# Date 2008-01-16 Time 01:52:10 PST -0800 (1200477130.75 s)
#phil __OFF__

Command line arguments: "../601.param" "adp.set_b_iso=10" "sites.shake=0.5" "main.number_of_macro_cycles=5" "--overwrite"

HOST = sunbird.lbl.gov
HOSTTYPE = x86_64-linux
USER = phzwart
PID = 4162
JOB_ID = 5158
SGE_ARCH = lx24-amd64
SGE_TASK_FIRST = 1
SGE_TASK_LAST = 1330
SGE_TASK_ID = 601

-------------------------------------------------------------------------------
  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: (69.8988, 48.1033, 87.2539, 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: 3.31, per 1000 atoms: 1.17


================================== 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: (69.8988, 48.1033, 87.2539, 90, 90, 90)
Space group: P 21 21 21 (No. 19)
Systematic absences: 0
Centric reflections: 2427
Resolution range: 15.0501 1.99071
Completeness in resolution range: 0.945506
Completeness with d_max=infinity: 0.942595

Number of F-obs in resolution range:                   19589
Number of F-obs <= 0:                                  0
Refinement resolution range: d_max =  15.0501
                             d_min =   1.9907

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: (69.8988, 48.1033, 87.2539, 90, 90, 90)
Space group: P 21 21 21 (No. 19)
Systematic absences: 0
Centric reflections: 2427
Resolution range: 15.0501 1.99071
Completeness in resolution range: 0.945506
Completeness with d_max=infinity: 0.942595

Test (R-free flags) flag value: 1

Number of work/free reflections by resolution:
                                         work  free  %free
  bin  1: 15.0505 -  4.2595 [2186/2214]  1964   222  10.2%
  bin  2:  4.2595 -  3.3936 [2082/2105]  1875   207   9.9%
  bin  3:  3.3936 -  2.9684 [2056/2081]  1850   206  10.0%
  bin  4:  2.9684 -  2.6987 [2054/2070]  1849   205  10.0%
  bin  5:  2.6987 -  2.5062 [2022/2059]  1816   206  10.2%
  bin  6:  2.5062 -  2.3590 [2026/2060]  1829   197   9.7%
  bin  7:  2.3590 -  2.2413 [2003/2040]  1803   200  10.0%
  bin  8:  2.2413 -  2.1440 [2008/2050]  1809   199   9.9%
  bin  9:  2.1440 -  2.0617 [1986/2025]  1788   198  10.0%
  bin 10:  2.0617 -  1.9907 [1166/2014]  1047   119  10.2%
                                overall 17630  1959  10.0%
Writing MTZ file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/trial/run_601/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: 0.15 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: 23
        2.42 -     3.04: 2159
        3.04 -     3.66: 4625
        3.66 -     4.28: 8865
        4.28 -     4.90: 12228
  Nonbonded interactions sorted by model distance:
             atom i - atom j             model   vdw sym.op. j
  " CE BMET A  47 " - " O  BHOH Z  74 "  1.806 3.460
  " O   HOH Z 277 " - " O   HOH Z 343 "  1.962 3.040 -x+1/2,-y+1,z+1/2
  " O   HOH Z  42 " - " O   HOH Z 183 "  2.043 3.040 -x+1,y+1/2,-z+1/2
  " O   HOH Z  70 " - " O   HOH Z 296 "  2.086 3.040 -x+1/2,-y+1,z+1/2
  " O   HOH Z 207 " - " O   HOH Z 341 "  2.092 3.040 -x+1/2,-y+1,z+1/2
  ... (remaining 27895 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_601/model_refine_001.eff

Writing geometry restraints to file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/trial/run_601/model_refine_001.geo

CPU time processing inputs: 9.25


============================ 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 = 69.89875 48.10325 87.2539 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: 1.99 - 15.05 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.5014   r_free= 0.4857   ksol= 0.00   Bsol= 0.00   scale= 0.768    |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (0.00,0.00,0.00,0.00,0.00,0.00); trace/3= 0.00                              |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.81 A                  |
| x-ray target function (ml) for work reflections: 6.301301                   |
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
| Bin     Resolution   Compl.  No. Refl.    R-factors          Targets        |
|number     range              work test   work   test        work        test|
|  1: 15.0505 -  4.7507 0.99   1411  158 0.4090 0.4275      6.6265      6.6544|
|  2:  4.7507 -  3.7906 0.99   1361  151 0.4412 0.4590      6.8575      6.9113|
|  3:  3.7906 -  3.3173 0.99   1341  148 0.4690 0.4230      6.7192      6.6704|
|  4:  3.3173 -  3.0167 0.99   1315  142 0.4994 0.4646      6.5551       6.489|
|  5:  3.0167 -  2.8019 0.98   1324  147 0.5405 0.5182      6.3906       6.418|
|  6:  2.8019 -  2.6377 0.99   1298  148 0.5327 0.4984      6.2958      6.1643|
|  7:  2.6377 -  2.5062 0.99   1304  152 0.5139 0.4768      6.2502      6.1812|
|  8:  2.5062 -  2.3976 0.99   1317  136 0.5297 0.4766       6.186      6.1565|
|  9:  2.3976 -  2.3056 0.99   1296  148 0.5387 0.5829      6.1116        6.21|
| 10:  2.3056 -  2.2263 0.98   1284  139 0.5695 0.5251      6.1245      6.1201|
| 11:  2.2263 -  2.1569 0.98   1282  148 0.5429 0.5568      6.0338      6.0378|
| 12:  2.1569 -  2.0954 1.00   1293  146 0.5354 0.4943        5.96      5.9834|
| 13:  2.0954 -  2.0404 0.96   1263  132 0.5298 0.5232      5.8876      5.8392|
| 14:  2.0404 -  1.9907 0.42    541   64 0.5669 0.4949      5.8893      5.7358|
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
|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: 15.0505 -  4.7507  1411   158  0.64  39.48   0.78     0.66      89725.79|
|  2:  4.7507 -  3.7906  1361   151  0.65  39.78   0.85     0.69     125488.26|
|  3:  3.7906 -  3.3173  1341   148  0.55  47.77   0.80     0.65     129459.55|
|  4:  3.3173 -  3.0167  1315   142  0.47  54.13   0.77     0.56     107241.61|
|  5:  3.0167 -  2.8019  1324   147  0.40  59.88   0.71     0.48      84989.79|
|  6:  2.8019 -  2.6377  1298   148  0.40  60.01   0.69     0.45      70508.81|
|  7:  2.6377 -  2.5062  1304   152  0.37  62.38   0.74     0.42      65343.25|
|  8:  2.5062 -  2.3976  1317   136  0.34  64.87   0.72     0.39      61319.76|
|  9:  2.3976 -  2.3056  1296   148  0.27  69.68   0.69     0.33      60438.32|
| 10:  2.3056 -  2.2263  1284   139  0.27  70.23   0.71     0.32      55127.88|
| 11:  2.2263 -  2.1569  1282   148  0.27  70.02   0.72     0.33      51072.26|
| 12:  2.1569 -  2.0954  1293   146  0.28  69.18   0.75     0.36      46176.34|
| 13:  2.0954 -  2.0404  1263   132  0.28  68.92   0.71     0.35      38977.63|
| 14:  2.0404 -  1.9907   541    64  0.30  67.75   0.71     0.32      29164.63|
|alpha:            min =        0.32 max =            0.69 mean =         0.46|
|beta:             min =    29164.63 max =       129459.55 mean =     74947.98|
|figures of merit: min =        0.00 max =            1.00 mean =         0.40|
|phase err.(work): min =        0.00 max =           90.00 mean =        59.70|
|phase err.(test): min =        0.00 max =           89.83 mean =        59.94|
|-----------------------------------------------------------------------------|

============================== 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 = 16.855302             wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 81.744   (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 1.619748              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 79.142   (deg)                 |
|-----------------------------------------------------------------------------|


