# Date 2008-01-16 Time 02:14:04 PST -0800 (1200478444.26 s)
#phil __OFF__

Command line arguments: "../744.param" "adp.set_b_iso=10" "sites.shake=0.5" "main.number_of_macro_cycles=5" "--overwrite"

HOST = thunderbird.lbl.gov
HOSTTYPE = x86_64-linux
USER = phzwart
PID = 25056
JOB_ID = 5158
SGE_ARCH = lx24-amd64
SGE_TASK_FIRST = 1
SGE_TASK_LAST = 1330
SGE_TASK_ID = 744

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

              phenix.refine: Macromolecular Structure Refinement

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

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

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

Processing inputs. This may take a minute or two.

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

  refinement.modify_start_model.sites.shake = 0.5

  refinement.main.number_of_macro_cycles = 5

Working crystal symmetry after inspecting all inputs:
  Unit cell: (70.6012, 45.9914, 87.2539, 90, 90, 90)
  Space group: P 21 21 21 (No. 19)

/net/cci-filer1/vol1/tmp/phzwart/tassos/trial/model.pdb
  Monomer Library directory:
    "/net/rosie/scratch3/phzwart/CCTBX/Sources/mon_lib"
  Total number of atoms: 2823
  Number of models: 1
  Model: 0
    Number of conformers: 2
    Conformer: "A"
      Number of atoms: 2769
      Number of chains: 2
        Number of residues, atoms: 302, 2333
          Classifications: {'peptide': 302}
          Modifications used: {'COO': 1}
          Link IDs: {'PTRANS': 7, 'CIS': 1, 'TRANS': 293}
        Number of residues, atoms: 436, 436
          Classifications: {'water': 436}
          Link IDs: {None: 435}
    Conformer: "B"
      Number of atoms: 2771
      Common with "A": 2717
      Number of chains: 2
        Number of residues, atoms: 302, 2333
          Classifications: {'peptide': 302}
          Modifications used: {'COO': 1}
          Link IDs: {'PTRANS': 7, 'CIS': 1, 'TRANS': 293}
          bond proxies already assigned to first conformer: 2332
        Number of residues, atoms: 438, 438
          Classifications: {'water': 438}
          Link IDs: {None: 437}
  Time building chain proxies: 3.26, per 1000 atoms: 1.15


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

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

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

Miller array info: /net/cci-filer1/vol1/tmp/phzwart/tassos/trial/1e0w.cns:FOBS,SIGMA
Observation type: xray.amplitude
Type of data: double, size=19589
Type of sigmas: double, size=19589
Number of Miller indices: 19589
Anomalous flag: False
Unit cell: (70.6012, 45.9914, 87.2539, 90, 90, 90)
Space group: P 21 21 21 (No. 19)
Systematic absences: 0
Centric reflections: 2427
Resolution range: 15.0892 1.96336
Completeness in resolution range: 0.93826
Completeness with d_max=infinity: 0.935482

Number of F-obs in resolution range:                   19589
Number of F-obs <= 0:                                  0
Refinement resolution range: d_max =  15.0892
                             d_min =   1.9634

Miller array info: /net/cci-filer1/vol1/tmp/phzwart/tassos/trial/1e0w.cns:TEST
Observation type: None
Type of data: int, size=19589
Type of sigmas: None
Number of Miller indices: 19589
Anomalous flag: False
Unit cell: (70.6012, 45.9914, 87.2539, 90, 90, 90)
Space group: P 21 21 21 (No. 19)
Systematic absences: 0
Centric reflections: 2427
Resolution range: 15.0892 1.96336
Completeness in resolution range: 0.93826
Completeness with d_max=infinity: 0.935482

Test (R-free flags) flag value: 1

Number of work/free reflections by resolution:
                                         work  free  %free
  bin  1: 15.0896 -  4.2023 [2193/2218]  1972   221  10.1%
  bin  2:  4.2023 -  3.3475 [2109/2129]  1901   208   9.9%
  bin  3:  3.3475 -  2.9279 [2081/2100]  1873   208  10.0%
  bin  4:  2.9279 -  2.6618 [2060/2090]  1850   210  10.2%
  bin  5:  2.6618 -  2.4719 [2048/2067]  1851   197   9.6%
  bin  6:  2.4719 -  2.3267 [2045/2070]  1834   211  10.3%
  bin  7:  2.3267 -  2.2105 [2016/2044]  1813   203  10.1%
  bin  8:  2.2105 -  2.1146 [2033/2069]  1826   207  10.2%
  bin  9:  2.1146 -  2.0334 [2014/2056]  1819   195   9.7%
  bin 10:  2.0334 -  1.9634 [ 990/2035]   891    99  10.0%
                                overall 17630  1959  10.0%
Writing MTZ file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/trial/run_744/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: 0.13 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: 40
        2.42 -     3.04: 2202
        3.04 -     3.66: 4712
        3.66 -     4.28: 9054
        4.28 -     4.90: 12328
  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
  " OG1 THR A  29 " - " O   HOH Z 245 "  1.883 3.040 x,y+1,z
  " O   HOH Z  70 " - " O   HOH Z 302 "  1.933 3.040 -x+1/2,-y+1,z+1/2
  " O   HOH Z  61 " - " O   HOH Z 246 "  1.941 3.040 x,y+1,z
  " O   HOH Z 201 " - " O   HOH Z 349 "  1.969 3.040 -x+1/2,-y+1,z+1/2
  ... (remaining 28331 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_744/model_refine_001.eff

Writing geometry restraints to file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/trial/run_744/model_refine_001.geo

CPU time processing inputs: 9.13


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

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

#phil __ON__
refinement {
  crystal_symmetry {
    unit_cell = 70.60125 45.9914 87.2539 90 90 90
    space_group = "P 21 21 21"
  }
  input {
    pdb {
      file_name = "/net/cci-filer1/vol1/tmp/phzwart/tassos/trial/model.pdb"
    }
    xray_data {
      file_name = "/net/cci-filer1/vol1/tmp/phzwart/tassos/trial/1e0w.cns"
      labels = "FOBS,SIGMA"
      r_free_flags {
        file_name = "/net/cci-filer1/vol1/tmp/phzwart/tassos/trial/1e0w.cns"
        label = "TEST"
        test_flag_value = 1
      }
    }
  }
  output {
    prefix = "model_refine"
    serial = 1
  }
  main {
    number_of_macro_cycles = 5
  }
  modify_start_model {
    adp {
      set_b_iso = 10
    }
    sites {
      shake = 0.5
    }
  }
}
#phil __OFF__


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


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


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

|--(resolution: 1.96 - 15.09 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.4847   r_free= 0.4757   ksol= 0.00   Bsol= 0.00   scale= 0.789    |
|                                                                             |
| 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:   0.74 A                  |
| x-ray target function (ml) for work reflections: 6.288341                   |
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
| Bin     Resolution   Compl.  No. Refl.    R-factors          Targets        |
|number     range              work test   work   test        work        test|
|  1: 15.0896 -  4.6877 0.99   1420  157 0.4116 0.3955      6.6153      6.6217|
|  2:  4.6877 -  3.7394 0.99   1373  156 0.4072 0.3679      6.8167      6.7503|
|  3:  3.7394 -  3.2722 0.99   1345  144 0.4291 0.3979      6.6638      6.6215|
|  4:  3.2722 -  2.9755 0.99   1340  151 0.4745 0.4619      6.5412      6.5037|
|  5:  2.9755 -  2.7636 0.99   1332  151 0.5210 0.5128      6.3674       6.385|
|  6:  2.7636 -  2.6016 0.99   1312  145 0.5136 0.5425      6.2724      6.2097|
|  7:  2.6016 -  2.4719 0.99   1325  140 0.5245 0.5039      6.2489      6.1893|
|  8:  2.4719 -  2.3647 0.98   1295  151 0.5315 0.4932      6.1711      6.1924|
|  9:  2.3647 -  2.2740 0.98   1307  143 0.5329 0.5438      6.1282      6.1988|
| 10:  2.2740 -  2.1957 1.00   1307  152 0.5237 0.5192       6.094      6.0529|
| 11:  2.1957 -  2.1273 0.98   1305  138 0.5106 0.5368      6.0381      6.0433|
| 12:  2.1273 -  2.0666 0.98   1288  144 0.5293 0.5669       5.948      5.9946|
| 13:  2.0666 -  2.0124 0.98   1267  141 0.5452 0.5589      5.8833       5.798|
| 14:  2.0124 -  1.9634 0.31    414   46 0.5625 0.4530      5.8719      5.8324|
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
|R-free likelihood based estimates for figures of merit, absolute phase error,|
|and distribution parameters alpha and beta (Acta Cryst. (1995). A51, 880-887)|
|                                                                             |
| Bin     Resolution      No. Refl.   FOM  Phase Scale    Alpha        Beta   |
|  #        range        work  test        error factor                       |
|  1: 15.0896 -  4.6877  1420   157  0.67  36.73   0.79     0.72      79858.35|
|  2:  4.6877 -  3.7394  1373   156  0.72  33.84   0.86     0.80     102132.14|
|  3:  3.7394 -  3.2722  1345   144  0.62  42.56   0.86     0.74     107912.30|
|  4:  3.2722 -  2.9755  1340   151  0.52  50.24   0.78     0.61      99164.78|
|  5:  2.9755 -  2.7636  1332   151  0.40  60.01   0.73     0.49      85242.98|
|  6:  2.7636 -  2.6016  1312   145  0.37  62.27   0.71     0.43      74366.24|
|  7:  2.6016 -  2.4719  1325   140  0.31  66.38   0.74     0.37      70263.82|
|  8:  2.4719 -  2.3647  1295   151  0.29  68.10   0.71     0.35      63581.93|
|  9:  2.3647 -  2.2740  1307   143  0.29  68.03   0.73     0.36      59109.03|
| 10:  2.2740 -  2.1957  1307   152  0.32  66.01   0.75     0.39      50471.27|
| 11:  2.1957 -  2.1273  1305   138  0.31  66.69   0.77     0.39      49102.93|
| 12:  2.1273 -  2.0666  1288   144  0.28  69.29   0.74     0.36      45451.92|
| 13:  2.0666 -  2.0124  1267   141  0.26  70.59   0.72     0.35      40131.13|
| 14:  2.0124 -  1.9634   414    46  0.33  65.75   0.69     0.37      30770.82|
|alpha:            min =        0.35 max =            0.80 mean =         0.49|
|beta:             min =    30770.82 max =       107912.30 mean =     70767.30|
|figures of merit: min =        0.00 max =            1.00 mean =         0.41|
|phase err.(work): min =        0.00 max =           90.00 mean =        58.37|
|phase err.(test): min =        0.00 max =           90.00 mean =        58.71|
|-----------------------------------------------------------------------------|

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

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

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 16.173540             wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 81.194   (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 1.401053              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 78.312   (deg)                 |
|-----------------------------------------------------------------------------|


