# Date 2008-01-16 Time 00:27:24 PST -0800 (1200472044.37 s)
#phil __OFF__

Command line arguments: "../25.param" "adp.set_b_iso=10" "sites.shake=0.5" "main.number_of_macro_cycles=5" "--overwrite"

HOST = sunbird.lbl.gov
HOSTTYPE = x86_64-linux
USER = phzwart
PID = 25285
JOB_ID = 5158
SGE_ARCH = lx24-amd64
SGE_TASK_FIRST = 1
SGE_TASK_LAST = 1330
SGE_TASK_ID = 25

-------------------------------------------------------------------------------
  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: (68.4938, 46.2261, 85.5261, 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: 3.27, per 1000 atoms: 1.16


================================== 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: (68.4938, 46.2261, 85.5261, 90, 90, 90)
Space group: P 21 21 21 (No. 19)
Systematic absences: 0
Centric reflections: 2427
Resolution range: 14.6791 1.95063
Completeness in resolution range: 0.962841
Completeness with d_max=infinity: 0.959822

Number of F-obs in resolution range:                   19589
Number of F-obs <= 0:                                  0
Refinement resolution range: d_max =  14.6791
                             d_min =   1.9506

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: (68.4938, 46.2261, 85.5261, 90, 90, 90)
Space group: P 21 21 21 (No. 19)
Systematic absences: 0
Centric reflections: 2427
Resolution range: 14.6791 1.95063
Completeness in resolution range: 0.962841
Completeness with d_max=infinity: 0.959822

Test (R-free flags) flag value: 1

Number of work/free reflections by resolution:
                                         work  free  %free
  bin  1: 14.6795 -  4.1733 [2148/2175]  1931   217  10.1%
  bin  2:  4.1733 -  3.3252 [2037/2053]  1836   201   9.9%
  bin  3:  3.3252 -  2.9086 [2036/2055]  1832   204  10.0%
  bin  4:  2.9086 -  2.6443 [2001/2031]  1799   202  10.1%
  bin  5:  2.6443 -  2.4557 [2001/2020]  1800   201  10.0%
  bin  6:  2.4557 -  2.3115 [1982/2007]  1786   196   9.9%
  bin  7:  2.3115 -  2.1962 [1973/2007]  1780   193   9.8%
  bin  8:  2.1962 -  2.1008 [1975/2006]  1775   200  10.1%
  bin  9:  2.1008 -  2.0202 [1945/1986]  1746   199  10.2%
  bin 10:  2.0202 -  1.9506 [1491/2005]  1345   146   9.8%
                                overall 17630  1959  10.0%
Writing MTZ file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/trial/run_25/model_refine_data.mtz


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

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

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

  Number of disulfides: simple=3, symmetry=0
    Simple disulfide: " SG  CYS A 168 " - " SG ACYS A 201 " distance=2.08
    Simple disulfide: " SG  CYS A 168 " - " SG BCYS A 201 " distance=1.98
    Simple disulfide: " SG  CYS A 254 " - " SG  CYS A 260 " distance=2.05
  Time building geometry restraints manager: 0.15 seconds
  Histogram of bond lengths:
        1.21 -     1.38: 943
        1.38 -     1.56: 1465
        1.56 -     1.73: 7
        1.73 -     1.90: 21
        1.90 -     2.08: 3
  Bond restraints sorted by residual:
             atom i - atom j            ideal  model  delta   weight residual
  " SG  CYS A 168 " - " SG BCYS A 201 " 2.031  1.983  0.048 2.50e+03 5.87e+00
  " C   GLN A  88 " - " N   GLN A  89 " 1.329  1.360 -0.031 5.10e+03 4.97e+00
  " SG  CYS A 168 " - " SG ACYS A 201 " 2.031  2.075 -0.044 2.50e+03 4.89e+00
  " CB  CYS A 201 " - " SG ACYS A 201 " 1.808  1.738  0.070 9.18e+02 4.46e+00
  " C   PRO A 198 " - " N   ILE A 199 " 1.329  1.301  0.028 5.10e+03 4.10e+00
  ... (remaining 2434 not shown)
  Histogram of nonbonded interaction distances:
        1.01 -     1.79: 8
        1.79 -     2.57: 101
        2.57 -     3.34: 4118
        3.34 -     4.12: 9711
        4.12 -     4.90: 15220
  Nonbonded interactions sorted by model distance:
             atom i - atom j             model   vdw sym.op. j
  " O   HOH Z  37 " - " O   HOH Z 416 "  1.009 3.040 -x+1,y-1/2,-z+1/2
  " O   HOH Z  52 " - " O   HOH Z 183 "  1.115 3.040 -x+1,y+1/2,-z+1/2
  " O   HOH Z  18 " - " O   HOH Z 102 "  1.462 3.040 -x+1,y+1/2,-z+1/2
  " NE2 GLN A  55 " - " O   ASN A 285 "  1.607 3.120 -x+1,y-1/2,-z+1/2
  " OE1 GLN A  55 " - " CB  ASN A 285 "  1.684 3.440 -x+1,y-1/2,-z+1/2
  ... (remaining 29153 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_25/model_refine_001.eff