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

|-Geometry statistics: start--------------------------------------------------|
|            Histogram of deviations from ideal values for                    |
| Bonds                | Angles                   |  Nonbonded contacts       |
| 0.000 - 0.140:   597 |   0.009 -   7.457:   713 |  1.196 -  1.566:        4 |
| 0.140 - 0.280:   585 |   7.457 -  14.906:   711 |  1.566 -  1.937:       24 |
| 0.280 - 0.420:   441 |  14.906 -  22.354:   630 |  1.937 -  2.307:      166 |
| 0.420 - 0.560:   366 |  22.354 -  29.802:   474 |  2.307 -  2.677:      678 |
| 0.560 - 0.700:   237 |  29.802 -  37.251:   338 |  2.677 -  3.048:     1488 |
| 0.700 - 0.840:   127 |  37.251 -  44.699:   241 |  3.048 -  3.418:     2580 |
| 0.840 - 0.980:    59 |  44.699 -  52.147:   125 |  3.418 -  3.789:     3871 |
| 0.980 - 1.120:    17 |  52.147 -  59.595:    51 |  3.789 -  4.159:     4997 |
| 1.120 - 1.260:     9 |  59.595 -  67.044:    13 |  4.159 -  4.530:     6481 |
| 1.260 - 1.400:     1 |  67.044 -  74.492:     3 |  4.530 -  4.900:     7640 |
|-----------------------------------------------------------------------------|
|-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 |       54.323 |
| planarity |      436 |   0.145    0.405  0.000 |     250.485 |              |
|  dihedral |      870 |  33.790  144.062  0.019 |      20.704 |              |
| nonbonded |     2439 |   4.092    4.900  1.196 |       1.798 |              |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 12.188)------------------------------------------|
|    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 = 12.188)------------------------------------------|
|    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: 1.99 - 15.05 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.5066   r_free= 0.4884   ksol= 0.00   Bsol= 0.00   scale= 0.740    |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (0.00,0.00,0.00,0.00,0.00,0.00); trace/3= 0.00                              |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.83 A                  |
| x-ray target function (ml) for work reflections: 6.302580                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.99 - 15.05 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.4953   r_free= 0.4799   ksol= 0.31   Bsol= 20.00   scale= 0.958   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (5.66,12.06,8.27,0.00,0.00,0.00); trace/3= 8.66                             |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.82 A                  |
| x-ray target function (ml) for work reflections: 6.294961                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 15.945897             wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 82.889   (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 1.497005              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 77.626   (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.4953      final r-factor (work) = 0.4277          |
| start r-factor (free) = 0.4799      final r-factor (free) = 0.4362          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 104.5514 = 15.95 * 0.50 * 6.2998 + 1.00 * 54.3232                           |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 49.8874 = 15.95 * 0.50 * 6.2394 + 1.00 * 0.1408                             |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 26     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.4277      final r-factor (work) = 0.3861          |
| start r-factor (free) = 0.4362      final r-factor (free) = 0.4327          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 9.3552 = 1.50 * 1.00 * 6.2394 + 1.00 * 0.0147                               |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 9.2692 = 1.50 * 1.00 * 6.1766 + 1.00 * 0.0228                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 27     |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 12.188)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.00    122.30  16.02    None  None   None       |
|    all(noH): 2823   0      0.00    122.30  16.02    None  None   None       |
|    Sol.    : 438    0      0.00    122.30  27.58    None  None   None       |
|    Mac.    : 2385   0      0.00    76.68   13.90    None  None   None       |
|    Hyd.    : 0      0      None    None    None     None  None   None       |
|    - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -      |
|       Distribution of isotropic (or equivalent) ADP for non-H atoms:        |
|    Bin#      value range     #atoms | Bin#      value range     #atoms      |
|      0:     0.000 -  12.230: 1381   |   5:    61.150 -  73.380:   25        |
|      1:    12.230 -  24.460:  836   |   6:    73.380 -  85.610:    5        |
|      2:    24.460 -  36.690:  383   |   7:    85.610 -  97.839:    3        |
|      3:    36.690 -  48.920:  134   |   8:    97.839 - 110.069:    0        |
|      4:    48.920 -  61.150:   54   |   9:   110.069 - 122.299:    2        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.3861 r_free = 0.4327             target_work(ml) = 6.168         |
| occupancies: max = 1.00  min = 0.30   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.3854 r_free = 0.4323             target_work(ml) = 6.167         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        8 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.99 - 15.05 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.3854   r_free= 0.4323   ksol= 0.31   Bsol= 20.00   scale= 1.100   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (5.66,12.06,8.27,0.00,0.00,0.00); trace/3= 8.66                             |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.62 A                  |
| x-ray target function (ml) for work reflections: 6.167143                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.99 - 15.05 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.3825   r_free= 0.4254   ksol= 0.28   Bsol= 31.24   scale= 0.993   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (1.84,6.99,4.19,0.00,0.00,0.00); trace/3= 4.34                              |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.64 A                  |
| x-ray target function (ml) for work reflections: 6.168406                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 7.924568              wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 102.110  (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 0.479630              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 131.117  (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.3825      final r-factor (work) = 0.3262          |
| start r-factor (free) = 0.4254      final r-factor (free) = 0.3934          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 24.5906 = 7.92 * 0.50 * 6.1708 + 1.00 * 0.1403                              |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 24.2437 = 7.92 * 0.50 * 6.0962 + 1.00 * 0.0888                              |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 28     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.3262      final r-factor (work) = 0.3203          |
| start r-factor (free) = 0.3934      final r-factor (free) = 0.3819          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 2.9468 = 0.48 * 1.00 * 6.0962 + 1.00 * 0.0229                               |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 2.9173 = 0.48 * 1.00 * 6.0625 + 1.00 * 0.0096                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 31     |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 12.188)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.00    109.42  14.45    None  None   None       |
|    all(noH): 2823   0      0.00    109.42  14.45    None  None   None       |
|    Sol.    : 438    0      0.00    109.42  26.61    None  None   None       |
|    Mac.    : 2385   0      0.00    64.80   12.22    None  None   None       |
|    Hyd.    : 0      0      None    None    None     None  None   None       |
|    - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -      |
|       Distribution of isotropic (or equivalent) ADP for non-H atoms:        |
|    Bin#      value range     #atoms | Bin#      value range     #atoms      |
|      0:     0.000 -  10.942: 1384   |   5:    54.710 -  65.652:   20        |
|      1:    10.942 -  21.884:  843   |   6:    65.652 -  76.594:    4        |
|      2:    21.884 -  32.826:  398   |   7:    76.594 -  87.536:    2        |
|      3:    32.826 -  43.768:  125   |   8:    87.536 -  98.478:    1        |
|      4:    43.768 -  54.710:   45   |   9:    98.478 - 109.420:    1        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.3203 r_free = 0.3819             target_work(ml) = 6.054         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        8 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.3200 r_free = 0.3817             target_work(ml) = 6.054         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:       13 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.99 - 15.05 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.3200   r_free= 0.3817   ksol= 0.28   Bsol= 31.24   scale= 1.019   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (1.84,6.99,4.19,0.00,0.00,0.00); trace/3= 4.34                              |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.52 A                  |
| x-ray target function (ml) for work reflections: 6.053576                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.99 - 15.05 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.3203   r_free= 0.3819   ksol= 0.29   Bsol= 31.24   scale= 0.993   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (1.31,5.37,2.98,0.00,0.00,0.00); trace/3= 3.22                              |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.53 A                  |
| x-ray target function (ml) for work reflections: 6.054773                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 9.206931              wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 101.102  (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 0.427979              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 127.804  (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.3203      final r-factor (work) = 0.2552          |
| start r-factor (free) = 0.3819      final r-factor (free) = 0.3041          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 27.9994 = 9.21 * 0.50 * 6.0629 + 1.00 * 0.0888                              |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 27.5523 = 9.21 * 0.50 * 5.9621 + 1.00 * 0.1058                              |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 28     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.2552      final r-factor (work) = 0.2374          |
| start r-factor (free) = 0.3041      final r-factor (free) = 0.2904          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 2.5623 = 0.43 * 1.00 * 5.9621 + 1.00 * 0.0106                               |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 2.5195 = 0.43 * 1.00 * 5.8087 + 1.00 * 0.0335                               |
|-----------------------------------------------------------------------------|
| number of iterations = 11      |    number of function evaluations = 34     |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 12.188)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.00    161.20  14.41    None  None   None       |
|    all(noH): 2823   0      0.00    161.20  14.41    None  None   None       |
|    Sol.    : 438    0      0.00    107.38  29.62    None  None   None       |
|    Mac.    : 2385   0      0.00    161.20  11.62    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 -  16.120: 1902   |   5:    80.598 -  96.717:    3        |
|      1:    16.120 -  32.239:  682   |   6:    96.717 - 112.837:    1        |
|      2:    32.239 -  48.359:  182   |   7:   112.837 - 128.956:    0        |
|      3:    48.359 -  64.478:   47   |   8:   128.956 - 145.076:    0        |
|      4:    64.478 -  80.598:    5   |   9:   145.076 - 161.195:    1        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.2374 r_free = 0.2904             target_work(ml) = 5.793         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:       13 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.2370 r_free = 0.2907             target_work(ml) = 5.793         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:       13 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.99 - 15.05 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.2370   r_free= 0.2907   ksol= 0.29   Bsol= 31.24   scale= 1.025   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (1.31,5.37,2.98,0.00,0.00,0.00); trace/3= 3.22                              |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.34 A                  |
| x-ray target function (ml) for work reflections: 5.792754                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.99 - 15.05 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.2360   r_free= 0.2899   ksol= 0.32   Bsol= 48.57   scale= 0.992   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (0.44,3.14,2.14,0.00,0.00,0.00); trace/3= 1.90                              |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.34 A                  |
| x-ray target function (ml) for work reflections: 5.791814                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 5.148742              wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 101.515  (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 0.537470              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 95.422   (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.2360      final r-factor (work) = 0.1872          |