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

|-Geometry statistics: start--------------------------------------------------|
|            Histogram of deviations from ideal values for                    |
| Bonds                | Angles                   |  Nonbonded contacts       |
| 0.000 - 0.140:   597 |   0.009 -   7.457:   713 |  1.196 -  1.566:        2 |
| 0.140 - 0.280:   585 |   7.457 -  14.906:   711 |  1.566 -  1.937:       34 |
| 0.280 - 0.420:   441 |  14.906 -  22.354:   630 |  1.937 -  2.307:      170 |
| 0.420 - 0.560:   366 |  22.354 -  29.802:   474 |  2.307 -  2.677:      693 |
| 0.560 - 0.700:   237 |  29.802 -  37.251:   338 |  2.677 -  3.048:     1516 |
| 0.700 - 0.840:   127 |  37.251 -  44.699:   241 |  3.048 -  3.418:     2633 |
| 0.840 - 0.980:    59 |  44.699 -  52.147:   125 |  3.418 -  3.789:     3956 |
| 0.980 - 1.120:    17 |  52.147 -  59.595:    51 |  3.789 -  4.159:     5093 |
| 1.120 - 1.260:     9 |  59.595 -  67.044:    13 |  4.159 -  4.530:     6553 |
| 1.260 - 1.400:     1 |  67.044 -  74.492:     3 |  4.530 -  4.900:     7714 |
|-----------------------------------------------------------------------------|
|-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 |       53.677 |
| planarity |      436 |   0.145    0.405  0.000 |     250.485 |              |
|  dihedral |      870 |  33.790  144.062  0.019 |      20.704 |              |
| nonbonded |     2439 |   4.089    4.900  1.196 |       2.006 |              |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 11.804)------------------------------------------|
|    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 = 11.804)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.01    19.99   9.86     None  None   None       |
|    all(noH): 2823   0      0.01    19.99   9.86     None  None   None       |
|    Sol.    : 438    0      0.06    19.99   10.10    None  None   None       |
|    Mac.    : 2385   0      0.01    19.98   9.82     None  None   None       |
|    Hyd.    : 0      0      None    None    None     None  None   None       |
|    - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -      |
|       Distribution of isotropic (or equivalent) ADP for non-H atoms:        |
|    Bin#      value range     #atoms | Bin#      value range     #atoms      |
|      0:     0.008 -   2.007:  301   |   5:    10.002 -  12.000:  285        |
|      1:     2.007 -   4.006:  276   |   6:    12.000 -  13.999:  292        |
|      2:     4.006 -   6.004:  309   |   7:    13.999 -  15.998:  289        |
|      3:     6.004 -   8.003:  285   |   8:    15.998 -  17.996:  266        |
|      4:     8.003 -  10.002:  251   |   9:    17.996 -  19.995:  269        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.96 - 15.09 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.4906   r_free= 0.4765   ksol= 0.00   Bsol= 0.00   scale= 0.760    |
|                                                                             |
| 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:   0.73 A                  |
| x-ray target function (ml) for work reflections: 6.290161                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.96 - 15.09 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.4765   r_free= 0.4620   ksol= 0.35   Bsol= 2.59   scale= 0.998    |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (7.18,10.00,9.22,0.00,0.00,0.00); trace/3= 8.80                             |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.75 A                  |
| x-ray target function (ml) for work reflections: 6.283362                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 13.444635             wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 82.546   (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 1.304877              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 76.388   (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.4765      final r-factor (work) = 0.3964          |
| start r-factor (free) = 0.4620      final r-factor (free) = 0.4183          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 95.9189 = 13.44 * 0.50 * 6.2839 + 1.00 * 53.6765                            |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 41.8753 = 13.44 * 0.50 * 6.2078 + 1.00 * 0.1444                             |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 26     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.3964      final r-factor (work) = 0.3543          |
| start r-factor (free) = 0.4183      final r-factor (free) = 0.4180          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 8.1149 = 1.30 * 1.00 * 6.2078 + 1.00 * 0.0144                               |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 8.0245 = 1.30 * 1.00 * 6.1361 + 1.00 * 0.0177                               |
|-----------------------------------------------------------------------------|
| number of iterations = 22      |    number of function evaluations = 24     |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 11.804)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.00    77.13   14.08    None  None   None       |
|    all(noH): 2823   0      0.00    77.13   14.08    None  None   None       |
|    Sol.    : 438    0      0.00    77.13   24.41    None  None   None       |
|    Mac.    : 2385   0      0.00    67.19   12.18    None  None   None       |
|    Hyd.    : 0      0      None    None    None     None  None   None       |
|    - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -      |
|       Distribution of isotropic (or equivalent) ADP for non-H atoms:        |
|    Bin#      value range     #atoms | Bin#      value range     #atoms      |
|      0:     0.000 -   7.713: 1004   |   5:    38.564 -  46.277:   68        |
|      1:     7.713 -  15.426:  844   |   6:    46.277 -  53.990:   36        |
|      2:    15.426 -  23.139:  438   |   7:    53.990 -  61.703:   19        |
|      3:    23.139 -  30.852:  264   |   8:    61.703 -  69.416:    7        |
|      4:    30.852 -  38.564:  142   |   9:    69.416 -  77.129:    1        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.3543 r_free = 0.4180             target_work(ml) = 6.126         |
| occupancies: max = 1.00  min = 0.30   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.3541 r_free = 0.4173             target_work(ml) = 6.126         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        2 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.96 - 15.09 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.3541   r_free= 0.4173   ksol= 0.35   Bsol= 2.59   scale= 1.121    |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (7.18,10.00,9.22,0.00,0.00,0.00); trace/3= 8.80                             |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.59 A                  |
| x-ray target function (ml) for work reflections: 6.125680                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.96 - 15.09 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.3511   r_free= 0.4101   ksol= 0.35   Bsol= 35.29   scale= 1.019   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (3.66,5.68,5.17,0.00,0.00,0.00); trace/3= 4.84                              |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.59 A                  |
| x-ray target function (ml) for work reflections: 6.125410                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 5.807550              wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 100.590  (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 0.620882              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 140.427  (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.3511      final r-factor (work) = 0.2921          |
| start r-factor (free) = 0.4101      final r-factor (free) = 0.3568          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 17.9526 = 5.81 * 0.50 * 6.1328 + 1.00 * 0.1444                              |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 17.6454 = 5.81 * 0.50 * 6.0499 + 1.00 * 0.0779                              |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 28     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.2921      final r-factor (work) = 0.2747          |
| start r-factor (free) = 0.3568      final r-factor (free) = 0.3428          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 3.7741 = 0.62 * 1.00 * 6.0499 + 1.00 * 0.0179                               |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 3.7108 = 0.62 * 1.00 * 5.9543 + 1.00 * 0.0138                               |
|-----------------------------------------------------------------------------|
| number of iterations = 11      |    number of function evaluations = 13     |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 11.804)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.00    81.26   14.05    None  None   None       |
|    all(noH): 2823   0      0.00    81.26   14.05    None  None   None       |
|    Sol.    : 438    0      0.00    81.26   29.14    None  None   None       |
|    Mac.    : 2385   0      0.00    62.95   11.28    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 -   8.126: 1124   |   5:    40.632 -  48.758:   53        |
|      1:     8.126 -  16.253:  774   |   6:    48.758 -  56.885:   26        |
|      2:    16.253 -  24.379:  427   |   7:    56.885 -  65.011:   17        |
|      3:    24.379 -  32.506:  245   |   8:    65.011 -  73.138:    2        |
|      4:    32.506 -  40.632:  154   |   9:    73.138 -  81.264:    1        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.2747 r_free = 0.3428             target_work(ml) = 5.940         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        2 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.2745 r_free = 0.3427             target_work(ml) = 5.940         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        4 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.96 - 15.09 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.2745   r_free= 0.3427   ksol= 0.35   Bsol= 35.29   scale= 1.061   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (3.66,5.68,5.17,0.00,0.00,0.00); trace/3= 4.84                              |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.43 A                  |
| x-ray target function (ml) for work reflections: 5.939553                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.96 - 15.09 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.2739   r_free= 0.3414   ksol= 0.32   Bsol= 42.12   scale= 1.012   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (2.29,3.26,3.55,0.00,0.00,0.00); trace/3= 3.03                              |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.43 A                  |
| x-ray target function (ml) for work reflections: 5.940601                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 6.305106              wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 99.024   (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 0.454602              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 118.888  (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.2739      final r-factor (work) = 0.2074          |
| start r-factor (free) = 0.3414      final r-factor (free) = 0.2687          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 18.8513 = 6.31 * 0.50 * 5.9550 + 1.00 * 0.0779                              |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 18.4516 = 6.31 * 0.50 * 5.8253 + 1.00 * 0.0869                              |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 27     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.2074      final r-factor (work) = 0.1874          |
| start r-factor (free) = 0.2687      final r-factor (free) = 0.2488          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 2.6619 = 0.45 * 1.00 * 5.8253 + 1.00 * 0.0136                               |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 2.5865 = 0.45 * 1.00 * 5.6345 + 1.00 * 0.0251                               |
|-----------------------------------------------------------------------------|
| number of iterations = 10      |    number of function evaluations = 11     |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 11.804)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.00    81.55   13.85    None  None   None       |
|    all(noH): 2823   0      0.00    81.55   13.85    None  None   None       |
|    Sol.    : 438    0      2.16    81.55   32.96    None  None   None       |
|    Mac.    : 2385   0      0.00    69.09   10.34    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 -   8.155: 1250   |   5:    40.776 -  48.931:   75        |
|      1:     8.155 -  16.310:  782   |   6:    48.931 -  57.086:   33        |
|      2:    16.310 -  24.466:  291   |   7:    57.086 -  65.241:   14        |
|      3:    24.466 -  32.621:  197   |   8:    65.241 -  73.397:    4        |
|      4:    32.621 -  40.776:  176   |   9:    73.397 -  81.552:    1        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.1874 r_free = 0.2488             target_work(ml) = 5.595         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        4 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.1871 r_free = 0.2482             target_work(ml) = 5.594         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        5 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.96 - 15.09 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1871   r_free= 0.2482   ksol= 0.32   Bsol= 42.12   scale= 1.039   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (2.29,3.26,3.55,0.00,0.00,0.00); trace/3= 3.03                              |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.24 A                  |
| x-ray target function (ml) for work reflections: 5.594109                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.96 - 15.09 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1862   r_free= 0.2473   ksol= 0.33   Bsol= 42.12   scale= 1.007   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (1.23,1.53,2.74,0.00,0.00,0.00); trace/3= 1.83                              |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.25 A                  |
| x-ray target function (ml) for work reflections: 5.593120                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 5.213080              wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 96.951   (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 0.582457              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 93.784   (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1862      final r-factor (work) = 0.1467          |
