# Date 2008-01-16 Time 01:40:21 PST -0800 (1200476421.71 s)
#phil __OFF__

Command line arguments: "../519.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 = 30305
JOB_ID = 5158
SGE_ARCH = lx24-amd64
SGE_TASK_FIRST = 1
SGE_TASK_LAST = 1330
SGE_TASK_ID = 519

-------------------------------------------------------------------------------
  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, 46.4607, 85.0941, 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: 3.32, per 1000 atoms: 1.18


================================== 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, 46.4607, 85.0941, 90, 90, 90)
Space group: P 21 21 21 (No. 19)
Systematic absences: 0
Centric reflections: 2427
Resolution range: 14.8779 1.97101
Completeness in resolution range: 0.972593
Completeness with d_max=infinity: 0.969512

Number of F-obs in resolution range:                   19589
Number of F-obs <= 0:                                  0
Refinement resolution range: d_max =  14.8779
                             d_min =   1.9710

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, 46.4607, 85.0941, 90, 90, 90)
Space group: P 21 21 21 (No. 19)
Systematic absences: 0
Centric reflections: 2427
Resolution range: 14.8779 1.97101
Completeness in resolution range: 0.972593
Completeness with d_max=infinity: 0.969512

Test (R-free flags) flag value: 1

Number of work/free reflections by resolution:
                                         work  free  %free
  bin  1: 14.8783 -  4.2172 [2104/2128]  1894   210  10.0%
  bin  2:  4.2172 -  3.3600 [2038/2057]  1834   204  10.0%
  bin  3:  3.3600 -  2.9390 [2009/2028]  1805   204  10.2%
  bin  4:  2.9390 -  2.6720 [1991/2021]  1797   194   9.7%
  bin  5:  2.6720 -  2.4814 [1977/1996]  1778   199  10.1%
  bin  6:  2.4814 -  2.3357 [1944/1969]  1751   193   9.9%
  bin  7:  2.3357 -  2.2191 [1967/1995]  1766   201  10.2%
  bin  8:  2.2191 -  2.1228 [1949/1985]  1757   192   9.9%
  bin  9:  2.1228 -  2.0413 [1939/1981]  1747   192   9.9%
  bin 10:  2.0413 -  1.9710 [1671/1981]  1501   170  10.2%
                                overall 17630  1959  10.0%
Writing MTZ file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/trial/run_519/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: 36
        2.42 -     3.04: 2227
        3.04 -     3.66: 4798
        3.66 -     4.28: 9137
        4.28 -     4.90: 12535
  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  52 " - " O   HOH Z 183 "  1.878 3.040 -x+1,y+1/2,-z+1/2
  " O   HOH Z 110 " - " O   HOH Z 355 "  1.979 3.040 -x+1/2,-y+1,z+1/2
  " O   HOH Z 178 " - " O   HOH Z 403 "  1.987 3.040 -x+1,y-1/2,-z+1/2
  " O   HOH Z 271 " - " O   HOH Z 342 "  2.040 3.040 -x+1/2,-y+1,z+1/2
  ... (remaining 28728 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_519/model_refine_001.eff

Writing geometry restraints to file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/trial/run_519/model_refine_001.geo

CPU time processing inputs: 9.57


============================ 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 46.4607 85.09415 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: 1.97 - 14.88 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.4574   r_free= 0.4451   ksol= 0.00   Bsol= 0.00   scale= 0.817    |
|                                                                             |
| 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:   0.66 A                  |
| x-ray target function (ml) for work reflections: 6.255489                   |
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
| Bin     Resolution   Compl.  No. Refl.    R-factors          Targets        |
|number     range              work test   work   test        work        test|
|  1: 14.8783 -  4.7035 0.99   1376  153 0.3812 0.3813      6.5505      6.5486|
|  2:  4.7035 -  3.7530 0.99   1323  146 0.3713 0.3502      6.7233      6.7029|
|  3:  3.7530 -  3.2844 0.99   1296  145 0.4032 0.3800      6.6236      6.6797|
|  4:  3.2844 -  2.9868 0.99   1281  144 0.4348 0.4001      6.5017       6.436|
|  5:  2.9868 -  2.7742 0.99   1281  143 0.4808 0.4947      6.3493      6.3303|
|  6:  2.7742 -  2.6116 0.99   1280  137 0.4832 0.5560      6.2668      6.2699|
|  7:  2.6116 -  2.4814 0.99   1271  143 0.4928 0.4256      6.2293      6.1766|
|  8:  2.4814 -  2.3738 0.98   1260  146 0.5100 0.4830      6.1819      6.1757|
|  9:  2.3738 -  2.2828 0.98   1260  135 0.4957 0.5062      6.1083      6.1055|
| 10:  2.2828 -  2.2043 0.99   1240  141 0.5089 0.4853      6.1181      6.1064|
| 11:  2.2043 -  2.1355 0.98   1263  136 0.5108 0.4500      6.0516      5.9893|
| 12:  2.1355 -  2.0747 0.97   1237  138 0.4975 0.4970       5.982      6.0206|
| 13:  2.0747 -  2.0202 1.00   1252  145 0.5195 0.5234      5.8919      5.8634|
| 14:  2.0202 -  1.9710 0.78   1010  107 0.5379 0.5298      5.8404      5.7632|
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
|R-free likelihood based estimates for figures of merit, absolute phase error,|
|and distribution parameters alpha and beta (Acta Cryst. (1995). A51, 880-887)|
|                                                                             |
| Bin     Resolution      No. Refl.   FOM  Phase Scale    Alpha        Beta   |
|  #        range        work  test        error factor                       |
|  1: 14.8783 -  4.7035  1376   153  0.69  35.31   0.81     0.73      72838.99|
|  2:  4.7035 -  3.7530  1323   146  0.73  32.37   0.90     0.81      92911.04|
|  3:  3.7530 -  3.2844  1296   145  0.65  39.28   0.88     0.78      96135.99|
|  4:  3.2844 -  2.9868  1281   144  0.59  44.81   0.84     0.69      85278.04|
|  5:  2.9868 -  2.7742  1281   143  0.48  53.15   0.76     0.57      73165.81|
|  6:  2.7742 -  2.6116  1280   137  0.46  55.45   0.75     0.52      65254.87|
|  7:  2.6116 -  2.4814  1271   143  0.43  57.17   0.75     0.50      60256.73|
|  8:  2.4814 -  2.3738  1260   146  0.43  57.44   0.75     0.51      54134.68|
|  9:  2.3738 -  2.2828  1260   135  0.45  55.70   0.75     0.52      46816.81|
| 10:  2.2828 -  2.2043  1240   141  0.47  54.71   0.77     0.54      41187.96|
| 11:  2.2043 -  2.1355  1263   136  0.45  55.75   0.78     0.55      38297.43|
| 12:  2.1355 -  2.0747  1237   138  0.42  58.76   0.79     0.51      38738.36|
| 13:  2.0747 -  2.0202  1252   145  0.33  65.70   0.76     0.40      36207.67|
| 14:  2.0202 -  1.9710  1010   107  0.25  71.64   0.72     0.27      32006.18|
|alpha:            min =        0.27 max =            0.81 mean =         0.57|
|beta:             min =    32006.18 max =        96135.99 mean =     60297.12|
|figures of merit: min =        0.00 max =            1.00 mean =         0.49|
|phase err.(work): min =        0.00 max =           89.96 mean =        52.16|
|phase err.(test): min =        0.00 max =           89.82 mean =        52.21|
|-----------------------------------------------------------------------------|

============================== 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 = 9.941448              wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 78.263   (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 0.955914              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 81.446   (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:        3 |
| 0.140 - 0.280:   585 |   7.457 -  14.906:   711 |  1.566 -  1.937:       26 |
| 0.280 - 0.420:   441 |  14.906 -  22.354:   630 |  1.937 -  2.307:      175 |
| 0.420 - 0.560:   366 |  22.354 -  29.802:   474 |  2.307 -  2.677:      701 |
| 0.560 - 0.700:   237 |  29.802 -  37.251:   338 |  2.677 -  3.048:     1547 |
| 0.700 - 0.840:   127 |  37.251 -  44.699:   241 |  3.048 -  3.418:     2680 |
| 0.840 - 0.980:    59 |  44.699 -  52.147:   125 |  3.418 -  3.789:     3984 |
| 0.980 - 1.120:    17 |  52.147 -  59.595:    51 |  3.789 -  4.159:     5145 |
| 1.120 - 1.260:     9 |  59.595 -  67.044:    13 |  4.159 -  4.530:     6652 |
| 1.260 - 1.400:     1 |  67.044 -  74.492:     3 |  4.530 -  4.900:     7802 |
|-----------------------------------------------------------------------------|
|-Geometry statistics: start--------------------------------------------------|
|      Type |    Count |    Deviation from ideal |     Targets | Target (sum) |
|           |          |    rmsd      max    min |             |              |
|      bond |     2439 |   0.414    1.400  0.000 |     454.651 |              |
|     angle |     3299 |  24.226   74.492  0.009 |     193.752 |              |
| chirality |      348 |   2.119    6.404  0.009 |     112.240 |       53.148 |
| planarity |      436 |   0.145    0.405  0.000 |     250.485 |              |
|  dihedral |      870 |  33.790  144.062  0.019 |      20.704 |              |
| nonbonded |     2439 |   4.089    4.900  1.196 |       1.904 |              |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 11.572)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      10.00   10.00   10.00    None  None   None       |
|    all(noH): 2823   0      10.00   10.00   10.00    None  None   None       |
|    Sol.    : 438    0      10.00   10.00   10.00    None  None   None       |
|    Mac.    : 2385   0      10.00   10.00   10.00    None  None   None       |
|    Hyd.    : 0      0      None    None    None     None  None   None       |
|    - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -      |
|       Distribution of isotropic (or equivalent) ADP for non-H atoms:        |
|    Bin#      value range     #atoms | Bin#      value range     #atoms      |
|      0:    10.000 -  10.000: 2823   |   5:    10.000 -  10.000:    0        |
|      1:    10.000 -  10.000:    0   |   6:    10.000 -  10.000:    0        |
|      2:    10.000 -  10.000:    0   |   7:    10.000 -  10.000:    0        |
|      3:    10.000 -  10.000:    0   |   8:    10.000 -  10.000:    0        |
|      4:    10.000 -  10.000:    0   |   9:    10.000 -  10.000:    0        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|

|-Occupancies statistics------------------------------------------------------|
| occupancies: max = 1.00   min = 0.30   number of occupancies < 0.1 = 0      |
|-----------------------------------------------------------------------------|