| start r-factor (free) = 0.2899      final r-factor (free) = 0.2370          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 15.0600 = 5.15 * 0.50 * 5.8089 + 1.00 * 0.1058                              |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 14.7404 = 5.15 * 0.50 * 5.6954 + 1.00 * 0.0784                              |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 28     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1872      final r-factor (work) = 0.1660          |
| start r-factor (free) = 0.2370      final r-factor (free) = 0.2100          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 3.1009 = 0.54 * 1.00 * 5.6954 + 1.00 * 0.0398                               |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 2.9797 = 0.54 * 1.00 * 5.5203 + 1.00 * 0.0127                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 27     |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 12.188)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.00    91.04   15.14    None  None   None       |
|    all(noH): 2823   0      0.00    91.04   15.14    None  None   None       |
|    Sol.    : 438    0      2.03    91.04   38.89    None  None   None       |
|    Mac.    : 2385   0      0.00    87.31   10.78    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 -   9.104: 1375   |   5:    45.521 -  54.625:   87        |
|      1:     9.104 -  18.209:  766   |   6:    54.625 -  63.730:   57        |
|      2:    18.209 -  27.313:  243   |   7:    63.730 -  72.834:   38        |
|      3:    27.313 -  36.417:  128   |   8:    72.834 -  81.938:   14        |
|      4:    36.417 -  45.521:  109   |   9:    81.938 -  91.042:    6        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.1660 r_free = 0.2100             target_work(ml) = 5.470         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:       13 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.1659 r_free = 0.2103             target_work(ml) = 5.470         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:       14 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.99 - 15.05 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1659   r_free= 0.2103   ksol= 0.32   Bsol= 48.57   scale= 1.006   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (0.44,3.14,2.14,0.00,0.00,0.00); trace/3= 1.90                              |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.22 A                  |
| x-ray target function (ml) for work reflections: 5.470059                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.99 - 15.05 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1660   r_free= 0.2104   ksol= 0.31   Bsol= 66.83   scale= 0.991   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (0.13,1.97,1.97,0.00,0.00,0.00); trace/3= 1.36                              |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.23 A                  |
| x-ray target function (ml) for work reflections: 5.471393                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 2.366896              wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 105.597  (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 0.495972              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 149.263  (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1660      final r-factor (work) = 0.1444          |
| start r-factor (free) = 0.2104      final r-factor (free) = 0.1903          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 6.6131 = 2.37 * 0.50 * 5.5216 + 1.00 * 0.0786                               |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 6.4642 = 2.37 * 0.50 * 5.4074 + 1.00 * 0.0647                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 28     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1444      final r-factor (work) = 0.1388          |
| start r-factor (free) = 0.1903      final r-factor (free) = 0.1860          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 2.6946 = 0.50 * 1.00 * 5.4074 + 1.00 * 0.0126                               |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 2.6609 = 0.50 * 1.00 * 5.3390 + 1.00 * 0.0129                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 30     |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 12.188)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.00    91.84   15.07    None  None   None       |
|    all(noH): 2823   0      0.00    91.84   15.07    None  None   None       |
|    Sol.    : 438    0      1.85    91.84   40.50    None  None   None       |
|    Mac.    : 2385   0      0.00    88.89   10.40    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 -   9.184: 1395   |   5:    45.919 -  55.102:   89        |
|      1:     9.184 -  18.367:  806   |   6:    55.102 -  64.286:   58        |
|      2:    18.367 -  27.551:  194   |   7:    64.286 -  73.470:   38        |
|      3:    27.551 -  36.735:   99   |   8:    73.470 -  82.653:   18        |
|      4:    36.735 -  45.919:  118   |   9:    82.653 -  91.837:    8        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.1388 r_free = 0.1860             target_work(ml) = 5.325         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:       14 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.1387 r_free = 0.1859             target_work(ml) = 5.325         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:       13 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.99 - 15.05 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1387   r_free= 0.1859   ksol= 0.31   Bsol= 66.83   scale= 0.994   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (0.13,1.97,1.97,0.00,0.00,0.00); trace/3= 1.36                              |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.19 A                  |
| x-ray target function (ml) for work reflections: 5.324985                   |
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
| Bin     Resolution   Compl.  No. Refl.    R-factors          Targets        |
|number     range              work test   work   test        work        test|
|  1: 15.0505 -  4.7507 0.99   1411  158 0.1064 0.1419      5.4627      5.6515|
|  2:  4.7507 -  3.7906 0.99   1361  151 0.0983 0.1210      5.5559       5.739|
|  3:  3.7906 -  3.3173 0.99   1341  148 0.1300 0.1810      5.6513      6.0016|
|  4:  3.3173 -  3.0167 0.99   1315  142 0.1532 0.1914      5.6308      5.7808|
|  5:  3.0167 -  2.8019 0.98   1324  147 0.1720 0.1757       5.526      5.5892|
|  6:  2.8019 -  2.6377 0.99   1298  148 0.1560 0.2440      5.4026      5.6388|
|  7:  2.6377 -  2.5062 0.99   1304  152 0.1542 0.1988      5.3455      5.5303|
|  8:  2.5062 -  2.3976 0.99   1317  136 0.1487 0.1974      5.2686      5.4846|
|  9:  2.3976 -  2.3056 0.99   1296  148 0.1564 0.2270      5.2201      5.5078|
| 10:  2.3056 -  2.2263 0.98   1284  139 0.1440 0.1975      5.1539      5.3438|
| 11:  2.2263 -  2.1569 0.98   1282  148 0.1460 0.2275      5.1114      5.4106|
| 12:  2.1569 -  2.0954 1.00   1293  146 0.1416 0.1890      5.0425      5.2806|
| 13:  2.0954 -  2.0404 0.96   1263  132 0.1492 0.2067      4.9859      5.1972|
| 14:  2.0404 -  1.9907 0.42    541   64 0.1366 0.2115      4.8725      5.0738|
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
|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: 15.0505 -  4.7507  1411   158  0.93  10.36   0.96     0.93       8525.09|
|  2:  4.7507 -  3.7906  1361   151  0.94   9.83   1.01     1.00      11535.23|
|  3:  3.7906 -  3.3173  1341   148  0.91  14.09   1.02     1.00      14174.85|
|  4:  3.3173 -  3.0167  1315   142  0.90  16.56   1.01     1.00      13893.25|
|  5:  3.0167 -  2.8019  1324   147  0.87  19.62   1.00     0.99      11888.90|
|  6:  2.8019 -  2.6377  1298   148  0.87  19.73   0.98     0.93       9903.16|
|  7:  2.6377 -  2.5062  1304   152  0.88  18.85   0.99     0.96       8622.97|
|  8:  2.5062 -  2.3976  1317   136  0.87  19.15   0.99     0.95       7871.37|
|  9:  2.3976 -  2.3056  1296   148  0.87  19.99   1.00     0.96       7132.10|
| 10:  2.3056 -  2.2263  1284   139  0.87  19.68   0.99     0.94       6387.31|
| 11:  2.2263 -  2.1569  1282   148  0.87  19.61   0.99     0.95       6071.08|
| 12:  2.1569 -  2.0954  1293   146  0.88  19.08   0.99     0.98       5446.13|
| 13:  2.0954 -  2.0404  1263   132  0.87  20.14   0.98     0.96       4802.48|
| 14:  2.0404 -  1.9907   541    64  0.88  18.23   0.94     0.90       3761.22|
|alpha:            min =        0.90 max =            1.00 mean =         0.96|
|beta:             min =     3761.22 max =        14174.85 mean =      8824.87|
|figures of merit: min =        0.00 max =            1.00 mean =         0.89|
|phase err.(work): min =        0.00 max =           89.91 mean =        17.38|
|phase err.(test): min =        0.00 max =           89.32 mean =        16.71|
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.99 - 15.05 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1386   r_free= 0.1858   ksol= 0.33   Bsol= 67.74   scale= 0.993   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-1.13,0.38,0.75,0.00,0.00,0.00); trace/3= 0.00                             |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.19 A                  |
| x-ray target function (ml) for work reflections: 5.324899                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.99 - 15.05 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1386   r_free= 0.1858   ksol= 0.33   Bsol= 67.74   scale= 0.993   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-1.13,0.38,0.75,0.00,0.00,0.00); trace/3= 0.00                             |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.19 A                  |
| x-ray target function (ml) for work reflections: 5.324899                   |
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
| Bin     Resolution   Compl.  No. Refl.    R-factors          Targets        |
|number     range              work test   work   test        work        test|
|  1: 15.0505 -  4.7507 0.99   1411  158 0.1065 0.1422      5.4641      5.6496|
|  2:  4.7507 -  3.7906 0.99   1361  151 0.0981 0.1207      5.5541      5.7363|
|  3:  3.7906 -  3.3173 0.99   1341  148 0.1301 0.1810      5.6511      6.0027|
|  4:  3.3173 -  3.0167 0.99   1315  142 0.1533 0.1915       5.631      5.7811|
|  5:  3.0167 -  2.8019 0.98   1324  147 0.1721 0.1754      5.5263      5.5882|
|  6:  2.8019 -  2.6377 0.99   1298  148 0.1558 0.2436      5.4017      5.6373|
|  7:  2.6377 -  2.5062 0.99   1304  152 0.1542 0.1992      5.3452      5.5305|
|  8:  2.5062 -  2.3976 0.99   1317  136 0.1485 0.1971      5.2686      5.4853|
|  9:  2.3976 -  2.3056 0.99   1296  148 0.1563 0.2274      5.2202      5.5088|
| 10:  2.3056 -  2.2263 0.98   1284  139 0.1439 0.1980      5.1542      5.3449|
| 11:  2.2263 -  2.1569 0.98   1282  148 0.1459 0.2273      5.1112      5.4109|
| 12:  2.1569 -  2.0954 1.00   1293  146 0.1415 0.1896      5.0423      5.2829|
| 13:  2.0954 -  2.0404 0.96   1263  132 0.1495 0.2062       4.986      5.1944|
| 14:  2.0404 -  1.9907 0.42    541   64 0.1365 0.2110      4.8723      5.0731|
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
|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: 15.0505 -  4.7507  1411   158  0.93  10.38   0.96     0.93       8578.74|
|  2:  4.7507 -  3.7906  1361   151  0.94   9.82   1.01     1.00      11514.47|
|  3:  3.7906 -  3.3173  1341   148  0.91  14.06   1.01     1.00      14129.98|
|  4:  3.3173 -  3.0167  1315   142  0.90  16.56   1.01     1.00      13891.20|
|  5:  3.0167 -  2.8019  1324   147  0.87  19.59   1.00     0.99      11865.70|
|  6:  2.8019 -  2.6377  1298   148  0.87  19.71   0.98     0.93       9885.75|
|  7:  2.6377 -  2.5062  1304   152  0.88  18.84   0.99     0.96       8617.76|
|  8:  2.5062 -  2.3976  1317   136  0.87  19.16   0.99     0.94       7880.85|
|  9:  2.3976 -  2.3056  1296   148  0.87  20.01   1.00     0.96       7147.57|
| 10:  2.3056 -  2.2263  1284   139  0.87  19.69   0.99     0.94       6397.22|
| 11:  2.2263 -  2.1569  1282   148  0.87  19.62   0.99     0.94       6081.35|
| 12:  2.1569 -  2.0954  1293   146  0.88  19.07   0.99     0.98       5446.28|
| 13:  2.0954 -  2.0404  1263   132  0.87  20.12   0.98     0.96       4794.19|
| 14:  2.0404 -  1.9907   541    64  0.88  18.22   0.94     0.90       3748.92|
|alpha:            min =        0.90 max =            1.00 mean =         0.96|
|beta:             min =     3748.92 max =        14129.98 mean =      8822.94|
|figures of merit: min =        0.00 max =            1.00 mean =         0.89|
|phase err.(work): min =        0.00 max =           89.92 mean =        17.37|
|phase err.(test): min =        0.00 max =           89.87 mean =        16.72|
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 12.188)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      1.28    93.12   16.35    None  None   None       |
|    all(noH): 2823   0      1.28    93.12   16.35    None  None   None       |
|    Sol.    : 438    0      3.13    93.12   41.78    None  None   None       |
|    Mac.    : 2385   0      1.28    90.17   11.69    None  None   None       |
|    Hyd.    : 0      0      None    None    None     None  None   None       |
|    - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -      |
|       Distribution of isotropic (or equivalent) ADP for non-H atoms:        |
|    Bin#      value range     #atoms | Bin#      value range     #atoms      |
|      0:     1.284 -  10.468: 1395   |   5:    47.203 -  56.387:   89        |
|      1:    10.468 -  19.652:  806   |   6:    56.387 -  65.570:   58        |
|      2:    19.652 -  28.835:  194   |   7:    65.570 -  74.754:   38        |
|      3:    28.835 -  38.019:   99   |   8:    74.754 -  83.938:   18        |
|      4:    38.019 -  47.203:  118   |   9:    83.938 -  93.121:    8        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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


