# Date 2008-01-16 Time 02:16:14 PST -0800 (1200478574.22 s)
#phil __OFF__

Command line arguments: "../763.param" "adp.set_b_iso=10" "sites.shake=0.5" "main.number_of_macro_cycles=5" "--overwrite"

HOST = moonbird.lbl.gov
HOSTTYPE = x86_64-linux
USER = phzwart
PID = 1006
JOB_ID = 5158
SGE_ARCH = lx24-amd64
SGE_TASK_FIRST = 1
SGE_TASK_LAST = 1330
SGE_TASK_ID = 763

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

              phenix.refine: Macromolecular Structure Refinement

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

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

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

Processing inputs. This may take a minute or two.

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

  refinement.modify_start_model.sites.shake = 0.5

  refinement.main.number_of_macro_cycles = 5

Working crystal symmetry after inspecting all inputs:
  Unit cell: (70.6012, 46.4607, 85.9581, 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: (70.6012, 46.4607, 85.9581, 90, 90, 90)
Space group: P 21 21 21 (No. 19)
Systematic absences: 0
Centric reflections: 2427
Resolution range: 15.0278 1.98157
Completeness in resolution range: 0.96865
Completeness with d_max=infinity: 0.965689

Number of F-obs in resolution range:                   19589
Number of F-obs <= 0:                                  0
Refinement resolution range: d_max =  15.0278
                             d_min =   1.9816

Miller array info: /net/cci-filer1/vol1/tmp/phzwart/tassos/trial/1e0w.cns:TEST
Observation type: None
Type of data: int, size=19589
Type of sigmas: None
Number of Miller indices: 19589
Anomalous flag: False
Unit cell: (70.6012, 46.4607, 85.9581, 90, 90, 90)
Space group: P 21 21 21 (No. 19)
Systematic absences: 0
Centric reflections: 2427
Resolution range: 15.0278 1.98157
Completeness in resolution range: 0.96865
Completeness with d_max=infinity: 0.965689

Test (R-free flags) flag value: 1

Number of work/free reflections by resolution:
                                         work  free  %free
  bin  1: 15.0283 -  4.2402 [2115/2140]  1905   210   9.9%
  bin  2:  4.2402 -  3.3781 [2042/2062]  1836   206  10.1%
  bin  3:  3.3781 -  2.9548 [2018/2037]  1815   203  10.1%
  bin  4:  2.9548 -  2.6863 [2003/2033]  1810   193   9.6%
  bin  5:  2.6863 -  2.4947 [1984/2003]  1785   199  10.0%
  bin  6:  2.4947 -  2.3482 [1968/1993]  1763   205  10.4%
  bin  7:  2.3482 -  2.2310 [1947/1975]  1752   195  10.0%
  bin  8:  2.2310 -  2.1342 [1975/2011]  1778   197  10.0%
  bin  9:  2.1342 -  2.0522 [1953/1995]  1762   191   9.8%
  bin 10:  2.0522 -  1.9816 [1584/1974]  1424   160  10.1%
                                overall 17630  1959  10.0%
Writing MTZ file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/trial/run_763/model_refine_data.mtz


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

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

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

  Number of disulfides: simple=3, symmetry=0
    Simple disulfide: " SG  CYS A 168 " - " SG ACYS A 201 " distance=2.08
    Simple disulfide: " SG  CYS A 168 " - " SG BCYS A 201 " distance=1.98
    Simple disulfide: " SG  CYS A 254 " - " SG  CYS A 260 " distance=2.05
  Time building geometry restraints manager: 0.14 seconds
  Histogram of bond lengths:
        1.21 -     1.38: 943
        1.38 -     1.56: 1465
        1.56 -     1.73: 7
        1.73 -     1.90: 21
        1.90 -     2.08: 3
  Bond restraints sorted by residual:
             atom i - atom j            ideal  model  delta   weight residual
  " SG  CYS A 168 " - " SG BCYS A 201 " 2.031  1.983  0.048 2.50e+03 5.87e+00
  " C   GLN A  88 " - " N   GLN A  89 " 1.329  1.360 -0.031 5.10e+03 4.97e+00
  " SG  CYS A 168 " - " SG ACYS A 201 " 2.031  2.075 -0.044 2.50e+03 4.89e+00
  " CB  CYS A 201 " - " SG ACYS A 201 " 1.808  1.738  0.070 9.18e+02 4.46e+00
  " C   PRO A 198 " - " N   ILE A 199 " 1.329  1.301  0.028 5.10e+03 4.10e+00
  ... (remaining 2434 not shown)
  Histogram of nonbonded interaction distances:
        1.81 -     2.42: 16
        2.42 -     3.04: 2202
        3.04 -     3.66: 4714
        3.66 -     4.28: 9117
        4.28 -     4.90: 12360
  Nonbonded interactions sorted by model distance:
             atom i - atom j             model   vdw sym.op. j
  " CE BMET A  47 " - " O  BHOH Z  74 "  1.806 3.460
  " CZ BARG A 275 " - " O  BHOH Z 338 "  2.218 3.270
  " O   HOH Z 204 " - " O   HOH Z 296 "  2.273 3.040 -x+1/2,-y+1,z+1/2
  " OG1 THR A  29 " - " O   HOH Z 245 "  2.305 3.040 x,y+1,z
  " O   HOH Z 280 " - " O   HOH Z 438 "  2.313 3.040 -x,y-1/2,-z+1/2
  ... (remaining 28404 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_763/model_refine_001.eff

Writing geometry restraints to file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/trial/run_763/model_refine_001.geo

CPU time processing inputs: 9.08


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

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

#phil __ON__
refinement {
  crystal_symmetry {
    unit_cell = 70.60125 46.4607 85.95805 90 90 90
    space_group = "P 21 21 21"
  }
  input {
    pdb {
      file_name = "/net/cci-filer1/vol1/tmp/phzwart/tassos/trial/model.pdb"
    }
    xray_data {
      file_name = "/net/cci-filer1/vol1/tmp/phzwart/tassos/trial/1e0w.cns"
      labels = "FOBS,SIGMA"
      r_free_flags {
        file_name = "/net/cci-filer1/vol1/tmp/phzwart/tassos/trial/1e0w.cns"
        label = "TEST"
        test_flag_value = 1
      }
    }
  }
  output {
    prefix = "model_refine"
    serial = 1
  }
  main {
    number_of_macro_cycles = 5
  }
  modify_start_model {
    adp {
      set_b_iso = 10
    }
    sites {
      shake = 0.5
    }
  }
}
#phil __OFF__


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


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


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

|--(resolution: 1.98 - 15.03 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.4352   r_free= 0.4188   ksol= 0.00   Bsol= 0.00   scale= 0.824    |
|                                                                             |
| 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:   0.58 A                  |
| x-ray target function (ml) for work reflections: 6.228906                   |
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
| Bin     Resolution   Compl.  No. Refl.    R-factors          Targets        |
|number     range              work test   work   test        work        test|
|  1: 15.0283 -  4.7293 0.99   1386  154 0.3707 0.3595      6.5273      6.4922|
|  2:  4.7293 -  3.7734 0.99   1324  146 0.3317 0.3261      6.6626      6.6291|
|  3:  3.7734 -  3.3022 0.99   1300  143 0.3700 0.3413      6.5552      6.5879|
|  4:  3.3022 -  3.0029 0.99   1285  148 0.4084 0.3657      6.4658      6.3776|
|  5:  3.0029 -  2.7891 0.99   1292  141 0.4601 0.4425      6.3154      6.3268|
|  6:  2.7891 -  2.6256 0.99   1281  141 0.4572 0.5065      6.2391      6.1994|
|  7:  2.6256 -  2.4947 0.99   1283  138 0.4827 0.4536      6.2117      6.2132|
|  8:  2.4947 -  2.3866 0.98   1253  147 0.4851 0.4312      6.1548      6.1233|
|  9:  2.3866 -  2.2950 0.98   1269  138 0.4680 0.4662      6.0849      6.0619|
| 10:  2.2950 -  2.2161 1.00   1266  142 0.4914 0.4761      6.0971      6.0907|
| 11:  2.2161 -  2.1470 0.97   1249  137 0.5022 0.4485      6.0328      5.9995|
| 12:  2.1470 -  2.0858 0.98   1256  141 0.4830 0.5013      5.9611      6.0035|
| 13:  2.0858 -  2.0310 0.99   1283  140 0.5090 0.5064      5.8781      5.8294|
| 14:  2.0310 -  1.9816 0.72    903  103 0.5201 0.4897      5.8462      5.7601|
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
|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: 15.0283 -  4.7293  1386   154  0.72  32.39   0.81     0.76      63360.97|
|  2:  4.7293 -  3.7734  1324   146  0.78  28.37   0.91     0.84      75085.20|
|  3:  3.7734 -  3.3022  1300   143  0.71  34.69   0.89     0.81      76732.14|
|  4:  3.3022 -  3.0029  1285   148  0.66  39.19   0.84     0.73      68809.64|
|  5:  3.0029 -  2.7891  1292   141  0.54  48.44   0.77     0.63      62401.73|
|  6:  2.7891 -  2.6256  1281   141  0.52  50.57   0.76     0.57      57210.52|
|  7:  2.6256 -  2.4947  1283   138  0.49  52.86   0.76     0.56      53801.12|
|  8:  2.4947 -  2.3866  1253   147  0.49  52.62   0.76     0.57      48284.90|
|  9:  2.3866 -  2.2950  1269   138  0.52  50.49   0.75     0.58      41837.90|
| 10:  2.2950 -  2.2161  1266   142  0.51  51.46   0.79     0.59      37285.34|
| 11:  2.2161 -  2.1470  1249   137  0.49  52.91   0.77     0.58      35789.07|
| 12:  2.1470 -  2.0858  1256   141  0.44  56.68   0.80     0.53      36454.86|
| 13:  2.0858 -  2.0310  1283   140  0.39  60.97   0.75     0.47      33537.96|
| 14:  2.0310 -  1.9816   903   103  0.39  60.57   0.73     0.42      27363.46|
|alpha:            min =        0.42 max =            0.84 mean =         0.62|
|beta:             min =    27363.46 max =        76732.14 mean =     52034.18|
|figures of merit: min =        0.00 max =            1.00 mean =         0.55|
|phase err.(work): min =        0.00 max =           89.99 mean =        47.56|
|phase err.(test): min =        0.00 max =           89.97 mean =        47.73|
|-----------------------------------------------------------------------------|

============================== 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 = 7.904284              wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 75.148   (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 0.705768              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 79.508   (deg)                 |
|-----------------------------------------------------------------------------|