| start r-factor (free) = 0.2473      final r-factor (free) = 0.2038          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 14.7798 = 5.21 * 0.50 * 5.6370 + 1.00 * 0.0869                              |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 14.3961 = 5.21 * 0.50 * 5.4948 + 1.00 * 0.0735                              |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 29     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1467      final r-factor (work) = 0.1328          |
| start r-factor (free) = 0.2038      final r-factor (free) = 0.1866          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 3.2141 = 0.58 * 1.00 * 5.4948 + 1.00 * 0.0136                               |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 3.1299 = 0.58 * 1.00 * 5.3544 + 1.00 * 0.0112                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 28     |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 11.804)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.00    81.01   13.91    None  None   None       |
|    all(noH): 2823   0      0.00    81.01   13.91    None  None   None       |
|    Sol.    : 438    0      2.69    81.01   37.51    None  None   None       |
|    Mac.    : 2385   0      0.00    78.03   9.58     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 -   8.101: 1332   |   5:    40.507 -  48.609:   97        |
|      1:     8.101 -  16.203:  799   |   6:    48.609 -  56.710:   82        |
|      2:    16.203 -  24.304:  220   |   7:    56.710 -  64.811:   46        |
|      3:    24.304 -  32.406:  135   |   8:    64.811 -  72.913:    4        |
|      4:    32.406 -  40.507:  103   |   9:    72.913 -  81.014:    5        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.1328 r_free = 0.1866             target_work(ml) = 5.303         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        5 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.1327 r_free = 0.1864             target_work(ml) = 5.303         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        5 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.96 - 15.09 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1327   r_free= 0.1864   ksol= 0.33   Bsol= 42.12   scale= 1.012   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (1.23,1.53,2.74,0.00,0.00,0.00); trace/3= 1.83                              |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.17 A                  |
| x-ray target function (ml) for work reflections: 5.302551                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.96 - 15.09 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1331   r_free= 0.1853   ksol= 0.32   Bsol= 49.66   scale= 1.006   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (1.16,1.06,2.71,0.00,0.00,0.00); trace/3= 1.64                              |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.17 A                  |
| x-ray target function (ml) for work reflections: 5.300059                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 3.177221              wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 125.010  (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 1.494412              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 140.296  (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1331      final r-factor (work) = 0.1219          |
| start r-factor (free) = 0.1853      final r-factor (free) = 0.1726          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 8.5801 = 3.18 * 0.50 * 5.3547 + 1.00 * 0.0735                               |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 8.4381 = 3.18 * 0.50 * 5.2688 + 1.00 * 0.0680                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 28     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1219      final r-factor (work) = 0.1181          |
| start r-factor (free) = 0.1726      final r-factor (free) = 0.1703          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 7.8849 = 1.49 * 1.00 * 5.2688 + 1.00 * 0.0111                               |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 7.8110 = 1.49 * 1.00 * 5.2181 + 1.00 * 0.0130                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 27     |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 11.804)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.00    90.56   14.11    None  None   None       |
|    all(noH): 2823   0      0.00    90.56   14.11    None  None   None       |
|    Sol.    : 438    0      2.75    90.22   39.58    None  None   None       |
|    Mac.    : 2385   0      0.00    90.56   9.44     None  None   None       |
|    Hyd.    : 0      0      None    None    None     None  None   None       |
|    - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -      |
|       Distribution of isotropic (or equivalent) ADP for non-H atoms:        |
|    Bin#      value range     #atoms | Bin#      value range     #atoms      |
|      0:     0.000 -   9.056: 1564   |   5:    45.280 -  54.336:   91        |
|      1:     9.056 -  18.112:  666   |   6:    54.336 -  63.392:   60        |
|      2:    18.112 -  27.168:  172   |   7:    63.392 -  72.448:   39        |
|      3:    27.168 -  36.224:  120   |   8:    72.448 -  81.504:   13        |
|      4:    36.224 -  45.280:   91   |   9:    81.504 -  90.560:    7        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.1181 r_free = 0.1703             target_work(ml) = 5.211         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        5 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.1181 r_free = 0.1702             target_work(ml) = 5.211         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        5 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.96 - 15.09 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1181   r_free= 0.1702   ksol= 0.32   Bsol= 49.66   scale= 1.003   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (1.16,1.06,2.71,0.00,0.00,0.00); trace/3= 1.64                              |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.17 A                  |
| x-ray target function (ml) for work reflections: 5.211009                   |
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
| Bin     Resolution   Compl.  No. Refl.    R-factors          Targets        |
|number     range              work test   work   test        work        test|
|  1: 15.0896 -  4.6877 0.99   1420  157 0.0982 0.1285       5.379      5.5735|
|  2:  4.6877 -  3.7394 0.99   1373  156 0.0865 0.1188      5.4573      5.6921|
|  3:  3.7394 -  3.2722 0.99   1345  144 0.1113 0.1597      5.5228      5.8484|
|  4:  3.2722 -  2.9755 0.99   1340  151 0.1297 0.1868      5.5019      5.6825|
|  5:  2.9755 -  2.7636 0.99   1332  151 0.1403 0.1788      5.3808      5.6094|
|  6:  2.7636 -  2.6016 0.99   1312  145 0.1304 0.2071      5.2541      5.5453|
|  7:  2.6016 -  2.4719 0.99   1325  140 0.1321 0.1748      5.2223      5.3763|
|  8:  2.4719 -  2.3647 0.98   1295  151 0.1288 0.1845      5.1458      5.4165|
|  9:  2.3647 -  2.2740 0.98   1307  143 0.1291 0.1953       5.115      5.4114|
| 10:  2.2740 -  2.1957 1.00   1307  152 0.1208 0.1873      5.0275      5.2565|
| 11:  2.1957 -  2.1273 0.98   1305  138 0.1201 0.2071      5.0252      5.4341|
| 12:  2.1273 -  2.0666 0.98   1288  144 0.1233 0.1881       4.945      5.2091|
| 13:  2.0666 -  2.0124 0.98   1267  141 0.1161 0.1782      4.8493      5.0627|
| 14:  2.0124 -  1.9634 0.31    414   46 0.1114 0.1603      4.7512      4.9266|
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
|R-free likelihood based estimates for figures of merit, absolute phase error,|
|and distribution parameters alpha and beta (Acta Cryst. (1995). A51, 880-887)|
|                                                                             |
| Bin     Resolution      No. Refl.   FOM  Phase Scale    Alpha        Beta   |
|  #        range        work  test        error factor                       |
|  1: 15.0896 -  4.6877  1420   157  0.94   9.48   0.98     0.95       7284.69|
|  2:  4.6877 -  3.7394  1373   156  0.95   8.40   1.02     1.00       9733.56|
|  3:  3.7394 -  3.2722  1345   144  0.93  12.48   1.04     1.03      11771.03|
|  4:  3.2722 -  2.9755  1340   151  0.91  15.36   1.02     0.99      11759.18|
|  5:  2.9755 -  2.7636  1332   151  0.89  17.11   1.00     0.98       9435.47|
|  6:  2.7636 -  2.6016  1312   145  0.89  17.42   0.99     0.95       7883.11|
|  7:  2.6016 -  2.4719  1325   140  0.89  16.85   0.99     0.96       7091.67|
|  8:  2.4719 -  2.3647  1295   151  0.89  17.49   0.99     0.96       6431.34|
|  9:  2.3647 -  2.2740  1307   143  0.89  17.84   0.99     0.94       6070.50|
| 10:  2.2740 -  2.1957  1307   152  0.89  17.46   1.00     0.96       5267.16|
| 11:  2.1957 -  2.1273  1305   138  0.88  18.12   0.99     0.93       5263.12|
| 12:  2.1273 -  2.0666  1288   144  0.89  17.71   1.01     1.00       4721.59|
| 13:  2.0666 -  2.0124  1267   141  0.88  18.91   1.00     0.97       4081.22|
| 14:  2.0124 -  1.9634   414    46  0.90  16.28   0.98     0.95       3214.09|
|alpha:            min =        0.93 max =            1.03 mean =         0.97|
|beta:             min =     3214.09 max =        11771.03 mean =      7385.32|
|figures of merit: min =        0.00 max =            1.00 mean =         0.90|
|phase err.(work): min =        0.00 max =           89.98 mean =        15.67|
|phase err.(test): min =        0.00 max =           89.22 mean =        15.00|
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.96 - 15.09 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1180   r_free= 0.1701   ksol= 0.32   Bsol= 51.41   scale= 1.006   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-0.44,-0.66,1.09,-0.00,0.00,0.00); trace/3= 0.00                           |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.17 A                  |
| x-ray target function (ml) for work reflections: 5.210777                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.96 - 15.09 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1180   r_free= 0.1701   ksol= 0.32   Bsol= 51.41   scale= 1.006   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-0.44,-0.66,1.09,-0.00,0.00,0.00); trace/3= 0.00                           |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.17 A                  |
| x-ray target function (ml) for work reflections: 5.210777                   |
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
| Bin     Resolution   Compl.  No. Refl.    R-factors          Targets        |
|number     range              work test   work   test        work        test|
|  1: 15.0896 -  4.6877 0.99   1420  157 0.0981 0.1282      5.3768      5.5732|
|  2:  4.6877 -  3.7394 0.99   1373  156 0.0866 0.1190       5.458      5.6935|
|  3:  3.7394 -  3.2722 0.99   1345  144 0.1113 0.1598      5.5235      5.8493|
|  4:  3.2722 -  2.9755 0.99   1340  151 0.1297 0.1867      5.5019      5.6821|
|  5:  2.9755 -  2.7636 0.99   1332  151 0.1402 0.1787      5.3804      5.6085|
|  6:  2.7636 -  2.6016 0.99   1312  145 0.1304 0.2070      5.2537      5.5449|
|  7:  2.6016 -  2.4719 0.99   1325  140 0.1321 0.1750      5.2221      5.3767|
|  8:  2.4719 -  2.3647 0.98   1295  151 0.1289 0.1844      5.1458      5.4161|
|  9:  2.3647 -  2.2740 0.98   1307  143 0.1290 0.1949      5.1149       5.411|
| 10:  2.2740 -  2.1957 1.00   1307  152 0.1207 0.1874      5.0276      5.2573|
| 11:  2.1957 -  2.1273 0.98   1305  138 0.1200 0.2071      5.0253      5.4344|
| 12:  2.1273 -  2.0666 0.98   1288  144 0.1233 0.1879      4.9448      5.2087|
| 13:  2.0666 -  2.0124 0.98   1267  141 0.1161 0.1779      4.8487      5.0615|
| 14:  2.0124 -  1.9634 0.31    414   46 0.1113 0.1600      4.7501       4.925|
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
|R-free likelihood based estimates for figures of merit, absolute phase error,|
|and distribution parameters alpha and beta (Acta Cryst. (1995). A51, 880-887)|
|                                                                             |
| Bin     Resolution      No. Refl.   FOM  Phase Scale    Alpha        Beta   |
|  #        range        work  test        error factor                       |
|  1: 15.0896 -  4.6877  1420   157  0.94   9.43   0.98     0.95       7244.12|
|  2:  4.6877 -  3.7394  1373   156  0.95   8.40   1.02     1.01       9730.74|
|  3:  3.7394 -  3.2722  1345   144  0.93  12.50   1.04     1.03      11799.58|
|  4:  3.2722 -  2.9755  1340   151  0.90  15.36   1.02     1.00      11758.49|
|  5:  2.9755 -  2.7636  1332   151  0.89  17.10   1.01     0.99       9424.68|
|  6:  2.7636 -  2.6016  1312   145  0.89  17.42   0.99     0.96       7875.47|
|  7:  2.6016 -  2.4719  1325   140  0.89  16.84   1.00     0.96       7087.90|
|  8:  2.4719 -  2.3647  1295   151  0.89  17.49   1.00     0.97       6429.64|
|  9:  2.3647 -  2.2740  1307   143  0.89  17.84   1.00     0.95       6069.92|
| 10:  2.2740 -  2.1957  1307   152  0.89  17.47   1.00     0.96       5270.03|
| 11:  2.1957 -  2.1273  1305   138  0.88  18.13   1.00     0.94       5267.22|
| 12:  2.1273 -  2.0666  1288   144  0.89  17.71   1.01     1.00       4720.54|
| 13:  2.0666 -  2.0124  1267   141  0.88  18.89   1.01     0.98       4076.22|
| 14:  2.0124 -  1.9634   414    46  0.90  16.24   0.99     0.96       3206.92|
|alpha:            min =        0.94 max =            1.03 mean =         0.98|
|beta:             min =     3206.92 max =        11799.58 mean =      7382.03|
|figures of merit: min =        0.00 max =            1.00 mean =         0.90|
|phase err.(work): min =        0.00 max =           89.98 mean =        15.67|
|phase err.(test): min =        0.00 max =           89.60 mean =        15.00|
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 11.804)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      1.75    92.31   15.87    None  None   None       |
|    all(noH): 2823   0      1.75    92.31   15.87    None  None   None       |
|    Sol.    : 438    0      4.50    91.97   41.34    None  None   None       |
|    Mac.    : 2385   0      1.75    92.31   11.19    None  None   None       |
|    Hyd.    : 0      0      None    None    None     None  None   None       |
|    - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -      |
|       Distribution of isotropic (or equivalent) ADP for non-H atoms:        |
|    Bin#      value range     #atoms | Bin#      value range     #atoms      |
|      0:     1.752 -  10.808: 1564   |   5:    47.032 -  56.088:   91        |
|      1:    10.808 -  19.864:  666   |   6:    56.088 -  65.144:   60        |
|      2:    19.864 -  28.920:  172   |   7:    65.144 -  74.200:   39        |
|      3:    28.920 -  37.976:  120   |   8:    74.200 -  83.256:   13        |
|      4:    37.976 -  47.032:   91   |   9:    83.256 -  92.312:    7        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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