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

Number of peaks found at mFobs-DFmodel map (map cutoff=3.00 sigma)= 338         
Filter by distance & map next to the model:
   mapped sites are within: 0.197 - 4.884
   number of sites selected in [dist_min= 0.70, dist_max= 6.00]: 335 from: 338
   mapped sites are within: 0.705 - 4.884

peak=    7.720 closest distance to " CG2 VAL A 230 " =    1.312
peak=    7.370 closest distance to " O   HOH Z 400 " =    1.115
peak=    6.747 closest distance to " CG1 ILE A 234 " =    1.447
peak=    6.720 closest distance to " O   HOH Z 120 " =    1.577
peak=    6.309 closest distance to " OD1 ASN A 301 " =    1.091
peak=    6.208 closest distance to " O   GLN A  11 " =    1.027
peak=    5.570 closest distance to " O   HOH Z 210 " =    1.671
peak=    5.407 closest distance to " CG  LEU A   5 " =    1.390
peak=    5.315 closest distance to " NH2 ARG A 156 " =    1.257
peak=    5.212 closest distance to " O   HOH Z 396 " =    1.249
peak=    5.098 closest distance to " CD2 LEU A 228 " =    1.260
peak=    5.050 closest distance to " O   HOH Z 117 " =    1.258
peak=    4.986 closest distance to " O   HOH Z 403 " =    2.233
peak=    4.978 closest distance to " CG1 VAL A 296 " =    1.220
peak=    4.955 closest distance to " O   HOH Z 128 " =    1.932
peak=    4.909 closest distance to " O   HOH Z 422 " =    1.094
peak=    4.864 closest distance to " O   HOH Z 404 " =    1.383
peak=    4.791 closest distance to " N   SER A 164 " =    0.972
peak=    4.756 closest distance to " NH2 ARG A  56 " =    2.237
peak=    4.747 closest distance to " O   HOH Z 426 " =    1.236
peak=    4.710 closest distance to " CG  PRO A 280 " =    0.908
peak=    4.692 closest distance to " O   HOH Z 248 " =    1.549
peak=    4.682 closest distance to " CB  VAL A 230 " =    1.258
peak=    4.673 closest distance to " CB  ARG A 275 " =    0.873
peak=    4.668 closest distance to " CB  VAL A 296 " =    1.144
peak=    4.607 closest distance to " CG  GLN A  77 " =    0.892
peak=    4.540 closest distance to " CB  SER A  63 " =    1.239
peak=    4.518 closest distance to " O   HOH Z 124 " =    1.499
peak=    4.504 closest distance to " CG AARG A 275 " =    1.181
peak=    4.405 closest distance to " O   HOH Z 126 " =    1.643
peak=    4.401 closest distance to " O   HOH Z 425 " =    1.686
peak=    4.385 closest distance to " CB  GLN A 223 " =    1.431
peak=    4.356 closest distance to " O   HOH Z 357 " =    2.291
peak=    4.346 closest distance to " O   HOH Z 412 " =    3.222
peak=    4.333 closest distance to " CD  ARG A  36 " =    1.063
peak=    4.317 closest distance to " O   HOH Z 139 " =    1.319
peak=    4.305 closest distance to " CA  TYR A  30 " =    0.954
peak=    4.284 closest distance to " O   HOH Z 431 " =    1.766
peak=    4.277 closest distance to " O   HOH Z 403 " =    1.491
peak=    4.271 closest distance to " O   HOH Z 154 " =    1.649
peak=    4.262 closest distance to " NE2 HIS A 115 " =    1.229
peak=    4.252 closest distance to " O   HOH Z 247 " =    1.508
peak=    4.247 closest distance to " CG  PRO A  54 " =    1.277
peak=    4.243 closest distance to " CD2 TRP A 179 " =    1.206
peak=    4.230 closest distance to " O   HOH Z 102 " =    1.592
peak=    4.227 closest distance to " NE2 GLN A  11 " =    1.016
peak=    4.223 closest distance to " CG1 ILE A 120 " =    1.139
peak=    4.215 closest distance to " NH1AARG A 145 " =    1.239
peak=    4.197 closest distance to " O   HOH Z 146 " =    1.874
peak=    4.189 closest distance to " CB  ASN A 285 " =    0.937
peak=    4.187 closest distance to " O   HOH Z 234 " =    3.477
peak=    4.173 closest distance to " O   HOH Z 193 " =    1.728
peak=    4.142 closest distance to " O   HOH Z  40 " =    2.215
peak=    4.124 closest distance to " O   HOH Z 261 " =    2.515
peak=    4.120 closest distance to " O   HOH Z 130 " =    2.620
peak=    4.107 closest distance to " NZ  LYS A  76 " =    1.014
peak=    4.105 closest distance to " OE1 GLU A   2 " =    1.409
peak=    4.096 closest distance to " O   HOH Z 394 " =    1.940
peak=    4.082 closest distance to " CB  GLN A 183 " =    1.245
peak=    4.079 closest distance to " CB  SER A  62 " =    1.028
peak=    4.061 closest distance to " CG  PRO A 198 " =    1.252
peak=    4.057 closest distance to " O   ASP A 124 " =    1.424
peak=    4.043 closest distance to " O   HOH Z 277 " =    2.689
peak=    4.015 closest distance to " CE1 HIS A 108 " =    1.161
peak=    4.002 closest distance to " CG1 VAL A 296 " =    1.749
peak=    3.994 closest distance to " O   ASP A 200 " =    1.569
peak=    3.964 closest distance to " CB  ALA A 299 " =    1.238
peak=    3.964 closest distance to " O   HOH Z 134 " =    2.387
peak=    3.960 closest distance to " CB  ARG A 275 " =    1.187
peak=    3.952 closest distance to " CB  GLU A 175 " =    1.312
peak=    3.950 closest distance to " CA  ARG A 195 " =    1.146
peak=    3.948 closest distance to " CB  PRO A  54 " =    0.985
peak=    3.932 closest distance to " O   HOH Z  53 " =    1.216
peak=    3.928 closest distance to " O   HOH Z  49 " =    1.479
peak=    3.914 closest distance to " CB  TRP A 179 " =    1.260
peak=    3.909 closest distance to " CZ  PHE A 218 " =    1.182
peak=    3.905 closest distance to " O   HOH Z 209 " =    2.238
peak=    3.898 closest distance to " CB  PHE A 283 " =    1.021
peak=    3.894 closest distance to " OD2 ASP A 298 " =    0.888
peak=    3.891 closest distance to " CG  ARG A  66 " =    0.959
peak=    3.877 closest distance to " CD  ARG A  36 " =    1.154
peak=    3.865 closest distance to " CB  VAL A 202 " =    1.379
peak=    3.865 closest distance to " OE1 GLN A  11 " =    2.228
peak=    3.864 closest distance to " N   ASP A 298 " =    0.954
peak=    3.840 closest distance to " O   HOH Z 418 " =    1.739
peak=    3.834 closest distance to " CD  LYS A 166 " =    1.702
peak=    3.831 closest distance to " O   VAL A  72 " =    1.208
peak=    3.812 closest distance to " O   HOH Z 144 " =    1.963
peak=    3.806 closest distance to " CB  ASN A 187 " =    1.191
peak=    3.782 closest distance to " CA  GLN A  11 " =    0.910
peak=    3.781 closest distance to " CB  SER A 141 " =    1.068
peak=    3.776 closest distance to " CB  GLN A  73 " =    1.182
peak=    3.773 closest distance to " O   HOH Z  80 " =    2.337
peak=    3.773 closest distance to " CB BVAL A  41 " =    1.277
peak=    3.768 closest distance to " CG2 VAL A 197 " =    1.192
peak=    3.766 closest distance to " O   HOH Z 176 " =    2.453
peak=    3.759 closest distance to " CA  TRP A  85 " =    1.173
peak=    3.755 closest distance to " CE  LYS A 119 " =    1.453
peak=    3.752 closest distance to " CB  ASN A 148 " =    1.342
peak=    3.747 closest distance to " O   HOH Z 369 " =    1.597
peak=    3.744 closest distance to " CA  SER A  12 " =    1.351
peak=    3.743 closest distance to " O   HOH Z 435 " =    1.819
peak=    3.742 closest distance to " O   HOH Z 401 " =    1.230
peak=    3.728 closest distance to " O   HOH Z 427 " =    2.879
peak=    3.724 closest distance to " CG2 VAL A 296 " =    1.012
peak=    3.721 closest distance to " CA  VAL A  41 " =    0.919
peak=    3.718 closest distance to " O   HOH Z  35 " =    1.820
peak=    3.712 closest distance to " O   HOH Z 126 " =    2.331
peak=    3.706 closest distance to " OG  SER A  62 " =    2.738
peak=    3.694 closest distance to " C   ALA A 299 " =    0.900
peak=    3.693 closest distance to " O   HOH Z  43 " =    1.596
peak=    3.693 closest distance to " O   HOH Z  44 " =    1.916
peak=    3.688 closest distance to " CA  ALA A 295 " =    1.025
peak=    3.684 closest distance to " CB  ALA A 248 " =    1.336
peak=    3.682 closest distance to " CA  ARG A  66 " =    1.083
peak=    3.680 closest distance to " O   HOH Z 371 " =    3.152
peak=    3.673 closest distance to " O   HOH Z 402 " =    1.605
peak=    3.672 closest distance to " OH  TYR A 116 " =    1.287
peak=    3.670 closest distance to " CB  VAL A 126 " =    0.832
peak=    3.668 closest distance to " CG2 ILE A 234 " =    1.158
peak=    3.657 closest distance to " O   HOH Z 183 " =    1.814
peak=    3.653 closest distance to " CD  ARG A  24 " =    1.254
peak=    3.651 closest distance to " O   HOH Z 342 " =    0.773
peak=    3.636 closest distance to " CG  GLN A  11 " =    1.352
peak=    3.636 closest distance to " CB  GLU A 128 " =    1.263
peak=    3.636 closest distance to " O   HOH Z 146 " =    1.690
peak=    3.635 closest distance to " CG1 ILE A  33 " =    1.233
peak=    3.630 closest distance to " O   HOH Z 273 " =    3.095
peak=    3.630 closest distance to " N   ALA A 256 " =    1.116
peak=    3.627 closest distance to " O   SER A  87 " =    2.336
peak=    3.626 closest distance to " O   HOH Z 301 " =    2.218
peak=    3.617 closest distance to " O  BHOH Z 338 " =    2.462
peak=    3.613 closest distance to " CB  GLU A 152 " =    1.071
peak=    3.608 closest distance to " O   HOH Z 265 " =    1.907
peak=    3.601 closest distance to " O   HOH Z 433 " =    2.185
peak=    3.601 closest distance to " O   HOH Z 418 " =    3.076
peak=    3.600 closest distance to " CB  THR A  31 " =    1.373
peak=    3.589 closest distance to " O   HOH Z 389 " =    2.187
peak=    3.580 closest distance to " O   HOH Z 232 " =    2.221
peak=    3.579 closest distance to " O   PRO A 198 " =    1.562
peak=    3.575 closest distance to " NH1 ARG A 269 " =    0.952
peak=    3.574 closest distance to " CB  MET A  40 " =    0.854
peak=    3.563 closest distance to " O   HOH Z  48 " =    1.784
peak=    3.563 closest distance to " CG  PRO A 243 " =    1.250
peak=    3.562 closest distance to " CG1 VAL A 153 " =    1.040
peak=    3.556 closest distance to " CB  GLN A  88 " =    1.276
peak=    3.553 closest distance to " NH2AARG A 145 " =    0.972
peak=    3.549 closest distance to " O   HOH Z 284 " =    2.960
peak=    3.547 closest distance to " O   HOH Z 415 " =    1.129
peak=    3.547 closest distance to " CD  LYS A 119 " =    2.157
peak=    3.543 closest distance to " CG  GLN A  11 " =    0.988
peak=    3.542 closest distance to " CG2 THR A 221 " =    1.245
peak=    3.538 closest distance to " O   HOH Z 130 " =    1.085
peak=    3.533 closest distance to " O   HOH Z  38 " =    1.598
peak=    3.530 closest distance to " O   HOH Z 327 " =    1.639
peak=    3.525 closest distance to " CA  SER A  62 " =    0.859
peak=    3.524 closest distance to " CD  GLN A  73 " =    1.185
peak=    3.524 closest distance to " O   ALA A 165 " =    1.288
peak=    3.524 closest distance to " O   HOH Z 423 " =    1.775
peak=    3.522 closest distance to " CG  ARG A  36 " =    1.099
peak=    3.512 closest distance to " CB  THR A 235 " =    1.296
peak=    3.511 closest distance to " N   ASN A  39 " =    1.237
peak=    3.510 closest distance to " ND2 ASN A 301 " =    0.945
peak=    3.509 closest distance to " O   HOH Z  67 " =    1.989
peak=    3.501 closest distance to " CE1 TYR A 186 " =    1.371