                ----------Modify initial isotropic ADP----------               

Randomizing
|-ADP statistics (Wilson B = 11.572)------------------------------------------|
|    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: 1.97 - 14.88 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.4652   r_free= 0.4504   ksol= 0.00   Bsol= 0.00   scale= 0.785    |
|                                                                             |
| 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:   0.67 A                  |
| x-ray target function (ml) for work reflections: 6.259321                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.97 - 14.88 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.4491   r_free= 0.4354   ksol= 0.36   Bsol= 2.23   scale= 1.012    |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (6.82,8.91,8.57,0.00,0.00,0.00); trace/3= 8.10                              |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.67 A                  |
| x-ray target function (ml) for work reflections: 6.248627                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 8.770364              wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 79.525   (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 0.887964              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 77.462   (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.4491      final r-factor (work) = 0.3563          |
| start r-factor (free) = 0.4354      final r-factor (free) = 0.3756          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 80.5938 = 8.77 * 0.50 * 6.2588 + 1.00 * 53.1478                             |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 27.0479 = 8.77 * 0.50 * 6.1388 + 1.00 * 0.1282                              |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 26     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.3563      final r-factor (work) = 0.3046          |
| start r-factor (free) = 0.3756      final r-factor (free) = 0.3446          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 5.4657 = 0.89 * 1.00 * 6.1388 + 1.00 * 0.0147                               |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 5.3532 = 0.89 * 1.00 * 6.0123 + 1.00 * 0.0145                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 27     |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 11.572)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.00    84.89   11.87    None  None   None       |
|    all(noH): 2823   0      0.00    84.89   11.87    None  None   None       |
|    Sol.    : 438    0      0.00    72.24   27.27    None  None   None       |
|    Mac.    : 2385   0      0.00    84.89   9.05     None  None   None       |
|    Hyd.    : 0      0      None    None    None     None  None   None       |
|    - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -      |
|       Distribution of isotropic (or equivalent) ADP for non-H atoms:        |
|    Bin#      value range     #atoms | Bin#      value range     #atoms      |
|      0:     0.000 -   8.489: 1448   |   5:    42.443 -  50.931:   40        |
|      1:     8.489 -  16.977:  741   |   6:    50.931 -  59.420:   11        |
|      2:    16.977 -  25.466:  291   |   7:    59.420 -  67.908:    7        |
|      3:    25.466 -  33.954:  166   |   8:    67.908 -  76.397:    4        |
|      4:    33.954 -  42.443:  113   |   9:    76.397 -  84.885:    2        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.3046 r_free = 0.3446             target_work(ml) = 5.980         |
| occupancies: max = 1.00  min = 0.30   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.3037 r_free = 0.3452             target_work(ml) = 5.979         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        8 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.97 - 14.88 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.3037   r_free= 0.3452   ksol= 0.36   Bsol= 2.23   scale= 1.099    |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (6.82,8.91,8.57,0.00,0.00,0.00); trace/3= 8.10                              |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.40 A                  |
| x-ray target function (ml) for work reflections: 5.979440                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.97 - 14.88 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.2994   r_free= 0.3402   ksol= 0.33   Bsol= 20.00   scale= 1.011   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (3.58,4.78,5.55,0.00,0.00,0.00); trace/3= 4.64                              |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.41 A                  |
| x-ray target function (ml) for work reflections: 5.976076                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 3.786103              wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 95.785   (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 0.417248              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 124.703  (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.2994      final r-factor (work) = 0.2070          |
| start r-factor (free) = 0.3402      final r-factor (free) = 0.2531          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 11.5063 = 3.79 * 0.50 * 6.0108 + 1.00 * 0.1275                              |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 11.0592 = 3.79 * 0.50 * 5.8079 + 1.00 * 0.0644                              |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 29     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.2070      final r-factor (work) = 0.1863          |
| start r-factor (free) = 0.2531      final r-factor (free) = 0.2347          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 2.4374 = 0.42 * 1.00 * 5.8079 + 1.00 * 0.0141                               |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 2.3884 = 0.42 * 1.00 * 5.6082 + 1.00 * 0.0483                               |
|-----------------------------------------------------------------------------|
| number of iterations = 16      |    number of function evaluations = 16     |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 11.572)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.00    85.19   11.92    None  None   None       |
|    all(noH): 2823   0      0.00    85.19   11.92    None  None   None       |
|    Sol.    : 438    0      1.13    67.69   31.54    None  None   None       |
|    Mac.    : 2385   0      0.00    85.19   8.32     None  None   None       |
|    Hyd.    : 0      0      None    None    None     None  None   None       |
|    - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -      |
|       Distribution of isotropic (or equivalent) ADP for non-H atoms:        |
|    Bin#      value range     #atoms | Bin#      value range     #atoms      |
|      0:     0.000 -   8.519: 1623   |   5:    42.593 -  51.112:   64        |
|      1:     8.519 -  17.037:  587   |   6:    51.112 -  59.630:   16        |
|      2:    17.037 -  25.556:  190   |   7:    59.630 -  68.149:    9        |
|      3:    25.556 -  34.074:  176   |   8:    68.149 -  76.667:    1        |
|      4:    34.074 -  42.593:  155   |   9:    76.667 -  85.186:    2        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.1863 r_free = 0.2347             target_work(ml) = 5.572         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        8 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.1859 r_free = 0.2339             target_work(ml) = 5.571         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        8 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.97 - 14.88 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1859   r_free= 0.2339   ksol= 0.33   Bsol= 20.00   scale= 1.048   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (3.58,4.78,5.55,0.00,0.00,0.00); trace/3= 4.64                              |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.21 A                  |
| x-ray target function (ml) for work reflections: 5.570608                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.97 - 14.88 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1847   r_free= 0.2337   ksol= 0.33   Bsol= 32.36   scale= 1.011   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (2.60,3.20,4.03,0.00,0.00,0.00); trace/3= 3.28                              |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.22 A                  |
| x-ray target function (ml) for work reflections: 5.568263                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 2.311510              wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 102.290  (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 1.216654              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 92.075   (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1847      final r-factor (work) = 0.1411          |
| start r-factor (free) = 0.2337      final r-factor (free) = 0.1872          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 6.5522 = 2.31 * 0.50 * 5.6135 + 1.00 * 0.0644                               |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 6.3602 = 2.31 * 0.50 * 5.4532 + 1.00 * 0.0577                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 27     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1411      final r-factor (work) = 0.1310          |
| start r-factor (free) = 0.1872      final r-factor (free) = 0.1776          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 6.6479 = 1.22 * 1.00 * 5.4532 + 1.00 * 0.0133                               |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 6.4579 = 1.22 * 1.00 * 5.2969 + 1.00 * 0.0134                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 28     |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 11.572)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.00    91.99   12.62    None  None   None       |
|    all(noH): 2823   0      0.00    91.99   12.62    None  None   None       |
|    Sol.    : 438    0      0.69    74.25   36.65    None  None   None       |
|    Mac.    : 2385   0      0.00    91.99   8.21     None  None   None       |
|    Hyd.    : 0      0      None    None    None     None  None   None       |
|    - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -      |
|       Distribution of isotropic (or equivalent) ADP for non-H atoms:        |
|    Bin#      value range     #atoms | Bin#      value range     #atoms      |
|      0:     0.000 -   9.199: 1748   |   5:    45.997 -  55.197:   94        |
|      1:     9.199 -  18.399:  524   |   6:    55.197 -  64.396:   51        |
|      2:    18.399 -  27.598:  142   |   7:    64.396 -  73.595:   14        |
|      3:    27.598 -  36.798:  131   |   8:    73.595 -  82.795:    2        |
|      4:    36.798 -  45.997:  115   |   9:    82.795 -  91.994:    2        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.1310 r_free = 0.1776             target_work(ml) = 5.269         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        8 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.1309 r_free = 0.1776             target_work(ml) = 5.269         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        8 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.97 - 14.88 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1309   r_free= 0.1776   ksol= 0.33   Bsol= 32.36   scale= 1.023   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (2.60,3.20,4.03,0.00,0.00,0.00); trace/3= 3.28                              |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.16 A                  |
| x-ray target function (ml) for work reflections: 5.268821                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.97 - 14.88 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1312   r_free= 0.1780   ksol= 0.32   Bsol= 35.30   scale= 1.012   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (2.41,2.69,3.56,0.00,0.00,0.00); trace/3= 2.89                              |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.16 A                  |
| x-ray target function (ml) for work reflections: 5.268314                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 1.683756              wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 116.378  (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 0.927379              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 112.911  (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1312      final r-factor (work) = 0.1190          |
| start r-factor (free) = 0.1780      final r-factor (free) = 0.1644          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 4.5179 = 1.68 * 0.50 * 5.2983 + 1.00 * 0.0574                               |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 4.4563 = 1.68 * 0.50 * 5.2281 + 1.00 * 0.0549                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 28     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1190      final r-factor (work) = 0.1167          |
| start r-factor (free) = 0.1644      final r-factor (free) = 0.1630          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 4.8619 = 0.93 * 1.00 * 5.2281 + 1.00 * 0.0134                               |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 4.8239 = 0.93 * 1.00 * 5.1837 + 1.00 * 0.0166                               |
|-----------------------------------------------------------------------------|
| number of iterations = 21      |    number of function evaluations = 23     |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 11.572)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.00    94.61   12.48    None  None   None       |