Writing geometry restraints to file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/trial/run_25/model_refine_001.geo

CPU time processing inputs: 11.09


============================ 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 = 68.49375 46.22605 85.5261 90 90 90
    space_group = "P 21 21 21"
  }
  input {
    pdb {
      file_name = "/net/cci-filer1/vol1/tmp/phzwart/tassos/trial/model.pdb"
    }
    xray_data {
      file_name = "/net/cci-filer1/vol1/tmp/phzwart/tassos/trial/1e0w.cns"
      labels = "FOBS,SIGMA"
      r_free_flags {
        file_name = "/net/cci-filer1/vol1/tmp/phzwart/tassos/trial/1e0w.cns"
        label = "TEST"
        test_flag_value = 1
      }
    }
  }
  output {
    prefix = "model_refine"
    serial = 1
  }
  main {
    number_of_macro_cycles = 5
  }
  modify_start_model {
    adp {
      set_b_iso = 10
    }
    sites {
      shake = 0.5
    }
  }
}
#phil __OFF__


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


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


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

|--(resolution: 1.95 - 14.68 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.4995   r_free= 0.4931   ksol= 0.00   Bsol= 0.00   scale= 0.795    |
|                                                                             |
| 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:   0.86 A                  |
| x-ray target function (ml) for work reflections: 6.294556                   |
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
| Bin     Resolution   Compl.  No. Refl.    R-factors          Targets        |
|number     range              work test   work   test        work        test|
|  1: 14.6795 -  4.6544 0.99   1390  153 0.4111 0.4111      6.6095       6.636|
|  2:  4.6544 -  3.7141 0.99   1327  151 0.4294 0.4263      6.8215       6.828|
|  3:  3.7141 -  3.2504 0.99   1316  146 0.4724 0.4520      6.7085      6.7502|
|  4:  3.2504 -  2.9559 0.99   1300  137 0.4848 0.4497      6.5584      6.4949|
|  5:  2.9559 -  2.7455 0.99   1296  146 0.5293 0.5297      6.3893      6.4086|
|  6:  2.7455 -  2.5845 0.99   1283  148 0.5376 0.5555      6.2985      6.2506|
|  7:  2.5845 -  2.4557 0.99   1286  144 0.5308 0.4955      6.2629      6.1791|
|  8:  2.4557 -  2.3493 0.98   1287  136 0.5428 0.5428      6.2025      6.2135|
|  9:  2.3493 -  2.2592 0.98   1258  147 0.5199 0.5516      6.1123      6.1697|
| 10:  2.2592 -  2.1815 0.98   1265  139 0.5419 0.5340      6.1303      6.1191|
| 11:  2.1815 -  2.1135 0.99   1279  140 0.5409 0.5521      6.0435       6.089|
| 12:  2.1135 -  2.0532 0.97   1260  138 0.5395 0.5392      5.9812      6.0411|
| 13:  2.0532 -  1.9993 0.99   1264  139 0.5528 0.4923      5.9047      5.8351|
| 14:  1.9993 -  1.9506 0.65    819   95 0.5503 0.5240        5.87       5.779|
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
|R-free likelihood based estimates for figures of merit, absolute phase error,|
|and distribution parameters alpha and beta (Acta Cryst. (1995). A51, 880-887)|
|                                                                             |
| Bin     Resolution      No. Refl.   FOM  Phase Scale    Alpha        Beta   |
|  #        range        work  test        error factor                       |
|  1: 14.6795 -  4.6544  1390   153  0.64  39.70   0.79     0.68      90515.82|
|  2:  4.6544 -  3.7141  1327   151  0.65  39.27   0.87     0.73     126756.96|
|  3:  3.7141 -  3.2504  1316   146  0.54  48.68   0.86     0.68     132319.93|
|  4:  3.2504 -  2.9559  1300   137  0.46  54.80   0.80     0.57     114465.39|
|  5:  2.9559 -  2.7455  1296   146  0.36  63.09   0.73     0.44      91997.57|
|  6:  2.7455 -  2.5845  1283   148  0.30  67.16   0.71     0.36      80978.13|
|  7:  2.5845 -  2.4557  1286   144  0.22  73.23   0.75     0.27      76620.80|
|  8:  2.4557 -  2.3493  1287   136  0.20  74.94   0.73     0.24      70366.81|
|  9:  2.3493 -  2.2592  1258   147  0.19  75.90   0.74     0.24      65570.15|
| 10:  2.2592 -  2.1815  1265   139  0.24  72.48   0.77     0.29      56461.76|
| 11:  2.1815 -  2.1135  1279   140  0.20  74.99   0.75     0.26      54108.69|
| 12:  2.1135 -  2.0532  1260   138  0.20  74.98   0.76     0.26      48760.00|
| 13:  2.0532 -  1.9993  1264   139  0.18  76.58   0.75     0.24      42657.03|
| 14:  1.9993 -  1.9506   819    95  0.24  71.81   0.74     0.28      32337.19|
|alpha:            min =        0.24 max =            0.73 mean =         0.40|
|beta:             min =    32337.19 max =       132319.93 mean =     79077.61|
|figures of merit: min =        0.00 max =            1.00 mean =         0.34|
|phase err.(work): min =        0.00 max =           90.00 mean =        64.34|
|phase err.(test): min =        0.00 max =           89.97 mean =        64.54|
|-----------------------------------------------------------------------------|