peak=    3.496 closest distance to " CB  LEU A 261 " =    1.170
peak=    3.491 closest distance to " CB  MET A 105 " =    1.218
peak=    3.489 closest distance to " N   GLU A  44 " =    1.349
peak=    3.484 closest distance to " CB  SER A 273 " =    1.098
peak=    3.481 closest distance to " CA  THR A 246 " =    0.957
peak=    3.475 closest distance to " O   HOH Z 214 " =    1.487
peak=    3.473 closest distance to " O   HOH Z 141 " =    1.662
peak=    3.461 closest distance to " O   HOH Z 189 " =    3.015
peak=    3.456 closest distance to " O   HOH Z 370 " =    1.144
peak=    3.445 closest distance to " CG1BVAL A 121 " =    1.410
peak=    3.437 closest distance to " O   HOH Z 414 " =    2.045
peak=    3.433 closest distance to " CG  LEU A 228 " =    1.321
peak=    3.432 closest distance to " CB  TRP A 179 " =    1.851
peak=    3.431 closest distance to " CG  LYS A  76 " =    1.099
peak=    3.430 closest distance to " CA  ASP A 191 " =    1.210
peak=    3.427 closest distance to " CB  GLU A  46 " =    1.178
peak=    3.423 closest distance to " O   LYS A 289 " =    0.955
peak=    3.421 closest distance to " O   HOH Z 279 " =    1.159
peak=    3.420 closest distance to " O   HOH Z 162 " =    2.280
peak=    3.419 closest distance to " O   HOH Z 281 " =    2.711
peak=    3.417 closest distance to " O   HOH Z 395 " =    1.465
peak=    3.416 closest distance to " CG  PRO A 213 " =    1.252
peak=    3.414 closest distance to " ND1 HIS A  81 " =    1.518
peak=    3.412 closest distance to " NZ  LYS A  48 " =    1.152
peak=    3.407 closest distance to " CA  CYS A 260 " =    1.302
peak=    3.403 closest distance to " O   HOH Z 155 " =    2.853
peak=    3.402 closest distance to " NE2 HIS A 108 " =    0.812
peak=    3.402 closest distance to " O   THR A 220 " =    1.149
peak=    3.401 closest distance to " O   HOH Z 227 " =    1.655
peak=    3.400 closest distance to " O   PRO A  90 " =    1.477
peak=    3.398 closest distance to " O   HOH Z 217 " =    2.839
peak=    3.398 closest distance to " CA  ALA A  51 " =    1.103
peak=    3.392 closest distance to " CB  ALA A 100 " =    1.350
peak=    3.391 closest distance to " O   HOH Z 368 " =    3.088
peak=    3.391 closest distance to " CD  ARG A 159 " =    0.858
peak=    3.390 closest distance to " CA  GLN A  73 " =    1.280
peak=    3.388 closest distance to " ND2 ASN A 110 " =    1.269
peak=    3.387 closest distance to " O   GLY A  91 " =    1.186
peak=    3.387 closest distance to " CB  TRP A 150 " =    1.529
peak=    3.384 closest distance to " O   HOH Z  54 " =    1.117
peak=    3.383 closest distance to " NE2 GLN A 194 " =    1.568
peak=    3.379 closest distance to " O   HOH Z 132 " =    2.530
peak=    3.374 closest distance to " N   GLY A  75 " =    0.927
peak=    3.374 closest distance to " CG2 THR A 220 " =    0.859
peak=    3.373 closest distance to " C   VAL A 265 " =    1.103
peak=    3.373 closest distance to " O   HOH Z 344 " =    2.993
peak=    3.373 closest distance to " CD2 LEU A 297 " =    0.827
peak=    3.373 closest distance to " CD  ARG A 269 " =    0.987
peak=    3.371 closest distance to " O   HOH Z 373 " =    1.635
peak=    3.367 closest distance to " O   HOH Z  48 " =    2.969
peak=    3.364 closest distance to " CZ3 TRP A 266 " =    1.118
peak=    3.364 closest distance to " O   HOH Z 176 " =    1.633
peak=    3.363 closest distance to " CA  ARG A 195 " =    1.496
peak=    3.362 closest distance to " OD2 ASP A 298 " =    3.293
peak=    3.361 closest distance to " O   HOH Z 359 " =    1.499
peak=    3.358 closest distance to " O   HOH Z 291 " =    1.500
peak=    3.356 closest distance to " O   ASP A 298 " =    0.829
peak=    3.355 closest distance to " O   HOH Z 419 " =    2.155
peak=    3.348 closest distance to " CA  ILE A 106 " =    0.745
peak=    3.341 closest distance to " O   HOH Z  63 " =    2.295
peak=    3.340 closest distance to " CB  SER A  97 " =    1.793
peak=    3.335 closest distance to " CB  SER A 146 " =    1.049
peak=    3.334 closest distance to " N   ILE A  33 " =    0.992
peak=    3.331 closest distance to " O   HOH Z 116 " =    1.144
peak=    3.330 closest distance to " O   HOH Z 299 " =    4.056
peak=    3.329 closest distance to " CB  ARG A 269 " =    1.823
peak=    3.328 closest distance to " CB  ARG A  79 " =    0.897
peak=    3.327 closest distance to " NE1 TRP A  92 " =    1.671
peak=    3.326 closest distance to " O   HOH Z  39 " =    1.538
peak=    3.322 closest distance to " CA  GLY A 196 " =    0.813
peak=    3.322 closest distance to " CB  VAL A 265 " =    1.329
peak=    3.321 closest distance to " CA  ASN A 217 " =    1.260
peak=    3.320 closest distance to " O   HOH Z  88 " =    2.977
peak=    3.317 closest distance to " CA  ALA A 248 " =    1.229
peak=    3.314 closest distance to " O   HOH Z 316 " =    3.052
peak=    3.312 closest distance to " CA  HIS A 115 " =    1.007
peak=    3.305 closest distance to " NH1 ARG A  14 " =    1.092
peak=    3.305 closest distance to " CB  ALA A 242 " =    0.966
peak=    3.304 closest distance to " O   VAL A  72 " =    0.970
peak=    3.303 closest distance to " O   HOH Z   9 " =    2.460
peak=    3.295 closest distance to " OE1 GLN A  88 " =    0.898
peak=    3.293 closest distance to " CG  MET A 185 " =    1.255
peak=    3.292 closest distance to " O   HOH Z 196 " =    1.399
peak=    3.291 closest distance to " CB  THR A  52 " =    0.873
peak=    3.290 closest distance to " CG2AVAL A  72 " =    1.782
peak=    3.284 closest distance to " O  BHOH Z 338 " =    0.958
peak=    3.283 closest distance to " CD ALYS A 290 " =    1.063
peak=    3.279 closest distance to " CB  MET A  47 " =    1.035
peak=    3.279 closest distance to " O   PRO A 213 " =    1.413
peak=    3.274 closest distance to " CB  PRO A 243 " =    1.160
peak=    3.270 closest distance to " CB  PHE A  16 " =    1.211
peak=    3.268 closest distance to " CE1 TYR A  30 " =    0.982
peak=    3.266 closest distance to " CB  TRP A 266 " =    1.093
peak=    3.260 closest distance to " NH1 ARG A  36 " =    1.259
peak=    3.260 closest distance to " NE  ARG A 195 " =    1.864
peak=    3.257 closest distance to " OG  SER A  62 " =    3.040
peak=    3.256 closest distance to " O   HOH Z 377 " =    1.310
peak=    3.254 closest distance to " O   HOH Z 394 " =    4.117
peak=    3.250 closest distance to " O   HOH Z 289 " =    1.683
peak=    3.249 closest distance to " CB  TYR A 169 " =    0.705
peak=    3.246 closest distance to " O   HOH Z 430 " =    2.151
peak=    3.242 closest distance to " OG BSER A 164 " =    2.074
peak=    3.241 closest distance to " O   HOH Z 294 " =    1.704
peak=    3.241 closest distance to " O   HOH Z 383 " =    2.122
peak=    3.238 closest distance to " O   HOH Z 388 " =    1.257
peak=    3.237 closest distance to " O   HOH Z 437 " =    2.331
peak=    3.236 closest distance to " O   HOH Z 142 " =    1.508
peak=    3.226 closest distance to " CD1 ILE A  33 " =    1.694
peak=    3.225 closest distance to " O   HOH Z   7 " =    0.982
peak=    3.224 closest distance to " CD2 LEU A   5 " =    1.313
peak=    3.222 closest distance to " O   HOH Z  78 " =    1.608
peak=    3.218 closest distance to " CB  PRO A 198 " =    1.334
peak=    3.217 closest distance to " O   HOH Z  66 " =    2.019
peak=    3.217 closest distance to " O   CYS A 168 " =    1.505
peak=    3.210 closest distance to " CD1 LEU A 222 " =    0.775
peak=    3.209 closest distance to " CA  ASP A 140 " =    1.291
peak=    3.207 closest distance to " O   HOH Z 409 " =    3.840
peak=    3.204 closest distance to " N   VAL A 126 " =    1.900
peak=    3.202 closest distance to " CA  GLY A  80 " =    0.901
peak=    3.201 closest distance to " O   HOH Z 214 " =    2.368
peak=    3.199 closest distance to " NZ  LYS A 117 " =    2.916
peak=    3.196 closest distance to " O   HOH Z 152 " =    2.073
peak=    3.195 closest distance to " OE1 GLN A 223 " =    3.174
peak=    3.191 closest distance to " O   HOH Z 393 " =    3.515
peak=    3.189 closest distance to " CD2 TYR A  68 " =    0.898
peak=    3.188 closest distance to " O   HOH Z 159 " =    1.214
peak=    3.188 closest distance to " CA  ASP A 149 " =    1.201
peak=    3.187 closest distance to " CA  TYR A 116 " =    1.437
peak=    3.184 closest distance to " O   HOH Z  90 " =    3.699
peak=    3.181 closest distance to " CG2 THR A  42 " =    0.788
peak=    3.178 closest distance to " OG ASER A 134 " =    2.871
peak=    3.177 closest distance to " O   GLU A   2 " =    1.650
peak=    3.170 closest distance to " O   HOH Z 417 " =    1.130
peak=    3.169 closest distance to " OE1 GLN A 223 " =    1.959
peak=    3.168 closest distance to " CB  SER A  26 " =    1.647
peak=    3.165 closest distance to " O   HOH Z 250 " =    1.606
peak=    3.163 closest distance to " O   HOH Z 139 " =    4.884
peak=    3.161 closest distance to " NH2BARG A 190 " =    1.886
peak=    3.160 closest distance to " CA  ILE A 120 " =    1.231
peak=    3.158 closest distance to " O   ARG A  14 " =    1.574
peak=    3.156 closest distance to " CG  GLU A  37 " =    0.928
peak=    3.155 closest distance to " O   HOH Z 148 " =    2.045
peak=    3.155 closest distance to " CB  GLU A 277 " =    0.908
peak=    3.153 closest distance to " CA  LEU A  83 " =    1.264
peak=    3.153 closest distance to " O   HOH Z 155 " =    1.603
peak=    3.153 closest distance to " CB  ARG A 190 " =    1.880
peak=    3.153 closest distance to " ND2 ASN A 249 " =    0.955
peak=    3.152 closest distance to " CD1 LEU A 228 " =    1.613
peak=    3.151 closest distance to " O   HOH Z 163 " =    2.087
peak=    3.150 closest distance to " CA  ILE A  33 " =    1.576
peak=    3.148 closest distance to " CA  ALA A 100 " =    1.141
peak=    3.145 closest distance to " CD  LYS A 289 " =    1.122
peak=    3.144 closest distance to " O   HOH Z 344 " =    1.847
peak=    3.138 closest distance to " CB  ASN A  69 " =    0.987
peak=    3.128 closest distance to " CB  ALA A 137 " =    1.521
peak=    3.128 closest distance to " O   HOH Z 158 " =    1.255
peak=    3.125 closest distance to " O   HOH Z 152 " =    1.645
peak=    3.117 closest distance to " C   ILE A 106 " =    1.805
peak=    3.114 closest distance to " CB  SER A  97 " =    1.128
peak=    3.111 closest distance to " CB  LYS A 289 " =    1.097
peak=    3.106 closest distance to " O   HOH Z  57 " =    1.967
peak=    3.104 closest distance to " N   SER A 271 " =    1.105
peak=    3.103 closest distance to " CZ3 TRP A  85 " =    0.889
peak=    3.086 closest distance to " CB  GLN A  58 " =    1.170
peak=    3.084 closest distance to " O   HOH Z  26 " =    1.175
peak=    3.066 closest distance to " SD  MET A 185 " =    1.412
peak=    3.053 closest distance to " O   HOH Z 193 " =    2.026
peak=    3.044 closest distance to " O   HOH Z 132 " =    2.704
peak=    3.038 closest distance to " O   HOH Z 421 " =    1.827
peak=    3.025 closest distance to " N   TYR A  15 " =    0.892