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

Number of peaks found at mFobs-DFmodel map (map cutoff=3.00 sigma)= 322         
Filter by distance & map next to the model:
   mapped sites are within: 0.285 - 5.330
   number of sites selected in [dist_min= 0.70, dist_max= 6.00]: 319 from: 322
   mapped sites are within: 0.713 - 5.330

peak=   10.193 closest distance to " CB  VAL A 230 " =    1.435
peak=    8.308 closest distance to " O   HOH Z 130 " =    1.762
peak=    8.051 closest distance to " CG2 VAL A 296 " =    1.251
peak=    6.550 closest distance to " CD2 LEU A   5 " =    1.273
peak=    6.404 closest distance to " CG  ARG A 138 " =    1.110
peak=    6.101 closest distance to " NE2 GLN A  11 " =    1.190
peak=    5.846 closest distance to " O   HOH Z  65 " =    1.481
peak=    5.684 closest distance to " O   HOH Z 222 " =    1.368
peak=    5.521 closest distance to " CD1AILE A 234 " =    1.061
peak=    5.495 closest distance to " NH2 ARG A  56 " =    2.095
peak=    5.432 closest distance to " O   HOH Z 142 " =    2.024
peak=    5.418 closest distance to " CG  PRO A  54 " =    1.377
peak=    5.358 closest distance to " CG  LEU A   5 " =    1.165
peak=    5.357 closest distance to " CG  LEU A 228 " =    1.143
peak=    5.241 closest distance to " O   HOH Z   9 " =    2.055
peak=    5.025 closest distance to " O   HOH Z 232 " =    2.253
peak=    4.956 closest distance to " O   HOH Z 427 " =    2.390
peak=    4.856 closest distance to " CB  PRO A  54 " =    1.054
peak=    4.806 closest distance to " O   HOH Z   7 " =    1.582
peak=    4.748 closest distance to " O   HOH Z 417 " =    1.674
peak=    4.736 closest distance to " O   HOH Z 425 " =    1.652
peak=    4.681 closest distance to " CB  VAL A 230 " =    1.183
peak=    4.677 closest distance to " O   HOH Z 369 " =    2.091
peak=    4.673 closest distance to " CB  GLN A 183 " =    1.259
peak=    4.665 closest distance to " O   HOH Z 126 " =    2.169
peak=    4.627 closest distance to " CB  GLN A 223 " =    1.554
peak=    4.599 closest distance to " NH1 ARG A 138 " =    1.005
peak=    4.506 closest distance to " O   HOH Z 127 " =    1.103
peak=    4.474 closest distance to " O   HOH Z  63 " =    1.567
peak=    4.472 closest distance to " O   HOH Z 287 " =    1.870
peak=    4.447 closest distance to " O   HOH Z   2 " =    1.866
peak=    4.330 closest distance to " O   HOH Z 392 " =    1.322
peak=    4.287 closest distance to " O   HOH Z 225 " =    1.553
peak=    4.285 closest distance to " O   HOH Z 380 " =    1.991
peak=    4.284 closest distance to " O   HOH Z 298 " =    1.800
peak=    4.281 closest distance to " O   HOH Z  78 " =    1.599
peak=    4.269 closest distance to " CB  SER A  63 " =    1.253
peak=    4.225 closest distance to " CB  VAL A 296 " =    1.132
peak=    4.220 closest distance to " CG  LEU A 167 " =    1.281
peak=    4.213 closest distance to " O   HOH Z 214 " =    2.293
peak=    4.202 closest distance to " CG  PRO A 198 " =    1.256
peak=    4.194 closest distance to " O   HOH Z  30 " =    1.994
peak=    4.191 closest distance to " CB  ARG A 275 " =    0.962
peak=    4.167 closest distance to " O   HOH Z 209 " =    2.324
peak=    4.166 closest distance to " O   HOH Z 427 " =    1.210
peak=    4.158 closest distance to " CB  SER A   3 " =    1.442
peak=    4.149 closest distance to " CB  ASN A  39 " =    0.998
peak=    4.145 closest distance to " O   HOH Z 139 " =    1.271
peak=    4.144 closest distance to " O   HOH Z 361 " =    1.379
peak=    4.140 closest distance to " CB  ASN A 148 " =    1.436
peak=    4.123 closest distance to " CG  PRO A 280 " =    0.873
peak=    4.121 closest distance to " O   HOH Z 424 " =    1.085
peak=    4.107 closest distance to " O   HOH Z 316 " =    3.030
peak=    4.093 closest distance to " CD  ARG A  66 " =    2.432
peak=    4.084 closest distance to " O   HOH Z  59 " =    1.598
peak=    4.079 closest distance to " CD2 LEU A 228 " =    1.250
peak=    4.063 closest distance to " CG  PRO A 213 " =    1.250
peak=    4.038 closest distance to " O   SER A  87 " =    2.393
peak=    4.024 closest distance to " O   HOH Z 272 " =    1.835
peak=    4.017 closest distance to " O   HOH Z 124 " =    1.297
peak=    4.011 closest distance to " O   HOH Z 133 " =    1.497
peak=    3.999 closest distance to " CB AVAL A  41 " =    1.134
peak=    3.982 closest distance to " O   HOH Z 158 " =    2.960
peak=    3.981 closest distance to " O   HOH Z   1 " =    1.924
peak=    3.965 closest distance to " CB  SER A 216 " =    0.951
peak=    3.951 closest distance to " O   HOH Z 195 " =    1.618
peak=    3.934 closest distance to " CB  ASP A 124 " =    0.768
peak=    3.929 closest distance to " O   HOH Z 410 " =    1.466
peak=    3.905 closest distance to " O   HOH Z 359 " =    1.281
peak=    3.902 closest distance to " O   HOH Z 419 " =    1.978
peak=    3.901 closest distance to " CB  VAL A 202 " =    1.624
peak=    3.898 closest distance to " O   HOH Z 418 " =    0.984
peak=    3.893 closest distance to " CH2 TRP A 266 " =    1.083
peak=    3.866 closest distance to " O   HOH Z 193 " =    1.708
peak=    3.862 closest distance to " CB  ASN A 142 " =    0.905
peak=    3.858 closest distance to " O   HOH Z 362 " =    1.840
peak=    3.850 closest distance to " O   HOH Z 422 " =    2.666
peak=    3.845 closest distance to " O   HOH Z 234 " =    3.868
peak=    3.836 closest distance to " O   HOH Z 425 " =    2.148
peak=    3.832 closest distance to " O   HOH Z  68 " =    2.104
peak=    3.830 closest distance to " CB  LEU A 228 " =    1.293
peak=    3.829 closest distance to " O   HOH Z 423 " =    1.572
peak=    3.820 closest distance to " O   HOH Z 193 " =    2.032
peak=    3.816 closest distance to " NH1AARG A 145 " =    1.149
peak=    3.812 closest distance to " O   HOH Z 373 " =    1.481
peak=    3.811 closest distance to " OG  SER A  62 " =    2.816
peak=    3.802 closest distance to " CE3 TRP A 150 " =    1.062
peak=    3.782 closest distance to " CB  GLU A 277 " =    3.565
peak=    3.780 closest distance to " CG  LYS A  76 " =    1.697
peak=    3.769 closest distance to " O   PRO A 198 " =    1.234
peak=    3.768 closest distance to " O   HOH Z 346 " =    1.664
peak=    3.767 closest distance to " O   HOH Z 327 " =    1.634
peak=    3.767 closest distance to " O   HOH Z 352 " =    1.665
peak=    3.766 closest distance to " CD  ARG A 159 " =    0.713
peak=    3.765 closest distance to " O   HOH Z 236 " =    1.552
peak=    3.764 closest distance to " CG  TRP A 179 " =    2.220
peak=    3.764 closest distance to " CB  TRP A 266 " =    1.073
peak=    3.754 closest distance to " O   PRO A 198 " =    1.568
peak=    3.753 closest distance to " O   HOH Z 112 " =    1.039
peak=    3.745 closest distance to " O   HOH Z 411 " =    3.559
peak=    3.744 closest distance to " CB  LEU A 237 " =    0.883
peak=    3.734 closest distance to " O   HOH Z 371 " =    2.745
peak=    3.731 closest distance to " CB  LYS A 117 " =    1.222
peak=    3.727 closest distance to " N   PHE A 130 " =    1.242
peak=    3.715 closest distance to " CB  GLN A  88 " =    1.367
peak=    3.714 closest distance to " O   HOH Z 375 " =    0.975
peak=    3.694 closest distance to " N   GLN A 278 " =    1.270
peak=    3.671 closest distance to " O   HOH Z 389 " =    1.320
peak=    3.670 closest distance to " O   HOH Z  55 " =    1.859
peak=    3.666 closest distance to " CA  ASN A 127 " =    1.120
peak=    3.665 closest distance to " O   HOH Z  61 " =    1.523
peak=    3.664 closest distance to " CD  GLN A 240 " =    1.598
peak=    3.662 closest distance to " O   HOH Z 368 " =    3.637
peak=    3.655 closest distance to " NH2AARG A 190 " =    1.665
peak=    3.647 closest distance to " O   HOH Z 145 " =    2.524
peak=    3.643 closest distance to " CB  TRP A 179 " =    1.401
peak=    3.640 closest distance to " ND1 HIS A  86 " =    1.858
peak=    3.630 closest distance to " CG  PRO A 243 " =    1.096
peak=    3.630 closest distance to " CB  GLU A 128 " =    1.084
peak=    3.625 closest distance to " NZ  LYS A 117 " =    3.200
peak=    3.621 closest distance to " O   HOH Z 146 " =    1.612
peak=    3.610 closest distance to " O   ASN A 209 " =    1.475
peak=    3.604 closest distance to " O   HOH Z  51 " =    1.510
peak=    3.604 closest distance to " O   HOH Z 414 " =    1.202
peak=    3.602 closest distance to " CB  SER A 276 " =    1.160
peak=    3.591 closest distance to " O   HOH Z  78 " =    2.133
peak=    3.591 closest distance to " O   HOH Z  59 " =    2.098
peak=    3.590 closest distance to " CA  ALA A  51 " =    1.101
peak=    3.588 closest distance to " O   HOH Z  76 " =    1.062
peak=    3.588 closest distance to " CB  THR A 157 " =    1.104
peak=    3.587 closest distance to " CG1 ILE A 151 " =    1.152
peak=    3.582 closest distance to " O   HOH Z 128 " =    2.125
peak=    3.582 closest distance to " CG  LEU A 281 " =    1.036
peak=    3.579 closest distance to " O   HOH Z  88 " =    3.487
peak=    3.577 closest distance to " O   HOH Z 175 " =    2.143
peak=    3.576 closest distance to " O   HOH Z 258 " =    2.150
peak=    3.569 closest distance to " O   HOH Z 329 " =    4.036
peak=    3.568 closest distance to " O   HOH Z  88 " =    2.964
peak=    3.564 closest distance to " O   HOH Z  39 " =    1.247
peak=    3.563 closest distance to " O   HOH Z 128 " =    1.881
peak=    3.558 closest distance to " O   HOH Z 425 " =    2.009
peak=    3.557 closest distance to " O   HOH Z 222 " =    2.057
peak=    3.553 closest distance to " N   SER A 271 " =    0.969
peak=    3.550 closest distance to " CG BARG A 102 " =    1.952
peak=    3.546 closest distance to " CB  MET A  40 " =    0.856
peak=    3.542 closest distance to " O   HOH Z 365 " =    3.014
peak=    3.540 closest distance to " CA  ALA A 160 " =    0.950
peak=    3.537 closest distance to " CA  TYR A  30 " =    0.934
peak=    3.535 closest distance to " O   HOH Z   3 " =    2.162
peak=    3.533 closest distance to " CB  SER A 212 " =    1.463
peak=    3.531 closest distance to " CG2 THR A 221 " =    1.192
peak=    3.528 closest distance to " CG2 VAL A 257 " =    0.776
peak=    3.526 closest distance to " O   HOH Z 109 " =    2.243
peak=    3.522 closest distance to " O   HOH Z 184 " =    1.459
peak=    3.520 closest distance to " OG  SER A  62 " =    3.075
peak=    3.517 closest distance to " O   HOH Z 438 " =    2.101
peak=    3.514 closest distance to " CB  ASN A 110 " =    1.059