============================== 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 = 21.411783             wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 83.122   (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 2.194468              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 83.632   (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 |  1.142 -  1.518:        9 |
| 0.140 - 0.280:   585 |   7.457 -  14.906:   711 |  1.518 -  1.894:       29 |
| 0.280 - 0.420:   441 |  14.906 -  22.354:   630 |  1.894 -  2.270:      180 |
| 0.420 - 0.560:   366 |  22.354 -  29.802:   474 |  2.270 -  2.645:      672 |
| 0.560 - 0.700:   237 |  29.802 -  37.251:   338 |  2.645 -  3.021:     1501 |
| 0.700 - 0.840:   127 |  37.251 -  44.699:   241 |  3.021 -  3.397:     2654 |
| 0.840 - 0.980:    59 |  44.699 -  52.147:   125 |  3.397 -  3.773:     4088 |
| 0.980 - 1.120:    17 |  52.147 -  59.595:    51 |  3.773 -  4.148:     5238 |
| 1.120 - 1.260:     9 |  59.595 -  67.044:    13 |  4.148 -  4.524:     6781 |
| 1.260 - 1.400:     1 |  67.044 -  74.492:     3 |  4.524 -  4.900:     7993 |
|-----------------------------------------------------------------------------|
|-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 |       52.629 |
| planarity |      436 |   0.145    0.405  0.000 |     250.485 |              |
|  dihedral |      870 |  33.790  144.062  0.019 |      20.704 |              |
| nonbonded |     2439 |   4.084    4.900  1.142 |       3.504 |              |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 11.264)------------------------------------------|
|    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 = 11.264)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.01    19.99   9.86     None  None   None       |
|    all(noH): 2823   0      0.01    19.99   9.86     None  None   None       |
|    Sol.    : 438    0      0.06    19.99   10.10    None  None   None       |
|    Mac.    : 2385   0      0.01    19.98   9.82     None  None   None       |
|    Hyd.    : 0      0      None    None    None     None  None   None       |
|    - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -      |
|       Distribution of isotropic (or equivalent) ADP for non-H atoms:        |
|    Bin#      value range     #atoms | Bin#      value range     #atoms      |
|      0:     0.008 -   2.007:  301   |   5:    10.002 -  12.000:  285        |
|      1:     2.007 -   4.006:  276   |   6:    12.000 -  13.999:  292        |
|      2:     4.006 -   6.004:  309   |   7:    13.999 -  15.998:  289        |
|      3:     6.004 -   8.003:  285   |   8:    15.998 -  17.996:  266        |
|      4:     8.003 -  10.002:  251   |   9:    17.996 -  19.995:  269        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.95 - 14.68 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.5032   r_free= 0.4969   ksol= 0.00   Bsol= 0.00   scale= 0.765    |
|                                                                             |
| 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:   0.86 A                  |
| x-ray target function (ml) for work reflections: 6.295447                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.95 - 14.68 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.4900   r_free= 0.4827   ksol= 0.36   Bsol= 0.00   scale= 0.997    |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (8.04,9.46,7.87,0.00,0.00,0.00); trace/3= 8.46                              |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.85 A                  |
| x-ray target function (ml) for work reflections: 6.286623                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 16.703451             wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 84.299   (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 1.838736              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 81.247   (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.4900      final r-factor (work) = 0.4200          |
| start r-factor (free) = 0.4827      final r-factor (free) = 0.4429          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 105.1817 = 16.70 * 0.50 * 6.2924 + 1.00 * 52.6291                           |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 52.1549 = 16.70 * 0.50 * 6.2256 + 1.00 * 0.1602                             |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 26     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.4200      final r-factor (work) = 0.3756          |
| start r-factor (free) = 0.4429      final r-factor (free) = 0.4217          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 11.4616 = 1.84 * 1.00 * 6.2256 + 1.00 * 0.0144                              |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 11.3484 = 1.84 * 1.00 * 6.1592 + 1.00 * 0.0231                              |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 28     |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 11.264)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.00    80.70   14.82    None  None   None       |
|    all(noH): 2823   0      0.00    80.70   14.82    None  None   None       |
|    Sol.    : 438    0      0.00    79.40   26.18    None  None   None       |