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

Number of peaks found at mFobs-DFmodel map (map cutoff=3.00 sigma)= 216         
Filter by distance & map next to the model:
   mapped sites are within: 0.526 - 5.531
   number of sites selected in [dist_min= 0.70, dist_max= 6.00]: 214 from: 216
   mapped sites are within: 0.728 - 5.531

peak=   -4.876 closest distance to " CG2 VAL A 230 " =    0.937
peak=   -4.674 closest distance to " OD1 ASN A 301 " =    0.764
peak=   -4.477 closest distance to " O   HOH Z 400 " =    0.881
peak=   -4.424 closest distance to " CD  ARG A  14 " =    3.170
peak=   -4.410 closest distance to " CD1 PHE A  59 " =    1.941
peak=   -4.409 closest distance to " CD  GLN A  58 " =    0.970
peak=   -4.403 closest distance to " CG  PRO A 243 " =    1.728
peak=   -4.372 closest distance to " CG1 VAL A 296 " =    0.959
peak=   -4.341 closest distance to " O   GLN A  11 " =    0.914
peak=   -4.332 closest distance to " CG1 VAL A 112 " =    2.535
peak=   -4.255 closest distance to " O   HOH Z 166 " =    1.498
peak=   -4.222 closest distance to " CD  GLN A 223 " =    1.479
peak=   -4.208 closest distance to " CA  ASP A 298 " =    1.086
peak=   -4.114 closest distance to " NH2 ARG A  36 " =    1.129
peak=   -4.055 closest distance to " O   HOH Z 411 " =    5.357
peak=   -4.051 closest distance to " C   VAL A 265 " =    1.007
peak=   -4.044 closest distance to " CA  SER A 276 " =    1.446
peak=   -4.033 closest distance to " O   PRO A 198 " =    1.242
peak=   -3.988 closest distance to " CG2BVAL A  41 " =    2.493
peak=   -3.987 closest distance to " O   HOH Z 151 " =    1.332
peak=   -3.957 closest distance to " O   HOH Z 351 " =    1.670
peak=   -3.888 closest distance to " O   HOH Z  13 " =    1.659
peak=   -3.858 closest distance to " N   ALA A 226 " =    2.155
peak=   -3.823 closest distance to " O   SER A  95 " =    1.974
peak=   -3.813 closest distance to " O   HOH Z 231 " =    1.867
peak=   -3.790 closest distance to " C   ASN A 285 " =    2.315
peak=   -3.781 closest distance to " O   HOH Z 388 " =    1.842
peak=   -3.768 closest distance to " O   ASP A 171 " =    1.062
peak=   -3.754 closest distance to " O   HOH Z 250 " =    1.703
peak=   -3.752 closest distance to " O   HOH Z 196 " =    1.608
peak=   -3.740 closest distance to " O   HOH Z  52 " =    2.148
peak=   -3.722 closest distance to " O   HOH Z 120 " =    1.545
peak=   -3.721 closest distance to " O   HOH Z 426 " =    2.147
peak=   -3.709 closest distance to " O   HOH Z  92 " =    1.332
peak=   -3.685 closest distance to " CD  GLN A  11 " =    1.299
peak=   -3.665 closest distance to " O   HOH Z 119 " =    1.903
peak=   -3.654 closest distance to " O   HOH Z 418 " =    1.454
peak=   -3.648 closest distance to " N   ALA A   1 " =    2.562
peak=   -3.648 closest distance to " O   HOH Z 174 " =    1.663
peak=   -3.645 closest distance to " O   ASP A 298 " =    1.647
peak=   -3.642 closest distance to " O   HOH Z 109 " =    3.379
peak=   -3.642 closest distance to " OD1 ASN A 148 " =    1.301
peak=   -3.640 closest distance to " CB  ALA A 248 " =    2.256
peak=   -3.636 closest distance to " CA  VAL A 197 " =    0.960
peak=   -3.635 closest distance to " CA  GLY A 241 " =    2.370
peak=   -3.628 closest distance to " O   HOH Z  37 " =    1.309
peak=   -3.625 closest distance to " CG2 ILE A  49 " =    2.691
peak=   -3.624 closest distance to " CZ3 TRP A  70 " =    1.471
peak=   -3.617 closest distance to " O   HOH Z  19 " =    2.091
peak=   -3.614 closest distance to " CD  ARG A 269 " =    2.486
peak=   -3.612 closest distance to " O   HOH Z 222 " =    1.274
peak=   -3.609 closest distance to " CA  SER A 164 " =    2.042
peak=   -3.597 closest distance to " O   HOH Z 384 " =    1.702
peak=   -3.592 closest distance to " CB  ALA A 161 " =    2.624
peak=   -3.592 closest distance to " CG  LEU A   5 " =    1.201
peak=   -3.585 closest distance to " N   SER A   3 " =    2.550
peak=   -3.585 closest distance to " O   HOH Z  60 " =    2.047
peak=   -3.582 closest distance to " O   HOH Z  30 " =    1.376
peak=   -3.579 closest distance to " CG2 THR A 279 " =    1.959
peak=   -3.576 closest distance to " OXT GLY A 302 " =    2.874
peak=   -3.575 closest distance to " O   HOH Z 165 " =    1.560
peak=   -3.569 closest distance to " O   HOH Z 221 " =    1.167
peak=   -3.564 closest distance to " O   PHE A  59 " =    2.235
peak=   -3.559 closest distance to " OG BSER A 210 " =    1.189
peak=   -3.551 closest distance to " CD  GLN A  77 " =    1.052
peak=   -3.550 closest distance to " OG  SER A  87 " =    1.750
peak=   -3.544 closest distance to " CA  GLU A 277 " =    1.138
peak=   -3.527 closest distance to " CD  ARG A  36 " =    0.976
peak=   -3.526 closest distance to " O   HOH Z 368 " =    2.049
peak=   -3.524 closest distance to " NH2 ARG A  66 " =    1.646
peak=   -3.520 closest distance to " C   GLY A 133 " =    1.189
peak=   -3.520 closest distance to " CA  TRP A 274 " =    0.982
peak=   -3.518 closest distance to " C   LEU A 222 " =    0.962
peak=   -3.510 closest distance to " CD1 LEU A 167 " =    2.113
peak=   -3.509 closest distance to " O   HOH Z 103 " =    2.205
peak=   -3.507 closest distance to " O   HOH Z 198 " =    1.295
peak=   -3.506 closest distance to " O   HOH Z 110 " =    1.438
peak=   -3.504 closest distance to " O   HOH Z 362 " =    4.377
peak=   -3.500 closest distance to " OD2 ASP A 298 " =    0.871
peak=   -3.496 closest distance to " CG  GLN A 103 " =    2.227
peak=   -3.495 closest distance to " O   HOH Z 369 " =    2.438
peak=   -3.492 closest distance to " CB  ALA A  10 " =    2.074
peak=   -3.483 closest distance to " O   HOH Z 423 " =    2.899
peak=   -3.480 closest distance to " ND2 ASN A  39 " =    1.295
peak=   -3.474 closest distance to " CG  ASP A  50 " =    2.289
peak=   -3.469 closest distance to " CG2 VAL A 189 " =    2.086
peak=   -3.459 closest distance to " OD1 ASP A 272 " =    1.653
peak=   -3.458 closest distance to " CD2 LEU A 237 " =    2.348
peak=   -3.455 closest distance to " OE2 GLU A 277 " =    2.826
peak=   -3.449 closest distance to " CA  GLY A 203 " =    2.372
peak=   -3.447 closest distance to " O   HOH Z 234 " =    4.069
peak=   -3.446 closest distance to " N   ALA A 295 " =    0.954
peak=   -3.442 closest distance to " O   HOH Z   7 " =    1.349
peak=   -3.440 closest distance to " CB  ALA A 291 " =    2.432
peak=   -3.438 closest distance to " CZ  TYR A 169 " =    1.614
peak=   -3.435 closest distance to " N   VAL A 230 " =    1.013
peak=   -3.429 closest distance to " CG  ASP A 231 " =    0.737
peak=   -3.422 closest distance to " N   ASP A 272 " =    1.243
peak=   -3.417 closest distance to " C   THR A 264 " =    1.409
peak=   -3.414 closest distance to " CG1 VAL A 197 " =    2.508
peak=   -3.411 closest distance to " OD1 ASP A 298 " =    2.364
peak=   -3.409 closest distance to " O   HOH Z 290 " =    0.923
peak=   -3.409 closest distance to " C   THR A 279 " =    1.172
peak=   -3.398 closest distance to " CG2 THR A 182 " =    2.302
peak=   -3.393 closest distance to " O   HOH Z 432 " =    1.001
peak=   -3.390 closest distance to " O   HOH Z   5 " =    1.748
peak=   -3.386 closest distance to " O   HOH Z 378 " =    1.207
peak=   -3.385 closest distance to " O   HOH Z 340 " =    1.259
peak=   -3.383 closest distance to " O   HOH Z 407 " =    3.303
peak=   -3.378 closest distance to " CD1 LEU A  25 " =    2.633
peak=   -3.373 closest distance to " CD2 LEU A 237 " =    2.530
peak=   -3.373 closest distance to " O   HOH Z 252 " =    1.290
peak=   -3.371 closest distance to " OE2 GLU A 128 " =    1.805
peak=   -3.369 closest distance to " CD  LYS A 289 " =    2.372
peak=   -3.366 closest distance to " O   HOH Z  64 " =    1.560
peak=   -3.364 closest distance to " O   HOH Z 331 " =    1.310
peak=   -3.362 closest distance to " CA  PRO A 198 " =    0.939
peak=   -3.362 closest distance to " O   HOH Z 411 " =    1.716
peak=   -3.359 closest distance to " O   SER A 276 " =    1.531
peak=   -3.352 closest distance to " CG  GLN A  58 " =    1.010
peak=   -3.351 closest distance to " CE  MET A 105 " =    2.186
peak=   -3.350 closest distance to " O   HOH Z 265 " =    1.317
peak=   -3.350 closest distance to " O   HOH Z 401 " =    1.443
peak=   -3.348 closest distance to " O   HOH Z 124 " =    1.432
peak=   -3.348 closest distance to " CA  TYR A  68 " =    2.708
peak=   -3.346 closest distance to " O   HOH Z 396 " =    2.388
peak=   -3.328 closest distance to " CE  LYS A 119 " =    2.063
peak=   -3.328 closest distance to " O   HOH Z 426 " =    0.950
peak=   -3.321 closest distance to " CZ  ARG A 259 " =    0.923
peak=   -3.320 closest distance to " O   HOH Z 301 " =    2.484
peak=   -3.314 closest distance to " CD2 LEU A 167 " =    1.858
peak=   -3.309 closest distance to " O   HOH Z 136 " =    1.275
peak=   -3.306 closest distance to " CA  ARG A  36 " =    1.311
peak=   -3.303 closest distance to " O   HOH Z  35 " =    1.117
peak=   -3.303 closest distance to " CD  GLN A 223 " =    0.839
peak=   -3.301 closest distance to " OD1 ASP A 171 " =    1.562
peak=   -3.299 closest distance to " CB  ALA A  43 " =    2.769
peak=   -3.299 closest distance to " SG BCYS A 201 " =    0.973
peak=   -3.296 closest distance to " CE2 TYR A 214 " =    1.804
peak=   -3.295 closest distance to " C   HIS A 108 " =    1.155
peak=   -3.290 closest distance to " OG  SER A  97 " =    2.400
peak=   -3.289 closest distance to " N   VAL A  72 " =    1.154
peak=   -3.288 closest distance to " O   HOH Z 132 " =    1.907
peak=   -3.286 closest distance to " CD2 LEU A 237 " =    2.265
peak=   -3.285 closest distance to " CB  ALA A   7 " =    2.431
peak=   -3.279 closest distance to " CD2 TYR A  30 " =    2.615
peak=   -3.279 closest distance to " O   HOH Z 394 " =    1.819
peak=   -3.278 closest distance to " O   SER A   3 " =    0.940
peak=   -3.278 closest distance to " OH  TYR A 247 " =    2.053
peak=   -3.275 closest distance to " CE3 TRP A 150 " =    2.355
peak=   -3.268 closest distance to " O   HOH Z 252 " =    4.235
peak=   -3.267 closest distance to " O   ASP A  27 " =    1.670
peak=   -3.263 closest distance to " CD2 TYR A 293 " =    1.826
peak=   -3.263 closest distance to " O   HOH Z 184 " =    1.179
peak=   -3.262 closest distance to " CG  ARG A 259 " =    2.444
peak=   -3.259 closest distance to " CZ  TYR A 172 " =    1.939
peak=   -3.255 closest distance to " CG  GLN A  73 " =    0.728
peak=   -3.253 closest distance to " O   ALA A  34 " =    2.442
peak=   -3.253 closest distance to " NE1 TRP A 266 " =    1.936
peak=   -3.249 closest distance to " O   HOH Z 425 " =    1.070
peak=   -3.243 closest distance to " O   HOH Z  93 " =    2.565
peak=   -3.243 closest distance to " CG  ASP A 286 " =    1.304
peak=   -3.240 closest distance to " O   HOH Z 150 " =    1.702
peak=   -3.240 closest distance to " O   HOH Z  17 " =    1.429
peak=   -3.239 closest distance to " OD2 ASP A 171 " =    1.947
peak=   -3.236 closest distance to " CZ  ARG A  79 " =    1.745
peak=   -3.234 closest distance to " CB  ALA A 100 " =    1.698
peak=   -3.233 closest distance to " CG  LEU A  83 " =    2.150
peak=   -3.229 closest distance to " CB  HIS A  86 " =    2.419
peak=   -3.227 closest distance to " CD1 LEU A 101 " =    2.510
peak=   -3.223 closest distance to " OG BSER A 134 " =    1.506
peak=   -3.221 closest distance to " O   HOH Z  11 " =    1.905
peak=   -3.213 closest distance to " O   HOH Z 269 " =    4.079
peak=   -3.209 closest distance to " O   HOH Z 108 " =    2.103
peak=   -3.201 closest distance to " O   HOH Z 253 " =    2.264
peak=   -3.199 closest distance to " N   ALA A  43 " =    2.649
peak=   -3.192 closest distance to " CD2 PHE A  59 " =    2.464
peak=   -3.181 closest distance to " O   HOH Z 216 " =    4.194
peak=   -3.180 closest distance to " O   HOH Z 210 " =    0.838
peak=   -3.179 closest distance to " CA  ASN A 127 " =    0.990
peak=   -3.178 closest distance to " O   VAL A 121 " =    0.836
peak=   -3.177 closest distance to " CD1 ILE A 109 " =    2.077
peak=   -3.175 closest distance to " ND2 ASN A  60 " =    1.489
peak=   -3.168 closest distance to " OE1 GLN A  88 " =    1.253
peak=   -3.166 closest distance to " O   HOH Z 285 " =    1.509
peak=   -3.165 closest distance to " O   HOH Z 118 " =    4.525
peak=   -3.161 closest distance to " CG1BVAL A  72 " =    5.531
peak=   -3.156 closest distance to " CD  PRO A 213 " =    2.186
peak=   -3.145 closest distance to " O   TYR A  15 " =    1.787
peak=   -3.142 closest distance to " O  BHOH Z 338 " =    1.262
peak=   -3.137 closest distance to " CD  ARG A 138 " =    2.540
peak=   -3.131 closest distance to " O   HOH Z 394 " =    5.455
peak=   -3.129 closest distance to " O   HOH Z  54 " =    1.385
peak=   -3.127 closest distance to " CD1 ILE A 263 " =    2.633
peak=   -3.125 closest distance to " CA  SER A 288 " =    1.174
peak=   -3.121 closest distance to " O   HOH Z  50 " =    1.230
peak=   -3.121 closest distance to " CB  MET A 188 " =    1.730
peak=   -3.121 closest distance to " OG BSER A  99 " =    1.156
peak=   -3.110 closest distance to " CD2 HIS A 115 " =    1.102
peak=   -3.104 closest distance to " SG  CYS A 260 " =    2.637
peak=   -3.103 closest distance to " OH  TYR A 169 " =    0.912
peak=   -3.103 closest distance to " CB  SER A 146 " =    2.140
peak=   -3.098 closest distance to " NE  ARG A 156 " =    1.845
peak=   -3.097 closest distance to " O   HOH Z 423 " =    1.252
peak=   -3.095 closest distance to " O   HOH Z 353 " =    1.482
peak=   -3.092 closest distance to " CD1 TYR A 247 " =    2.403
peak=   -3.083 closest distance to " OG1 THR A  82 " =    1.390
peak=   -3.082 closest distance to " C   MET A 188 " =    1.146
peak=   -3.071 closest distance to " O   HOH Z  90 " =    3.283
peak=   -3.049 closest distance to " CZ3 TRP A 266 " =    1.605
peak=   -3.038 closest distance to " O   HOH Z   1 " =    1.997
peak=   -3.036 closest distance to " O   HOH Z 265 " =    1.916
peak=   -3.030 closest distance to " NH1 ARG A 219 " =    1.889
peak=   -3.013 closest distance to " O   PHE A  59 " =    2.122