peak=    3.513 closest distance to " CB  VAL A 265 " =    1.302
peak=    3.505 closest distance to " CB  HIS A 108 " =    0.836
peak=    3.504 closest distance to " O   HOH Z 193 " =    1.654
peak=    3.498 closest distance to " O   HOH Z 133 " =    2.525
peak=    3.491 closest distance to " CA  LYS A 117 " =    1.168
peak=    3.489 closest distance to " O   HOH Z 405 " =    1.454
peak=    3.481 closest distance to " N   TYR A  15 " =    1.117
peak=    3.477 closest distance to " ND2BASN A 224 " =    0.825
peak=    3.477 closest distance to " CB  ARG A 190 " =    1.693
peak=    3.473 closest distance to " O   HOH Z 181 " =    2.335
peak=    3.468 closest distance to " O   HOH Z  58 " =    1.901
peak=    3.467 closest distance to " CG2 ILE A 234 " =    0.901
peak=    3.465 closest distance to " CE  LYS A  76 " =    0.855
peak=    3.463 closest distance to " O   HOH Z  20 " =    1.666
peak=    3.460 closest distance to " CA  SER A  87 " =    0.990
peak=    3.458 closest distance to " CA  GLY A 267 " =    1.212
peak=    3.458 closest distance to " CG  GLN A  89 " =    1.506
peak=    3.457 closest distance to " O   HOH Z 180 " =    2.139
peak=    3.454 closest distance to " O   HOH Z   1 " =    1.734
peak=    3.452 closest distance to " O   HOH Z  44 " =    2.121
peak=    3.447 closest distance to " CB  GLN A  89 " =    1.186
peak=    3.441 closest distance to " O   HOH Z 153 " =    3.702
peak=    3.440 closest distance to " O   HOH Z  10 " =    1.747
peak=    3.438 closest distance to " O   ILE A  20 " =    1.994
peak=    3.431 closest distance to " CA  ILE A 234 " =    1.061
peak=    3.428 closest distance to " O   HOH Z 368 " =    1.861
peak=    3.426 closest distance to " CG2 ILE A  20 " =    1.704
peak=    3.421 closest distance to " O   HOH Z 133 " =    2.561
peak=    3.418 closest distance to " OE2 GLU A   2 " =    1.965
peak=    3.408 closest distance to " O   HOH Z 145 " =    2.045
peak=    3.408 closest distance to " CE3 TRP A 274 " =    1.261
peak=    3.403 closest distance to " CZ3 TRP A  92 " =    1.190
peak=    3.402 closest distance to " O   HOH Z 290 " =    0.929
peak=    3.397 closest distance to " CD  LYS A 166 " =    1.417
peak=    3.396 closest distance to " NH2BARG A 145 " =    1.975
peak=    3.396 closest distance to " CA  THR A 221 " =    0.957
peak=    3.395 closest distance to " O   HOH Z 189 " =    2.917
peak=    3.393 closest distance to " O   MET A 105 " =    1.732
peak=    3.391 closest distance to " O   HOH Z 424 " =    2.496
peak=    3.389 closest distance to " CB  MET A  47 " =    1.210
peak=    3.383 closest distance to " O   HOH Z 403 " =    1.497
peak=    3.382 closest distance to " NH2BARG A 190 " =    1.415
peak=    3.382 closest distance to " O   HOH Z  88 " =    3.550
peak=    3.378 closest distance to " O   HOH Z 356 " =    1.321
peak=    3.377 closest distance to " CZ  PHE A 218 " =    1.127
peak=    3.376 closest distance to " O   HOH Z 222 " =    1.882
peak=    3.372 closest distance to " O   HOH Z 385 " =    3.743
peak=    3.370 closest distance to " NH2AARG A 145 " =    1.138
peak=    3.370 closest distance to " CB  ARG A 139 " =    1.046
peak=    3.368 closest distance to " O   HOH Z 250 " =    1.337
peak=    3.365 closest distance to " CD1 ILE A  33 " =    1.798
peak=    3.360 closest distance to " CG  GLN A  88 " =    1.168
peak=    3.356 closest distance to " ND2 ASN A 249 " =    0.807
peak=    3.353 closest distance to " O   HOH Z 350 " =    1.448
peak=    3.351 closest distance to " CB  ALA A 114 " =    1.557
peak=    3.351 closest distance to " O   HOH Z  97 " =    2.000
peak=    3.346 closest distance to " O   HOH Z 305 " =    3.486
peak=    3.343 closest distance to " N   ALA A 256 " =    0.983
peak=    3.339 closest distance to " CB  GLU A 236 " =    1.190
peak=    3.337 closest distance to " OG1 THR A 221 " =    1.337
peak=    3.333 closest distance to " O   HOH Z 233 " =    1.718
peak=    3.326 closest distance to " O   HOH Z 154 " =    1.918
peak=    3.322 closest distance to " CD1 LEU A 300 " =    1.168
peak=    3.322 closest distance to " ND2 ASN A 187 " =    1.669
peak=    3.320 closest distance to " OG BSER A 164 " =    2.186
peak=    3.317 closest distance to " CD  ARG A 138 " =    1.118
peak=    3.315 closest distance to " O   HOH Z 409 " =    2.394
peak=    3.309 closest distance to " O   HOH Z 357 " =    2.054
peak=    3.306 closest distance to " CG  ARG A 159 " =    0.932
peak=    3.303 closest distance to " CA  ASN A 215 " =    1.219
peak=    3.301 closest distance to " CA  ALA A 299 " =    0.961
peak=    3.299 closest distance to " N   ASN A 127 " =    1.351
peak=    3.293 closest distance to " CB  LEU A 143 " =    1.052
peak=    3.291 closest distance to " O   HOH Z  44 " =    2.580
peak=    3.290 closest distance to " CD  ARG A 269 " =    1.002
peak=    3.287 closest distance to " CE3 TRP A  85 " =    1.194
peak=    3.286 closest distance to " O   HOH Z 130 " =    2.696
peak=    3.286 closest distance to " CB  SER A 210 " =    0.915
peak=    3.285 closest distance to " ND2 ASN A 110 " =    1.785
peak=    3.283 closest distance to " O   HOH Z 209 " =    2.395
peak=    3.282 closest distance to " CA  ALA A 291 " =    0.862
peak=    3.279 closest distance to " O   HOH Z 353 " =    1.742
peak=    3.276 closest distance to " O   HOH Z 207 " =    2.285
peak=    3.276 closest distance to " CB  ALA A   1 " =    4.634
peak=    3.275 closest distance to " CA  MET A 105 " =    0.879
peak=    3.275 closest distance to " O   HOH Z 213 " =    2.253
peak=    3.275 closest distance to " OH  TYR A 116 " =    1.067
peak=    3.272 closest distance to " CB  ASN A 187 " =    1.097
peak=    3.271 closest distance to " CB  ARG A  79 " =    1.396
peak=    3.269 closest distance to " O   HOH Z 116 " =    3.111
peak=    3.268 closest distance to " CA  ALA A 158 " =    1.137
peak=    3.268 closest distance to " CB  SER A  26 " =    1.604
peak=    3.266 closest distance to " CB  GLU A 152 " =    1.328
peak=    3.262 closest distance to " CB  SER A 273 " =    0.887
peak=    3.260 closest distance to " O   HOH Z 148 " =    2.223
peak=    3.260 closest distance to " CG1BVAL A  72 " =    0.747
peak=    3.259 closest distance to " O   HOH Z 343 " =    3.214
peak=    3.259 closest distance to " CA  ILE A 106 " =    0.749
peak=    3.255 closest distance to " CG AARG A 275 " =    1.190
peak=    3.252 closest distance to " NE2 GLN A  58 " =    4.068
peak=    3.250 closest distance to " OG BSER A 212 " =    2.830
peak=    3.250 closest distance to " O   HOH Z  50 " =    1.598
peak=    3.245 closest distance to " CA  TYR A 116 " =    1.415
peak=    3.244 closest distance to " CA  PHE A 283 " =    1.378
peak=    3.241 closest distance to " CE1 TYR A 186 " =    1.253
peak=    3.238 closest distance to " CZ  PHE A  38 " =    1.199
peak=    3.238 closest distance to " CG BARG A 190 " =    1.314
peak=    3.233 closest distance to " CA  ARG A 102 " =    1.137
peak=    3.232 closest distance to " NH1BARG A 145 " =    1.305
peak=    3.231 closest distance to " O   HOH Z  22 " =    2.114
peak=    3.227 closest distance to " OG BSER A  99 " =    2.167
peak=    3.225 closest distance to " O   HOH Z 392 " =    2.126
peak=    3.225 closest distance to " CB  VAL A 250 " =    1.058
peak=    3.225 closest distance to " OD2 ASP A 286 " =    2.585
peak=    3.224 closest distance to " N   SER A  97 " =    0.861
peak=    3.220 closest distance to " O   HOH Z 371 " =    1.891
peak=    3.219 closest distance to " O   HOH Z 189 " =    3.142
peak=    3.219 closest distance to " CA  ARG A 195 " =    1.228
peak=    3.212 closest distance to " CG1 ILE A  49 " =    1.436
peak=    3.206 closest distance to " O   HOH Z  40 " =    2.044
peak=    3.199 closest distance to " N   GLU A   2 " =    1.423
peak=    3.198 closest distance to " O   HOH Z 368 " =    2.707
peak=    3.197 closest distance to " NE  ARG A  56 " =    3.461
peak=    3.196 closest distance to " O   HOH Z  88 " =    3.507
peak=    3.179 closest distance to " CG1 ILE A  33 " =    1.285
peak=    3.176 closest distance to " O   HOH Z 341 " =    2.418
peak=    3.175 closest distance to " O   HOH Z 273 " =    2.890
peak=    3.172 closest distance to " CA  THR A 264 " =    0.738
peak=    3.167 closest distance to " O   HOH Z 303 " =    2.868
peak=    3.164 closest distance to " CB  ALA A 248 " =    0.919
peak=    3.153 closest distance to " NZ BLYS A 290 " =    0.965
peak=    3.146 closest distance to " CB  LEU A 300 " =    0.883
peak=    3.144 closest distance to " O   HOH Z 430 " =    2.544
peak=    3.144 closest distance to " O   HOH Z 325 " =    2.218
peak=    3.143 closest distance to " O   HOH Z 421 " =    3.202
peak=    3.134 closest distance to " CB  GLU A 175 " =    0.920
peak=    3.132 closest distance to " ND1 HIS A  81 " =    1.897
peak=    3.131 closest distance to " CG1 VAL A 153 " =    0.898
peak=    3.125 closest distance to " O   HOH Z 389 " =    1.621
peak=    3.120 closest distance to " O   HOH Z 323 " =    1.702
peak=    3.117 closest distance to " CA  ALA A 233 " =    0.974
peak=    3.114 closest distance to " O   HOH Z 113 " =    2.146
peak=    3.107 closest distance to " O   HOH Z 145 " =    1.861
peak=    3.107 closest distance to " O   HOH Z 344 " =    2.947
peak=    3.107 closest distance to " O   GLY A 302 " =    2.170
peak=    3.103 closest distance to " O   HOH Z  94 " =    2.347
peak=    3.100 closest distance to " O   HOH Z 299 " =    4.358
peak=    3.097 closest distance to " N   ALA A   1 " =    2.417
peak=    3.094 closest distance to " N   SER A 135 " =    1.244
peak=    3.090 closest distance to " O   HOH Z 438 " =    2.999
peak=    3.087 closest distance to " O   HOH Z 430 " =    1.635
peak=    3.086 closest distance to " CA  ARG A 139 " =    0.882
peak=    3.085 closest distance to " O   HOH Z   3 " =    2.247
peak=    3.085 closest distance to " OE1 GLU A   2 " =    1.461
peak=    3.085 closest distance to " O   HOH Z 412 " =    5.330
peak=    3.083 closest distance to " O   HOH Z 281 " =    2.285
peak=    3.077 closest distance to " OG ASER A 212 " =    1.782
peak=    3.075 closest distance to " CB  ARG A 138 " =    1.184
peak=    3.071 closest distance to " O   HOH Z 172 " =    2.452
peak=    3.042 closest distance to " O   ASP A 200 " =    1.397
peak=    3.031 closest distance to " CB  ARG A  79 " =    0.883
peak=    3.022 closest distance to " CA  LEU A 282 " =    1.122