|    all(noH): 2823   0      0.00    94.61   12.48    None  None   None       |
|    Sol.    : 438    0      1.28    76.81   36.37    None  None   None       |
|    Mac.    : 2385   0      0.00    94.61   8.09     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 -   9.461: 1792   |   5:    47.306 -  56.767:   82        |
|      1:     9.461 -  18.922:  510   |   6:    56.767 -  66.228:   41        |
|      2:    18.922 -  28.384:  139   |   7:    66.228 -  75.690:   18        |
|      3:    28.384 -  37.845:  124   |   8:    75.690 -  85.151:    1        |
|      4:    37.845 -  47.306:  113   |   9:    85.151 -  94.612:    3        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.1167 r_free = 0.1630             target_work(ml) = 5.177         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        8 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.1166 r_free = 0.1630             target_work(ml) = 5.177         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        6 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.97 - 14.88 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1166   r_free= 0.1630   ksol= 0.32   Bsol= 35.30   scale= 1.012   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (2.41,2.69,3.56,0.00,0.00,0.00); trace/3= 2.89                              |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.15 A                  |
| x-ray target function (ml) for work reflections: 5.176771                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.97 - 14.88 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1166   r_free= 0.1630   ksol= 0.32   Bsol= 35.30   scale= 1.013   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (2.48,2.69,3.55,0.00,0.00,0.00); trace/3= 2.91                              |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.15 A                  |
| x-ray target function (ml) for work reflections: 5.176722                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 2.696978              wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 114.112  (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 0.302924              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 106.283  (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1166      final r-factor (work) = 0.1095          |
| start r-factor (free) = 0.1630      final r-factor (free) = 0.1592          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 7.0449 = 2.70 * 0.50 * 5.1836 + 1.00 * 0.0549                               |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 7.0097 = 2.70 * 0.50 * 5.1491 + 1.00 * 0.0662                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 28     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1095      final r-factor (work) = 0.1094          |
| start r-factor (free) = 0.1592      final r-factor (free) = 0.1569          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 1.5834 = 0.30 * 1.00 * 5.1491 + 1.00 * 0.0236                               |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 1.5668 = 0.30 * 1.00 * 5.1356 + 1.00 * 0.0111                               |
|-----------------------------------------------------------------------------|
| number of iterations = 24      |    number of function evaluations = 29     |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 11.572)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.00    94.36   12.07    None  None   None       |
|    all(noH): 2823   0      0.00    94.36   12.07    None  None   None       |
|    Sol.    : 438    0      1.47    76.05   34.85    None  None   None       |
|    Mac.    : 2385   0      0.00    94.36   7.89     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 -   9.436: 1833   |   5:    47.180 -  56.616:   74        |
|      1:     9.436 -  18.872:  484   |   6:    56.616 -  66.052:   36        |
|      2:    18.872 -  28.308:  148   |   7:    66.052 -  75.488:   14        |
|      3:    28.308 -  37.744:  125   |   8:    75.488 -  84.924:    1        |
|      4:    37.744 -  47.180:  105   |   9:    84.924 -  94.360:    3        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.1094 r_free = 0.1569             target_work(ml) = 5.127         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        6 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.1093 r_free = 0.1568             target_work(ml) = 5.127         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        6 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.97 - 14.88 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1093   r_free= 0.1568   ksol= 0.32   Bsol= 35.30   scale= 1.011   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (2.48,2.69,3.55,0.00,0.00,0.00); trace/3= 2.91                              |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.14 A                  |
| x-ray target function (ml) for work reflections: 5.126851                   |
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
| Bin     Resolution   Compl.  No. Refl.    R-factors          Targets        |
|number     range              work test   work   test        work        test|
|  1: 14.8783 -  4.7035 0.99   1376  153 0.0971 0.1233      5.3611      5.4943|
|  2:  4.7035 -  3.7530 0.99   1323  146 0.0838 0.1140      5.4178      5.6408|
|  3:  3.7530 -  3.2844 0.99   1296  145 0.1032 0.1523      5.4636      5.8449|
|  4:  3.2844 -  2.9868 0.99   1281  144 0.1201 0.1601      5.4523      5.6065|
|  5:  2.9868 -  2.7742 0.99   1281  143 0.1246 0.1709      5.2989      5.5134|
|  6:  2.7742 -  2.6116 0.99   1280  137 0.1139 0.1764      5.1826      5.4111|
|  7:  2.6116 -  2.4814 0.99   1271  143 0.1250 0.1634      5.1517      5.3864|
|  8:  2.4814 -  2.3738 0.98   1260  146 0.1144 0.1765      5.0656       5.357|
|  9:  2.3738 -  2.2828 0.98   1260  135 0.1138 0.1735       5.023      5.2746|
| 10:  2.2828 -  2.2043 0.99   1240  141 0.1072 0.1692      4.9365      5.2155|
| 11:  2.2043 -  2.1355 0.98   1263  136 0.1123 0.1786      4.9324      5.2681|
| 12:  2.1355 -  2.0747 0.97   1237  138 0.1091 0.1625      4.8666      5.1877|
| 13:  2.0747 -  2.0202 1.00   1252  145 0.1129 0.1705      4.7978      5.0612|
| 14:  2.0202 -  1.9710 0.78   1010  107 0.1070 0.1705      4.6708      4.9138|
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
|R-free likelihood based estimates for figures of merit, absolute phase error,|
|and distribution parameters alpha and beta (Acta Cryst. (1995). A51, 880-887)|
|                                                                             |
| Bin     Resolution      No. Refl.   FOM  Phase Scale    Alpha        Beta   |
|  #        range        work  test        error factor                       |
|  1: 14.8783 -  4.7035  1376   153  0.94   8.71   0.99     0.96       6664.75|
|  2:  4.7035 -  3.7530  1323   146  0.95   7.69   1.03     1.02       8723.17|
|  3:  3.7530 -  3.2844  1296   145  0.93  11.20   1.04     1.03      10328.71|
|  4:  3.2844 -  2.9868  1281   144  0.92  13.41   1.02     1.00      10206.05|
|  5:  2.9868 -  2.7742  1281   143  0.90  15.41   1.00     0.96       7862.83|
|  6:  2.7742 -  2.6116  1280   137  0.91  15.24   0.99     0.96       6788.60|
|  7:  2.6116 -  2.4814  1271   143  0.90  15.93   0.99     0.96       6134.70|
|  8:  2.4814 -  2.3738  1260   146  0.91  14.93   1.00     0.98       5266.21|
|  9:  2.3738 -  2.2828  1260   135  0.91  15.08   1.02     1.00       4994.84|
| 10:  2.2828 -  2.2043  1240   141  0.91  14.98   1.01     0.98       4194.92|
| 11:  2.2043 -  2.1355  1263   136  0.90  16.29   1.01     0.98       4345.43|
| 12:  2.1355 -  2.0747  1237   138  0.92  14.74   1.02     1.00       3805.25|
| 13:  2.0747 -  2.0202  1252   145  0.90  15.88   1.02     1.02       3365.62|
| 14:  2.0202 -  1.9710  1010   107  0.92  14.47   1.00     0.97       2549.36|
|alpha:            min =        0.96 max =            1.03 mean =         0.99|
|beta:             min =     2549.36 max =        10328.71 mean =      6173.85|
|figures of merit: min =        0.00 max =            1.00 mean =         0.92|
|phase err.(work): min =        0.00 max =           89.95 mean =        13.79|
|phase err.(test): min =        0.00 max =           89.35 mean =        13.28|
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.97 - 14.88 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1093   r_free= 0.1568   ksol= 0.32   Bsol= 40.51   scale= 1.011   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-0.43,-0.24,0.67,0.00,0.00,0.00); trace/3= 0.00                            |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.14 A                  |
| x-ray target function (ml) for work reflections: 5.126689                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.97 - 14.88 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1093   r_free= 0.1568   ksol= 0.32   Bsol= 40.51   scale= 1.011   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-0.43,-0.24,0.67,0.00,0.00,0.00); trace/3= 0.00                            |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.14 A                  |
| x-ray target function (ml) for work reflections: 5.126689                   |
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
| Bin     Resolution   Compl.  No. Refl.    R-factors          Targets        |
|number     range              work test   work   test        work        test|
|  1: 14.8783 -  4.7035 0.99   1376  153 0.0972 0.1234      5.3619      5.4957|
|  2:  4.7035 -  3.7530 0.99   1323  146 0.0840 0.1143      5.4197      5.6426|
|  3:  3.7530 -  3.2844 0.99   1296  145 0.1033 0.1522      5.4646      5.8454|
|  4:  3.2844 -  2.9868 0.99   1281  144 0.1200 0.1601       5.452      5.6058|
|  5:  2.9868 -  2.7742 0.99   1281  143 0.1246 0.1708      5.2982       5.512|
|  6:  2.7742 -  2.6116 0.99   1280  137 0.1138 0.1762      5.1818      5.4104|
|  7:  2.6116 -  2.4814 0.99   1271  143 0.1249 0.1633      5.1507       5.386|
|  8:  2.4814 -  2.3738 0.98   1260  146 0.1143 0.1763       5.065      5.3555|
|  9:  2.3738 -  2.2828 0.98   1260  135 0.1138 0.1736      5.0225       5.275|
| 10:  2.2828 -  2.2043 0.99   1240  141 0.1071 0.1691      4.9361      5.2152|
| 11:  2.2043 -  2.1355 0.98   1263  136 0.1122 0.1784      4.9321      5.2679|
| 12:  2.1355 -  2.0747 0.97   1237  138 0.1091 0.1624      4.8664      5.1875|
| 13:  2.0747 -  2.0202 1.00   1252  145 0.1130 0.1705      4.7974      5.0611|
| 14:  2.0202 -  1.9710 0.78   1010  107 0.1070 0.1702        4.67      4.9126|
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
|R-free likelihood based estimates for figures of merit, absolute phase error,|
|and distribution parameters alpha and beta (Acta Cryst. (1995). A51, 880-887)|
|                                                                             |
| Bin     Resolution      No. Refl.   FOM  Phase Scale    Alpha        Beta   |
|  #        range        work  test        error factor                       |
|  1: 14.8783 -  4.7035  1376   153  0.94   8.72   0.99     0.96       6683.10|
|  2:  4.7035 -  3.7530  1323   146  0.95   7.71   1.03     1.02       8745.66|
|  3:  3.7530 -  3.2844  1296   145  0.93  11.22   1.04     1.03      10346.98|
|  4:  3.2844 -  2.9868  1281   144  0.92  13.41   1.02     1.00      10196.89|
|  5:  2.9868 -  2.7742  1281   143  0.90  15.40   1.00     0.96       7849.26|
|  6:  2.7742 -  2.6116  1280   137  0.91  15.23   0.99     0.96       6777.06|
|  7:  2.6116 -  2.4814  1271   143  0.90  15.91   0.99     0.96       6121.17|
|  8:  2.4814 -  2.3738  1260   146  0.91  14.92   1.00     0.98       5257.08|
|  9:  2.3738 -  2.2828  1260   135  0.91  15.07   1.02     1.00       4989.83|
| 10:  2.2828 -  2.2043  1240   141  0.91  14.98   1.01     0.98       4192.23|
| 11:  2.2043 -  2.1355  1263   136  0.90  16.29   1.01     0.98       4344.16|
| 12:  2.1355 -  2.0747  1237   138  0.92  14.73   1.02     1.00       3802.74|
| 13:  2.0747 -  2.0202  1252   145  0.90  15.87   1.02     1.02       3361.41|
| 14:  2.0202 -  1.9710  1010   107  0.92  14.45   1.00     0.97       2543.70|
|alpha:            min =        0.96 max =            1.03 mean =         0.99|
|beta:             min =     2543.70 max =        10346.98 mean =      6172.76|
|figures of merit: min =        0.00 max =            1.00 mean =         0.92|
|phase err.(work): min =        0.00 max =           89.97 mean =        13.78|
|phase err.(test): min =        0.00 max =           89.23 mean =        13.27|
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 11.572)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      2.91    97.27   14.98    None  None   None       |
|    all(noH): 2823   0      2.91    97.27   14.98    None  None   None       |
|    Sol.    : 438    0      4.37    78.96   37.75    None  None   None       |
|    Mac.    : 2385   0      2.91    97.27   10.80    None  None   None       |
|    Hyd.    : 0      0      None    None    None     None  None   None       |
|    - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -      |
|       Distribution of isotropic (or equivalent) ADP for non-H atoms:        |
|    Bin#      value range     #atoms | Bin#      value range     #atoms      |
|      0:     2.906 -  12.342: 1833   |   5:    50.086 -  59.522:   74        |
|      1:    12.342 -  21.778:  484   |   6:    59.522 -  68.958:   36        |
|      2:    21.778 -  31.214:  148   |   7:    68.958 -  78.394:   14        |
|      3:    31.214 -  40.650:  125   |   8:    78.394 -  87.830:    1        |
|      4:    40.650 -  50.086:  105   |   9:    87.830 -  97.266:    3        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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