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

|-Geometry statistics: start--------------------------------------------------|
|            Histogram of deviations from ideal values for                    |
| Bonds                | Angles                   |  Nonbonded contacts       |
| 0.000 - 0.140:   597 |   0.009 -   7.457:   713 |  1.196 -  1.566:        2 |
| 0.140 - 0.280:   585 |   7.457 -  14.906:   711 |  1.566 -  1.937:       21 |
| 0.280 - 0.420:   441 |  14.906 -  22.354:   630 |  1.937 -  2.307:      174 |
| 0.420 - 0.560:   366 |  22.354 -  29.802:   474 |  2.307 -  2.677:      679 |
| 0.560 - 0.700:   237 |  29.802 -  37.251:   338 |  2.677 -  3.048:     1514 |
| 0.700 - 0.840:   127 |  37.251 -  44.699:   241 |  3.048 -  3.418:     2661 |
| 0.840 - 0.980:    59 |  44.699 -  52.147:   125 |  3.418 -  3.789:     3935 |
| 0.980 - 1.120:    17 |  52.147 -  59.595:    51 |  3.789 -  4.159:     5101 |
| 1.120 - 1.260:     9 |  59.595 -  67.044:    13 |  4.159 -  4.530:     6580 |
| 1.260 - 1.400:     1 |  67.044 -  74.492:     3 |  4.530 -  4.900:     7734 |
|-----------------------------------------------------------------------------|
|-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 |       53.601 |
| planarity |      436 |   0.145    0.405  0.000 |     250.485 |              |
|  dihedral |      870 |  33.790  144.062  0.019 |      20.704 |              |
| nonbonded |     2439 |   4.090    4.900  1.196 |       1.713 |              |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 11.806)------------------------------------------|
|    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 = 11.806)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.01    19.99   9.86     None  None   None       |
|    all(noH): 2823   0      0.01    19.99   9.86     None  None   None       |
|    Sol.    : 438    0      0.06    19.99   10.10    None  None   None       |
|    Mac.    : 2385   0      0.01    19.98   9.82     None  None   None       |
|    Hyd.    : 0      0      None    None    None     None  None   None       |
|    - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -      |
|       Distribution of isotropic (or equivalent) ADP for non-H atoms:        |
|    Bin#      value range     #atoms | Bin#      value range     #atoms      |
|      0:     0.008 -   2.007:  301   |   5:    10.002 -  12.000:  285        |
|      1:     2.007 -   4.006:  276   |   6:    12.000 -  13.999:  292        |
|      2:     4.006 -   6.004:  309   |   7:    13.999 -  15.998:  289        |
|      3:     6.004 -   8.003:  285   |   8:    15.998 -  17.996:  266        |
|      4:     8.003 -  10.002:  251   |   9:    17.996 -  19.995:  269        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.98 - 15.03 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.4431   r_free= 0.4266   ksol= 0.00   Bsol= 0.00   scale= 0.792    |
|                                                                             |
| 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:   0.59 A                  |
| x-ray target function (ml) for work reflections: 6.234603                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.98 - 15.03 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.4263   r_free= 0.4080   ksol= 0.35   Bsol= 8.14   scale= 1.030    |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (7.71,9.51,8.11,0.00,0.00,0.00); trace/3= 8.44                              |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.59 A                  |
| x-ray target function (ml) for work reflections: 6.223357                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 7.254071              wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 77.084   (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 0.691224              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 76.787   (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.4263      final r-factor (work) = 0.3209          |
| start r-factor (free) = 0.4080      final r-factor (free) = 0.3433          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 76.2341 = 7.25 * 0.50 * 6.2401 + 1.00 * 53.6011                             |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 22.1610 = 7.25 * 0.50 * 6.0775 + 1.00 * 0.1177                              |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 26     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.3209      final r-factor (work) = 0.2603          |
| start r-factor (free) = 0.3433      final r-factor (free) = 0.3006          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 4.2156 = 0.69 * 1.00 * 6.0775 + 1.00 * 0.0147                               |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 4.0957 = 0.69 * 1.00 * 5.9072 + 1.00 * 0.0125                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 27     |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 11.806)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.00    69.01   10.93    None  None   None       |
|    all(noH): 2823   0      0.00    69.01   10.93    None  None   None       |
|    Sol.    : 438    0      0.00    65.13   27.33    None  None   None       |
|    Mac.    : 2385   0      0.00    69.01   7.92     None  None   None       |
|    Hyd.    : 0      0      None    None    None     None  None   None       |
|    - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -      |
|       Distribution of isotropic (or equivalent) ADP for non-H atoms:        |
|    Bin#      value range     #atoms | Bin#      value range     #atoms      |
|      0:     0.000 -   6.901: 1352   |   5:    34.506 -  41.407:   75        |
|      1:     6.901 -  13.803:  739   |   6:    41.407 -  48.309:   49        |
|      2:    13.803 -  20.704:  281   |   7:    48.309 -  55.210:   11        |
|      3:    20.704 -  27.605:  171   |   8:    55.210 -  62.111:    9        |
|      4:    27.605 -  34.506:  133   |   9:    62.111 -  69.012:    3        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.2603 r_free = 0.3006             target_work(ml) = 5.849         |
| occupancies: max = 1.00  min = 0.30   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.2598 r_free = 0.3008             target_work(ml) = 5.847         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        2 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.98 - 15.03 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.2598   r_free= 0.3008   ksol= 0.35   Bsol= 8.14   scale= 1.102    |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (7.71,9.51,8.11,0.00,0.00,0.00); trace/3= 8.44                              |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.30 A                  |
| x-ray target function (ml) for work reflections: 5.847490                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.98 - 15.03 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.2533   r_free= 0.2924   ksol= 0.33   Bsol= 29.88   scale= 1.006   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (4.17,5.00,5.04,0.00,0.00,0.00); trace/3= 4.74                              |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.33 A                  |
| x-ray target function (ml) for work reflections: 5.841917                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 3.613341              wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 94.232   (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 0.375582              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 118.875  (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.2533      final r-factor (work) = 0.1698          |
| start r-factor (free) = 0.2924      final r-factor (free) = 0.2146          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 10.8017 = 3.61 * 0.50 * 5.9139 + 1.00 * 0.1173                              |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 10.2782 = 3.61 * 0.50 * 5.6546 + 1.00 * 0.0621                              |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 28     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1698      final r-factor (work) = 0.1518          |
| start r-factor (free) = 0.2146      final r-factor (free) = 0.1978          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 2.1360 = 0.38 * 1.00 * 5.6546 + 1.00 * 0.0123                               |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 2.1041 = 0.38 * 1.00 * 5.4308 + 1.00 * 0.0644                               |
|-----------------------------------------------------------------------------|
| number of iterations = 13      |    number of function evaluations = 14     |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 11.806)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.00    70.88   11.14    None  None   None       |
|    all(noH): 2823   0      0.00    70.88   11.14    None  None   None       |
|    Sol.    : 438    0      0.00    66.43   31.32    None  None   None       |
|    Mac.    : 2385   0      0.00    70.88   7.44     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 -   7.088: 1547   |   5:    35.439 -  42.527:  131        |
|      1:     7.088 -  14.176:  624   |   6:    42.527 -  49.615:   57        |
|      2:    14.176 -  21.264:  186   |   7:    49.615 -  56.703:   17        |
|      3:    21.264 -  28.351:  123   |   8:    56.703 -  63.790:   10        |
|      4:    28.351 -  35.439:  126   |   9:    63.790 -  70.878:    2        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.1518 r_free = 0.1978             target_work(ml) = 5.394         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        2 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.1517 r_free = 0.1977             target_work(ml) = 5.393         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        3 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.98 - 15.03 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1517   r_free= 0.1977   ksol= 0.33   Bsol= 29.88   scale= 1.034   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (4.17,5.00,5.04,0.00,0.00,0.00); trace/3= 4.74                              |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.18 A                  |
| x-ray target function (ml) for work reflections: 5.393467                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.98 - 15.03 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1512   r_free= 0.1962   ksol= 0.32   Bsol= 37.25   scale= 1.002   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (3.18,3.37,4.24,0.00,0.00,0.00); trace/3= 3.60                              |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.18 A                  |
| x-ray target function (ml) for work reflections: 5.391634                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 2.375763              wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 109.936  (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 1.694655              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 90.641   (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1512      final r-factor (work) = 0.1252          |
| start r-factor (free) = 0.1962      final r-factor (free) = 0.1693          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 6.5231 = 2.38 * 0.50 * 5.4391 + 1.00 * 0.0621                               |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 6.3645 = 2.38 * 0.50 * 5.3078 + 1.00 * 0.0594                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 28     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1252      final r-factor (work) = 0.1193          |
| start r-factor (free) = 0.1693      final r-factor (free) = 0.1644          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 9.0092 = 1.69 * 1.00 * 5.3078 + 1.00 * 0.0143                               |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 8.8395 = 1.69 * 1.00 * 5.2079 + 1.00 * 0.0138                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 27     |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 11.806)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.00    83.55   11.94    None  None   None       |
|    all(noH): 2823   0      0.00    83.55   11.94    None  None   None       |
|    Sol.    : 438    0      0.55    76.46   35.60    None  None   None       |
|    Mac.    : 2385   0      0.00    83.55   7.59     None  None   None       |
|    Hyd.    : 0      0      None    None    None     None  None   None       |
|    - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -      |
|       Distribution of isotropic (or equivalent) ADP for non-H atoms:        |
|    Bin#      value range     #atoms | Bin#      value range     #atoms      |
|      0:     0.000 -   8.355: 1729   |   5:    41.774 -  50.128:   98        |
|      1:     8.355 -  16.710:  522   |   6:    50.128 -  58.483:   59        |
|      2:    16.710 -  25.064:  150   |   7:    58.483 -  66.838:   32        |
|      3:    25.064 -  33.419:  119   |   8:    66.838 -  75.193:   10        |
|      4:    33.419 -  41.774:   99   |   9:    75.193 -  83.547:    5        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.1193 r_free = 0.1644             target_work(ml) = 5.192         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        3 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.1192 r_free = 0.1643             target_work(ml) = 5.191         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        3 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.98 - 15.03 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1192   r_free= 0.1643   ksol= 0.32   Bsol= 37.25   scale= 1.011   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (3.18,3.37,4.24,0.00,0.00,0.00); trace/3= 3.60                              |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.15 A                  |
| x-ray target function (ml) for work reflections: 5.191246                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.98 - 15.03 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1194   r_free= 0.1644   ksol= 0.32   Bsol= 42.59   scale= 1.006   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (3.07,3.09,4.14,0.00,0.00,0.00); trace/3= 3.43                              |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.15 A                  |