|    Mac.    : 2385   0      0.00    80.70   12.74    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 -   8.070: 1046   |   5:    40.348 -  48.417:   85        |
|      1:     8.070 -  16.139:  761   |   6:    48.417 -  56.487:   41        |
|      2:    16.139 -  24.209:  457   |   7:    56.487 -  64.557:   23        |
|      3:    24.209 -  32.278:  266   |   8:    64.557 -  72.626:    9        |
|      4:    32.278 -  40.348:  128   |   9:    72.626 -  80.696:    7        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.3756 r_free = 0.4217             target_work(ml) = 6.142         |
| occupancies: max = 1.00  min = 0.30   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.3750 r_free = 0.4211             target_work(ml) = 6.141         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:       12 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.95 - 14.68 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.3750   r_free= 0.4211   ksol= 0.36   Bsol= 0.00   scale= 1.119    |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (8.04,9.46,7.87,0.00,0.00,0.00); trace/3= 8.46                              |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.59 A                  |
| x-ray target function (ml) for work reflections: 6.140857                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.95 - 14.68 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.3728   r_free= 0.4152   ksol= 0.34   Bsol= 24.90   scale= 1.033   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (4.70,5.34,5.05,0.00,0.00,0.00); trace/3= 5.03                              |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.59 A                  |
| x-ray target function (ml) for work reflections: 6.140104                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 8.857648              wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 98.968   (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 0.702661              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 123.926  (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.3728      final r-factor (work) = 0.2932          |
| start r-factor (free) = 0.4152      final r-factor (free) = 0.3510          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 27.4154 = 8.86 * 0.50 * 6.1541 + 1.00 * 0.1602                              |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 26.8559 = 8.86 * 0.50 * 6.0418 + 1.00 * 0.0977                              |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 28     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.2932      final r-factor (work) = 0.2678          |
| start r-factor (free) = 0.3510      final r-factor (free) = 0.3304          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 4.2699 = 0.70 * 1.00 * 6.0418 + 1.00 * 0.0245                               |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 4.1718 = 0.70 * 1.00 * 5.9166 + 1.00 * 0.0144                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 25     |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 11.264)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.00    94.75   14.15    None  None   None       |
|    all(noH): 2823   0      0.00    94.75   14.15    None  None   None       |
|    Sol.    : 438    0      0.00    84.36   31.86    None  None   None       |
|    Mac.    : 2385   0      0.00    94.75   10.90    None  None   None       |
|    Hyd.    : 0      0      None    None    None     None  None   None       |
|    - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -      |
|       Distribution of isotropic (or equivalent) ADP for non-H atoms:        |
|    Bin#      value range     #atoms | Bin#      value range     #atoms      |
|      0:     0.000 -   9.475: 1389   |   5:    47.377 -  56.852:   67        |
|      1:     9.475 -  18.951:  736   |   6:    56.852 -  66.327:   19        |
|      2:    18.951 -  28.426:  307   |   7:    66.327 -  75.803:    8        |
|      3:    28.426 -  37.901:  189   |   8:    75.803 -  85.278:    4        |
|      4:    37.901 -  47.377:  103   |   9:    85.278 -  94.753:    1        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.2678 r_free = 0.3304             target_work(ml) = 5.889         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:       12 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.2675 r_free = 0.3303             target_work(ml) = 5.889         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:       15 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.95 - 14.68 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.2675   r_free= 0.3303   ksol= 0.34   Bsol= 24.90   scale= 1.082   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (4.70,5.34,5.05,0.00,0.00,0.00); trace/3= 5.03                              |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.37 A                  |
| x-ray target function (ml) for work reflections: 5.889064                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.95 - 14.68 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.2649   r_free= 0.3292   ksol= 0.34   Bsol= 35.49   scale= 1.024   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (2.38,2.91,3.34,0.00,0.00,0.00); trace/3= 2.88                              |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.37 A                  |