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

Number of peaks found at mFobs-DFmodel map (map cutoff=3.00 sigma)= 312         
Filter by distance & map next to the model:
   mapped sites are within: 0.361 - 5.674
   number of sites selected in [dist_min= 0.70, dist_max= 6.00]: 310 from: 312
   mapped sites are within: 0.709 - 5.674

peak=   11.305 closest distance to " CB  VAL A 230 " =    1.438
peak=   10.037 closest distance to " CG2 VAL A 296 " =    1.359
peak=    5.966 closest distance to " NE2 GLN A  11 " =    1.155
peak=    5.962 closest distance to " CG  LEU A   5 " =    1.183
peak=    5.495 closest distance to " NH2 ARG A  56 " =    2.092
peak=    5.487 closest distance to " CD2 LEU A   5 " =    1.203
peak=    5.440 closest distance to " O   HOH Z 142 " =    1.851
peak=    5.366 closest distance to " CD1AILE A 234 " =    1.003
peak=    5.170 closest distance to " O   HOH Z 124 " =    1.487
peak=    5.099 closest distance to " O   HOH Z 193 " =    1.702
peak=    5.096 closest distance to " CG  LEU A 228 " =    1.194
peak=    5.095 closest distance to " O   HOH Z 427 " =    2.655
peak=    5.071 closest distance to " O   HOH Z 278 " =    1.025
peak=    5.041 closest distance to " O   HOH Z 126 " =    1.967
peak=    5.018 closest distance to " CB  GLN A 183 " =    1.253
peak=    4.934 closest distance to " O   HOH Z 232 " =    2.370
peak=    4.662 closest distance to " CG  PRO A 213 " =    1.205
peak=    4.605 closest distance to " O   HOH Z 272 " =    1.847
peak=    4.579 closest distance to " C   PRO A 198 " =    1.556
peak=    4.549 closest distance to " O   SER A  87 " =    2.310
peak=    4.537 closest distance to " CB  ARG A 275 " =    0.881
peak=    4.532 closest distance to " CB  GLN A 223 " =    1.519
peak=    4.516 closest distance to " O   HOH Z 316 " =    2.823
peak=    4.509 closest distance to " O   HOH Z 236 " =    1.968
peak=    4.464 closest distance to " CB  VAL A 230 " =    1.124
peak=    4.452 closest distance to " O   HOH Z 298 " =    1.796
peak=    4.419 closest distance to " CB  SER A  63 " =    1.242
peak=    4.405 closest distance to " CB  GLU A 152 " =    1.253
peak=    4.359 closest distance to " CB  ARG A  79 " =    1.489
peak=    4.358 closest distance to " OD1 ASN A  69 " =    2.601
peak=    4.341 closest distance to " CB  ASN A 148 " =    1.423
peak=    4.274 closest distance to " O   HOH Z 203 " =    1.672
peak=    4.258 closest distance to " CB  SER A   3 " =    1.367
peak=    4.179 closest distance to " O   HOH Z  44 " =    1.793
peak=    4.171 closest distance to " O   HOH Z 368 " =    1.888
peak=    4.163 closest distance to " CG1BVAL A  72 " =    1.487
peak=    4.134 closest distance to " O   HOH Z 411 " =    3.740
peak=    4.130 closest distance to " CB  VAL A 265 " =    1.319
peak=    4.128 closest distance to " O   HOH Z 425 " =    1.377
peak=    4.094 closest distance to " ND2 ASN A 187 " =    1.573
peak=    4.085 closest distance to " O   HOH Z 209 " =    2.246
peak=    4.080 closest distance to " CB  TRP A 179 " =    1.353
peak=    4.066 closest distance to " O   HOH Z  61 " =    1.577
peak=    4.063 closest distance to " O   HOH Z 227 " =    2.202
peak=    4.061 closest distance to " O   HOH Z 144 " =    2.267
peak=    4.058 closest distance to " O   HOH Z 369 " =    1.989
peak=    4.051 closest distance to " CB  TYR A 169 " =    1.022
peak=    4.021 closest distance to " O   HOH Z 263 " =    1.478
peak=    4.013 closest distance to " O   HOH Z   9 " =    1.935
peak=    4.012 closest distance to " O   HOH Z 234 " =    3.444
peak=    4.006 closest distance to " CD2 LEU A 228 " =    1.178
peak=    4.001 closest distance to " CG  PRO A 198 " =    1.182
peak=    3.997 closest distance to " CB  VAL A 296 " =    1.083
peak=    3.991 closest distance to " N   PHE A 130 " =    1.357
peak=    3.990 closest distance to " O   HOH Z 202 " =    1.123
peak=    3.988 closest distance to " O   HOH Z 403 " =    1.742
peak=    3.950 closest distance to " O   HOH Z  85 " =    1.263
peak=    3.943 closest distance to " O   HOH Z  93 " =    2.294
peak=    3.933 closest distance to " O   HOH Z 303 " =    2.218
peak=    3.924 closest distance to " O   HOH Z  68 " =    2.245
peak=    3.915 closest distance to " O   HOH Z 346 " =    1.544
peak=    3.912 closest distance to " OD2 ASP A 286 " =    2.618
peak=    3.908 closest distance to " O   HOH Z 130 " =    2.624
peak=    3.893 closest distance to " CB  ARG A 139 " =    1.052
peak=    3.893 closest distance to " O   HOH Z 322 " =    2.047
peak=    3.890 closest distance to " NZ  LYS A 117 " =    2.955
peak=    3.884 closest distance to " CB  GLN A  88 " =    1.304
peak=    3.873 closest distance to " O   HOH Z 128 " =    1.948
peak=    3.859 closest distance to " O   HOH Z 193 " =    1.793
peak=    3.846 closest distance to " CB  TRP A 266 " =    1.037
peak=    3.842 closest distance to " CG2 THR A 221 " =    1.274
peak=    3.839 closest distance to " O   HOH Z 227 " =    1.742
peak=    3.830 closest distance to " O   HOH Z 250 " =    1.320
peak=    3.828 closest distance to " O   HOH Z 130 " =    2.245
peak=    3.816 closest distance to " O   HOH Z 189 " =    2.596
peak=    3.815 closest distance to " O   HOH Z 371 " =    2.783
peak=    3.813 closest distance to " CB  GLU A 128 " =    1.030
peak=    3.812 closest distance to " O   HOH Z  59 " =    1.732
peak=    3.797 closest distance to " O   HOH Z 117 " =    1.962
peak=    3.786 closest distance to " O   HOH Z  78 " =    1.710
peak=    3.780 closest distance to " OG BSER A 164 " =    2.164
peak=    3.769 closest distance to " CB BVAL A  41 " =    1.277
peak=    3.767 closest distance to " O   HOH Z 273 " =    2.751
peak=    3.755 closest distance to " CB  ASN A 148 " =    1.901
peak=    3.752 closest distance to " CB  VAL A 202 " =    1.635
peak=    3.746 closest distance to " CG  LEU A 167 " =    1.131
peak=    3.744 closest distance to " O   HOH Z  55 " =    2.356
peak=    3.742 closest distance to " O   HOH Z   3 " =    1.956
peak=    3.741 closest distance to " O   HOH Z 389 " =    1.776
peak=    3.733 closest distance to " CA  ASN A 215 " =    1.108
peak=    3.711 closest distance to " CB  SER A 216 " =    0.883
peak=    3.706 closest distance to " O   HOH Z  22 " =    2.119
peak=    3.701 closest distance to " O   HOH Z  40 " =    1.767
peak=    3.697 closest distance to " O   HOH Z 222 " =    2.359
peak=    3.693 closest distance to " CA  PHE A 283 " =    1.495
peak=    3.685 closest distance to " O   HOH Z 344 " =    1.151
peak=    3.678 closest distance to " O   HOH Z 419 " =    1.897
peak=    3.678 closest distance to " O   HOH Z  61 " =    1.554
peak=    3.669 closest distance to " O   HOH Z  10 " =    1.756
peak=    3.661 closest distance to " O   HOH Z 284 " =    2.949
peak=    3.654 closest distance to " O   HOH Z   9 " =    1.151
peak=    3.652 closest distance to " O   HOH Z 158 " =    3.073
peak=    3.652 closest distance to " CG2 ILE A 120 " =    1.278
peak=    3.646 closest distance to " O   HOH Z 141 " =    1.604
peak=    3.642 closest distance to " N   ARG A 156 " =    1.300
peak=    3.639 closest distance to " CA  LYS A 290 " =    1.284
peak=    3.635 closest distance to " O   HOH Z 426 " =    1.489
peak=    3.634 closest distance to " O   HOH Z 405 " =    1.102
peak=    3.631 closest distance to " O   HOH Z 344 " =    2.839
peak=    3.628 closest distance to " O   HOH Z 345 " =    3.277
peak=    3.627 closest distance to " N   ASN A  39 " =    1.161
peak=    3.627 closest distance to " O   HOH Z 425 " =    2.044
peak=    3.625 closest distance to " O   HOH Z 175 " =    2.164
peak=    3.617 closest distance to " O   HOH Z 422 " =    2.497
peak=    3.609 closest distance to " CA  TYR A  30 " =    0.989
peak=    3.608 closest distance to " O   HOH Z 193 " =    1.807
peak=    3.601 closest distance to " CG BARG A 102 " =    1.804
peak=    3.601 closest distance to " CD2 TRP A 179 " =    1.432
peak=    3.599 closest distance to " CB  LEU A 143 " =    1.129
peak=    3.594 closest distance to " O   HOH Z 180 " =    2.100
peak=    3.584 closest distance to " CG  MET A 185 " =    1.035
peak=    3.582 closest distance to " CA  ALA A 248 " =    1.334
peak=    3.568 closest distance to " CG  PRO A 243 " =    1.185
peak=    3.567 closest distance to " CD1 ILE A  33 " =    1.638
peak=    3.565 closest distance to " OE1 GLU A   2 " =    2.105
peak=    3.552 closest distance to " O   HOH Z  48 " =    1.509
peak=    3.551 closest distance to " O   HOH Z 374 " =    2.479
peak=    3.549 closest distance to " O   HOH Z  78 " =    2.548
peak=    3.546 closest distance to " CA  ASN A 127 " =    1.010
peak=    3.542 closest distance to " CB  MET A  40 " =    0.844
peak=    3.536 closest distance to " O   HOH Z   7 " =    1.331
peak=    3.534 closest distance to " O   HOH Z 392 " =    3.121
peak=    3.532 closest distance to " O   HOH Z  43 " =    2.137
peak=    3.531 closest distance to " CB  ASN A  39 " =    0.817
peak=    3.528 closest distance to " OG BSER A 134 " =    3.300
peak=    3.527 closest distance to " CA  ALA A  21 " =    1.158
peak=    3.526 closest distance to " CD BLYS A 290 " =    1.211
peak=    3.523 closest distance to " CA  LYS A 117 " =    1.191
peak=    3.510 closest distance to " CA  THR A 264 " =    0.860
peak=    3.507 closest distance to " O   HOH Z 423 " =    2.557
peak=    3.499 closest distance to " CB  SER A  26 " =    1.611
peak=    3.497 closest distance to " O   HOH Z   1 " =    1.697
peak=    3.496 closest distance to " CE  MET A  93 " =    1.533
peak=    3.495 closest distance to " OG  SER A  62 " =    2.985
peak=    3.494 closest distance to " CG1 ILE A  33 " =    1.383
peak=    3.488 closest distance to " O   HOH Z 132 " =    2.417
peak=    3.483 closest distance to " O   HOH Z 130 " =    0.913
peak=    3.475 closest distance to " O   HOH Z  30 " =    1.314
peak=    3.475 closest distance to " O   HOH Z 368 " =    3.627
peak=    3.475 closest distance to " O   HOH Z 133 " =    1.476
peak=    3.467 closest distance to " CA  VAL A 126 " =    0.949
peak=    3.464 closest distance to " O   HOH Z 213 " =    2.143