| x-ray target function (ml) for work reflections: 5.191483                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 1.541646              wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 136.858  (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 0.151617              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 130.554  (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1194      final r-factor (work) = 0.1157          |
| start r-factor (free) = 0.1644      final r-factor (free) = 0.1611          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 4.0739 = 1.54 * 0.50 * 5.2081 + 1.00 * 0.0593                               |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 4.0462 = 1.54 * 0.50 * 5.1795 + 1.00 * 0.0537                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 28     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1157      final r-factor (work) = 0.1170          |
| start r-factor (free) = 0.1611      final r-factor (free) = 0.1585          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 0.7991 = 0.15 * 1.00 * 5.1795 + 1.00 * 0.0138                               |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 0.7958 = 0.15 * 1.00 * 5.1813 + 1.00 * 0.0102                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 35     |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 11.806)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.00    83.00   11.64    None  None   None       |
|    all(noH): 2823   0      0.00    83.00   11.64    None  None   None       |
|    Sol.    : 438    0      1.51    73.77   34.23    None  None   None       |
|    Mac.    : 2385   0      0.00    83.00   7.49     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 -   8.300: 1755   |   5:    41.501 -  49.801:   97        |
|      1:     8.300 -  16.601:  529   |   6:    49.801 -  58.102:   54        |
|      2:    16.601 -  24.901:  132   |   7:    58.102 -  66.402:   26        |
|      3:    24.901 -  33.201:  121   |   8:    66.402 -  74.702:   10        |
|      4:    33.201 -  41.501:   96   |   9:    74.702 -  83.002:    3        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.1170 r_free = 0.1585             target_work(ml) = 5.168         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        3 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.1169 r_free = 0.1583             target_work(ml) = 5.167         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        4 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.98 - 15.03 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1169   r_free= 0.1583   ksol= 0.32   Bsol= 42.59   scale= 1.005   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (3.07,3.09,4.14,0.00,0.00,0.00); trace/3= 3.43                              |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.14 A                  |
| x-ray target function (ml) for work reflections: 5.167373                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.98 - 15.03 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1169   r_free= 0.1582   ksol= 0.32   Bsol= 42.59   scale= 1.002   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (2.97,2.91,4.05,0.00,0.00,0.00); trace/3= 3.31                              |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.15 A                  |
| x-ray target function (ml) for work reflections: 5.167235                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 2.787969              wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 152.155  (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 5.804792              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 141.945  (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1169      final r-factor (work) = 0.1107          |
| start r-factor (free) = 0.1582      final r-factor (free) = 0.1543          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 7.2750 = 2.79 * 0.50 * 5.1803 + 1.00 * 0.0537                               |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 7.2335 = 2.79 * 0.50 * 5.1408 + 1.00 * 0.0672                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 28     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1107      final r-factor (work) = 0.1086          |
| start r-factor (free) = 0.1543      final r-factor (free) = 0.1561          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 29.8517 = 5.80 * 1.00 * 5.1408 + 1.00 * 0.0102                              |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 29.7202 = 5.80 * 1.00 * 5.1176 + 1.00 * 0.0138                              |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 27     |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 11.806)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.00    90.96   11.88    None  None   None       |
|    all(noH): 2823   0      0.00    90.96   11.88    None  None   None       |
|    Sol.    : 438    0      1.09    83.67   35.33    None  None   None       |
|    Mac.    : 2385   0      0.00    90.96   7.57     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 -   9.096: 1818   |   5:    45.481 -  54.577:   84        |
|      1:     9.096 -  18.192:  482   |   6:    54.577 -  63.673:   40        |
|      2:    18.192 -  27.289:  142   |   7:    63.673 -  72.769:   20        |
|      3:    27.289 -  36.385:  123   |   8:    72.769 -  81.865:    8        |
|      4:    36.385 -  45.481:  103   |   9:    81.865 -  90.962:    3        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.1086 r_free = 0.1561             target_work(ml) = 5.127         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        4 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.1085 r_free = 0.1561             target_work(ml) = 5.127         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        4 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.98 - 15.03 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1085   r_free= 0.1561   ksol= 0.32   Bsol= 42.59   scale= 1.003   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (2.97,2.91,4.05,0.00,0.00,0.00); trace/3= 3.31                              |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.14 A                  |
| x-ray target function (ml) for work reflections: 5.126506                   |
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
| Bin     Resolution   Compl.  No. Refl.    R-factors          Targets        |
|number     range              work test   work   test        work        test|
|  1: 15.0283 -  4.7293 0.99   1386  154 0.0960 0.1272      5.3618      5.5112|
|  2:  4.7293 -  3.7734 0.99   1324  146 0.0833 0.1100      5.4147      5.5982|
|  3:  3.7734 -  3.3022 0.99   1300  143 0.1042 0.1493       5.464      5.8387|
|  4:  3.3022 -  3.0029 0.99   1285  148 0.1175 0.1594      5.4347      5.5887|
|  5:  3.0029 -  2.7891 0.99   1292  141 0.1271 0.1716      5.3071      5.5646|
|  6:  2.7891 -  2.6256 0.99   1281  141 0.1140 0.1819      5.1825      5.4464|
|  7:  2.6256 -  2.4947 0.99   1283  138 0.1267 0.1521      5.1634      5.3261|
|  8:  2.4947 -  2.3866 0.98   1253  147 0.1134 0.1784       5.056      5.3661|
|  9:  2.3866 -  2.2950 0.98   1269  138 0.1146 0.1712      5.0369      5.2568|
| 10:  2.2950 -  2.2161 1.00   1266  142 0.1052 0.1801      4.9408      5.2858|
| 11:  2.2161 -  2.1470 0.97   1249  137 0.1108 0.1625        4.94      5.2029|
| 12:  2.1470 -  2.0858 0.98   1256  141 0.1087 0.1728      4.8613      5.2283|
| 13:  2.0858 -  2.0310 0.99   1283  140 0.1089 0.1719      4.7712      5.0606|
| 14:  2.0310 -  1.9816 0.72    903  103 0.0986 0.1603      4.6439       4.878|
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
|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: 15.0283 -  4.7293  1386   154  0.94   8.80   0.98     0.96       6872.92|
|  2:  4.7293 -  3.7734  1324   146  0.95   7.62   1.02     1.01       8699.69|
|  3:  3.7734 -  3.3022  1300   143  0.94  11.00   1.03     1.03      10066.83|
|  4:  3.3022 -  3.0029  1285   148  0.92  13.34   1.01     1.00      10060.15|
|  5:  3.0029 -  2.7891  1292   141  0.90  15.71   0.99     0.97       8120.03|
|  6:  2.7891 -  2.6256  1281   141  0.91  15.37   0.99     0.96       6899.02|
|  7:  2.6256 -  2.4947  1283   138  0.90  15.60   0.99     0.96       6144.40|
|  8:  2.4947 -  2.3866  1253   147  0.91  15.04   0.99     0.96       5186.29|
|  9:  2.3866 -  2.2950  1269   138  0.91  15.37   1.00     0.98       5107.81|
| 10:  2.2950 -  2.2161  1266   142  0.91  15.23   1.00     0.96       4325.08|
| 11:  2.2161 -  2.1470  1249   137  0.90  16.58   1.00     0.97       4474.75|
| 12:  2.1470 -  2.0858  1256   141  0.92  14.63   1.01     0.99       3823.92|
| 13:  2.0858 -  2.0310  1283   140  0.90  15.82   1.00     0.99       3277.68|
| 14:  2.0310 -  1.9816   903   103  0.92  14.18   0.98     0.95       2518.37|
|alpha:            min =        0.95 max =            1.03 mean =         0.98|
|beta:             min =     2518.37 max =        10066.83 mean =      6216.53|
|figures of merit: min =        0.00 max =            1.00 mean =         0.92|
|phase err.(work): min =        0.00 max =           89.90 mean =        13.81|
|phase err.(test): min =        0.00 max =           89.93 mean =        13.35|
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.98 - 15.03 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1085   r_free= 0.1561   ksol= 0.32   Bsol= 46.03   scale= 1.007   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-0.32,-0.42,0.74,-0.00,0.00,0.00); trace/3= 0.00                           |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.14 A                  |
| x-ray target function (ml) for work reflections: 5.126552                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.98 - 15.03 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1085   r_free= 0.1561   ksol= 0.32   Bsol= 46.03   scale= 1.007   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-0.32,-0.42,0.74,-0.00,0.00,0.00); trace/3= 0.00                           |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.14 A                  |
| x-ray target function (ml) for work reflections: 5.126552                   |
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
| Bin     Resolution   Compl.  No. Refl.    R-factors          Targets        |
|number     range              work test   work   test        work        test|
|  1: 15.0283 -  4.7293 0.99   1386  154 0.0960 0.1273      5.3625       5.512|
|  2:  4.7293 -  3.7734 0.99   1324  146 0.0833 0.1100       5.415      5.5982|
|  3:  3.7734 -  3.3022 0.99   1300  143 0.1042 0.1493       5.464       5.839|
|  4:  3.3022 -  3.0029 0.99   1285  148 0.1175 0.1594      5.4347      5.5888|
|  5:  3.0029 -  2.7891 0.99   1292  141 0.1271 0.1715       5.307      5.5643|
|  6:  2.7891 -  2.6256 0.99   1281  141 0.1140 0.1819      5.1824      5.4464|
|  7:  2.6256 -  2.4947 0.99   1283  138 0.1267 0.1521      5.1635      5.3265|
|  8:  2.4947 -  2.3866 0.98   1253  147 0.1134 0.1784      5.0561      5.3659|
|  9:  2.3866 -  2.2950 0.98   1269  138 0.1146 0.1712      5.0369      5.2568|
| 10:  2.2950 -  2.2161 1.00   1266  142 0.1051 0.1801      4.9408      5.2859|
| 11:  2.2161 -  2.1470 0.97   1249  137 0.1108 0.1624        4.94      5.2026|
| 12:  2.1470 -  2.0858 0.98   1256  141 0.1087 0.1728      4.8611      5.2283|
| 13:  2.0858 -  2.0310 0.99   1283  140 0.1089 0.1718      4.7711      5.0602|
| 14:  2.0310 -  1.9816 0.72    903  103 0.0986 0.1602      4.6438      4.8779|
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
|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: 15.0283 -  4.7293  1386   154  0.94   8.81   0.98     0.96       6884.14|
|  2:  4.7293 -  3.7734  1324   146  0.95   7.63   1.02     1.01       8707.69|
|  3:  3.7734 -  3.3022  1300   143  0.94  11.00   1.03     1.03      10069.47|
|  4:  3.3022 -  3.0029  1285   148  0.92  13.34   1.01     1.00      10059.37|
|  5:  3.0029 -  2.7891  1292   141  0.90  15.71   1.00     0.97       8118.16|
|  6:  2.7891 -  2.6256  1281   141  0.91  15.37   0.99     0.97       6897.76|
|  7:  2.6256 -  2.4947  1283   138  0.90  15.60   0.99     0.96       6145.32|
|  8:  2.4947 -  2.3866  1253   147  0.91  15.04   0.99     0.97       5186.28|
|  9:  2.3866 -  2.2950  1269   138  0.91  15.37   1.01     0.98       5108.74|
| 10:  2.2950 -  2.2161  1266   142  0.91  15.23   1.01     0.96       4324.22|
| 11:  2.2161 -  2.1470  1249   137  0.90  16.58   1.01     0.97       4474.20|
| 12:  2.1470 -  2.0858  1256   141  0.92  14.63   1.02     1.00       3822.49|
| 13:  2.0858 -  2.0310  1283   140  0.90  15.81   1.01     0.99       3276.69|
| 14:  2.0310 -  1.9816   903   103  0.92  14.18   0.99     0.96       2517.41|
|alpha:            min =        0.96 max =            1.03 mean =         0.98|
|beta:             min =     2517.41 max =        10069.47 mean =      6217.73|
|figures of merit: min =        0.00 max =            1.00 mean =         0.92|
|phase err.(work): min =        0.00 max =           89.90 mean =        13.81|
|phase err.(test): min =        0.00 max =           89.93 mean =        13.35|
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 11.806)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      3.43    94.40   15.31    None  None   None       |
|    all(noH): 2823   0      3.43    94.40   15.31    None  None   None       |
|    Sol.    : 438    0      4.52    87.10   38.76    None  None   None       |
|    Mac.    : 2385   0      3.43    94.40   11.01    None  None   None       |
|    Hyd.    : 0      0      None    None    None     None  None   None       |
|    - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -      |
|       Distribution of isotropic (or equivalent) ADP for non-H atoms:        |
|    Bin#      value range     #atoms | Bin#      value range     #atoms      |
|      0:     3.435 -  12.531: 1818   |   5:    48.915 -  58.011:   84        |
|      1:    12.531 -  21.627:  482   |   6:    58.011 -  67.108:   40        |
|      2:    21.627 -  30.723:  142   |   7:    67.108 -  76.204:   20        |
|      3:    30.723 -  39.819:  123   |   8:    76.204 -  85.300:    8        |
|      4:    39.819 -  48.915:  103   |   9:    85.300 -  94.396:    3        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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


