " =    1.410
peak=   -3.268 closest distance to " CD1 LEU A 282 " =    2.532
peak=   -3.259 closest distance to " O   HOH Z 256 " =    1.050
peak=   -3.255 closest distance to " O   PHE A 218 " =    1.608
peak=   -3.252 closest distance to " CA  GLY A  57 " =    2.093
peak=   -3.251 closest distance to " N   VAL A 189 " =    1.740
peak=   -3.249 closest distance to " O   GLY A 203 " =    2.533
peak=   -3.246 closest distance to " O   HOH Z 365 " =    1.337
peak=   -3.244 closest distance to " O   HOH Z 231 " =    1.955
peak=   -3.237 closest distance to " NH2AARG A 275 " =    5.311
peak=   -3.236 closest distance to " O   HOH Z  54 " =    1.109
peak=   -3.235 closest distance to " N   SER A 206 " =    2.056
peak=   -3.235 closest distance to " CG  ARG A 219 " =    2.265
peak=   -3.229 closest distance to " N   ALA A   1 " =    1.087
peak=   -3.228 closest distance to " O   HOH Z 359 " =    3.395
peak=   -3.228 closest distance to " CG  LEU A 228 " =    0.886
peak=   -3.227 closest distance to " O   HOH Z 111 " =    1.664
peak=   -3.226 closest distance to " O   HOH Z 185 " =    2.075
peak=   -3.225 closest distance to " CZ  TYR A 169 " =    1.957
peak=   -3.225 closest distance to " OG BSER A 210 " =    2.371
peak=   -3.225 closest distance to " O   HOH Z 276 " =    1.355
peak=   -3.223 closest distance to " O   HOH Z 337 " =    1.653
peak=   -3.216 closest distance to " CA  ASN A 127 " =    1.285
peak=   -3.215 closest distance to " N   GLU A 277 " =    1.293
peak=   -3.213 closest distance to " O   HOH Z 428 " =    2.464
peak=   -3.213 closest distance to " O   HOH Z 126 " =    1.902
peak=   -3.211 closest distance to " O   HOH Z 238 " =    1.036
peak=   -3.200 closest distance to " CB  PRO A 243 " =    2.630
peak=   -3.199 closest distance to " CG  ARG A 259 " =    2.434
peak=   -3.198 closest distance to " OG  SER A 245 " =    1.550
peak=   -3.197 closest distance to " OD2 ASP A 171 " =    2.266
peak=   -3.197 closest distance to " O   ARG A 145 " =    1.334
peak=   -3.197 closest distance to " CG  HIS A 108 " =    0.957
peak=   -3.195 closest distance to " O   HOH Z 414 " =    1.757
peak=   -3.195 closest distance to " CG  GLU A 277 " =    1.104
peak=   -3.194 closest distance to " O   HOH Z  52 " =    2.058
peak=   -3.193 closest distance to " N   ALA A 248 " =    1.683
peak=   -3.192 closest distance to " CZ  ARG A 259 " =    0.922
peak=   -3.190 closest distance to " O   HOH Z 429 " =    1.467
peak=   -3.190 closest distance to " C   TYR A 172 " =    1.551
peak=   -3.188 closest distance to " CD2 TYR A 116 " =    2.200
peak=   -3.184 closest distance to " O   HOH Z 188 " =    0.924
peak=   -3.182 closest distance to " OH  TYR A 214 " =    1.082
peak=   -3.174 closest distance to " CB  ALA A 131 " =    1.839
peak=   -3.173 closest distance to " C   ILE A 239 " =    1.888
peak=   -3.172 closest distance to " CB  ASN A  45 " =    2.049
peak=   -3.172 closest distance to " O   HOH Z 135 " =    1.866
peak=   -3.169 closest distance to " O   HOH Z  52 " =    1.520
peak=   -3.153 closest distance to " O   HOH Z 129 " =    4.409
peak=   -3.153 closest distance to " CE2 TRP A  70 " =    2.435
peak=   -3.149 closest distance to " N   GLN A  11 " =    1.003
peak=   -3.147 closest distance to " C   ARG A  79 " =    2.652
peak=   -3.146 closest distance to " O   PRO A 163 " =    1.842
peak=   -3.145 closest distance to " O   LYS A 193 " =    1.549
peak=   -3.144 closest distance to " O   HOH Z 136 " =    2.999
peak=   -3.140 closest distance to " O   HOH Z 198 " =    1.985
peak=   -3.139 closest distance to " CB  PHE A 155 " =    2.560
peak=   -3.137 closest distance to " OG1 THR A 178 " =    1.181
peak=   -3.129 closest distance to " O   HOH Z 174 " =    2.746
peak=   -3.127 closest distance to " CD  ARG A 139 " =    1.813
peak=   -3.126 closest distance to " C   PHE A  59 " =    0.971
peak=   -3.124 closest distance to " C   ARG A 269 " =    1.326
peak=   -3.121 closest distance to " CB  SER A  62 " =    5.356
peak=   -3.117 closest distance to " O   HOH Z 108 " =    1.518
peak=   -3.114 closest distance to " CA  HIS A 207 " =    1.170
peak=   -3.113 closest distance to " O   HOH Z 360 " =    1.012
peak=   -3.107 closest distance to " CG2 ILE A 151 " =    2.412
peak=   -3.106 closest distance to " NE  ARG A  79 " =    1.000
peak=   -3.106 closest distance to " OG BSER A  99 " =    1.418
peak=   -3.102 closest distance to " O   HOH Z 147 " =    1.060
peak=   -3.099 closest distance to " CB  ALA A 161 " =    1.655
peak=   -3.097 closest distance to " OD1 ASN A  69 " =    0.883
peak=   -3.097 closest distance to " CZ3 TRP A 123 " =    1.743
peak=   -3.095 closest distance to " O   HOH Z 393 " =    2.786
peak=   -3.087 closest distance to " OG BSER A  12 " =    1.281
peak=   -3.087 closest distance to " OE2 GLU A 152 " =    1.094
peak=   -3.085 closest distance to " NH2 ARG A 219 " =    2.135
peak=   -3.083 closest distance to " CD1 ILE A  33 " =    2.264
peak=   -3.081 closest distance to " CG  ASP A 231 " =    0.785
peak=   -3.078 closest distance to " C   GLU A 236 " =    1.022
peak=   -3.077 closest distance to " O   HOH Z 298 " =    0.940
peak=   -3.071 closest distance to " CB  ASN A 301 " =    1.903
peak=   -3.066 closest distance to " O   HOH Z 189 " =    1.266
peak=   -3.056 closest distance to " OD1 ASP A  27 " =    0.959
peak=   -3.055 closest distance to " CB  ALA A  43 " =    2.428