peak=    3.459 closest distance to " CG2 VAL A 257 " =    0.849
peak=    3.456 closest distance to " CG  GLN A  88 " =    1.035
peak=    3.453 closest distance to " CE1 TYR A 186 " =    1.286
peak=    3.453 closest distance to " O   HOH Z  47 " =    1.681
peak=    3.451 closest distance to " CD  PRO A 243 " =    1.394
peak=    3.447 closest distance to " ND2 ASN A 110 " =    1.801
peak=    3.444 closest distance to " C   ALA A 299 " =    0.977
peak=    3.443 closest distance to " O   HOH Z 130 " =    2.224
peak=    3.437 closest distance to " CB  ILE A  20 " =    1.457
peak=    3.432 closest distance to " O   HOH Z 303 " =    1.705
peak=    3.429 closest distance to " CB  GLU A 277 " =    3.498
peak=    3.429 closest distance to " CA  ALA A  51 " =    0.987
peak=    3.428 closest distance to " O   HOH Z   2 " =    1.630
peak=    3.427 closest distance to " O   ALA A   1 " =    1.684
peak=    3.426 closest distance to " OG  SER A  22 " =    2.710
peak=    3.424 closest distance to " CG2 ILE A  20 " =    1.552
peak=    3.423 closest distance to " O   HOH Z 412 " =    1.942
peak=    3.423 closest distance to " CG  MET A 185 " =    1.237
peak=    3.421 closest distance to " O   HOH Z 251 " =    1.547
peak=    3.419 closest distance to " O   HOH Z 299 " =    4.175
peak=    3.414 closest distance to " O   HOH Z 371 " =    1.747
peak=    3.413 closest distance to " O   HOH Z 151 " =    1.549
peak=    3.413 closest distance to " NH1 ARG A 138 " =    1.242
peak=    3.404 closest distance to " NZ  LYS A  48 " =    2.210
peak=    3.403 closest distance to " O   HOH Z 108 " =    2.203
peak=    3.394 closest distance to " CG  ARG A  66 " =    2.451
peak=    3.390 closest distance to " CA  ALA A 158 " =    1.130
peak=    3.390 closest distance to " CB  ASN A 142 " =    1.021
peak=    3.384 closest distance to " O   HOH Z 248 " =    1.701
peak=    3.380 closest distance to " O   HOH Z 214 " =    2.129
peak=    3.376 closest distance to " O   HOH Z  59 " =    1.996
peak=    3.376 closest distance to " O   HOH Z 126 " =    1.506
peak=    3.374 closest distance to " O   HOH Z   1 " =    1.620
peak=    3.360 closest distance to " O   HOH Z 260 " =    1.324
peak=    3.352 closest distance to " O  BHOH Z 338 " =    2.395
peak=    3.351 closest distance to " O   HOH Z 234 " =    1.912
peak=    3.348 closest distance to " O   HOH Z  59 " =    2.236
peak=    3.347 closest distance to " CD  GLN A 194 " =    1.419
peak=    3.346 closest distance to " NH2 ARG A 156 " =    1.102
peak=    3.344 closest distance to " CA  SER A  87 " =    0.927
peak=    3.344 closest distance to " O   HOH Z 334 " =    1.499
peak=    3.342 closest distance to " CD1 ILE A 106 " =    1.183
peak=    3.341 closest distance to " CA  ILE A 234 " =    0.940
peak=    3.338 closest distance to " CB  ARG A 190 " =    1.701
peak=    3.337 closest distance to " CA  ARG A 275 " =    1.863
peak=    3.329 closest distance to " O   HOH Z 151 " =    1.608
peak=    3.328 closest distance to " CD1 LEU A 300 " =    1.265
peak=    3.320 closest distance to " CE  LYS A  76 " =    0.968
peak=    3.318 closest distance to " ND1 HIS A  86 " =    1.760
peak=    3.315 closest distance to " O   HOH Z  80 " =    1.671
peak=    3.315 closest distance to " OE2 GLU A  53 " =    2.031
peak=    3.313 closest distance to " O   HOH Z  48 " =    1.502
peak=    3.311 closest distance to " CD1 LEU A 228 " =    1.725
peak=    3.309 closest distance to " CA  VAL A  41 " =    0.850
peak=    3.309 closest distance to " CG  LYS A 119 " =    1.115
peak=    3.303 closest distance to " O   HOH Z  58 " =    1.408
peak=    3.301 closest distance to " O   HOH Z 423 " =    1.773
peak=    3.299 closest distance to " O   HOH Z 134 " =    1.361
peak=    3.296 closest distance to " O   HOH Z  71 " =    1.213
peak=    3.294 closest distance to " CG  GLN A  89 " =    1.437
peak=    3.293 closest distance to " N   SER A 135 " =    1.401
peak=    3.293 closest distance to " O   HOH Z 437 " =    2.161
peak=    3.288 closest distance to " O   HOH Z 128 " =    1.964
peak=    3.288 closest distance to " CG1BVAL A 121 " =    0.967
peak=    3.288 closest distance to " O   HOH Z 380 " =    1.617
peak=    3.282 closest distance to " CG  GLN A  77 " =    2.361
peak=    3.282 closest distance to " CB  THR A 157 " =    1.004
peak=    3.275 closest distance to " O   HOH Z 128 " =    2.132
peak=    3.273 closest distance to " CG  PRO A 280 " =    0.747
peak=    3.273 closest distance to " CG AARG A 275 " =    1.046
peak=    3.272 closest distance to " N   VAL A 126 " =    1.183
peak=    3.270 closest distance to " O   HOH Z 272 " =    2.273
peak=    3.268 closest distance to " O   HOH Z 135 " =    1.950
peak=    3.267 closest distance to " OG1 THR A 294 " =    2.390
peak=    3.267 closest distance to " O   HOH Z 192 " =    1.952
peak=    3.257 closest distance to " O   HOH Z 189 " =    2.624
peak=    3.254 closest distance to " CB  ALA A 248 " =    1.012
peak=    3.253 closest distance to " O   HOH Z 109 " =    2.491
peak=    3.253 closest distance to " O   HOH Z 336 " =    1.783
peak=    3.251 closest distance to " CG1 ILE A 151 " =    1.233
peak=    3.251 closest distance to " O   HOH Z 329 " =    3.764
peak=    3.249 closest distance to " O   HOH Z 438 " =    2.148
peak=    3.247 closest distance to " CB  ASP A 140 " =    0.786
peak=    3.246 closest distance to " O   MET A 105 " =    1.801
peak=    3.243 closest distance to " CG  GLU A 277 " =    2.134
peak=    3.242 closest distance to " O   HOH Z 209 " =    2.290
peak=    3.234 closest distance to " O   HOH Z 366 " =    2.969
peak=    3.233 closest distance to " NH2AARG A 190 " =    1.812
peak=    3.232 closest distance to " CB  ASN A 215 " =    1.458
peak=    3.231 closest distance to " CB  LEU A 255 " =    0.810
peak=    3.231 closest distance to " O   PRO A 198 " =    1.225
peak=    3.230 closest distance to " O   HOH Z 402 " =    1.386
peak=    3.230 closest distance to " CB  LEU A 228 " =    1.357
peak=    3.213 closest distance to " O   HOH Z 196 " =    1.413
peak=    3.213 closest distance to " CG2 THR A 294 " =    1.560
peak=    3.205 closest distance to " O   HOH Z 108 " =    0.962
peak=    3.203 closest distance to " CD2 LEU A 255 " =    1.619
peak=    3.201 closest distance to " CB  PRO A  54 " =    0.802
peak=    3.200 closest distance to " CD2 LEU A 297 " =    0.984
peak=    3.199 closest distance to " CB  VAL A 268 " =    0.841
peak=    3.197 closest distance to " CA  GLN A 194 " =    1.281
peak=    3.197 closest distance to " NE AARG A 275 " =    1.242
peak=    3.197 closest distance to " O   HOH Z 236 " =    1.524
peak=    3.196 closest distance to " O   HOH Z 258 " =    2.238
peak=    3.192 closest distance to " O   HOH Z 407 " =    2.283
peak=    3.190 closest distance to " CD  ARG A 269 " =    1.078
peak=    3.187 closest distance to " O   HOH Z 172 " =    3.542
peak=    3.185 closest distance to " CB  THR A  31 " =    1.707
peak=    3.180 closest distance to " O   HOH Z 172 " =    5.674
peak=    3.179 closest distance to " CB  GLN A 278 " =    0.787
peak=    3.173 closest distance to " CA  ASN A 176 " =    1.020
peak=    3.169 closest distance to " O   HOH Z  80 " =    2.271
peak=    3.167 closest distance to " CA  LEU A 101 " =    1.400
peak=    3.166 closest distance to " CA  ALA A 233 " =    1.072
peak=    3.164 closest distance to " O   HOH Z  21 " =    1.763
peak=    3.164 closest distance to " O   HOH Z 285 " =    1.675
peak=    3.164 closest distance to " CB  ALA A 291 " =    1.501
peak=    3.164 closest distance to " O   HOH Z 250 " =    1.364
peak=    3.163 closest distance to " O   HOH Z 261 " =    1.487
peak=    3.162 closest distance to " CD  LYS A 166 " =    1.295
peak=    3.162 closest distance to " CB  ALA A   9 " =    1.593
peak=    3.154 closest distance to " O   HOH Z 383 " =    2.098
peak=    3.150 closest distance to " CA  GLY A 267 " =    0.960
peak=    3.148 closest distance to " NH1BARG A 145 " =    1.381
peak=    3.140 closest distance to " CA  LEU A 282 " =    1.198
peak=    3.140 closest distance to " O   THR A  31 " =    1.535
peak=    3.139 closest distance to " O   HOH Z  88 " =    2.527
peak=    3.138 closest distance to " O   HOH Z 173 " =    2.150
peak=    3.137 closest distance to " O   GLN A  58 " =    1.465
peak=    3.134 closest distance to " OG ASER A  99 " =    1.528
peak=    3.132 closest distance to " CD1 LEU A 261 " =    1.238
peak=    3.124 closest distance to " O   HOH Z 250 " =    1.752
peak=    3.123 closest distance to " O   HOH Z 286 " =    2.259
peak=    3.121 closest distance to " O   HOH Z 118 " =    1.328
peak=    3.113 closest distance to " ND1 HIS A  81 " =    1.591
peak=    3.112 closest distance to " O   HOH Z 245 " =    1.377
peak=    3.110 closest distance to " CB  LYS A 117 " =    1.188
peak=    3.106 closest distance to " CB  ASP A 124 " =    0.709
peak=    3.099 closest distance to " CH2 TRP A 274 " =    2.343
peak=    3.098 closest distance to " O   HOH Z 271 " =    1.851
peak=    3.097 closest distance to " O   HOH Z   9 " =    1.761
peak=    3.096 closest distance to " OD1 ASN A  45 " =    1.381
peak=    3.095 closest distance to " CB  ALA A   1 " =    4.642
peak=    3.092 closest distance to " CB  ALA A 180 " =    1.194
peak=    3.091 closest distance to " O   HOH Z 409 " =    3.115
peak=    3.090 closest distance to " O   HOH Z 280 " =    2.473
peak=    3.089 closest distance to " O   HOH Z 326 " =    1.872
peak=    3.084 closest distance to " CB  TYR A  30 " =    1.589
peak=    3.077 closest distance to " N   ASP A 162 " =    1.304
peak=    3.073 closest distance to " O   HOH Z 112 " =    1.777
peak=    3.066 closest distance to " CB  ARG A 138 " =    0.979
peak=    3.064 closest distance to " O   HOH Z 406 " =    1.583
peak=    3.064 closest distance to " O   HOH Z 341 " =    2.380
peak=    3.060 closest distance to " N   ASN A 127 " =    1.273
peak=    3.046 closest distance to " O   HOH Z 353 " =    2.497
peak=    3.044 closest distance to " CD  ARG A 138 " =    0.837
peak=    3.029 closest distance to " O   HOH Z 433 " =    1.785
peak=    3.010 closest distance to " O   HOH Z 175 " =    2.079