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

Number of peaks found at mFobs-DFmodel map (map cutoff=3.00 sigma)= 304         
Filter by distance & map next to the model:
   mapped sites are within: 0.356 - 4.211
   number of sites selected in [dist_min= 0.70, dist_max= 6.00]: 301 from: 304
   mapped sites are within: 0.714 - 4.211

peak=   11.525 closest distance to " CB  VAL A 230 " =    1.445
peak=    7.619 closest distance to " CG2 VAL A 296 " =    1.143
peak=    5.994 closest distance to " CD2 LEU A   5 " =    1.201
peak=    5.938 closest distance to " NE2 GLN A  11 " =    1.161
peak=    5.899 closest distance to " CG  LEU A   5 " =    1.177
peak=    5.846 closest distance to " NH2 ARG A  56 " =    2.170
peak=    5.717 closest distance to " CG  PRO A  54 " =    1.253
peak=    5.449 closest distance to " CG  LEU A 228 " =    1.119
peak=    5.380 closest distance to " O   HOH Z 144 " =    1.833
peak=    5.303 closest distance to " O   HOH Z 232 " =    2.337
peak=    5.271 closest distance to " CB  GLN A 183 " =    1.253
peak=    5.010 closest distance to " CB  GLN A 223 " =    1.515
peak=    4.948 closest distance to " O   HOH Z 126 " =    1.966
peak=    4.894 closest distance to " O   HOH Z 427 " =    2.798
peak=    4.891 closest distance to " CB  VAL A 296 " =    1.064
peak=    4.825 closest distance to " CB  PRO A  54 " =    0.962
peak=    4.809 closest distance to " CB  SER A  63 " =    1.324
peak=    4.740 closest distance to " O   HOH Z 209 " =    2.263
peak=    4.548 closest distance to " CB  VAL A 230 " =    1.134
peak=    4.510 closest distance to " O   HOH Z 425 " =    1.443
peak=    4.504 closest distance to " CG  PRO A 213 " =    1.175
peak=    4.501 closest distance to " O   HOH Z 316 " =    3.006
peak=    4.478 closest distance to " CB  GLU A 152 " =    1.252
peak=    4.471 closest distance to " C   PRO A 198 " =    1.538
peak=    4.469 closest distance to " CD2 LEU A 228 " =    1.137
peak=    4.467 closest distance to " O   HOH Z 193 " =    1.727
peak=    4.441 closest distance to " CB  SER A   3 " =    1.346
peak=    4.435 closest distance to " O   HOH Z  61 " =    1.659
peak=    4.399 closest distance to " CB  ASN A 148 " =    1.356
peak=    4.393 closest distance to " O   HOH Z 369 " =    2.149
peak=    4.366 closest distance to " O   HOH Z 298 " =    1.757
peak=    4.358 closest distance to " O   HOH Z  78 " =    1.756
peak=    4.354 closest distance to " O   HOH Z 203 " =    1.676
peak=    4.328 closest distance to " O   HOH Z 272 " =    1.840
peak=    4.324 closest distance to " CB  ARG A 275 " =    0.906
peak=    4.278 closest distance to " O   HOH Z 346 " =    1.608
peak=    4.264 closest distance to " O   SER A  87 " =    2.363
peak=    4.234 closest distance to " O   HOH Z 126 " =    1.635
peak=    4.221 closest distance to " CB  ARG A  79 " =    1.439
peak=    4.219 closest distance to " O   HOH Z 236 " =    2.089
peak=    4.153 closest distance to " CA  TYR A  30 " =    0.981
peak=    4.145 closest distance to " CB  TYR A 169 " =    0.768
peak=    4.137 closest distance to " O   HOH Z 158 " =    3.065
peak=    4.136 closest distance to " O   HOH Z 403 " =    1.719
peak=    4.134 closest distance to " OD1 ASN A  69 " =    2.659
peak=    4.132 closest distance to " CB  VAL A 265 " =    1.320
peak=    4.113 closest distance to " CB  TRP A 266 " =    1.035
peak=    4.104 closest distance to " CG  PRO A 198 " =    1.128
peak=    4.068 closest distance to " CD  ARG A  66 " =    2.696
peak=    4.059 closest distance to " O   HOH Z 411 " =    3.731
peak=    4.053 closest distance to " ND2 ASN A 187 " =    1.425
peak=    4.028 closest distance to " O   HOH Z  55 " =    2.429
peak=    4.004 closest distance to " O   HOH Z 261 " =    2.229
peak=    4.002 closest distance to " O   HOH Z  43 " =    1.845
peak=    3.987 closest distance to " O   HOH Z 303 " =    2.121
peak=    3.980 closest distance to " CB  SER A 216 " =    0.836
peak=    3.977 closest distance to " CG2 VAL A 257 " =    0.849
peak=    3.970 closest distance to " O   HOH Z 368 " =    2.091
peak=    3.954 closest distance to " O   HOH Z  30 " =    1.481
peak=    3.934 closest distance to " OG BSER A 164 " =    2.175
peak=    3.930 closest distance to " O   HOH Z  78 " =    2.106
peak=    3.911 closest distance to " O   HOH Z  97 " =    2.015
peak=    3.907 closest distance to " O   HOH Z 189 " =    2.755
peak=    3.906 closest distance to " O   HOH Z   2 " =    1.470
peak=    3.896 closest distance to " CB  GLU A 128 " =    1.030
peak=    3.894 closest distance to " O   HOH Z 193 " =    1.734
peak=    3.890 closest distance to " O   HOH Z 313 " =    1.864
peak=    3.874 closest distance to " O   HOH Z 263 " =    1.619
peak=    3.863 closest distance to " CB  TRP A 179 " =    1.410
peak=    3.861 closest distance to " NZ  LYS A 117 " =    3.052
peak=    3.843 closest distance to " CB BVAL A  41 " =    1.235
peak=    3.834 closest distance to " O   HOH Z 128 " =    2.063
peak=    3.829 closest distance to " CA  ALA A  51 " =    1.013
peak=    3.825 closest distance to " CB  ASP A 140 " =    0.890
peak=    3.822 closest distance to " O   HOH Z  59 " =    1.789
peak=    3.814 closest distance to " O   HOH Z  88 " =    3.172
peak=    3.814 closest distance to " O   HOH Z 280 " =    2.932
peak=    3.812 closest distance to " CB  ARG A 139 " =    0.976
peak=    3.809 closest distance to " CG  GLN A  88 " =    1.068
peak=    3.802 closest distance to " O   HOH Z 133 " =    1.589
peak=    3.795 closest distance to " N   PHE A 130 " =    1.276
peak=    3.793 closest distance to " CB  ASN A 142 " =    1.061
peak=    3.790 closest distance to " O   HOH Z   9 " =    2.062
peak=    3.783 closest distance to " O   HOH Z  10 " =    1.746
peak=    3.778 closest distance to " O   HOH Z 234 " =    3.628
peak=    3.778 closest distance to " O   HOH Z 389 " =    1.925
peak=    3.764 closest distance to " CG1BVAL A  72 " =    1.578
peak=    3.756 closest distance to " CA  ASN A 215 " =    1.239
peak=    3.745 closest distance to " O   HOH Z  68 " =    2.152
peak=    3.743 closest distance to " CB  ASN A 187 " =    1.204
peak=    3.725 closest distance to " O   HOH Z   9 " =    1.159
peak=    3.716 closest distance to " O   HOH Z 197 " =    3.226
peak=    3.715 closest distance to " O   HOH Z 422 " =    2.567
peak=    3.703 closest distance to " CA  ALA A 158 " =    1.231
peak=    3.703 closest distance to " OD2 ASP A 286 " =    2.773
peak=    3.698 closest distance to " CG  PRO A 243 " =    1.119
peak=    3.691 closest distance to " O   HOH Z 180 " =    2.129
peak=    3.678 closest distance to " CB  GLU A 277 " =    3.539
peak=    3.674 closest distance to " O   HOH Z 290 " =    0.955
peak=    3.671 closest distance to " CD1 ILE A  33 " =    1.641
peak=    3.669 closest distance to " CB  LEU A 143 " =    1.182
peak=    3.669 closest distance to " O   HOH Z 227 " =    1.729
peak=    3.666 closest distance to " CG  LEU A 167 " =    1.171
peak=    3.662 closest distance to " CB  THR A  82 " =    1.312
peak=    3.661 closest distance to " O   HOH Z 286 " =    2.349
peak=    3.657 closest distance to " CG2 THR A 221 " =    1.225
peak=    3.653 closest distance to " O   HOH Z   1 " =    1.730
peak=    3.645 closest distance to " CB  THR A 157 " =    1.125
peak=    3.642 closest distance to " O   HOH Z 250 " =    1.348
peak=    3.635 closest distance to " O   HOH Z 371 " =    2.853
peak=    3.630 closest distance to " O   HOH Z 425 " =    2.064
peak=    3.623 closest distance to " CD BLYS A 290 " =    1.143
peak=    3.610 closest distance to " O   HOH Z 248 " =    1.642
peak=    3.604 closest distance to " O   HOH Z 214 " =    2.087
peak=    3.603 closest distance to " O   HOH Z 305 " =    3.418
peak=    3.603 closest distance to " CD2 TRP A 179 " =    1.376
peak=    3.593 closest distance to " CD  ARG A 159 " =    0.714
peak=    3.588 closest distance to " O   HOH Z 437 " =    1.881
peak=    3.586 closest distance to " O   HOH Z 423 " =    2.682
peak=    3.576 closest distance to " O   HOH Z 222 " =    2.460
peak=    3.568 closest distance to " O   HOH Z 175 " =    2.261
peak=    3.563 closest distance to " O   HOH Z 273 " =    2.778
peak=    3.558 closest distance to " CA  THR A 264 " =    0.745
peak=    3.558 closest distance to " CB  ASN A  39 " =    0.944
peak=    3.552 closest distance to " CB  VAL A 202 " =    1.605
peak=    3.551 closest distance to " CD2 LEU A 255 " =    1.620
peak=    3.549 closest distance to " CZ  PHE A 218 " =    1.101
peak=    3.547 closest distance to " O   HOH Z   3 " =    1.869
peak=    3.535 closest distance to " CA  LYS A 117 " =    1.202
peak=    3.535 closest distance to " CD1 LEU A 228 " =    1.902
peak=    3.533 closest distance to " O   HOH Z  61 " =    1.535
peak=    3.530 closest distance to " CA  SER A 146 " =    1.761
peak=    3.528 closest distance to " O   HOH Z 435 " =    2.027
peak=    3.524 closest distance to " CA  LYS A 290 " =    1.275
peak=    3.518 closest distance to " O   HOH Z   7 " =    1.347
peak=    3.517 closest distance to " O   HOH Z 124 " =    1.318
peak=    3.516 closest distance to " CE  LYS A  76 " =    0.936
peak=    3.512 closest distance to " O   HOH Z 132 " =    2.483
peak=    3.507 closest distance to " O   HOH Z 147 " =    1.709
peak=    3.504 closest distance to " O   HOH Z   1 " =    1.753
peak=    3.502 closest distance to " CB  ARG A 190 " =    1.593
peak=    3.501 closest distance to " CB  HIS A 108 " =    0.834
peak=    3.499 closest distance to " O   HOH Z  58 " =    1.534
peak=    3.498 closest distance to " O   HOH Z  40 " =    1.892
peak=    3.498 closest distance to " ND1 HIS A  86 " =    1.744
peak=    3.498 closest distance to " CB  ALA A   9 " =    1.591
peak=    3.496 closest distance to " O   HOH Z 419 " =    1.952
peak=    3.491 closest distance to " O   HOH Z 303 " =    1.827