================= 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    :  0.5014 0.4857   6.301301e+00   6.284351e+00
   1_bss:  0.4953 0.4799   6.294961e+00   6.281545e+00
   1_xyz:  0.4277 0.4362   6.228398e+00   6.234511e+00
   1_adp:  0.3861 0.4327   6.167808e+00   6.227197e+00
   1_occ:  0.3854 0.4323   6.167143e+00   6.227244e+00
   2_bss:  0.3825 0.4254   6.168406e+00   6.226953e+00
   2_xyz:  0.3262 0.3934   6.064902e+00   6.175041e+00
   2_adp:  0.3203 0.3819   6.054042e+00   6.157683e+00
   2_occ:  0.3200 0.3817   6.053576e+00   6.157470e+00
   3_bss:  0.3203 0.3819   6.054773e+00   6.158305e+00
   3_xyz:  0.2552 0.3041   5.844283e+00   5.987114e+00
   3_adp:  0.2374 0.2904   5.792564e+00   5.952413e+00
   3_occ:  0.2370 0.2907   5.792754e+00   5.954315e+00
   4_bss:  0.2360 0.2899   5.791814e+00   5.953334e+00
   4_xyz:  0.1872 0.2370   5.579616e+00   5.770423e+00
   4_adp:  0.1660 0.2100   5.470054e+00   5.666103e+00
   4_occ:  0.1659 0.2103   5.470059e+00   5.666507e+00
   5_bss:  0.1660 0.2104   5.471393e+00   5.665924e+00
   5_xyz:  0.1444 0.1903   5.356249e+00   5.566853e+00
   5_adp:  0.1388 0.1860   5.325220e+00   5.539678e+00
   5_occ:  0.1387 0.1859   5.324985e+00   5.539432e+00
   5_bss:  0.1386 0.1858   5.324899e+00   5.539168e+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:  0.311  20.000   5.659  12.063   8.270   0.000   0.000   0.000
   1_xyz:  0.311  20.000   5.659  12.063   8.270   0.000   0.000   0.000
   1_adp:  0.311  20.000   5.659  12.063   8.270   0.000   0.000   0.000
   1_occ:  0.311  20.000   5.659  12.063   8.270   0.000   0.000   0.000
   2_bss:  0.284  31.242   1.844   6.985   4.188   0.000   0.000   0.000
   2_xyz:  0.284  31.242   1.844   6.985   4.188   0.000   0.000   0.000
   2_adp:  0.284  31.242   1.844   6.985   4.188   0.000   0.000   0.000
   2_occ:  0.284  31.242   1.844   6.985   4.188   0.000   0.000   0.000
   3_bss:  0.289  31.242   1.307   5.371   2.984   0.000   0.000   0.000
   3_xyz:  0.289  31.242   1.307   5.371   2.984   0.000   0.000   0.000
   3_adp:  0.289  31.242   1.307   5.371   2.984   0.000   0.000   0.000
   3_occ:  0.289  31.242   1.307   5.371   2.984   0.000   0.000   0.000
   4_bss:  0.316  48.571   0.440   3.136   2.138   0.000   0.000   0.000
   4_xyz:  0.316  48.571   0.440   3.136   2.138   0.000   0.000   0.000
   4_adp:  0.316  48.571   0.440   3.136   2.138   0.000   0.000   0.000
   4_occ:  0.316  48.571   0.440   3.136   2.138   0.000   0.000   0.000
   5_bss:  0.312  66.830   0.129   1.974   1.974   0.000   0.000   0.000
   5_xyz:  0.312  66.830   0.129   1.974   1.974   0.000   0.000   0.000
   5_adp:  0.312  66.830   0.129   1.974   1.974   0.000   0.000   0.000
   5_occ:  0.312  66.830   0.129   1.974   1.974   0.000   0.000   0.000
   5_bss:  0.328  67.737  -1.130   0.383   0.747   0.000   0.000   0.000
------------------------------------------------------------------------
 stage     <pher>    fom   alpha         beta
   0    :  59.720 0.3981  0.4607    74938.323
   1_bss:  59.901 0.3947  0.5862    74064.271
   1_xyz:  50.924 0.5086  0.7379    57288.821
   1_adp:  49.960 0.5203  0.8282    55599.668
   1_occ:  49.966 0.5202  0.8268    55572.067
   2_bss:  49.616 0.5246  0.7232    55157.301
   2_xyz:  44.793 0.5842  0.8054    46173.313
   2_adp:  43.203 0.6042  0.8225    43850.006
   2_occ:  43.158 0.6048  0.8229    43789.996
   3_bss:  43.043 0.6061  0.7939    43632.383
   3_xyz:  32.342 0.7313  0.9303    25902.320
   3_adp:  30.472 0.7527  0.9472    23563.254
   3_occ:  30.567 0.7516  0.9454    23673.236
   4_bss:  30.444 0.7530  0.9059    23553.899
   4_xyz:  23.371 0.8281  0.9604    14433.893
   4_adp:  20.450 0.8573  0.9692    11501.686
   4_occ:  20.460 0.8573  0.9692    11524.683
   5_bss:  20.449 0.8575  0.9515    11548.353
   5_xyz:  18.082 0.8796  0.9648     9283.675
   5_adp:  17.317 0.8870  0.9637     8824.666
   5_occ:  17.310 0.8870  0.9636     8823.735
   5_bss:  17.306 0.8871  0.9617     8821.806
------------------------------------------------------------------------
 stage       angl   bond   chir   dihe   plan   repu  geom_target
   0    :  24.226  0.414  2.119 33.790  0.145  4.092   5.4323e+01
   1_bss:  24.226  0.414  2.119 33.790  0.145  4.092   5.4323e+01
   1_xyz:   1.669  0.013  0.107 18.206  0.007  4.123   1.4078e-01
   1_adp:   1.669  0.013  0.107 18.206  0.007  4.123   1.4078e-01
   1_occ:   1.669  0.013  0.107 18.206  0.007  4.123   1.4078e-01
   2_bss:   1.669  0.013  0.107 18.206  0.007  4.123   1.4078e-01
   2_xyz:   1.228  0.009  0.080 16.390  0.005  4.108   8.8800e-02
   2_adp:   1.228  0.009  0.080 16.390  0.005  4.108   8.8800e-02
   2_occ:   1.228  0.009  0.080 16.390  0.005  4.108   8.8800e-02
   3_bss:   1.228  0.009  0.080 16.390  0.005  4.108   8.8800e-02
   3_xyz:   1.386  0.011  0.098 15.998  0.005  4.113   1.0583e-01
   3_adp:   1.386  0.011  0.098 15.998  0.005  4.113   1.0583e-01
   3_occ:   1.386  0.011  0.098 15.998  0.005  4.113   1.0583e-01
   4_bss:   1.386  0.011  0.098 15.998  0.005  4.113   1.0583e-01
   4_xyz:   1.123  0.009  0.077 15.498  0.005  4.133   7.8371e-02
   4_adp:   1.123  0.009  0.077 15.498  0.005  4.133   7.8371e-02
   4_occ:   1.123  0.009  0.077 15.498  0.005  4.133   7.8371e-02
   5_bss:   1.123  0.009  0.077 15.498  0.005  4.133   7.8371e-02
   5_xyz:   1.045  0.007  0.078 15.094  0.003  4.124   6.4745e-02
   5_adp:   1.045  0.007  0.078 15.094  0.003  4.124   6.4745e-02
   5_occ:   1.045  0.007  0.078 15.094  0.003  4.124   6.4745e-02
   5_bss:   1.045  0.007  0.078 15.094  0.003  4.124   6.4745e-02
------------------------------------------------------------------------
                      Maximal deviations:
 stage       angl   bond   chir   dihe   plan   repu       |grad|
   0    :  74.492  1.400  6.404144.062  0.405  1.196   7.0425e+00
   1_bss:  74.492  1.400  6.404144.062  0.405  1.196   7.0425e+00
   1_xyz:  14.888  0.115  0.477 88.027  0.040  2.260   1.0089e-01
   1_adp:  14.888  0.115  0.477 88.027  0.040  2.260   1.0089e-01
   1_occ:  14.888  0.115  0.477 88.027  0.040  2.260   1.0089e-01
   2_bss:  14.888  0.115  0.477 88.027  0.040  2.260   1.0089e-01
   2_xyz:   7.682  0.081  0.311 85.154  0.038  2.202   8.4505e-02
   2_adp:   7.682  0.081  0.311 85.154  0.038  2.202   8.4505e-02
   2_occ:   7.682  0.081  0.311 85.154  0.038  2.202   8.4505e-02
   3_bss:   7.682  0.081  0.311 85.154  0.038  2.202   8.4505e-02
   3_xyz:   8.364  0.107  0.316 85.339  0.032  2.200   9.2953e-02
   3_adp:   8.364  0.107  0.316 85.339  0.032  2.200   9.2953e-02
   3_occ:   8.364  0.107  0.316 85.339  0.032  2.200   9.2953e-02
   4_bss:   8.364  0.107  0.316 85.339  0.032  2.200   9.2953e-02
   4_xyz:   7.148  0.060  0.268 88.522  0.050  2.173   7.3510e-02
   4_adp:   7.148  0.060  0.268 88.522  0.050  2.173   7.3510e-02
   4_occ:   7.148  0.060  0.268 88.522  0.050  2.173   7.3510e-02
   5_bss:   7.148  0.060  0.268 88.522  0.050  2.173   7.3510e-02
   5_xyz:   7.233  0.040  0.324 80.326  0.030  2.231   4.3059e-02
   5_adp:   7.233  0.040  0.324 80.326  0.030  2.231   4.3059e-02
   5_occ:   7.233  0.040  0.324 80.326  0.030  2.231   4.3059e-02
   5_bss:   7.233  0.040  0.324 80.326  0.030  2.231   4.3059e-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: 122.30   0.00  16.02  76.68   0.00  13.90 122.30   0.00  27.58
   1_occ: 122.30   0.00  16.02  76.68   0.00  13.90 122.30   0.00  27.58
   2_bss: 122.30   0.00  16.02  76.68   0.00  13.90 122.30   0.00  27.58
   2_xyz: 122.30   0.00  16.02  76.68   0.00  13.90 122.30   0.00  27.58
   2_adp: 109.42   0.00  14.45  64.80   0.00  12.22 109.42   0.00  26.61
   2_occ: 109.42   0.00  14.45  64.80   0.00  12.22 109.42   0.00  26.61
   3_bss: 109.42   0.00  14.45  64.80   0.00  12.22 109.42   0.00  26.61
   3_xyz: 109.42   0.00  14.45  64.80   0.00  12.22 109.42   0.00  26.61
   3_adp: 161.20   0.00  14.41 161.20   0.00  11.62 107.38   0.00  29.62
   3_occ: 161.20   0.00  14.41 161.20   0.00  11.62 107.38   0.00  29.62
   4_bss: 161.20   0.00  14.41 161.20   0.00  11.62 107.38   0.00  29.62
   4_xyz: 161.20   0.00  14.41 161.20   0.00  11.62 107.38   0.00  29.62
   4_adp:  91.04   0.00  15.14  87.31   0.00  10.78  91.04   2.03  38.89
   4_occ:  91.04   0.00  15.14  87.31   0.00  10.78  91.04   2.03  38.89
   5_bss:  91.04   0.00  15.14  87.31   0.00  10.78  91.04   2.03  38.89
   5_xyz:  91.04   0.00  15.14  87.31   0.00  10.78  91.04   2.03  38.89
   5_adp:  91.84   0.00  15.07  88.89   0.00  10.40  91.84   1.85  40.50
   5_occ:  91.84   0.00  15.07  88.89   0.00  10.40  91.84   1.85  40.50
   5_bss:  93.12   1.28  16.35  90.17   1.28  11.69  93.12   3.13  41.78
------------------------------------------------------------------------
 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:    1.134    0.008    0.406
   1_adp:    1.134    0.008    0.406
   1_occ:    1.134    0.008    0.406
   2_bss:    1.134    0.008    0.406
   2_xyz:    1.554    0.044    0.550
   2_adp:    1.554    0.044    0.550
   2_occ:    1.554    0.044    0.550
   3_bss:    1.554    0.044    0.550
   3_xyz:    1.760    0.039    0.721
   3_adp:    1.760    0.039    0.721
   3_occ:    1.760    0.039    0.721
   4_bss:    1.760    0.039    0.721
   4_xyz:    1.918    0.080    0.833
   4_adp:    1.918    0.080    0.833
   4_occ:    1.918    0.080    0.833
   5_bss:    1.918    0.080    0.833
   5_xyz:    1.910    0.058    0.866
   5_adp:    1.910    0.058    0.866
   5_occ:    1.910    0.058    0.866
   5_bss:    1.910    0.058    0.866
------------------------------------------------------------------------