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

Number of peaks found at mFobs-DFmodel map (map cutoff=3.00 sigma)= 214         
Filter by distance & map next to the model:
   mapped sites are within: 0.580 - 5.330
   number of sites selected in [dist_min= 0.70, dist_max= 6.00]: 212 from: 214
   mapped sites are within: 0.752 - 5.330

peak=   -5.251 closest distance to " CG2 VAL A 230 " =    0.752
peak=   -4.905 closest distance to " CD  ARG A 156 " =    2.024
peak=   -4.494 closest distance to " SG  CYS A 254 " =    3.208
peak=   -4.281 closest distance to " CD1 LEU A 255 " =    2.795
peak=   -4.214 closest distance to " O   HOH Z  11 " =    1.916
peak=   -4.209 closest distance to " O   HOH Z 290 " =    1.085
peak=   -4.166 closest distance to " O   HOH Z 231 " =    1.848
peak=   -4.163 closest distance to " C   HIS A 108 " =    1.207
peak=   -4.160 closest distance to " CB  PRO A 243 " =    2.636
peak=   -4.139 closest distance to " N   GLN A  58 " =    1.820
peak=   -4.108 closest distance to " CG2 VAL A 296 " =    1.551
peak=   -4.101 closest distance to " OG BSER A 134 " =    1.170
peak=   -4.065 closest distance to " O   HOH Z 266 " =    4.670
peak=   -3.963 closest distance to " O   HOH Z 166 " =    1.554
peak=   -3.962 closest distance to " O   HOH Z 351 " =    1.529
peak=   -3.950 closest distance to " O   PRO A 198 " =    1.287
peak=   -3.950 closest distance to " CA  GLY A  23 " =    2.025
peak=   -3.941 closest distance to " O   HOH Z 389 " =    1.879
peak=   -3.940 closest distance to " O   VAL A  67 " =    2.735
peak=   -3.908 closest distance to " O   ALA A 161 " =    1.652
peak=   -3.885 closest distance to " O   HOH Z 211 " =    1.504
peak=   -3.861 closest distance to " CE2 TYR A  30 " =    2.835
peak=   -3.858 closest distance to " CG2 VAL A 296 " =    0.945
peak=   -3.807 closest distance to " CA  VAL A  67 " =    2.748
peak=   -3.798 closest distance to " NH2 ARG A  79 " =    1.936
peak=   -3.779 closest distance to " CG  GLN A 223 " =    2.035
peak=   -3.773 closest distance to " OXT GLY A 302 " =    2.855
peak=   -3.772 closest distance to " N   ALA A 248 " =    1.649
peak=   -3.767 closest distance to " CZ  PHE A  59 " =    1.476
peak=   -3.765 closest distance to " O   PRO A 163 " =    1.990
peak=   -3.761 closest distance to " O   HOH Z  47 " =    1.565
peak=   -3.734 closest distance to " CA  GLY A  98 " =    1.894
peak=   -3.730 closest distance to " CB  TYR A  15 " =    2.148
peak=   -3.719 closest distance to " C   ILE A 239 " =    2.176
peak=   -3.712 closest distance to " N   HIS A 115 " =    2.087
peak=   -3.704 closest distance to " CD1 LEU A 101 " =    2.335
peak=   -3.700 closest distance to " O   HOH Z 140 " =    1.525
peak=   -3.695 closest distance to " CB  PRO A 163 " =    2.562
peak=   -3.695 closest distance to " O   HOH Z 103 " =    1.761
peak=   -3.692 closest distance to " CB  ALA A 248 " =    1.977
peak=   -3.664 closest distance to " CG1 VAL A 112 " =    2.837
peak=   -3.633 closest distance to " C   ASP A 231 " =    2.568
peak=   -3.633 closest distance to " CE2 PHE A 218 " =    2.574
peak=   -3.633 closest distance to " OG BSER A 134 " =    1.614
peak=   -3.630 closest distance to " CA  GLY A 133 " =    1.989
peak=   -3.620 closest distance to " N   SER A 276 " =    1.253
peak=   -3.599 closest distance to " NH1 ARG A  56 " =    2.540
peak=   -3.597 closest distance to " O   HOH Z 388 " =    2.121
peak=   -3.588 closest distance to " O   HOH Z 407 " =    3.038
peak=   -3.579 closest distance to " CD1 LEU A 228 " =    2.086
peak=   -3.577 closest distance to " CB  ALA A 161 " =    2.530
peak=   -3.571 closest distance to " O   ALA A  51 " =    1.304
peak=   -3.555 closest distance to " CE  MET A 105 " =    2.167
peak=   -3.552 closest distance to " CD1 PHE A  59 " =    1.898
peak=   -3.543 closest distance to " O   HOH Z  11 " =    2.081
peak=   -3.538 closest distance to " C   ASN A 285 " =    2.215
peak=   -3.531 closest distance to " O   HOH Z 111 " =    4.374
peak=   -3.523 closest distance to " CG2 THR A 178 " =    2.199
peak=   -3.521 closest distance to " N   THR A 157 " =    1.406
peak=   -3.519 closest distance to " O   HOH Z 198 " =    2.246
peak=   -3.516 closest distance to " O   HOH Z 191 " =    5.330
peak=   -3.515 closest distance to " O   PRO A 198 " =    1.262
peak=   -3.507 closest distance to " O   HOH Z 423 " =    2.178
peak=   -3.493 closest distance to " CG  PHE A 283 " =    2.585
peak=   -3.491 closest distance to " CG  ASP A 231 " =    0.758
peak=   -3.490 closest distance to " O   HOH Z 298 " =    1.266
peak=   -3.486 closest distance to " C   ASN A 187 " =    1.896
peak=   -3.483 closest distance to " O   ALA A   8 " =    1.819
peak=   -3.483 closest distance to " O   HOH Z 426 " =    2.387
peak=   -3.480 closest distance to " O   GLY A  80 " =    2.473
peak=   -3.471 closest distance to " CB  ASP A 132 " =    2.323
peak=   -3.469 closest distance to " CG  LEU A 228 " =    1.003
peak=   -3.464 closest distance to " O   HOH Z  60 " =    2.206
peak=   -3.459 closest distance to " O   SER A  22 " =    2.387
peak=   -3.450 closest distance to " CG  MET A 105 " =    0.894
peak=   -3.449 closest distance to " OE1 GLN A  73 " =    2.423
peak=   -3.446 closest distance to " NE2 GLN A 194 " =    2.841
peak=   -3.444 closest distance to " CG2AVAL A  41 " =    2.949
peak=   -3.436 closest distance to " O   HOH Z 185 " =    2.159
peak=   -3.421 closest distance to " O   HOH Z 102 " =    1.639
peak=   -3.420 closest distance to " OG BSER A 212 " =    2.042
peak=   -3.417 closest distance to " O   HOH Z 377 " =    0.897
peak=   -3.416 closest distance to " O   HOH Z 148 " =    1.918
peak=   -3.413 closest distance to " O   HOH Z  93 " =    1.524
peak=   -3.413 closest distance to " O   PHE A 218 " =    1.569
peak=   -3.410 closest distance to " CD1 ILE A 199 " =    2.431
peak=   -3.408 closest distance to " ND2 ASN A 187 " =    1.584
peak=   -3.400 closest distance to " C   ALA A 158 " =    1.269
peak=   -3.398 closest distance to " O   HOH Z 359 " =    3.266
peak=   -3.395 closest distance to " O   HOH Z 309 " =    2.485
peak=   -3.394 closest distance to " O   PRO A 243 " =    2.579
peak=   -3.390 closest distance to " O   HOH Z 423 " =    1.224
peak=   -3.388 closest distance to " O   HOH Z  90 " =    2.603
peak=   -3.380 closest distance to " CD  LYS A 289 " =    2.523
peak=   -3.374 closest distance to " O   HOH Z 369 " =    2.155
peak=   -3.370 closest distance to " O   HOH Z 313 " =    1.740
peak=   -3.363 closest distance to " CE3 TRP A 274 " =    2.359
peak=   -3.362 closest distance to " N   ALA A   9 " =    1.484
peak=   -3.361 closest distance to " O   HOH Z 348 " =    1.814
peak=   -3.356 closest distance to " O   HOH Z 385 " =    2.023
peak=   -3.353 closest distance to " OG  SER A   3 " =    1.452
peak=   -3.352 closest distance to " CD2 LEU A 300 " =    2.751
peak=   -3.351 closest distance to " CG2 VAL A 296 " =    1.921
peak=   -3.350 closest distance to " N   GLN A  77 " =    1.713
peak=   -3.347 closest distance to " CG1 VAL A 197 " =    2.261
peak=   -3.344 closest distance to " CB  ALA A  43 " =    2.326
peak=   -3.344 closest distance to " NE2 GLN A  88 " =    2.113
peak=   -3.340 closest distance to " CG  PRO A 163 " =    2.719
peak=   -3.333 closest distance to " CB  ASP A 132 " =    2.312
peak=   -3.332 closest distance to " CB  ALA A 248 " =    2.403
peak=   -3.332 closest distance to " CD  GLU A 152 " =    2.563
peak=   -3.330 closest distance to " OD1 ASN A 301 " =    1.982
peak=   -3.325 closest distance to " O   HOH Z 198 " =    1.377
peak=   -3.316 closest distance to " O   ASP A 270 " =    1.767
peak=   -3.312 closest distance to " NZ  LYS A 119 " =    3.345
peak=   -3.312 closest distance to " CA  ASP A 298 " =    1.052
peak=   -3.310 closest distance to " O   HOH Z 134 " =    2.823
peak=   -3.308 closest distance to " CG  TRP A 266 " =    1.824
peak=   -3.306 closest distance to " OG  SER A  97 " =    2.056
peak=   -3.305 closest distance to " O   HOH Z 114 " =    2.819
peak=   -3.301 closest distance to " O   HOH Z 312 " =    1.525
peak=   -3.300 closest distance to " CB  PHE A 192 " =    1.732
peak=   -3.299 closest distance to " O   MET A  40 " =    2.639
peak=   -3.297 closest distance to " CB  ALA A 244 " =    2.048
peak=   -3.294 closest distance to " CG1 VAL A 112 " =    2.636
peak=   -3.291 closest distance to " O   HOH Z  38 " =    2.042
peak=   -3.288 closest distance to " CG1 VAL A 125 " =    2.181
peak=   -3.284 closest distance to " NH1AARG A 275 " =    1.906
peak=   -3.284 closest distance to " CD  GLN A  88 " =    0.959
peak=   -3.275 closest distance to " CA  GLY A 241 " =    2.201
peak=   -3.275 closest distance to " OD2 ASP A 191 " =    1.351
peak=   -3.275 closest distance to " CB  SER A 258 " =    2.136
peak=   -3.274 closest distance to " O   HOH Z 131 " =    4.106
peak=   -3.270 closest distance to " O   HOH Z  13 " =    1.596
peak=   -3.263 closest distance to " CG2 VAL A 257 " =    2.823
peak=   -3.253 closest distance to " O   HOH Z 222 " =    3.246
peak=   -3.252 closest distance to " CB  ASN A  39 " =    2.185
peak=   -3.251 closest distance to " O   HOH Z 165 " =    2.064
peak=   -3.248 closest distance to " O   TRP A  70 " =    1.484
peak=   -3.247 closest distance to " O   HOH Z 426 " =    1.686
peak=   -3.243 closest distance to " O   HOH Z 350 " =    1.797
peak=   -3.242 closest distance to " O   HOH Z  56 " =    2.141
peak=   -3.242 closest distance to " OG ASER A 134 " =    1.316
peak=   -3.242 closest distance to " O   HOH Z  52 " =    1.503
peak=   -3.236 closest distance to " CB  ILE A  33 " =    2.911
peak=   -3.234 closest distance to " CG2 VAL A 112 " =    2.508
peak=   -3.231 closest distance to " O   HOH Z 281 " =    2.902
peak=   -3.231 closest distance to " SG ACYS A 201 " =    2.061
peak=   -3.227 closest distance to " O   HOH Z 250 " =    1.422
peak=   -3.227 closest distance to " OG  SER A 206 " =    1.586
peak=   -3.226 closest distance to " O   HOH Z 410 " =    2.108
peak=   -3.225 closest distance to " C   GLN A 205 " =    1.979
peak=   -3.225 closest distance to " OG ASER A 216 " =    1.015
peak=   -3.217 closest distance to " N   THR A 235 " =    1.307
peak=   -3.211 closest distance to " CG  PRO A  90 " =    1.556
peak=   -3.210 closest distance to " CG  GLU A 152 " =    1.543
peak=   -3.209 closest distance to " CG  GLN A 278 " =    2.098
peak=   -3.208 closest distance to " CA  GLY A 133 " =    2.164
peak=   -3.203 closest distance to " CZ  TYR A 169 " =    1.650
peak=   -3.202 closest distance to " O   HOH Z 143 " =    1.337
peak=   -3.201 closest distance to " CG1AVAL A  41 " =    2.906
peak=   -3.199 closest distance to " O   HOH Z 210 " =    1.135
peak=   -3.197 closest distance to " CD1 TYR A 247 " =    2.707
peak=   -3.195 closest distance to " O   HOH Z  71 " =    1.207
peak=   -3.194 closest distance to " CG1 VAL A 250 " =    2.769
peak=   -3.194 closest distance to " CG  GLU A   2 " =    2.113
peak=   -3.193 closest distance to " CG  GLN A  58 " =    1.313
peak=   -3.191 closest distance to " CG  LYS A 193 " =    2.327
peak=   -3.191 closest distance to " O   HOH Z 228 " =    1.579
peak=   -3.190 closest distance to " CD2 TYR A 293 " =    2.103
peak=   -3.185 closest distance to " CZ  ARG A 259 " =    0.869
peak=   -3.183 closest distance to " O   GLY A  75 " =    1.852
peak=   -3.183 closest distance to " ND2 ASN A  45 " =    1.027
peak=   -3.183 closest distance to " O   ASP A 191 " =    1.480
peak=   -3.181 closest distance to " CB  ALA A  64 " =    2.485
peak=   -3.180 closest distance to " CD2 LEU A 237 " =    2.829
peak=   -3.178 closest distance to " O   HOH Z 393 " =    3.469
peak=   -3.172 closest distance to " O   HOH Z  64 " =    2.174
peak=   -3.168 closest distance to " N   PHE A  59 " =    1.999
peak=   -3.164 closest distance to " O   HOH Z 411 " =    3.830
peak=   -3.163 closest distance to " O   HOH Z 368 " =    2.241
peak=   -3.161 closest distance to " ND2 ASN A 142 " =    1.945
peak=   -3.161 closest distance to " NH2AARG A 275 " =    5.117
peak=   -3.160 closest distance to " O   HOH Z 158 " =    2.185
peak=   -3.156 closest distance to " CA  ASP A  27 " =    2.352
peak=   -3.154 closest distance to " CA  GLY A  35 " =    2.020
peak=   -3.153 closest distance to " O   GLN A 240 " =    1.779
peak=   -3.149 closest distance to " OD2 ASP A 270 " =    1.453
peak=   -3.147 closest distance to " C   LEU A 143 " =    1.098
peak=   -3.145 closest distance to " N   MET A 105 " =    2.625
peak=   -3.144 closest distance to " OG  SER A  62 " =    1.455
peak=   -3.142 closest distance to " OE1 GLN A  88 " =    1.158
peak=   -3.130 closest distance to " N   ALA A 226 " =    1.960
peak=   -3.126 closest distance to " O   HOH Z 166 " =    1.992
peak=   -3.125 closest distance to " O   HOH Z 192 " =    2.464
peak=   -3.118 closest distance to " OE1 GLN A  77 " =    1.840
peak=   -3.117 closest distance to " CE1 HIS A  81 " =    1.479
peak=   -3.117 closest distance to " CZ3 TRP A 179 " =    1.340
peak=   -3.110 closest distance to " O   VAL A 189 " =    2.633
peak=   -3.110 closest distance to " CA  GLY A 241 " =    3.016
peak=   -3.109 closest distance to " O   HOH Z  97 " =    1.694
peak=   -3.108 closest distance to " CA  ALA A 227 " =    2.302
peak=   -3.095 closest distance to " C   MET A 188 " =    1.571
peak=   -3.090 closest distance to " OG1 THR A 178 " =    1.180
peak=   -3.090 closest distance to " O   HOH Z  78 " =    1.841
peak=   -3.088 closest distance to " N   ALA A 248 " =    2.430
peak=   -3.085 closest distance to " O   HOH Z 353 " =    2.014
peak=   -3.081 closest distance to " O   HOH Z 427 " =    1.482
peak=   -3.068 closest distance to " O   HOH Z 175 " =    4.263
peak=   -3.060 closest distance to " CB  SER A 210 " =    1.335
peak=   -3.047 closest distance to " OE2 GLU A 152 " =    1.260
peak=   -3.031 closest distance to " O   HOH Z 234 " =    3.931