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

Number of peaks found at mFobs-DFmodel map (map cutoff=3.00 sigma)= 217         
Filter by distance & map next to the model:
   mapped sites are within: 0.721 - 5.979
   number of sites selected in [dist_min= 0.70, dist_max= 6.00]: 216 from: 217
   mapped sites are within: 0.721 - 5.979

peak=   -4.668 closest distance to " OG BSER A 134 " =    1.461
peak=   -4.436 closest distance to " CD  ARG A  14 " =    3.081
peak=   -4.338 closest distance to " O   HOH Z 131 " =    4.004
peak=   -4.257 closest distance to " CG2 VAL A 230 " =    0.867
peak=   -4.212 closest distance to " CG  ARG A 138 " =    0.971
peak=   -4.192 closest distance to " O   HOH Z 266 " =    5.031
peak=   -4.146 closest distance to " O   SER A 135 " =    1.484
peak=   -4.121 closest distance to " CD1 LEU A 255 " =    2.954
peak=   -4.120 closest distance to " CB  PRO A 243 " =    2.639
peak=   -4.083 closest distance to " CE2 PHE A 218 " =    2.488
peak=   -4.013 closest distance to " CB  ALA A  43 " =    2.461
peak=   -4.002 closest distance to " CA  ASP A  27 " =    2.417
peak=   -3.928 closest distance to " CG  GLN A 223 " =    2.494
peak=   -3.899 closest distance to " N   THR A 157 " =    1.479
peak=   -3.853 closest distance to " O   HOH Z 185 " =    2.173
peak=   -3.841 closest distance to " N   PRO A 163 " =    1.531
peak=   -3.840 closest distance to " O   VAL A  67 " =    2.450
peak=   -3.838 closest distance to " CD  ARG A 156 " =    2.018
peak=   -3.827 closest distance to " CB  VAL A 230 " =    1.104
peak=   -3.812 closest distance to " O   HOH Z  43 " =    1.883
peak=   -3.801 closest distance to " O   SER A  22 " =    2.526
peak=   -3.784 closest distance to " CZ2 TRP A 274 " =    0.906
peak=   -3.779 closest distance to " O   HOH Z 238 " =    0.904
peak=   -3.761 closest distance to " CB  ASP A 132 " =    2.404
peak=   -3.756 closest distance to " OE1 GLU A 277 " =    2.236
peak=   -3.744 closest distance to " O   PRO A 198 " =    1.215
peak=   -3.741 closest distance to " O   HOH Z  52 " =    1.436
peak=   -3.737 closest distance to " CD2 TYR A 293 " =    1.858
peak=   -3.736 closest distance to " O   HOH Z 231 " =    0.721
peak=   -3.731 closest distance to " CA  GLY A  98 " =    1.873
peak=   -3.729 closest distance to " O   HOH Z 389 " =    1.397
peak=   -3.714 closest distance to " O   HOH Z 377 " =    1.873
peak=   -3.714 closest distance to " OG  SER A  87 " =    1.313
peak=   -3.703 closest distance to " CE2 TYR A  30 " =    2.642
peak=   -3.692 closest distance to " N   ALA A  43 " =    2.627
peak=   -3.683 closest distance to " C   HIS A 108 " =    1.215
peak=   -3.679 closest distance to " CG2 VAL A 202 " =    2.710
peak=   -3.677 closest distance to " CD  LYS A 289 " =    2.400
peak=   -3.669 closest distance to " CB  ALA A   9 " =    2.338
peak=   -3.666 closest distance to " ND2 ASN A 249 " =    2.321
peak=   -3.666 closest distance to " CA  GLY A 241 " =    2.269
peak=   -3.666 closest distance to " CB  TRP A  85 " =    2.570
peak=   -3.650 closest distance to " CB  ALA A 248 " =    2.097
peak=   -3.650 closest distance to " CG2 VAL A 296 " =    1.551
peak=   -3.642 closest distance to " O   HOH Z 359 " =    1.630
peak=   -3.641 closest distance to " CD  ARG A 138 " =    1.479
peak=   -3.636 closest distance to " ND2 ASN A 187 " =    1.577
peak=   -3.624 closest distance to " O   HOH Z 350 " =    1.762
peak=   -3.618 closest distance to " NH2 ARG A  79 " =    2.079
peak=   -3.604 closest distance to " O   PRO A 243 " =    2.451
peak=   -3.603 closest distance to " O   HOH Z  11 " =    1.833
peak=   -3.587 closest distance to " O   HOH Z 292 " =    1.615
peak=   -3.586 closest distance to " O   HOH Z 407 " =    3.044
peak=   -3.581 closest distance to " O   ALA A  84 " =    1.671
peak=   -3.579 closest distance to " NH2AARG A 275 " =    5.353
peak=   -3.578 closest distance to " O   HOH Z 211 " =    1.262
peak=   -3.576 closest distance to " O   MET A  40 " =    2.884
peak=   -3.573 closest distance to " O   HOH Z 134 " =    3.924
peak=   -3.570 closest distance to " O   HOH Z  39 " =    1.113
peak=   -3.566 closest distance to " CA  GLY A 203 " =    2.406
peak=   -3.557 closest distance to " O   HOH Z 111 " =    1.823
peak=   -3.552 closest distance to " O   HOH Z 298 " =    2.870
peak=   -3.551 closest distance to " CD1 LEU A 101 " =    2.283
peak=   -3.540 closest distance to " O   HOH Z 359 " =    3.383
peak=   -3.532 closest distance to " O   PRO A 163 " =    1.990
peak=   -3.529 closest distance to " CB  ASN A  39 " =    2.218
peak=   -3.521 closest distance to " OG  SER A  62 " =    4.391
peak=   -3.519 closest distance to " O   VAL A 189 " =    2.547
peak=   -3.517 closest distance to " CB  ALA A 227 " =    2.376
peak=   -3.510 closest distance to " CD2 LEU A   5 " =    1.017
peak=   -3.510 closest distance to " O   HOH Z  51 " =    0.764
peak=   -3.499 closest distance to " OG  SER A 141 " =    1.869
peak=   -3.496 closest distance to " OE2 GLU A 152 " =    1.159
peak=   -3.494 closest distance to " CB  GLN A  55 " =    1.225
peak=   -3.493 closest distance to " O   GLY A  80 " =    2.537
peak=   -3.485 closest distance to " CD  LYS A 166 " =    2.389
peak=   -3.484 closest distance to " N   VAL A  72 " =    1.715
peak=   -3.484 closest distance to " O   HOH Z 198 " =    2.154
peak=   -3.480 closest distance to " C   MET A 188 " =    1.541
peak=   -3.463 closest distance to " CG  PRO A 163 " =    2.508
peak=   -3.462 closest distance to " CB  PHE A 130 " =    1.345
peak=   -3.459 closest distance to " CD2 LEU A 237 " =    2.783
peak=   -3.456 closest distance to " CG1 VAL A 250 " =    2.634
peak=   -3.451 closest distance to " CG2 THR A  52 " =    3.166
peak=   -3.443 closest distance to " OD2 ASP A  27 " =    1.726
peak=   -3.438 closest distance to " O   HOH Z 352 " =    2.067
peak=   -3.434 closest distance to " O   HOH Z 134 " =    3.375
peak=   -3.434 closest distance to " CB  TYR A  15 " =    2.118
peak=   -3.433 closest distance to " O   HOH Z 231 " =    1.918
peak=   -3.431 closest distance to " O   HOH Z 389 " =    2.133
peak=   -3.431 closest distance to " CB  PRO A  90 " =    1.677
peak=   -3.416 closest distance to " CG2 VAL A 296 " =    1.089
peak=   -3.416 closest distance to " N   ARG A 138 " =    1.503
peak=   -3.411 closest distance to " O   HOH Z 394 " =    1.507
peak=   -3.404 closest distance to " OG  SER A  97 " =    2.205
peak=   -3.403 closest distance to " O   HOH Z 114 " =    3.108
peak=   -3.403 closest distance to " O   HOH Z 427 " =    1.752
peak=   -3.400 closest distance to " ND2 ASN A  45 " =    1.246
peak=   -3.400 closest distance to " O   ARG A 145 " =    1.309
peak=   -3.397 closest distance to " O   HOH Z 351 " =    1.617
peak=   -3.396 closest distance to " O   HOH Z 339 " =    1.785
peak=   -3.391 closest distance to " CG  TRP A 266 " =    1.755
peak=   -3.388 closest distance to " CZ  TYR A 169 " =    1.655
peak=   -3.387 closest distance to " CA  ASN A 127 " =    1.139
peak=   -3.383 closest distance to " CG  MET A 105 " =    0.967
peak=   -3.377 closest distance to " O   HOH Z 166 " =    1.802
peak=   -3.377 closest distance to " CG  GLN A  58 " =    1.016
peak=   -3.375 closest distance to " O   HOH Z 103 " =    1.528
peak=   -3.375 closest distance to " ND2 ASN A 252 " =    2.061
peak=   -3.373 closest distance to " OG  SER A 245 " =    1.323
peak=   -3.371 closest distance to " OG ASER A 134 " =    1.157
peak=   -3.366 closest distance to " O   HOH Z 377 " =    1.227
peak=   -3.363 closest distance to " NH2 ARG A 219 " =    1.709
peak=   -3.361 closest distance to " O   HOH Z  24 " =    1.147
peak=   -3.357 closest distance to " ND2 ASN A 285 " =    2.053
peak=   -3.355 closest distance to " N   ALA A 248 " =    1.500
peak=   -3.351 closest distance to " CA  GLY A  35 " =    2.068
peak=   -3.345 closest distance to " CB  ALA A 161 " =    2.462
peak=   -3.341 closest distance to " CZ  PHE A  59 " =    1.513
peak=   -3.333 closest distance to " O   HOH Z 216 " =    1.617
peak=   -3.333 closest distance to " O   HOH Z 368 " =    2.409
peak=   -3.327 closest distance to " OD1 ASP A 191 " =    1.897
peak=   -3.324 closest distance to " CB  PRO A 163 " =    2.371
peak=   -3.323 closest distance to " CG  LEU A 281 " =    1.720
peak=   -3.320 closest distance to " O   HOH Z 368 " =    1.467
peak=   -3.319 closest distance to " CE2 TRP A  70 " =    2.355
peak=   -3.318 closest distance to " OH  TYR A 172 " =    1.797
peak=   -3.318 closest distance to " O   HOH Z 191 " =    5.472
peak=   -3.312 closest distance to " O   ALA A   1 " =    1.363
peak=   -3.311 closest distance to " CB  ALA A 131 " =    1.977
peak=   -3.309 closest distance to " ND2 ASN A  60 " =    1.400
peak=   -3.309 closest distance to " N   SER A 276 " =    1.347
peak=   -3.309 closest distance to " O   GLY A 211 " =    1.192
peak=   -3.308 closest distance to " CE  MET A 105 " =    2.375
peak=   -3.308 closest distance to " N   ASP A 171 " =    2.573
peak=   -3.307 closest distance to " C   ARG A 269 " =    1.370
peak=   -3.307 closest distance to " CG2 ILE A  49 " =    2.859
peak=   -3.305 closest distance to " OD2 ASP A  50 " =    1.573
peak=   -3.296 closest distance to " CE1 PHE A  59 " =    2.043
peak=   -3.292 closest distance to " N   ALA A 226 " =    2.125
peak=   -3.283 closest distance to " O   HOH Z 353 " =    1.446
peak=   -3.276 closest distance to " O   HOH Z  60 " =    1.830
peak=   -3.273 closest distance to " O   HOH Z 208 " =    2.145
peak=   -3.272 closest distance to " O   HOH Z 275 " =    1.711
peak=   -3.265 closest distance to " O   ILE A  49 " =    1.667
peak=   -3.264 closest distance to " CB  ARG A  79 " =    2.561
peak=   -3.264 closest distance to " CB  PRO A  54 " =    2.400
peak=   -3.262 closest distance to " CE BMET A  47 " =    1.000
peak=   -3.261 closest distance to " CG  PHE A 283 " =    2.637
peak=   -3.258 closest distance to " O   ASP A 270 " =    1.448
peak=   -3.257 closest distance to " O   HOH Z  90 " =    2.958
peak=   -3.254 closest distance to " O   HOH Z 313 " =    1.400
peak=   -3.251 closest distance to " CG  GLN A 240 " =    2.364
peak=   -3.250 closest distance to " O   HOH Z 435 " =    2.370
peak=   -3.247 closest distance to " O   HOH Z 357 " =    1.905
peak=   -3.246 closest distance to " O   HOH Z 100 " =    1.237
peak=   -3.240 closest distance to " O   HOH Z 426 " =    2.181
peak=   -3.236 closest distance to " O   HOH Z  60 " =    2.316
peak=   -3.226 closest distance to " O   HOH Z 286 " =    1.775
peak=   -3.224 closest distance to " O   HOH Z 111 " =    1.144
peak=   -3.220 closest distance to " OG  SER A  63 " =    1.343
peak=   -3.219 closest distance to " CD2 PHE A 225 " =    1.028
peak=   -3.219 closest distance to " C   ALA A 158 " =    1.382
peak=   -3.213 closest distance to " CG  ASN A 301 " =    1.959
peak=   -3.211 closest distance to " O   HOH Z 111 " =    4.701
peak=   -3.205 closest distance to " CD2 HIS A 207 " =    2.423
peak=   -3.204 closest distance to " CG1 VAL A 112 " =    2.581
peak=   -3.203 closest distance to " O   ALA A  10 " =    1.759
peak=   -3.200 closest distance to " O   PRO A 198 " =    1.390
peak=   -3.198 closest distance to " O   HOH Z 140 " =    1.353
peak=   -3.197 closest distance to " CA  GLY A 133 " =    1.998
peak=   -3.196 closest distance to " CA  TYR A  68 " =    1.155
peak=   -3.196 closest distance to " OG  SER A 206 " =    1.709
peak=   -3.191 closest distance to " O   ALA A   1 " =    1.719
peak=   -3.191 closest distance to " C   GLU A 236 " =    0.917
peak=   -3.190 closest distance to " CG2 ILE A  20 " =    2.820
peak=   -3.183 closest distance to " O   HOH Z 207 " =    2.042
peak=   -3.183 closest distance to " O   GLU A 152 " =    1.618
peak=   -3.179 closest distance to " O   HOH Z 415 " =    1.296
peak=   -3.175 closest distance to " C   LEU A 143 " =    1.222
peak=   -3.172 closest distance to " CD1 LEU A 228 " =    2.335
peak=   -3.171 closest distance to " O   HOH Z 122 " =    2.145
peak=   -3.165 closest distance to " CD1 ILE A  33 " =    2.373
peak=   -3.164 closest distance to " CB  CYS A 254 " =    2.001
peak=   -3.162 closest distance to " OE1 GLN A  88 " =    1.199
peak=   -3.160 closest distance to " O   HOH Z 256 " =    1.368
peak=   -3.159 closest distance to " O   HOH Z  67 " =    3.075
peak=   -3.156 closest distance to " O   HOH Z 166 " =    1.371
peak=   -3.156 closest distance to " O   SER A 271 " =    2.076
peak=   -3.152 closest distance to " CG  GLN A 278 " =    2.121
peak=   -3.151 closest distance to " CZ3 TRP A 179 " =    1.240
peak=   -3.150 closest distance to " CG2 THR A 178 " =    2.226
peak=   -3.143 closest distance to " O   HOH Z 102 " =    1.520
peak=   -3.143 closest distance to " CG1 VAL A 296 " =    1.350
peak=   -3.137 closest distance to " O   HOH Z 336 " =    5.979
peak=   -3.130 closest distance to " O   HOH Z   2 " =    1.855
peak=   -3.121 closest distance to " O   TYR A  30 " =    2.678
peak=   -3.120 closest distance to " CD1 LEU A 297 " =    2.222
peak=   -3.109 closest distance to " OD1 ASN A 187 " =    1.670
peak=   -3.103 closest distance to " CB  ALA A 114 " =    2.423
peak=   -3.100 closest distance to " OXT GLY A 302 " =    3.279
peak=   -3.085 closest distance to " O   HOH Z  68 " =    1.278
peak=   -3.082 closest distance to " CD1 PHE A  61 " =    2.953
peak=   -3.081 closest distance to " O   HOH Z  52 " =    2.028
peak=   -3.081 closest distance to " CD2 TYR A 293 " =    2.739
peak=   -3.078 closest distance to " O   HOH Z 384 " =    2.314
peak=   -3.077 closest distance to " CA  GLY A  57 " =    2.166
peak=   -3.076 closest distance to " O   HOH Z 318 " =    1.919
peak=   -3.074 closest distance to " CB  ASP A 132 " =    2.184
peak=   -3.073 closest distance to " CD2 LEU A 297 " =    2.080
peak=   -3.050 closest distance to " O   HOH Z 421 " =    3.197
peak=   -3.050 closest distance to " O   TRP A  70 " =    1.449
peak=   -3.050 closest distance to " CB  HIS A  81 " =    1.115
peak=   -3.048 closest distance to " OG BSER A 134 " =    1.831
peak=   -3.020 closest distance to " O   HOH Z  64 " =    2.574
peak=   -3.018 closest distance to " CD  PRO A 243 " =    2.056