| x-ray target function (ml) for work reflections: 5.886196                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 5.346281              wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 100.420  (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 0.261664              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 114.667  (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.2649      final r-factor (work) = 0.1938          |
| start r-factor (free) = 0.3292      final r-factor (free) = 0.2472          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 15.9154 = 5.35 * 0.50 * 5.9174 + 1.00 * 0.0974                              |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 15.4888 = 5.35 * 0.50 * 5.7661 + 1.00 * 0.0752                              |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 28     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1938      final r-factor (work) = 0.1738          |
| start r-factor (free) = 0.2472      final r-factor (free) = 0.2273          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 1.5230 = 0.26 * 1.00 * 5.7661 + 1.00 * 0.0142                               |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 1.4622 = 0.26 * 1.00 * 5.5530 + 1.00 * 0.0092                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 28     |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 11.264)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.00    92.29   13.77    None  None   None       |
|    all(noH): 2823   0      0.00    92.29   13.77    None  None   None       |
|    Sol.    : 438    0      2.49    76.23   35.01    None  None   None       |
|    Mac.    : 2385   0      0.00    92.29   9.86     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 -   9.229: 1513   |   5:    46.144 -  55.373:   80        |
|      1:     9.229 -  18.458:  702   |   6:    55.373 -  64.601:   24        |
|      2:    18.458 -  27.686:  210   |   7:    64.601 -  73.830:   11        |
|      3:    27.686 -  36.915:  149   |   8:    73.830 -  83.059:    4        |
|      4:    36.915 -  46.144:  129   |   9:    83.059 -  92.288:    1        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.1738 r_free = 0.2273             target_work(ml) = 5.513         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:       15 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.1731 r_free = 0.2269             target_work(ml) = 5.511         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:       11 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.95 - 14.68 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1731   r_free= 0.2269   ksol= 0.34   Bsol= 35.49   scale= 1.054   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (2.38,2.91,3.34,0.00,0.00,0.00); trace/3= 2.88                              |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.19 A                  |
| x-ray target function (ml) for work reflections: 5.511006                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.95 - 14.68 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1719   r_free= 0.2256   ksol= 0.32   Bsol= 31.96   scale= 1.016   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (0.87,1.42,2.28,0.00,0.00,0.00); trace/3= 1.53                              |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.19 A                  |
| x-ray target function (ml) for work reflections: 5.508453                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 3.608202              wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 101.710  (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 0.172819              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 140.701  (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1719      final r-factor (work) = 0.1359          |
| start r-factor (free) = 0.2256      final r-factor (free) = 0.1813          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 10.1073 = 3.61 * 0.50 * 5.5607 + 1.00 * 0.0752                              |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 9.8291 = 3.61 * 0.50 * 5.4112 + 1.00 * 0.0667                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 28     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1359      final r-factor (work) = 0.1300          |
| start r-factor (free) = 0.1813      final r-factor (free) = 0.1731          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 0.9442 = 0.17 * 1.00 * 5.4112 + 1.00 * 0.0091                               |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 0.9200 = 0.17 * 1.00 * 5.2758 + 1.00 * 0.0082                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 32     |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 11.264)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.00    89.88   13.57    None  None   None       |
|    all(noH): 2823   0      0.00    89.88   13.57    None  None   None       |
|    Sol.    : 438    0      2.42    75.13   35.47    None  None   None       |
|    Mac.    : 2385   0      0.00    89.88   9.55     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 -   8.988: 1542   |   5:    44.939 -  53.927:  101        |
|      1:     8.988 -  17.976:  699   |   6:    53.927 -  62.915:   32        |
|      2:    17.976 -  26.964:  170   |   7:    62.915 -  71.903:   10        |