================= 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    :  0.4574 0.4451   6.255489e+00   6.239158e+00
   1_bss:  0.4491 0.4354   6.248627e+00   6.227588e+00
   1_xyz:  0.3563 0.3756   6.101410e+00   6.129787e+00
   1_adp:  0.3046 0.3446   5.980161e+00   6.071780e+00
   1_occ:  0.3037 0.3452   5.979440e+00   6.073358e+00
   2_bss:  0.2994 0.3402   5.976076e+00   6.065966e+00
   2_xyz:  0.2070 0.2531   5.661604e+00   5.828646e+00
   2_adp:  0.1863 0.2347   5.572182e+00   5.758643e+00
   2_occ:  0.1859 0.2339   5.570608e+00   5.756469e+00
   3_bss:  0.1847 0.2337   5.568263e+00   5.754578e+00
   3_xyz:  0.1411 0.1872   5.331099e+00   5.549645e+00
   3_adp:  0.1310 0.1776   5.269142e+00   5.496783e+00
   3_occ:  0.1309 0.1776   5.268821e+00   5.496439e+00
   4_bss:  0.1312 0.1780   5.268314e+00   5.494945e+00
   4_xyz:  0.1190 0.1644   5.191283e+00   5.431117e+00
   4_adp:  0.1167 0.1630   5.177102e+00   5.417252e+00
   4_occ:  0.1166 0.1630   5.176771e+00   5.416799e+00
   5_bss:  0.1166 0.1630   5.176722e+00   5.416790e+00
   5_xyz:  0.1095 0.1592   5.135538e+00   5.394893e+00
   5_adp:  0.1094 0.1569   5.127326e+00   5.381212e+00
   5_occ:  0.1093 0.1568   5.126851e+00   5.380621e+00
   5_bss:  0.1093 0.1568   5.126689e+00   5.380449e+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:  0.358   2.229   6.816   8.915   8.568   0.000   0.000   0.000
   1_xyz:  0.358   2.229   6.816   8.915   8.568   0.000   0.000   0.000
   1_adp:  0.358   2.229   6.816   8.915   8.568   0.000   0.000   0.000
   1_occ:  0.358   2.229   6.816   8.915   8.568   0.000   0.000   0.000
   2_bss:  0.329  20.000   3.585   4.780   5.553   0.000   0.000   0.000
   2_xyz:  0.329  20.000   3.585   4.780   5.553   0.000   0.000   0.000
   2_adp:  0.329  20.000   3.585   4.780   5.553   0.000   0.000   0.000
   2_occ:  0.329  20.000   3.585   4.780   5.553   0.000   0.000   0.000
   3_bss:  0.325  32.364   2.602   3.199   4.034   0.000   0.000   0.000
   3_xyz:  0.325  32.364   2.602   3.199   4.034   0.000   0.000   0.000
   3_adp:  0.325  32.364   2.602   3.199   4.034   0.000   0.000   0.000
   3_occ:  0.325  32.364   2.602   3.199   4.034   0.000   0.000   0.000
   4_bss:  0.320  35.299   2.407   2.690   3.560   0.000   0.000   0.000
   4_xyz:  0.320  35.299   2.407   2.690   3.560   0.000   0.000   0.000
   4_adp:  0.320  35.299   2.407   2.690   3.560   0.000   0.000   0.000
   4_occ:  0.320  35.299   2.407   2.690   3.560   0.000   0.000   0.000
   5_bss:  0.320  35.299   2.484   2.691   3.554   0.000   0.000   0.000
   5_xyz:  0.320  35.299   2.484   2.691   3.554   0.000   0.000   0.000
   5_adp:  0.320  35.299   2.484   2.691   3.554   0.000   0.000   0.000
   5_occ:  0.320  35.299   2.484   2.691   3.554   0.000   0.000   0.000
   5_bss:  0.323  40.512  -0.426  -0.242   0.668   0.000   0.000   0.000
------------------------------------------------------------------------
 stage     <pher>    fom   alpha         beta
   0    :  52.164 0.4944  0.5710    60301.564
   1_bss:  52.222 0.4913  0.7125    57297.788
   1_xyz:  41.191 0.6278  0.8935    39366.473
   1_adp:  35.691 0.6942  1.0029    32244.550
   1_occ:  35.828 0.6926  0.9994    32354.065
   2_bss:  35.388 0.6973  0.8904    31509.560
   2_xyz:  25.358 0.8072  0.9954    16337.747
   2_adp:  22.699 0.8355  1.0165    13986.032
   2_occ:  22.633 0.8362  1.0166    13893.300
   3_bss:  22.533 0.8370  0.9689    13816.813
   3_xyz:  17.460 0.8851  0.9961     8761.673
   3_adp:  16.182 0.8969  0.9969     7906.202
   3_occ:  16.176 0.8970  0.9968     7901.725
   4_bss:  16.135 0.8973  0.9824     7862.604
   4_xyz:  14.730 0.9089  0.9887     6779.634
   4_adp:  14.429 0.9117  0.9866     6625.890
   4_occ:  14.423 0.9118  0.9865     6616.675
   5_bss:  14.423 0.9118  0.9874     6617.381
   5_xyz:  14.044 0.9146  0.9888     6336.832
   5_adp:  13.745 0.9171  0.9880     6184.773
   5_occ:  13.735 0.9171  0.9879     6174.321
   5_bss:  13.731 0.9172  0.9879     6173.230
------------------------------------------------------------------------
 stage       angl   bond   chir   dihe   plan   repu  geom_target
   0    :  24.226  0.414  2.119 33.790  0.145  4.089   5.3148e+01
   1_bss:  24.226  0.414  2.119 33.790  0.145  4.089   5.3148e+01
   1_xyz:   1.602  0.012  0.103 18.206  0.006  4.117   1.2823e-01
   1_adp:   1.602  0.012  0.103 18.206  0.006  4.117   1.2823e-01
   1_occ:   1.602  0.012  0.103 18.206  0.006  4.117   1.2823e-01
   2_bss:   1.602  0.012  0.103 18.206  0.006  4.117   1.2823e-01
   2_xyz:   0.999  0.006  0.072 16.026  0.004  4.116   6.4439e-02
   2_adp:   0.999  0.006  0.072 16.026  0.004  4.116   6.4439e-02
   2_occ:   0.999  0.006  0.072 16.026  0.004  4.116   6.4439e-02
   3_bss:   0.999  0.006  0.072 16.026  0.004  4.116   6.4439e-02
   3_xyz:   0.963  0.006  0.073 15.752  0.003  4.116   5.7679e-02
   3_adp:   0.963  0.006  0.073 15.752  0.003  4.116   5.7679e-02
   3_occ:   0.963  0.006  0.073 15.752  0.003  4.116   5.7679e-02
   4_bss:   0.963  0.006  0.073 15.752  0.003  4.116   5.7679e-02
   4_xyz:   0.911  0.005  0.071 15.719  0.003  4.111   5.4878e-02
   4_adp:   0.911  0.005  0.071 15.719  0.003  4.111   5.4878e-02
   4_occ:   0.911  0.005  0.071 15.719  0.003  4.111   5.4878e-02
   5_bss:   0.911  0.005  0.071 15.719  0.003  4.111   5.4878e-02
   5_xyz:   1.051  0.007  0.081 15.855  0.004  4.113   6.6180e-02
   5_adp:   1.051  0.007  0.081 15.855  0.004  4.113   6.6180e-02
   5_occ:   1.051  0.007  0.081 15.855  0.004  4.113   6.6180e-02
   5_bss:   1.051  0.007  0.081 15.855  0.004  4.113   6.6180e-02
------------------------------------------------------------------------
                      Maximal deviations:
 stage       angl   bond   chir   dihe   plan   repu       |grad|
   0    :  74.492  1.400  6.404144.062  0.405  1.196   6.8894e+00
   1_bss:  74.492  1.400  6.404144.062  0.405  1.196   6.8894e+00
   1_xyz:  12.909  0.160  0.435 86.609  0.035  2.268   9.2559e-02
   1_adp:  12.909  0.160  0.435 86.609  0.035  2.268   9.2559e-02
   1_occ:  12.909  0.160  0.435 86.609  0.035  2.268   9.2559e-02
   2_bss:  12.909  0.160  0.435 86.609  0.035  2.268   9.2559e-02
   2_xyz:   6.504  0.051  0.305 87.477  0.035  2.351   5.0567e-02
   2_adp:   6.504  0.051  0.305 87.477  0.035  2.351   5.0567e-02
   2_occ:   6.504  0.051  0.305 87.477  0.035  2.351   5.0567e-02
   3_bss:   6.504  0.051  0.305 87.477  0.035  2.351   5.0567e-02
   3_xyz:   6.377  0.044  0.382 86.726  0.028  2.321   3.7129e-02
   3_adp:   6.377  0.044  0.382 86.726  0.028  2.321   3.7129e-02
   3_occ:   6.377  0.044  0.382 86.726  0.028  2.321   3.7129e-02
   4_bss:   6.377  0.044  0.382 86.726  0.028  2.321   3.7129e-02
   4_xyz:   6.795  0.044  0.376 83.939  0.024  2.345   6.1988e-02
   4_adp:   6.795  0.044  0.376 83.939  0.024  2.345   6.1988e-02
   4_occ:   6.795  0.044  0.376 83.939  0.024  2.345   6.1988e-02
   5_bss:   6.795  0.044  0.376 83.939  0.024  2.345   6.1988e-02
   5_xyz:   6.559  0.043  0.507 83.859  0.025  2.269   4.8289e-02
   5_adp:   6.559  0.043  0.507 83.859  0.025  2.269   4.8289e-02
   5_occ:   6.559  0.043  0.507 83.859  0.025  2.269   4.8289e-02
   5_bss:   6.559  0.043  0.507 83.859  0.025  2.269   4.8289e-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:  84.89   0.00  11.87  84.89   0.00   9.05  72.24   0.00  27.27
   1_occ:  84.89   0.00  11.87  84.89   0.00   9.05  72.24   0.00  27.27
   2_bss:  84.89   0.00  11.87  84.89   0.00   9.05  72.24   0.00  27.27
   2_xyz:  84.89   0.00  11.87  84.89   0.00   9.05  72.24   0.00  27.27
   2_adp:  85.19   0.00  11.92  85.19   0.00   8.32  67.69   1.13  31.54
   2_occ:  85.19   0.00  11.92  85.19   0.00   8.32  67.69   1.13  31.54
   3_bss:  85.19   0.00  11.92  85.19   0.00   8.32  67.69   1.13  31.54
   3_xyz:  85.19   0.00  11.92  85.19   0.00   8.32  67.69   1.13  31.54
   3_adp:  91.99   0.00  12.62  91.99   0.00   8.21  74.25   0.69  36.65
   3_occ:  91.99   0.00  12.62  91.99   0.00   8.21  74.25   0.69  36.65
   4_bss:  91.99   0.00  12.62  91.99   0.00   8.21  74.25   0.69  36.65
   4_xyz:  91.99   0.00  12.62  91.99   0.00   8.21  74.25   0.69  36.65
   4_adp:  94.61   0.00  12.48  94.61   0.00   8.09  76.81   1.28  36.37
   4_occ:  94.61   0.00  12.48  94.61   0.00   8.09  76.81   1.28  36.37
   5_bss:  94.61   0.00  12.48  94.61   0.00   8.09  76.81   1.28  36.37
   5_xyz:  94.61   0.00  12.48  94.61   0.00   8.09  76.81   1.28  36.37
   5_adp:  94.36   0.00  12.07  94.36   0.00   7.89  76.05   1.47  34.85
   5_occ:  94.36   0.00  12.07  94.36   0.00   7.89  76.05   1.47  34.85
   5_bss:  97.27   2.91  14.98  97.27   2.91  10.80  78.96   4.37  37.75
------------------------------------------------------------------------
 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:    1.212    0.015    0.406
   1_adp:    1.212    0.015    0.406
   1_occ:    1.212    0.015    0.406
   2_bss:    1.212    0.015    0.406
   2_xyz:    1.451    0.022    0.544
   2_adp:    1.451    0.022    0.544
   2_occ:    1.451    0.022    0.544
   3_bss:    1.451    0.022    0.544
   3_xyz:    1.455    0.063    0.593
   3_adp:    1.455    0.063    0.593
   3_occ:    1.455    0.063    0.593
   4_bss:    1.455    0.063    0.593
   4_xyz:    1.635    0.031    0.623
   4_adp:    1.635    0.031    0.623
   4_occ:    1.635    0.031    0.623
   5_bss:    1.635    0.031    0.623
   5_xyz:    1.694    0.021    0.636
   5_adp:    1.694    0.021    0.636
   5_occ:    1.694    0.021    0.636
   5_bss:    1.694    0.021    0.636
------------------------------------------------------------------------