================= 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    :  0.5041 0.4939   6.306876e+00   6.291657e+00
   1_bss:  0.4959 0.4812   6.303588e+00   6.286993e+00
   1_xyz:  0.4308 0.4577   6.238517e+00   6.265307e+00
   1_adp:  0.3942 0.4612   6.199197e+00   6.264275e+00
   1_occ:  0.3940 0.4609   6.198898e+00   6.264650e+00
   2_bss:  0.3926 0.4577   6.200949e+00   6.264728e+00
   2_xyz:  0.3424 0.4269   6.102662e+00   6.218438e+00
   2_adp:  0.3276 0.4134   6.079268e+00   6.201838e+00
   2_occ:  0.3275 0.4135   6.079465e+00   6.202475e+00
   3_bss:  0.3274 0.4115   6.078960e+00   6.201384e+00
   3_xyz:  0.2646 0.3357   5.891625e+00   6.054135e+00
   3_adp:  0.2338 0.3216   5.812824e+00   6.013516e+00
   3_occ:  0.2336 0.3219   5.812354e+00   6.013871e+00
   4_bss:  0.2329 0.3216   5.810978e+00   6.013047e+00
   4_xyz:  0.1910 0.2650   5.629295e+00   5.855070e+00
   4_adp:  0.1718 0.2370   5.529900e+00   5.761523e+00
   4_occ:  0.1715 0.2367   5.528378e+00   5.760121e+00
   5_bss:  0.1716 0.2366   5.526532e+00   5.757574e+00
   5_xyz:  0.1504 0.2107   5.413506e+00   5.658402e+00
   5_adp:  0.1438 0.1986   5.369685e+00   5.606544e+00
   5_occ:  0.1436 0.1982   5.368271e+00   5.605180e+00
   5_bss:  0.1440 0.1981   5.368002e+00   5.604649e+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:  0.368  20.000   5.862   8.894   9.111   0.000   0.000   0.000
   1_xyz:  0.368  20.000   5.862   8.894   9.111   0.000   0.000   0.000
   1_adp:  0.368  20.000   5.862   8.894   9.111   0.000   0.000   0.000
   1_occ:  0.368  20.000   5.862   8.894   9.111   0.000   0.000   0.000
   2_bss:  0.362  46.006   2.979   5.040   5.300   0.000   0.000   0.000
   2_xyz:  0.362  46.006   2.979   5.040   5.300   0.000   0.000   0.000
   2_adp:  0.362  46.006   2.979   5.040   5.300   0.000   0.000   0.000
   2_occ:  0.362  46.006   2.979   5.040   5.300   0.000   0.000   0.000
   3_bss:  0.326  50.855   1.706   2.766   3.395   0.000   0.000   0.000
   3_xyz:  0.326  50.855   1.706   2.766   3.395   0.000   0.000   0.000
   3_adp:  0.326  50.855   1.706   2.766   3.395   0.000   0.000   0.000
   3_occ:  0.326  50.855   1.706   2.766   3.395   0.000   0.000   0.000
   4_bss:  0.311  54.713   1.045   1.451   2.659   0.000   0.000   0.000
   4_xyz:  0.311  54.713   1.045   1.451   2.659   0.000   0.000   0.000
   4_adp:  0.311  54.713   1.045   1.451   2.659   0.000   0.000   0.000
   4_occ:  0.311  54.713   1.045   1.451   2.659   0.000   0.000   0.000
   5_bss:  0.321  52.591   0.747   0.644   2.461   0.000   0.000   0.000
   5_xyz:  0.321  52.591   0.747   0.644   2.461   0.000   0.000   0.000
   5_adp:  0.321  52.591   0.747   0.644   2.461   0.000   0.000   0.000
   5_occ:  0.321  52.591   0.747   0.644   2.461   0.000   0.000   0.000
   5_bss:  0.321  53.684  -0.501  -0.741   1.242   0.000   0.000   0.000
------------------------------------------------------------------------
 stage     <pher>    fom   alpha         beta
   0    :  63.350 0.3500  0.4247    80189.717
   1_bss:  62.356 0.3624  0.5537    78675.845
   1_xyz:  56.437 0.4382  0.6545    68276.170
   1_adp:  56.527 0.4365  0.7217    68331.823
   1_occ:  56.577 0.4359  0.7202    68566.430