peak=    3.489 closest distance to " CB  ASN A 110 " =    1.166
peak=    3.477 closest distance to " CA  TYR A  30 " =    1.048
peak=    3.470 closest distance to " CA  PHE A 283 " =    1.304
peak=    3.466 closest distance to " CB  LEU A 228 " =    1.292
peak=    3.462 closest distance to " O   HOH Z 368 " =    3.610
peak=    3.460 closest distance to " O   HOH Z  44 " =    1.608
peak=    3.449 closest distance to " O   HOH Z 271 " =    2.045
peak=    3.448 closest distance to " O   HOH Z 112 " =    1.670
peak=    3.443 closest distance to " CE1 TYR A 186 " =    1.340
peak=    3.441 closest distance to " O   HOH Z 227 " =    2.133
peak=    3.438 closest distance to " O   HOH Z 145 " =    3.487
peak=    3.432 closest distance to " O   HOH Z  63 " =    1.316
peak=    3.432 closest distance to " NH2 ARG A 156 " =    1.080
peak=    3.429 closest distance to " O   MET A 105 " =    1.831
peak=    3.428 closest distance to " O   HOH Z 193 " =    1.921
peak=    3.426 closest distance to " CG1 ILE A  33 " =    1.274
peak=    3.421 closest distance to " CB  MET A  40 " =    0.860
peak=    3.420 closest distance to " CG  MET A 185 " =    1.247
peak=    3.417 closest distance to " CA  ALA A  21 " =    1.139
peak=    3.416 closest distance to " O   HOH Z 426 " =    1.590
peak=    3.414 closest distance to " OE2 GLU A  53 " =    1.965
peak=    3.412 closest distance to " CB  GLN A  88 " =    1.281
peak=    3.408 closest distance to " CA  VAL A  41 " =    0.846
peak=    3.407 closest distance to " O   HOH Z 344 " =    2.939
peak=    3.406 closest distance to " CB  SER A 212 " =    1.170
peak=    3.399 closest distance to " O   HOH Z 130 " =    2.215
peak=    3.395 closest distance to " CB  ARG A  79 " =    0.867
peak=    3.394 closest distance to " O   HOH Z 380 " =    1.597
peak=    3.391 closest distance to " O   HOH Z 329 " =    3.837
peak=    3.391 closest distance to " CA  ALA A 291 " =    0.917
peak=    3.389 closest distance to " CB  THR A  31 " =    1.687
peak=    3.389 closest distance to " O   HOH Z 172 " =    3.383
peak=    3.389 closest distance to " CE  LYS A  48 " =    1.065
peak=    3.387 closest distance to " O   HOH Z 145 " =    1.868
peak=    3.380 closest distance to " CB  ALA A 291 " =    1.478
peak=    3.377 closest distance to " CB  LYS A 117 " =    1.194
peak=    3.377 closest distance to " O   HOH Z 405 " =    1.116
peak=    3.376 closest distance to " O   LYS A 290 " =    2.411
peak=    3.376 closest distance to " O   HOH Z 409 " =    3.046
peak=    3.368 closest distance to " CA  ARG A  36 " =    1.053
peak=    3.366 closest distance to " CB  SER A 273 " =    0.864
peak=    3.365 closest distance to " O   HOH Z 366 " =    2.829
peak=    3.362 closest distance to " O  BHOH Z 338 " =    2.431
peak=    3.359 closest distance to " CB  ASN A 224 " =    1.016
peak=    3.355 closest distance to " CG1 ILE A  49 " =    1.397
peak=    3.354 closest distance to " ND2 ASN A 110 " =    1.754
peak=    3.354 closest distance to " CG BARG A 102 " =    1.853
peak=    3.353 closest distance to " O   HOH Z 148 " =    3.351
peak=    3.347 closest distance to " O   ALA A 291 " =    1.574
peak=    3.347 closest distance to " ND1 HIS A  81 " =    1.665
peak=    3.342 closest distance to " CA  VAL A 126 " =    0.878
peak=    3.340 closest distance to " CA  LEU A 282 " =    1.141
peak=    3.338 closest distance to " N   ARG A 156 " =    1.271
peak=    3.337 closest distance to " NH1AARG A 145 " =    1.057
peak=    3.336 closest distance to " CG1 VAL A 153 " =    0.952
peak=    3.331 closest distance to " CA  GLY A 267 " =    0.811
peak=    3.319 closest distance to " O   GLN A 278 " =    1.303
peak=    3.309 closest distance to " O   HOH Z 423 " =    1.664
peak=    3.308 closest distance to " NH2BARG A 145 " =    1.929
peak=    3.308 closest distance to " OG  SER A  62 " =    2.967
peak=    3.307 closest distance to " O   HOH Z 353 " =    2.606
peak=    3.306 closest distance to " O   HOH Z 126 " =    1.506
peak=    3.305 closest distance to " CA  ASN A  74 " =    1.256
peak=    3.305 closest distance to " O   HOH Z 108 " =    2.349
peak=    3.303 closest distance to " O   HOH Z  93 " =    2.590
peak=    3.300 closest distance to " O   HOH Z 303 " =    3.068
peak=    3.299 closest distance to " N   ASN A 127 " =    1.322
peak=    3.297 closest distance to " O   HOH Z 128 " =    1.935
peak=    3.297 closest distance to " O   HOH Z 371 " =    1.733
peak=    3.290 closest distance to " CB  ALA A  34 " =    1.064
peak=    3.290 closest distance to " N   VAL A 126 " =    1.290
peak=    3.288 closest distance to " CD1 ILE A 106 " =    1.051
peak=    3.286 closest distance to " CB  ILE A  20 " =    1.470
peak=    3.285 closest distance to " OG  SER A  22 " =    2.862
peak=    3.284 closest distance to " O   HOH Z 299 " =    4.211
peak=    3.275 closest distance to " CA  TYR A 116 " =    1.407
peak=    3.273 closest distance to " O   ALA A 158 " =    1.437
peak=    3.268 closest distance to " O   HOH Z 345 " =    3.468
peak=    3.267 closest distance to " CA  ARG A 102 " =    1.115
peak=    3.261 closest distance to " O   HOH Z 128 " =    2.184
peak=    3.261 closest distance to " O   HOH Z 133 " =    2.384
peak=    3.259 closest distance to " O   HOH Z 189 " =    2.841
peak=    3.259 closest distance to " O   HOH Z 341 " =    2.271
peak=    3.257 closest distance to " N   SER A 135 " =    1.348
peak=    3.252 closest distance to " CB  VAL A 268 " =    0.841
peak=    3.252 closest distance to " O   HOH Z 135 " =    1.932
peak=    3.252 closest distance to " C   ALA A 299 " =    0.981
peak=    3.250 closest distance to " O   HOH Z 213 " =    2.261
peak=    3.247 closest distance to " CB  SER A  62 " =    1.225
peak=    3.246 closest distance to " OG  SER A  62 " =    2.905
peak=    3.244 closest distance to " CG  MET A 185 " =    1.052
peak=    3.242 closest distance to " O   HOH Z  85 " =    2.007
peak=    3.242 closest distance to " O   HOH Z 109 " =    2.504
peak=    3.241 closest distance to " CG2 VAL A 197 " =    1.096
peak=    3.239 closest distance to " CD  LYS A 166 " =    1.379
peak=    3.226 closest distance to " O   HOH Z 336 " =    1.974
peak=    3.226 closest distance to " CA  THR A 221 " =    0.950
peak=    3.222 closest distance to " O   HOH Z 423 " =    1.506
peak=    3.220 closest distance to " CA  ARG A 195 " =    1.194
peak=    3.213 closest distance to " CG2 ILE A 120 " =    1.203
peak=    3.213 closest distance to " CG  GLN A  89 " =    1.460
peak=    3.212 closest distance to " CB  TRP A 150 " =    1.340
peak=    3.209 closest distance to " CG  GLN A  77 " =    2.436
peak=    3.208 closest distance to " CB  TYR A  30 " =    1.600
peak=    3.202 closest distance to " NE2 HIS A 207 " =    1.727
peak=    3.202 closest distance to " NH2BARG A 190 " =    1.765
peak=    3.195 closest distance to " O   HOH Z 291 " =    1.562
peak=    3.193 closest distance to " CA  SER A  87 " =    1.012
peak=    3.190 closest distance to " OE1 GLU A   2 " =    2.088
peak=    3.188 closest distance to " O   HOH Z 124 " =    2.019
peak=    3.188 closest distance to " O   HOH Z 417 " =    2.050
peak=    3.183 closest distance to " CD1 LEU A 300 " =    1.230
peak=    3.180 closest distance to " CG1 ILE A 151 " =    1.020
peak=    3.179 closest distance to " NH2AARG A 275 " =    3.589
peak=    3.176 closest distance to " O   HOH Z 279 " =    2.208
peak=    3.176 closest distance to " O   HOH Z  21 " =    1.641
peak=    3.176 closest distance to " CB  LEU A 255 " =    0.758
peak=    3.172 closest distance to " O   HOH Z 407 " =    2.260
peak=    3.171 closest distance to " CG2 ILE A  20 " =    1.475
peak=    3.169 closest distance to " O   TRP A 274 " =    1.866
peak=    3.169 closest distance to " O   HOH Z   2 " =    1.487
peak=    3.168 closest distance to " OD1BASN A 224 " =    2.278
peak=    3.167 closest distance to " CA  ILE A 234 " =    0.966
peak=    3.165 closest distance to " O   HOH Z 417 " =    3.336
peak=    3.155 closest distance to " CG  ARG A 138 " =    1.154
peak=    3.155 closest distance to " O   HOH Z 359 " =    1.182
peak=    3.154 closest distance to " O   HOH Z 116 " =    1.656
peak=    3.154 closest distance to " O   HOH Z 411 " =    1.744
peak=    3.144 closest distance to " CD  ARG A 138 " =    0.888
peak=    3.140 closest distance to " O   HOH Z 261 " =    1.358
peak=    3.138 closest distance to " O   HOH Z 285 " =    2.862
peak=    3.135 closest distance to " O   HOH Z 359 " =    3.801
peak=    3.135 closest distance to " CB  ARG A 138 " =    0.901
peak=    3.130 closest distance to " CG  GLN A 278 " =    1.277
peak=    3.124 closest distance to " O   HOH Z 156 " =    3.288
peak=    3.120 closest distance to " CA  MET A 105 " =    0.979
peak=    3.117 closest distance to " CD  LYS A 119 " =    1.429
peak=    3.110 closest distance to " CB  VAL A 250 " =    1.073
peak=    3.110 closest distance to " O   HOH Z 325 " =    2.327
peak=    3.109 closest distance to " CB  ILE A 120 " =    1.416
peak=    3.107 closest distance to " O   HOH Z 173 " =    2.097
peak=    3.105 closest distance to " O   HOH Z  88 " =    2.623
peak=    3.102 closest distance to " OG  SER A 206 " =    1.229
peak=    3.096 closest distance to " NZ  LYS A  76 " =    1.299
peak=    3.094 closest distance to " O   HOH Z  89 " =    2.261
peak=    3.093 closest distance to " CA  GLN A 194 " =    1.302
peak=    3.092 closest distance to " O   ALA A   1 " =    1.703
peak=    3.088 closest distance to " CG  ARG A 159 " =    0.942
peak=    3.082 closest distance to " OG BSER A  99 " =    2.139
peak=    3.079 closest distance to " CB  GLN A 205 " =    1.204
peak=    3.073 closest distance to " O   HOH Z 245 " =    1.342
peak=    3.067 closest distance to " O   HOH Z 285 " =    1.959
peak=    3.054 closest distance to " CB  SER A 245 " =    3.181