CPU time actual refinement: 354.65


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

Writing refined structure to PDB file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/trial/run_519/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_519/model_refine_001_2mFobs-DFmodel.map
Writing mFobs-DFmodel XPLOR map to file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/trial/run_519/model_refine_001_mFobs-DFmodel.map
Writing map coefficients to MTZ file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/trial/run_519/model_refine_001_map_coeffs.mtz

Writing default parameters for subsequent refinement:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/trial/run_519/model_refine_002.def


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

Pure refinement (no I/O, processing, etc)= 354.51 
  Macro-tasks:
    bulk solvent and scale       = 48.66  
    individual site refinement   = 149.79 
    weights calculation          = 32.87  
    collect and process          = 6.46   
    model show statistics        = 0.12   
    TOTAL for macro-tasks        = 237.90 
  Micro-tasks:
    mask                            = 1.81   
    f_calc                          = 108.08 
    alpha_beta                      = 8.21   
    target                          = 1.12   
    gradients_wrt_atomic_parameters = 120.56 
    fmodel                         = 7.94   
    r_factors                      = 0.29   
    phase_errors                   = 10.56  
    foms                           = 0.20   
    TOTAL for micro-tasks          = 258.77 
NUMBER OF MASK CALCS=  4
Time per interpreted Python bytecode instruction: 4.846 micro seconds
Total CPU time: 6.14 minutes
from_scatterers_fft:    669 calls, 107.67 s
gradients_fft:          614 calls, 106.02 s

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

# Date 2008-01-16 Time 01:46:30 PST -0800 (1200476790.28 s)
Start R-work = 0.4574, R-free = 0.4451 (no bulk solvent and anisotropic scale)
Final R-work = 0.1269, R-free = 0.1736 (no bulk solvent and anisotropic scale)

Start R-work = 0.4491, R-free = 0.4354
Final R-work = 0.1093, R-free = 0.1568