   2_bss:  56.317 0.4392  0.6466    68155.705
   2_xyz:  49.848 0.5204  0.7674    55324.052
   2_adp:  47.245 0.5536  0.8186    51686.164
   2_occ:  47.310 0.5527  0.8172    51752.828
   3_bss:  47.082 0.5554  0.7696    51223.883
   3_xyz:  35.903 0.6899  0.9303    31555.271
   3_adp:  33.279 0.7203  0.9435    28073.874
   3_occ:  33.294 0.7201  0.9432    28075.655
   4_bss:  33.210 0.7211  0.9146    27974.990
   4_xyz:  26.904 0.7899  0.9666    18213.396
   4_adp:  23.331 0.8280  0.9760    14435.183
   4_occ:  23.281 0.8284  0.9758    14359.456
   5_bss:  23.213 0.8289  0.9612    14257.603
   5_xyz:  20.378 0.8573  0.9772    11377.020
   5_adp:  18.911 0.8721  0.9756    10266.645
   5_occ:  18.883 0.8723  0.9751    10215.051
   5_bss:  18.860 0.8725  0.9685    10187.382
------------------------------------------------------------------------
 stage       angl   bond   chir   dihe   plan   repu  geom_target
   0    :  24.226  0.414  2.119 33.790  0.145  4.089   5.3482e+01
   1_bss:  24.226  0.414  2.119 33.790  0.145  4.089   5.3482e+01
   1_xyz:   1.757  0.014  0.108 18.566  0.006  4.104   1.5450e-01
   1_adp:   1.757  0.014  0.108 18.566  0.006  4.104   1.5450e-01
   1_occ:   1.757  0.014  0.108 18.566  0.006  4.104   1.5450e-01
   2_bss:   1.757  0.014  0.108 18.566  0.006  4.104   1.5450e-01
   2_xyz:   1.286  0.009  0.085 16.965  0.006  4.125   1.0684e-01
   2_adp:   1.286  0.009  0.085 16.965  0.006  4.125   1.0684e-01
   2_occ:   1.286  0.009  0.085 16.965  0.006  4.125   1.0684e-01
   3_bss:   1.286  0.009  0.085 16.965  0.006  4.125   1.0684e-01
   3_xyz:   1.343  0.011  0.098 16.691  0.005  4.125   1.0664e-01
   3_adp:   1.343  0.011  0.098 16.691  0.005  4.125   1.0664e-01
   3_occ:   1.343  0.011  0.098 16.691  0.005  4.125   1.0664e-01
   4_bss:   1.343  0.011  0.098 16.691  0.005  4.125   1.0664e-01
   4_xyz:   1.069  0.008  0.078 15.701  0.004  4.111   7.1357e-02
   4_adp:   1.069  0.008  0.078 15.701  0.004  4.111   7.1357e-02
   4_occ:   1.069  0.008  0.078 15.701  0.004  4.111   7.1357e-02
   5_bss:   1.069  0.008  0.078 15.701  0.004  4.111   7.1357e-02
   5_xyz:   0.942  0.006  0.069 15.427  0.003  4.109   5.7282e-02
   5_adp:   0.942  0.006  0.069 15.427  0.003  4.109   5.7282e-02
   5_occ:   0.942  0.006  0.069 15.427  0.003  4.109   5.7282e-02
   5_bss:   0.942  0.006  0.069 15.427  0.003  4.109   5.7282e-02
------------------------------------------------------------------------
                      Maximal deviations:
 stage       angl   bond   chir   dihe   plan   repu       |grad|
   0    :  74.492  1.400  6.404144.062  0.405  1.196   6.9293e+00
   1_bss:  74.492  1.400  6.404144.062  0.405  1.196   6.9293e+00
   1_xyz:  13.661  0.197  0.426 88.616  0.034  2.083   1.0345e-01
   1_adp:  13.661  0.197  0.426 88.616  0.034  2.083   1.0345e-01
   1_occ:  13.661  0.197  0.426 88.616  0.034  2.083   1.0345e-01
   2_bss:  13.661  0.197  0.426 88.616  0.034  2.083   1.0345e-01
   2_xyz:   8.242  0.072  0.338 89.692  0.044  1.905   6.3009e-02
   2_adp:   8.242  0.072  0.338 89.692  0.044  1.905   6.3009e-02
   2_occ:   8.242  0.072  0.338 89.692  0.044  1.905   6.3009e-02