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

Number of peaks found at mFobs-DFmodel map (map cutoff=3.00 sigma)= 213         
Filter by distance & map next to the model:
   mapped sites are within: 0.737 - 5.448
   number of sites selected in [dist_min= 0.70, dist_max= 6.00]: 212 from: 213
   mapped sites are within: 0.737 - 5.448

peak=   -4.646 closest distance to " CD  ARG A 156 " =    2.011
peak=   -4.481 closest distance to " CG2 VAL A 230 " =    0.862
peak=   -4.427 closest distance to " SG  CYS A 254 " =    3.305
peak=   -4.426 closest distance to " OG BSER A 134 " =    1.242
peak=   -4.328 closest distance to " O   HOH Z 266 " =    4.941
peak=   -4.325 closest distance to " CB  PRO A 243 " =    2.648
peak=   -4.247 closest distance to " CG  GLN A 223 " =    2.002
peak=   -4.196 closest distance to " O   HOH Z 435 " =    2.802
peak=   -4.099 closest distance to " C   HIS A 108 " =    1.174
peak=   -3.995 closest distance to " CG2 VAL A 296 " =    1.421
peak=   -3.970 closest distance to " O   HOH Z 231 " =    1.864
peak=   -3.939 closest distance to " CE2 TYR A  30 " =    2.806
peak=   -3.932 closest distance to " CB  PRO A 280 " =    2.068
peak=   -3.881 closest distance to " CE2 PHE A 218 " =    2.551
peak=   -3.853 closest distance to " CG1 VAL A 112 " =    2.754
peak=   -3.846 closest distance to " N   ALA A  43 " =    2.524
peak=   -3.817 closest distance to " OD1 ASN A 187 " =    1.629
peak=   -3.815 closest distance to " O   HOH Z  52 " =    1.436
peak=   -3.811 closest distance to " CB  ALA A 248 " =    2.016
peak=   -3.808 closest distance to " O   HOH Z 290 " =    1.194
peak=   -3.800 closest distance to " O   HOH Z 389 " =    1.944
peak=   -3.793 closest distance to " OG  SER A  87 " =    1.268
peak=   -3.791 closest distance to " O   PRO A 163 " =    2.014
peak=   -3.785 closest distance to " O   HOH Z 350 " =    1.663
peak=   -3.784 closest distance to " O   VAL A  67 " =    2.620
peak=   -3.774 closest distance to " CE  MET A 105 " =    2.307
peak=   -3.774 closest distance to " CB  PRO A 163 " =    2.496
peak=   -3.772 closest distance to " OXT GLY A 302 " =    2.978
peak=   -3.759 closest distance to " O   HOH Z  11 " =    1.944
peak=   -3.755 closest distance to " O   VAL A  67 " =    2.741
peak=   -3.753 closest distance to " NH2 ARG A  79 " =    1.950
peak=   -3.753 closest distance to " O   ARG A 145 " =    1.545
peak=   -3.735 closest distance to " CB  ALA A 291 " =    2.401
peak=   -3.718 closest distance to " CZ  PHE A  59 " =    1.482
peak=   -3.707 closest distance to " O   HOH Z 166 " =    2.196
peak=   -3.702 closest distance to " ND2 ASN A  45 " =    1.631
peak=   -3.699 closest distance to " CD1 LEU A 228 " =    2.183
peak=   -3.690 closest distance to " N   GLN A  58 " =    1.682
peak=   -3.677 closest distance to " CB  PHE A 192 " =    1.794
peak=   -3.673 closest distance to " CB  ALA A 248 " =    2.382
peak=   -3.669 closest distance to " O   HOH Z 351 " =    1.498
peak=   -3.645 closest distance to " O   HOH Z 198 " =    2.251
peak=   -3.642 closest distance to " CD  LYS A 289 " =    2.462
peak=   -3.624 closest distance to " NZ  LYS A 119 " =    3.379
peak=   -3.619 closest distance to " O   HOH Z 185 " =    2.134
peak=   -3.595 closest distance to " O   HOH Z 140 " =    1.520
peak=   -3.580 closest distance to " O   HOH Z 313 " =    1.697
peak=   -3.575 closest distance to " N   THR A 157 " =    1.445
peak=   -3.569 closest distance to " C   LEU A 222 " =    0.785
peak=   -3.568 closest distance to " CZ3 TRP A 179 " =    1.190
peak=   -3.567 closest distance to " CG  TRP A 266 " =    1.827
peak=   -3.564 closest distance to " O   HOH Z 394 " =    1.515
peak=   -3.559 closest distance to " O   GLY A  80 " =    2.496
peak=   -3.556 closest distance to " CG2 THR A 178 " =    2.234
peak=   -3.549 closest distance to " CG  ASP A 231 " =    0.737
peak=   -3.546 closest distance to " C   ALA A 158 " =    1.302
peak=   -3.543 closest distance to " O   HOH Z 211 " =    1.521
peak=   -3.537 closest distance to " O   HOH Z  90 " =    2.767
peak=   -3.530 closest distance to " O   HOH Z  60 " =    2.086
peak=   -3.529 closest distance to " O   PRO A 198 " =    1.238
peak=   -3.525 closest distance to " CA  GLY A 241 " =    2.229
peak=   -3.514 closest distance to " CD1 LEU A 101 " =    2.789
peak=   -3.509 closest distance to " O   VAL A 189 " =    2.598
peak=   -3.503 closest distance to " CB  ALA A 291 " =    2.146
peak=   -3.502 closest distance to " O   HOH Z 114 " =    2.941
peak=   -3.502 closest distance to " ND2 ASN A 187 " =    1.695
peak=   -3.500 closest distance to " CA  ASP A  27 " =    2.444
peak=   -3.498 closest distance to " O   HOH Z 407 " =    3.126
peak=   -3.497 closest distance to " O   HOH Z  43 " =    1.832
peak=   -3.496 closest distance to " O   HOH Z 102 " =    1.604
peak=   -3.485 closest distance to " O   HOH Z 166 " =    1.452
peak=   -3.482 closest distance to " C   ASN A 187 " =    1.798
peak=   -3.479 closest distance to " N   ALA A 248 " =    1.584
peak=   -3.477 closest distance to " CD2 LEU A 300 " =    2.769
peak=   -3.473 closest distance to " CD2 LEU A 237 " =    2.737
peak=   -3.471 closest distance to " OH  TYR A 214 " =    1.226
peak=   -3.469 closest distance to " CG1 VAL A 112 " =    2.602
peak=   -3.467 closest distance to " O   HOH Z 198 " =    1.604
peak=   -3.464 closest distance to " CA  GLY A 203 " =    2.308
peak=   -3.461 closest distance to " O   HOH Z 281 " =    2.751
peak=   -3.461 closest distance to " CD1 LEU A 101 " =    2.377
peak=   -3.457 closest distance to " CA  ASN A 110 " =    2.393
peak=   -3.456 closest distance to " CD  GLN A  58 " =    1.132
peak=   -3.454 closest distance to " O   SER A  22 " =    2.226
peak=   -3.452 closest distance to " O   HOH Z 166 " =    2.076
peak=   -3.449 closest distance to " N   THR A 235 " =    1.279
peak=   -3.444 closest distance to " CB  ALA A  43 " =    2.466
peak=   -3.443 closest distance to " O   HOH Z 191 " =    5.448
peak=   -3.442 closest distance to " CG  PHE A 283 " =    2.643
peak=   -3.441 closest distance to " O   MET A  40 " =    2.707
peak=   -3.436 closest distance to " CG1 VAL A 197 " =    2.272
peak=   -3.435 closest distance to " O   PRO A 198 " =    1.331
peak=   -3.426 closest distance to " CG1 VAL A 296 " =    1.374
peak=   -3.425 closest distance to " N   ALA A 226 " =    2.107
peak=   -3.424 closest distance to " CD2 LEU A   5 " =    1.116
peak=   -3.422 closest distance to " CD  ARG A 139 " =    1.595
peak=   -3.422 closest distance to " O   ALA A 161 " =    1.641
peak=   -3.421 closest distance to " NH2BARG A 275 " =    1.591
peak=   -3.419 closest distance to " CD1 PHE A  59 " =    2.006
peak=   -3.413 closest distance to " CB  TYR A  15 " =    2.145
peak=   -3.413 closest distance to " N   PHE A  59 " =    2.110
peak=   -3.408 closest distance to " O   HOH Z 359 " =    3.330
peak=   -3.400 closest distance to " CA  GLY A  98 " =    1.884
peak=   -3.389 closest distance to " CG  GLN A 278 " =    2.167
peak=   -3.388 closest distance to " O   HOH Z 139 " =    2.949
peak=   -3.381 closest distance to " CD2 TYR A 247 " =    2.496
peak=   -3.377 closest distance to " NH1 ARG A  36 " =    2.011
peak=   -3.376 closest distance to " O   HOH Z 103 " =    1.762
peak=   -3.366 closest distance to " OD1 ASN A 148 " =    1.492
peak=   -3.363 closest distance to " CG  PRO A 163 " =    2.506
peak=   -3.361 closest distance to " OG BSER A 134 " =    1.634
peak=   -3.356 closest distance to " OD2 ASP A 171 " =    2.249
peak=   -3.355 closest distance to " O   SER A 135 " =    1.469
peak=   -3.350 closest distance to " CB  ALA A 131 " =    2.029
peak=   -3.348 closest distance to " O   HOH Z 423 " =    1.140
peak=   -3.345 closest distance to " O   HOH Z 309 " =    2.527
peak=   -3.345 closest distance to " CG1 VAL A 250 " =    2.720
peak=   -3.344 closest distance to " NE2 GLN A  88 " =    2.035
peak=   -3.344 closest distance to " CE BMET A  47 " =    1.692
peak=   -3.333 closest distance to " CA  ASP A 298 " =    1.029
peak=   -3.332 closest distance to " O   HOH Z  13 " =    1.745
peak=   -3.328 closest distance to " OG  SER A  62 " =    1.640
peak=   -3.328 closest distance to " O   HOH Z 131 " =    4.113
peak=   -3.323 closest distance to " OD2 ASP A 191 " =    1.400
peak=   -3.323 closest distance to " C   MET A 188 " =    1.429
peak=   -3.318 closest distance to " CB  ASP A 132 " =    2.335
peak=   -3.317 closest distance to " O   HOH Z 165 " =    2.076
peak=   -3.317 closest distance to " N   SER A 276 " =    1.290
peak=   -3.306 closest distance to " NH2AARG A 275 " =    5.219
peak=   -3.305 closest distance to " CG1 VAL A 230 " =    1.894
peak=   -3.299 closest distance to " OG ASER A 134 " =    1.059
peak=   -3.299 closest distance to " CG2 ILE A  20 " =    2.801
peak=   -3.295 closest distance to " CG  LYS A 193 " =    2.461
peak=   -3.293 closest distance to " O   TYR A  30 " =    2.881
peak=   -3.293 closest distance to " C   ASN A 285 " =    2.420
peak=   -3.292 closest distance to " O   HOH Z 134 " =    3.504
peak=   -3.290 closest distance to " O   ALA A  51 " =    1.346
peak=   -3.281 closest distance to " O   HOH Z 292 " =    1.815
peak=   -3.280 closest distance to " OG  SER A  97 " =    2.161
peak=   -3.279 closest distance to " O   HOH Z 113 " =    2.492
peak=   -3.274 closest distance to " O   SER A 210 " =    1.960
peak=   -3.271 closest distance to " O   HOH Z   9 " =    1.520
peak=   -3.269 closest distance to " O   HOH Z 111 " =    4.496
peak=   -3.266 closest distance to " CE3 TRP A 150 " =    2.079
peak=   -3.265 closest distance to " O   HOH Z 111 " =    2.486
peak=   -3.265 closest distance to " C   LEU A 143 " =    1.072
peak=   -3.260 closest distance to " CZ  PHE A 192 " =    2.834
peak=   -3.244 closest distance to " O   HOH Z 275 " =    1.410
peak=   -3.243 closest distance to " CA  GLY A 133 " =    1.967
peak=   -3.238 closest distance to " OD1 ASP A 191 " =    1.502
peak=   -3.231 closest distance to " O   HOH Z 388 " =    2.175
peak=   -3.231 closest distance to " CA  ASN A 127 " =    1.133
peak=   -3.231 closest distance to " O   HOH Z 426 " =    1.659
peak=   -3.228 closest distance to " CG  MET A 105 " =    0.943
peak=   -3.227 closest distance to " CB  ASP A 132 " =    2.306
peak=   -3.226 closest distance to " CD1 ILE A 199 " =    2.503
peak=   -3.226 closest distance to " O   HOH Z 369 " =    2.240
peak=   -3.225 closest distance to " O   HOH Z 346 " =    1.775
peak=   -3.218 closest distance to " O   HOH Z 389 " =    1.427
peak=   -3.216 closest distance to " O   GLY A 203 " =    2.388
peak=   -3.213 closest distance to " OG1 THR A 178 " =    1.240
peak=   -3.211 closest distance to " CZ2 TRP A 274 " =    0.866
peak=   -3.211 closest distance to " OG  SER A  26 " =    1.213
peak=   -3.210 closest distance to " N   HIS A 115 " =    2.049
peak=   -3.209 closest distance to " CZ  TYR A 169 " =    1.519
peak=   -3.208 closest distance to " CB  VAL A 230 " =    1.032
peak=   -3.204 closest distance to " O   GLY A  75 " =    2.075
peak=   -3.197 closest distance to " O   HOH Z 410 " =    2.124
peak=   -3.197 closest distance to " O   HOH Z  97 " =    1.514
peak=   -3.196 closest distance to " O   HOH Z  38 " =    1.819
peak=   -3.190 closest distance to " CG  GLU A 152 " =    1.544
peak=   -3.190 closest distance to " CA  GLY A 241 " =    3.097
peak=   -3.188 closest distance to " N   ALA A 248 " =    2.556
peak=   -3.188 closest distance to " O   THR A  18 " =    1.562
peak=   -3.184 closest distance to " O   HOH Z 295 " =    1.548
peak=   -3.178 closest distance to " O   HOH Z  51 " =    1.222
peak=   -3.175 closest distance to " OXT GLY A 302 " =    3.463
peak=   -3.174 closest distance to " C   LYS A  76 " =    1.610
peak=   -3.174 closest distance to " O   HOH Z 111 " =    1.116
peak=   -3.171 closest distance to " N   ALA A 248 " =    1.870
peak=   -3.168 closest distance to " SG BCYS A 201 " =    1.987
peak=   -3.168 closest distance to " O   PHE A 218 " =    1.515
peak=   -3.162 closest distance to " O   HOH Z 149 " =    2.283
peak=   -3.162 closest distance to " CZ2 TRP A 179 " =    2.371
peak=   -3.151 closest distance to " NE2 GLN A 223 " =    1.785
peak=   -3.143 closest distance to " O   HOH Z 436 " =    1.475
peak=   -3.138 closest distance to " ND2 ASN A  69 " =    1.750
peak=   -3.138 closest distance to " O   HOH Z 423 " =    2.132
peak=   -3.137 closest distance to " OE2 GLU A 152 " =    1.194
peak=   -3.129 closest distance to " ND2 ASN A 249 " =    2.150
peak=   -3.129 closest distance to " O   HOH Z 359 " =    1.652
peak=   -3.126 closest distance to " CB  ASN A  39 " =    2.215
peak=   -3.123 closest distance to " O   TRP A  70 " =    1.457
peak=   -3.123 closest distance to " O   HOH Z 148 " =    1.815
peak=   -3.121 closest distance to " O   HOH Z 189 " =    1.938
peak=   -3.109 closest distance to " O   HOH Z 371 " =    2.339
peak=   -3.107 closest distance to " O   LYS A 289 " =    3.160
peak=   -3.107 closest distance to " O   HOH Z   2 " =    1.874
peak=   -3.106 closest distance to " CG  LEU A 101 " =    2.345
peak=   -3.103 closest distance to " ND2 ASN A  60 " =    1.697
peak=   -3.102 closest distance to " CG  ASP A  50 " =    2.320
peak=   -3.095 closest distance to " O   GLN A 240 " =    2.417
peak=   -3.070 closest distance to " CA  GLY A 133 " =    2.253
peak=   -3.068 closest distance to " CG2 THR A 157 " =    2.200
peak=   -3.056 closest distance to " O   HOH Z 234 " =    4.040
peak=   -3.055 closest distance to " CB  LEU A  83 " =    2.386
peak=   -3.054 closest distance to " O   HOH Z 383 " =    1.060
peak=   -3.035 closest distance to " CB  ALA A   9 " =    2.549
peak=   -3.033 closest distance to " O   GLY A  80 " =    2.588
peak=   -3.015 closest distance to " CD2 LEU A 300 " =    2.659
peak=   -3.010 closest distance to " CG2 VAL A 202 " =    2.615
peak=   -2.977 closest distance to " O   HOH Z 417 " =    2.694