================= 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    :  0.4847 0.4757   6.288341e+00   6.270429e+00
   1_bss:  0.4765 0.4620   6.283362e+00   6.263069e+00
   1_xyz:  0.3964 0.4183   6.185385e+00   6.215254e+00
   1_adp:  0.3543 0.4180   6.126304e+00   6.210551e+00
   1_occ:  0.3541 0.4173   6.125680e+00   6.210690e+00
   2_bss:  0.3511 0.4101   6.125410e+00   6.208404e+00
   2_xyz:  0.2921 0.3568   5.974734e+00   6.103132e+00
   2_adp:  0.2747 0.3428   5.939627e+00   6.075941e+00
   2_occ:  0.2745 0.3427   5.939553e+00   6.076307e+00
   3_bss:  0.2739 0.3414   5.940601e+00   6.075874e+00
   3_xyz:  0.2074 0.2687   5.684604e+00   5.865734e+00
   3_adp:  0.1874 0.2488   5.595263e+00   5.800342e+00
   3_occ:  0.1871 0.2482   5.594109e+00   5.799408e+00
   4_bss:  0.1862 0.2473   5.593120e+00   5.797475e+00
   4_xyz:  0.1467 0.2038   5.393466e+00   5.631828e+00
   4_adp:  0.1328 0.1866   5.303227e+00   5.540601e+00
   4_occ:  0.1327 0.1864   5.302551e+00   5.539990e+00
   5_bss:  0.1331 0.1853   5.300059e+00   5.536800e+00
   5_xyz:  0.1219 0.1726   5.229852e+00   5.475394e+00
   5_adp:  0.1181 0.1703   5.211335e+00   5.461447e+00
   5_occ:  0.1181 0.1702   5.211009e+00   5.461050e+00
   5_bss:  0.1180 0.1701   5.210777e+00   5.460970e+00
------------------------------------------------------------------------
 stage     k_sol   b_sol     b11     b22     b33     b12     b13     b23
   0    :  0.000   0.000   0.000   0.000   0.000   0.000   0.000   0.000
   1_bss:  0.349   2.590   7.179   9.997   9.223   0.000   0.000   0.000
   1_xyz:  0.349   2.590   7.179   9.997   9.223   0.000   0.000   0.000
   1_adp:  0.349   2.590   7.179   9.997   9.223   0.000   0.000   0.000
   1_occ:  0.349   2.590   7.179   9.997   9.223   0.000   0.000   0.000
   2_bss:  0.347  35.287   3.662   5.675   5.172   0.000   0.000   0.000
   2_xyz:  0.347  35.287   3.662   5.675   5.172   0.000   0.000   0.000
   2_adp:  0.347  35.287   3.662   5.675   5.172   0.000   0.000   0.000
   2_occ:  0.347  35.287   3.662   5.675   5.172   0.000   0.000   0.000
   3_bss:  0.320  42.119   2.287   3.260   3.553   0.000   0.000   0.000
   3_xyz:  0.320  42.119   2.287   3.260   3.553   0.000   0.000   0.000
   3_adp:  0.320  42.119   2.287   3.260   3.553   0.000   0.000   0.000
   3_occ:  0.320  42.119   2.287   3.260   3.553   0.000   0.000   0.000
   4_bss:  0.325  42.119   1.228   1.531   2.740   0.000   0.000   0.000
   4_xyz:  0.325  42.119   1.228   1.531   2.740   0.000   0.000   0.000
   4_adp:  0.325  42.119   1.228   1.531   2.740   0.000   0.000   0.000
   4_occ:  0.325  42.119   1.228   1.531   2.740   0.000   0.000   0.000
   5_bss:  0.321  49.657   1.156   1.055   2.706   0.000   0.000   0.000
   5_xyz:  0.321  49.657   1.156   1.055   2.706   0.000   0.000   0.000
   5_adp:  0.321  49.657   1.156   1.055   2.706   0.000   0.000   0.000
   5_occ:  0.321  49.657   1.156   1.055   2.706   0.000   0.000   0.000
   5_bss:  0.315  51.409  -0.436  -0.657   1.092  -0.000   0.000   0.000
------------------------------------------------------------------------
 stage     <pher>    fom   alpha         beta
   0    :  58.406 0.4139  0.4902    70765.390
   1_bss:  57.901 0.4194  0.6397    68793.319
   1_xyz:  50.579 0.5113  0.7592    54602.122
   1_adp:  49.090 0.5299  0.8432    53011.635
   1_occ:  49.093 0.5299  0.8419    53039.372
   2_bss:  48.431 0.5382  0.7510    52031.549
   2_xyz:  39.035 0.6527  0.8939    35959.020
   2_adp:  36.923 0.6783  0.9273    33368.954
   2_occ:  36.977 0.6777  0.9260    33399.756
   3_bss:  36.825 0.6795  0.8705    33259.116
   3_xyz:  27.056 0.7885  0.9775    18786.434
   3_adp:  24.330 0.8179  0.9963    15805.478
   3_occ:  24.292 0.8183  0.9962    15740.721
   4_bss:  24.245 0.8188  0.9550    15681.598
   4_xyz:  19.823 0.8627  0.9780    10705.122
   4_adp:  17.622 0.8837  0.9786     8908.615
   4_occ:  17.610 0.8838  0.9784     8887.220
   5_bss:  17.519 0.8844  0.9721     8780.896
   5_xyz:  15.991 0.8980  0.9781     7619.546
   5_adp:  15.605 0.9017  0.9715     7397.896
   5_occ:  15.602 0.9017  0.9713     7385.059
   5_bss:  15.599 0.9017  0.9752     7381.767
------------------------------------------------------------------------
 stage       angl   bond   chir   dihe   plan   repu  geom_target
   0    :  24.226  0.414  2.119 33.790  0.145  4.089   5.3677e+01
   1_bss:  24.226  0.414  2.119 33.790  0.145  4.089   5.3677e+01
   1_xyz:   1.704  0.013  0.107 18.391  0.006  4.106   1.4443e-01
   1_adp:   1.704  0.013  0.107 18.391  0.006  4.106   1.4443e-01
   1_occ:   1.704  0.013  0.107 18.391  0.006  4.106   1.4443e-01
   2_bss:   1.704  0.013  0.107 18.391  0.006  4.106   1.4443e-01
   2_xyz:   1.105  0.008  0.076 16.142  0.005  4.121   7.7883e-02
   2_adp:   1.105  0.008  0.076 16.142  0.005  4.121   7.7883e-02
   2_occ:   1.105  0.008  0.076 16.142  0.005  4.121   7.7883e-02
   3_bss:   1.105  0.008  0.076 16.142  0.005  4.121   7.7883e-02
   3_xyz:   1.195  0.009  0.089 16.263  0.005  4.124   8.6861e-02
   3_adp:   1.195  0.009  0.089 16.263  0.005  4.124   8.6861e-02
   3_occ:   1.195  0.009  0.089 16.263  0.005  4.124   8.6861e-02
   4_bss:   1.195  0.009  0.089 16.263  0.005  4.124   8.6861e-02
   4_xyz:   1.114  0.008  0.083 15.777  0.004  4.109   7.3546e-02
   4_adp:   1.114  0.008  0.083 15.777  0.004  4.109   7.3546e-02
   4_occ:   1.114  0.008  0.083 15.777  0.004  4.109   7.3546e-02
   5_bss:   1.114  0.008  0.083 15.777  0.004  4.109   7.3546e-02
   5_xyz:   1.063  0.008  0.082 15.671  0.004  4.114   6.8016e-02
   5_adp:   1.063  0.008  0.082 15.671  0.004  4.114   6.8016e-02
   5_occ:   1.063  0.008  0.082 15.671  0.004  4.114   6.8016e-02
   5_bss:   1.063  0.008  0.082 15.671  0.004  4.114   6.8016e-02
------------------------------------------------------------------------
                      Maximal deviations:
 stage       angl   bond   chir   dihe   plan   repu       |grad|
   0    :  74.492  1.400  6.404144.062  0.405  1.196   6.9572e+00
   1_bss:  74.492  1.400  6.404144.062  0.405  1.196   6.9572e+00
   1_xyz:  13.281  0.188  0.407 86.645  0.035  2.122   1.0043e-01
   1_adp:  13.281  0.188  0.407 86.645  0.035  2.122   1.0043e-01
   1_occ:  13.281  0.188  0.407 86.645  0.035  2.122   1.0043e-01
   2_bss:  13.281  0.188  0.407 86.645  0.035  2.122   1.0043e-01
   2_xyz:   6.413  0.075  0.280 85.287  0.045  2.194   8.1584e-02
   2_adp:   6.413  0.075  0.280 85.287  0.045  2.194   8.1584e-02
   2_occ:   6.413  0.075  0.280 85.287  0.045  2.194   8.1584e-02
   3_bss:   6.413  0.075  0.280 85.287  0.045  2.194   8.1584e-02
   3_xyz:   8.207  0.059  0.405 87.062  0.034  2.201   1.3015e-01
   3_adp:   8.207  0.059  0.405 87.062  0.034  2.201   1.3015e-01
   3_occ:   8.207  0.059  0.405 87.062  0.034  2.201   1.3015e-01
   4_bss:   8.207  0.059  0.405 87.062  0.034  2.201   1.3015e-01
   4_xyz:   8.261  0.066  0.396 84.295  0.028  2.259   5.6569e-02
   4_adp:   8.261  0.066  0.396 84.295  0.028  2.259   5.6569e-02
   4_occ:   8.261  0.066  0.396 84.295  0.028  2.259   5.6569e-02
   5_bss:   8.261  0.066  0.396 84.295  0.028  2.259   5.6569e-02
   5_xyz:   8.905  0.049  0.462 82.599  0.030  2.297   4.8610e-02
   5_adp:   8.905  0.049  0.462 82.599  0.030  2.297   4.8610e-02
   5_occ:   8.905  0.049  0.462 82.599  0.030  2.297   4.8610e-02
   5_bss:   8.905  0.049  0.462 82.599  0.030  2.297   4.8610e-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:  77.13   0.00  14.08  67.19   0.00  12.18  77.13   0.00  24.41
   1_occ:  77.13   0.00  14.08  67.19   0.00  12.18  77.13   0.00  24.41
   2_bss:  77.13   0.00  14.08  67.19   0.00  12.18  77.13   0.00  24.41
   2_xyz:  77.13   0.00  14.08  67.19   0.00  12.18  77.13   0.00  24.41
   2_adp:  81.26   0.00  14.05  62.95   0.00  11.28  81.26   0.00  29.14
   2_occ:  81.26   0.00  14.05  62.95   0.00  11.28  81.26   0.00  29.14
   3_bss:  81.26   0.00  14.05  62.95   0.00  11.28  81.26   0.00  29.14
   3_xyz:  81.26   0.00  14.05  62.95   0.00  11.28  81.26   0.00  29.14
   3_adp:  81.55   0.00  13.85  69.09   0.00  10.34  81.55   2.16  32.96
   3_occ:  81.55   0.00  13.85  69.09   0.00  10.34  81.55   2.16  32.96
   4_bss:  81.55   0.00  13.85  69.09   0.00  10.34  81.55   2.16  32.96
   4_xyz:  81.55   0.00  13.85  69.09   0.00  10.34  81.55   2.16  32.96
   4_adp:  81.01   0.00  13.91  78.03   0.00   9.58  81.01   2.69  37.51
   4_occ:  81.01   0.00  13.91  78.03   0.00   9.58  81.01   2.69  37.51
   5_bss:  81.01   0.00  13.91  78.03   0.00   9.58  81.01   2.69  37.51
   5_xyz:  81.01   0.00  13.91  78.03   0.00   9.58  81.01   2.69  37.51
   5_adp:  90.56   0.00  14.11  90.56   0.00   9.44  90.22   2.75  39.58
   5_occ:  90.56   0.00  14.11  90.56   0.00   9.44  90.22   2.75  39.58
   5_bss:  92.31   1.75  15.87  92.31   1.75  11.19  91.97   4.50  41.34
------------------------------------------------------------------------
 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:    1.266    0.023    0.411
   1_adp:    1.266    0.023    0.411
   1_occ:    1.266    0.023    0.411
   2_bss:    1.266    0.023    0.411
   2_xyz:    1.553    0.049    0.540
   2_adp:    1.553    0.049    0.540
   2_occ:    1.553    0.049    0.540
   3_bss:    1.553    0.049    0.540
   3_xyz:    1.597    0.014    0.683
   3_adp:    1.597    0.014    0.683
   3_occ:    1.597    0.014    0.683
   4_bss:    1.597    0.014    0.683
   4_xyz:    1.801    0.043    0.752
   4_adp:    1.801    0.043    0.752
   4_occ:    1.801    0.043    0.752
   5_bss:    1.801    0.043    0.752
   5_xyz:    1.876    0.031    0.773
   5_adp:    1.876    0.031    0.773
   5_occ:    1.876    0.031    0.773
   5_bss:    1.876    0.031    0.773
------------------------------------------------------------------------