   3_bss:   8.242  0.072  0.338 89.692  0.044  1.905   6.3009e-02
   3_xyz:   7.017  0.054  0.326 82.085  0.043  2.120   9.7792e-02
   3_adp:   7.017  0.054  0.326 82.085  0.043  2.120   9.7792e-02
   3_occ:   7.017  0.054  0.326 82.085  0.043  2.120   9.7792e-02
   4_bss:   7.017  0.054  0.326 82.085  0.043  2.120   9.7792e-02
   4_xyz:   7.366  0.048  0.307 76.636  0.030  2.332   6.4237e-02
   4_adp:   7.366  0.048  0.307 76.636  0.030  2.332   6.4237e-02
   4_occ:   7.366  0.048  0.307 76.636  0.030  2.332   6.4237e-02
   5_bss:   7.366  0.048  0.307 76.636  0.030  2.332   6.4237e-02
   5_xyz:   6.535  0.050  0.255 80.432  0.032  2.351   3.4215e-02
   5_adp:   6.535  0.050  0.255 80.432  0.032  2.351   3.4215e-02
   5_occ:   6.535  0.050  0.255 80.432  0.032  2.351   3.4215e-02
   5_bss:   6.535  0.050  0.255 80.432  0.032  2.351   3.4215e-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:  88.55   0.00  16.18  82.56   0.00  14.68  88.55   0.00  24.35
   1_occ:  88.55   0.00  16.18  82.56   0.00  14.68  88.55   0.00  24.35
   2_bss:  88.55   0.00  16.18  82.56   0.00  14.68  88.55   0.00  24.35
   2_xyz:  88.55   0.00  16.18  82.56   0.00  14.68  88.55   0.00  24.35
   2_adp:  82.18   0.00  15.47  71.69   0.00  13.44  82.18   0.00  26.53
   2_occ:  82.18   0.00  15.47  71.69   0.00  13.44  82.18   0.00  26.53
   3_bss:  82.18   0.00  15.47  71.69   0.00  13.44  82.18   0.00  26.53
   3_xyz:  82.18   0.00  15.47  71.69   0.00  13.44  82.18   0.00  26.53
   3_adp:  99.29   0.00  17.35  93.64   0.00  13.04  99.29   0.00  40.83
   3_occ:  99.29   0.00  17.35  93.64   0.00  13.04  99.29   0.00  40.83
   4_bss:  99.29   0.00  17.35  93.64   0.00  13.04  99.29   0.00  40.83
   4_xyz:  99.29   0.00  17.35  93.64   0.00  13.04  99.29   0.00  40.83
   4_adp:  99.23   0.00  16.35  99.23   0.00  11.30  96.34   2.16  43.83
   4_occ:  99.23   0.00  16.35  99.23   0.00  11.30  96.34   2.16  43.83
   5_bss:  99.23   0.00  16.35  99.23   0.00  11.30  96.34   2.16  43.83
   5_xyz:  99.23   0.00  16.35  99.23   0.00  11.30  96.34   2.16  43.83
   5_adp: 125.37   0.00  15.59 125.37   0.00  10.54  97.06   3.32  43.09
   5_occ: 125.37   0.00  15.59 125.37   0.00  10.54  97.06   3.32  43.09
   5_bss: 126.46   1.09  16.69 126.46   1.09  11.64  98.15   4.41  44.18
------------------------------------------------------------------------
 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:    1.310    0.020    0.414
   1_adp:    1.310    0.020    0.414
   1_occ:    1.310    0.020    0.414
   2_bss:    1.310    0.020    0.414
   2_xyz:    1.696    0.046    0.583
   2_adp:    1.696    0.046    0.583
   2_occ:    1.696    0.046    0.583
   3_bss:    1.696    0.046    0.583
   3_xyz:    1.760    0.081    0.763
   3_adp:    1.760    0.081    0.763
   3_occ:    1.760    0.081    0.763
   4_bss:    1.760    0.081    0.763
   4_xyz:    1.907    0.029    0.849
   4_adp:    1.907    0.029    0.849
   4_occ:    1.907    0.029    0.849
   5_bss:    1.907    0.029    0.849
   5_xyz:    1.983    0.091    0.889
   5_adp:    1.983    0.091    0.889
   5_occ:    1.983    0.091    0.889
   5_bss:    1.983    0.091    0.889
------------------------------------------------------------------------