================= 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    :  0.4352 0.4188   6.228906e+00   6.205516e+00
   1_bss:  0.4263 0.4080   6.223357e+00   6.192295e+00
   1_xyz:  0.3209 0.3433   6.023295e+00   6.064869e+00
   1_adp:  0.2603 0.3006   5.848740e+00   5.956161e+00
   1_occ:  0.2598 0.3008   5.847490e+00   5.957115e+00
   2_bss:  0.2533 0.2924   5.841917e+00   5.948607e+00
   2_xyz:  0.1698 0.2146   5.488240e+00   5.668857e+00
   2_adp:  0.1518 0.1978   5.393812e+00   5.596304e+00
   2_occ:  0.1517 0.1977   5.393467e+00   5.596047e+00
   3_bss:  0.1512 0.1962   5.391634e+00   5.593477e+00
   3_xyz:  0.1252 0.1693   5.230046e+00   5.457589e+00
   3_adp:  0.1193 0.1644   5.191798e+00   5.426241e+00
   3_occ:  0.1192 0.1643   5.191246e+00   5.425438e+00
   4_bss:  0.1194 0.1644   5.191483e+00   5.424273e+00
   4_xyz:  0.1157 0.1611   5.172855e+00   5.412858e+00
   4_adp:  0.1170 0.1585   5.168203e+00   5.393096e+00
   4_occ:  0.1169 0.1583   5.167373e+00   5.391908e+00
   5_bss:  0.1169 0.1582   5.167235e+00   5.391805e+00
   5_xyz:  0.1107 0.1543   5.127763e+00   5.369337e+00
   5_adp:  0.1086 0.1561   5.126755e+00   5.381304e+00
   5_occ:  0.1085 0.1561   5.126506e+00   5.381018e+00
   5_bss:  0.1085 0.1561   5.126552e+00   5.381058e+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:  0.349   8.139   7.712   9.507   8.106   0.000   0.000   0.000
   1_xyz:  0.349   8.139   7.712   9.507   8.106   0.000   0.000   0.000
   1_adp:  0.349   8.139   7.712   9.507   8.106   0.000   0.000   0.000
   1_occ:  0.349   8.139   7.712   9.507   8.106   0.000   0.000   0.000
   2_bss:  0.333  29.875   4.166   5.004   5.044   0.000   0.000   0.000
   2_xyz:  0.333  29.875   4.166   5.004   5.044   0.000   0.000   0.000
   2_adp:  0.333  29.875   4.166   5.004   5.044   0.000   0.000   0.000
   2_occ:  0.333  29.875   4.166   5.004   5.044   0.000   0.000   0.000
   3_bss:  0.318  37.255   3.180   3.370   4.244   0.000   0.000   0.000
   3_xyz:  0.318  37.255   3.180   3.370   4.244   0.000   0.000   0.000
   3_adp:  0.318  37.255   3.180   3.370   4.244   0.000   0.000   0.000
   3_occ:  0.318  37.255   3.180   3.370   4.244   0.000   0.000   0.000
   4_bss:  0.323  42.592   3.073   3.089   4.136   0.000   0.000   0.000
   4_xyz:  0.323  42.592   3.073   3.089   4.136   0.000   0.000   0.000
   4_adp:  0.323  42.592   3.073   3.089   4.136   0.000   0.000   0.000
   4_occ:  0.323  42.592   3.073   3.089   4.136   0.000   0.000   0.000
   5_bss:  0.323  42.592   2.967   2.906   4.055   0.000   0.000   0.000
   5_xyz:  0.323  42.592   2.967   2.906   4.055   0.000   0.000   0.000
   5_adp:  0.323  42.592   2.967   2.906   4.055   0.000   0.000   0.000
   5_occ:  0.323  42.592   2.967   2.906   4.055   0.000   0.000   0.000
   5_bss:  0.323  46.026  -0.322  -0.417   0.739  -0.000   0.000   0.000
------------------------------------------------------------------------
 stage     <pher>    fom   alpha         beta
   0    :  47.575 0.5520  0.6222    52031.857
   1_bss:  47.655 0.5485  0.7908    49413.981
   1_xyz:  37.008 0.6772  0.9529    32405.237
   1_adp:  29.746 0.7616  1.0581    23300.243
   1_occ:  29.785 0.7611  1.0562    23284.951
   2_bss:  29.288 0.7664  0.9303    22600.212
   2_xyz:  20.473 0.8569  1.0014    11348.852
   2_adp:  18.497 0.8762  1.0114     9754.797
   2_occ:  18.489 0.8762  1.0113     9742.017
   3_bss:  18.389 0.8770  0.9708     9652.035
   3_xyz:  15.434 0.9028  0.9856     7234.264
   3_adp:  14.763 0.9087  0.9864     6837.736
   3_occ:  14.747 0.9088  0.9864     6824.618
   4_bss:  14.725 0.9090  0.9805     6820.827
   4_xyz:  14.402 0.9120  0.9802     6607.273
   4_adp:  13.914 0.9161  0.9836     6369.532
   4_occ:  13.890 0.9162  0.9836     6352.236
   5_bss:  13.886 0.9163  0.9793     6349.945
   5_xyz:  13.517 0.9189  0.9813     6086.380
   5_adp:  13.774 0.9170  0.9769     6219.577
   5_occ:  13.768 0.9171  0.9768     6216.342
   5_bss:  13.769 0.9171  0.9813     6217.540
------------------------------------------------------------------------
 stage       angl   bond   chir   dihe   plan   repu  geom_target
   0    :  24.226  0.414  2.119 33.790  0.145  4.090   5.3601e+01
   1_bss:  24.226  0.414  2.119 33.790  0.145  4.090   5.3601e+01
   1_xyz:   1.516  0.011  0.100 17.875  0.006  4.120   1.1770e-01
   1_adp:   1.516  0.011  0.100 17.875  0.006  4.120   1.1770e-01
   1_occ:   1.516  0.011  0.100 17.875  0.006  4.120   1.1770e-01
   2_bss:   1.516  0.011  0.100 17.875  0.006  4.120   1.1770e-01
   2_xyz:   0.988  0.007  0.074 15.938  0.004  4.119   6.2113e-02
   2_adp:   0.988  0.007  0.074 15.938  0.004  4.119   6.2113e-02
   2_occ:   0.988  0.007  0.074 15.938  0.004  4.119   6.2113e-02
   3_bss:   0.988  0.007  0.074 15.938  0.004  4.119   6.2113e-02
   3_xyz:   0.978  0.006  0.077 15.864  0.003  4.122   5.9419e-02
   3_adp:   0.978  0.006  0.077 15.864  0.003  4.122   5.9419e-02
   3_occ:   0.978  0.006  0.077 15.864  0.003  4.122   5.9419e-02
   4_bss:   0.978  0.006  0.077 15.864  0.003  4.122   5.9419e-02
   4_xyz:   0.908  0.005  0.073 15.677  0.003  4.117   5.3662e-02
   4_adp:   0.908  0.005  0.073 15.677  0.003  4.117   5.3662e-02
   4_occ:   0.908  0.005  0.073 15.677  0.003  4.117   5.3662e-02
   5_bss:   0.908  0.005  0.073 15.677  0.003  4.117   5.3662e-02
   5_xyz:   1.052  0.008  0.086 15.651  0.004  4.111   6.7234e-02
   5_adp:   1.052  0.008  0.086 15.651  0.004  4.111   6.7234e-02
   5_occ:   1.052  0.008  0.086 15.651  0.004  4.111   6.7234e-02
   5_bss:   1.052  0.008  0.086 15.651  0.004  4.111   6.7234e-02
------------------------------------------------------------------------
                      Maximal deviations:
 stage       angl   bond   chir   dihe   plan   repu       |grad|
   0    :  74.492  1.400  6.404144.062  0.405  1.196   6.9496e+00
   1_bss:  74.492  1.400  6.404144.062  0.405  1.196   6.9496e+00
   1_xyz:  12.711  0.144  0.418 89.150  0.034  2.250   8.6919e-02
   1_adp:  12.711  0.144  0.418 89.150  0.034  2.250   8.6919e-02
   1_occ:  12.711  0.144  0.418 89.150  0.034  2.250   8.6919e-02
   2_bss:  12.711  0.144  0.418 89.150  0.034  2.250   8.6919e-02
   2_xyz:   6.414  0.067  0.332 81.622  0.045  2.304   4.6935e-02
   2_adp:   6.414  0.067  0.332 81.622  0.045  2.304   4.6935e-02
   2_occ:   6.414  0.067  0.332 81.622  0.045  2.304   4.6935e-02
   3_bss:   6.414  0.067  0.332 81.622  0.045  2.304   4.6935e-02
   3_xyz:   7.840  0.053  0.460 83.604  0.031  2.305   3.7238e-02
   3_adp:   7.840  0.053  0.460 83.604  0.031  2.305   3.7238e-02
   3_occ:   7.840  0.053  0.460 83.604  0.031  2.305   3.7238e-02
   4_bss:   7.840  0.053  0.460 83.604  0.031  2.305   3.7238e-02
   4_xyz:   7.234  0.044  0.421 83.401  0.034  2.395   3.0587e-02
   4_adp:   7.234  0.044  0.421 83.401  0.034  2.395   3.0587e-02
   4_occ:   7.234  0.044  0.421 83.401  0.034  2.395   3.0587e-02
   5_bss:   7.234  0.044  0.421 83.401  0.034  2.395   3.0587e-02
   5_xyz:   6.907  0.045  0.585 84.395  0.038  2.276   5.3099e-02
   5_adp:   6.907  0.045  0.585 84.395  0.038  2.276   5.3099e-02
   5_occ:   6.907  0.045  0.585 84.395  0.038  2.276   5.3099e-02
   5_bss:   6.907  0.045  0.585 84.395  0.038  2.276   5.3099e-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:  69.01   0.00  10.93  69.01   0.00   7.92  65.13   0.00  27.33
   1_occ:  69.01   0.00  10.93  69.01   0.00   7.92  65.13   0.00  27.33
   2_bss:  69.01   0.00  10.93  69.01   0.00   7.92  65.13   0.00  27.33
   2_xyz:  69.01   0.00  10.93  69.01   0.00   7.92  65.13   0.00  27.33
   2_adp:  70.88   0.00  11.14  70.88   0.00   7.44  66.43   0.00  31.32
   2_occ:  70.88   0.00  11.14  70.88   0.00   7.44  66.43   0.00  31.32
   3_bss:  70.88   0.00  11.14  70.88   0.00   7.44  66.43   0.00  31.32
   3_xyz:  70.88   0.00  11.14  70.88   0.00   7.44  66.43   0.00  31.32
   3_adp:  83.55   0.00  11.94  83.55   0.00   7.59  76.46   0.55  35.60
   3_occ:  83.55   0.00  11.94  83.55   0.00   7.59  76.46   0.55  35.60
   4_bss:  83.55   0.00  11.94  83.55   0.00   7.59  76.46   0.55  35.60
   4_xyz:  83.55   0.00  11.94  83.55   0.00   7.59  76.46   0.55  35.60
   4_adp:  83.00   0.00  11.64  83.00   0.00   7.49  73.77   1.51  34.23
   4_occ:  83.00   0.00  11.64  83.00   0.00   7.49  73.77   1.51  34.23
   5_bss:  83.00   0.00  11.64  83.00   0.00   7.49  73.77   1.51  34.23
   5_xyz:  83.00   0.00  11.64  83.00   0.00   7.49  73.77   1.51  34.23
   5_adp:  90.96   0.00  11.88  90.96   0.00   7.57  83.67   1.09  35.33
   5_occ:  90.96   0.00  11.88  90.96   0.00   7.57  83.67   1.09  35.33
   5_bss:  94.40   3.43  15.31  94.40   3.43  11.01  87.10   4.52  38.76
------------------------------------------------------------------------
 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:    1.172    0.017    0.402
   1_adp:    1.172    0.017    0.402
   1_occ:    1.172    0.017    0.402
   2_bss:    1.172    0.017    0.402
   2_xyz:    1.318    0.040    0.518
   2_adp:    1.318    0.040    0.518
   2_occ:    1.318    0.040    0.518
   3_bss:    1.318    0.040    0.518
   3_xyz:    1.530    0.050    0.548
   3_adp:    1.530    0.050    0.548
   3_occ:    1.530    0.050    0.548
   4_bss:    1.530    0.050    0.548
   4_xyz:    1.672    0.035    0.563
   4_adp:    1.672    0.035    0.563
   4_occ:    1.672    0.035    0.563
   5_bss:    1.672    0.035    0.563
   5_xyz:    1.700    0.063    0.571
   5_adp:    1.700    0.063    0.571
   5_occ:    1.700    0.063    0.571
   5_bss:    1.700    0.063    0.571
------------------------------------------------------------------------