CPU time actual refinement: 342.86


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

Writing refined structure to PDB file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/trial/run_744/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_744/model_refine_001_2mFobs-DFmodel.map
Writing mFobs-DFmodel XPLOR map to file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/trial/run_744/model_refine_001_mFobs-DFmodel.map
Writing map coefficients to MTZ file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/trial/run_744/model_refine_001_map_coeffs.mtz

Writing default parameters for subsequent refinement:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/trial/run_744/model_refine_002.def


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

Pure refinement (no I/O, processing, etc)= 342.71 
  Macro-tasks:
    bulk solvent and scale       = 40.96  
    individual site refinement   = 145.13 
    weights calculation          = 32.16  
    collect and process          = 6.52   
    model show statistics        = 0.13   
    TOTAL for macro-tasks        = 224.90 
  Micro-tasks:
    mask                            = 2.34   
    f_calc                          = 106.73 
    alpha_beta                      = 8.49   
    target                          = 1.18   
    gradients_wrt_atomic_parameters = 117.64 
    fmodel                         = 7.49   
    r_factors                      = 0.17   
    phase_errors                   = 10.35  
    foms                           = 0.27   
    TOTAL for micro-tasks          = 254.66 
NUMBER OF MASK CALCS=  5
Time per interpreted Python bytecode instruction: 4.783 micro seconds
Total CPU time: 5.94 minutes
from_scatterers_fft:    653 calls, 106.31 s
gradients_fft:          598 calls, 104.01 s

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

# Date 2008-01-16 Time 02:19:59 PST -0800 (1200478799.46 s)
Start R-work = 0.4847, R-free = 0.4757 (no bulk solvent and anisotropic scale)
Final R-work = 0.1346, R-free = 0.1849 (no bulk solvent and anisotropic scale)

Start R-work = 0.4765, R-free = 0.4620
Final R-work = 0.1180, R-free = 0.1701