CPU time actual refinement: 343.66


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

Writing refined structure to PDB file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/trial/run_613/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_613/model_refine_001_2mFobs-DFmodel.map
Writing mFobs-DFmodel XPLOR map to file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/trial/run_613/model_refine_001_mFobs-DFmodel.map
Writing map coefficients to MTZ file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/trial/run_613/model_refine_001_map_coeffs.mtz

Writing default parameters for subsequent refinement:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/trial/run_613/model_refine_002.def


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

Pure refinement (no I/O, processing, etc)= 343.49 
  Macro-tasks:
    bulk solvent and scale       = 41.31  
    individual site refinement   = 144.42 
    weights calculation          = 32.20  
    collect and process          = 6.32   
    model show statistics        = 0.13   
    TOTAL for macro-tasks        = 224.38 
  Micro-tasks:
    mask                            = 2.92   
    f_calc                          = 107.75 
    alpha_beta                      = 8.16   
    target                          = 1.15   
    gradients_wrt_atomic_parameters = 117.80 
    fmodel                         = 6.83   
    r_factors                      = 0.27   
    phase_errors                   = 9.90   
    foms                           = 0.21   
    TOTAL for micro-tasks          = 254.99 
NUMBER OF MASK CALCS=  6
Time per interpreted Python bytecode instruction: 4.814 micro seconds
Total CPU time: 5.95 minutes
from_scatterers_fft:    652 calls, 107.35 s
gradients_fft:          597 calls, 104.61 s

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

# Date 2008-01-16 Time 02:01:49 PST -0800 (1200477709.43 s)
Start R-work = 0.5041, R-free = 0.4939 (no bulk solvent and anisotropic scale)
Final R-work = 0.1591, R-free = 0.2132 (no bulk solvent and anisotropic scale)

Start R-work = 0.4959, R-free = 0.4812
Final R-work = 0.1440, R-free = 0.1981