CPU time actual refinement: 356.61


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

Writing refined structure to PDB file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/trial/run_601/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_601/model_refine_001_2mFobs-DFmodel.map
Writing mFobs-DFmodel XPLOR map to file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/trial/run_601/model_refine_001_mFobs-DFmodel.map
Writing map coefficients to MTZ file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/trial/run_601/model_refine_001_map_coeffs.mtz

Writing default parameters for subsequent refinement:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/trial/run_601/model_refine_002.def


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

Pure refinement (no I/O, processing, etc)= 356.46 
  Macro-tasks:
    bulk solvent and scale       = 41.71  
    individual site refinement   = 155.03 
    weights calculation          = 33.57  
    collect and process          = 6.34   
    model show statistics        = 0.14   
    TOTAL for macro-tasks        = 236.79 
  Micro-tasks:
    mask                            = 2.48   
    f_calc                          = 112.38 
    alpha_beta                      = 8.28   
    target                          = 1.17   
    gradients_wrt_atomic_parameters = 123.86 
    fmodel                         = 7.59   
    r_factors                      = 0.18   
    phase_errors                   = 9.95   
    foms                           = 0.22   
    TOTAL for micro-tasks          = 266.11 
NUMBER OF MASK CALCS=  5
Time per interpreted Python bytecode instruction: 4.938 micro seconds
Total CPU time: 6.17 minutes
from_scatterers_fft:    657 calls, 112.01 s
gradients_fft:          601 calls, 109.64 s

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

# Date 2008-01-16 Time 01:58:20 PST -0800 (1200477500.74 s)
Start R-work = 0.5014, R-free = 0.4857 (no bulk solvent and anisotropic scale)
Final R-work = 0.1547, R-free = 0.2009 (no bulk solvent and anisotropic scale)

Start R-work = 0.4953, R-free = 0.4799
Final R-work = 0.1386, R-free = 0.1858