CPU time actual refinement: 325.19


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

Writing refined structure to PDB file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/trial/run_763/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_763/model_refine_001_2mFobs-DFmodel.map
Writing mFobs-DFmodel XPLOR map to file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/trial/run_763/model_refine_001_mFobs-DFmodel.map
Writing map coefficients to MTZ file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/trial/run_763/model_refine_001_map_coeffs.mtz

Writing default parameters for subsequent refinement:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/trial/run_763/model_refine_002.def


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

Pure refinement (no I/O, processing, etc)= 325.03 
  Macro-tasks:
    bulk solvent and scale       = 42.53  
    individual site refinement   = 127.72 
    weights calculation          = 32.03  
    collect and process          = 6.52   
    model show statistics        = 0.13   
    TOTAL for macro-tasks        = 208.93 
  Micro-tasks:
    mask                            = 1.72   
    f_calc                          = 98.49  
    alpha_beta                      = 8.19   
    target                          = 1.19   
    gradients_wrt_atomic_parameters = 108.25 
    fmodel                         = 7.03   
    r_factors                      = 0.21   
    phase_errors                   = 10.82  
    foms                           = 0.28   
    TOTAL for micro-tasks          = 236.18 
NUMBER OF MASK CALCS=  4
Time per interpreted Python bytecode instruction: 4.598 micro seconds
Total CPU time: 5.64 minutes
from_scatterers_fft:    648 calls, 98.22 s
gradients_fft:          592 calls, 95.21 s

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

# Date 2008-01-16 Time 02:21:52 PST -0800 (1200478912.55 s)
Start R-work = 0.4352, R-free = 0.4188 (no bulk solvent and anisotropic scale)
Final R-work = 0.1260, R-free = 0.1726 (no bulk solvent and anisotropic scale)

Start R-work = 0.4263, R-free = 0.4080
Final R-work = 0.1085, R-free = 0.1561