|      3:    26.964 -  35.951:  146   |   8:    71.903 -  80.890:    6        |
|      4:    35.951 -  44.939:  116   |   9:    80.890 -  89.878:    1        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.1300 r_free = 0.1731             target_work(ml) = 5.251         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:       11 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.1297 r_free = 0.1730             target_work(ml) = 5.249         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:       12 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.95 - 14.68 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1297   r_free= 0.1730   ksol= 0.32   Bsol= 31.96   scale= 1.025   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (0.87,1.42,2.28,0.00,0.00,0.00); trace/3= 1.53                              |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.15 A                  |
| x-ray target function (ml) for work reflections: 5.248971                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.95 - 14.68 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1299   r_free= 0.1723   ksol= 0.32   Bsol= 31.96   scale= 1.015   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (0.44,1.01,2.07,0.00,0.00,0.00); trace/3= 1.17                              |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.15 A                  |
| x-ray target function (ml) for work reflections: 5.247900                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 2.104149              wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 112.311  (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 0.471643              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 153.522  (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1299      final r-factor (work) = 0.1201          |
| start r-factor (free) = 0.1723      final r-factor (free) = 0.1622          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 5.6174 = 2.10 * 0.50 * 5.2760 + 1.00 * 0.0667                               |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 5.5434 = 2.10 * 0.50 * 5.2124 + 1.00 * 0.0596                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 27     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1201      final r-factor (work) = 0.1169          |
| start r-factor (free) = 0.1622      final r-factor (free) = 0.1616          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 2.4666 = 0.47 * 1.00 * 5.2124 + 1.00 * 0.0082                               |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 2.4497 = 0.47 * 1.00 * 5.1730 + 1.00 * 0.0099                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 28     |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 11.264)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.00    91.76   13.80    None  None   None       |
|    all(noH): 2823   0      0.00    91.76   13.80    None  None   None       |
|    Sol.    : 438    0      3.03    80.95   37.20    None  None   None       |
|    Mac.    : 2385   0      0.00    91.76   9.50     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 -   9.176: 1588   |   5:    45.881 -  55.057:   93        |
|      1:     9.176 -  18.353:  672   |   6:    55.057 -  64.234:   51        |
|      2:    18.353 -  27.529:  157   |   7:    64.234 -  73.410:   12        |
|      3:    27.529 -  36.705:  123   |   8:    73.410 -  82.586:    6        |
|      4:    36.705 -  45.881:  119   |   9:    82.586 -  91.762:    2        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.1169 r_free = 0.1616             target_work(ml) = 5.171         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:       12 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.1168 r_free = 0.1616             target_work(ml) = 5.171         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:       12 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.95 - 14.68 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1168   r_free= 0.1616   ksol= 0.32   Bsol= 31.96   scale= 1.016   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (0.44,1.01,2.07,0.00,0.00,0.00); trace/3= 1.17                              |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.14 A                  |
| x-ray target function (ml) for work reflections: 5.170580                   |
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
| Bin     Resolution   Compl.  No. Refl.    R-factors          Targets        |
|number     range              work test   work   test        work        test|
|  1: 14.6795 -  4.6544 0.99   1390  153 0.1045 0.1311      5.4203      5.5548|
|  2:  4.6544 -  3.7141 0.99   1327  151 0.0911 0.1209      5.4855      5.6982|
|  3:  3.7141 -  3.2504 0.99   1316  146 0.1130 0.1429      5.5252       5.814|
|  4:  3.2504 -  2.9559 0.99   1300  137 0.1264 0.1726      5.4821      5.6644|
|  5:  2.9559 -  2.7455 0.99   1296  146 0.1359 0.1742       5.355      5.5388|
|  6:  2.7455 -  2.5845 0.99   1283  148 0.1260 0.1969      5.2276      5.4922|
|  7:  2.5845 -  2.4557 0.99   1286  144 0.1267 0.1614      5.1717      5.3387|
|  8:  2.4557 -  2.3493 0.98   1287  136 0.1206 0.1640      5.1005      5.3335|
|  9:  2.3493 -  2.2592 0.98   1258  147 0.1225 0.1816      5.0466      5.3436|
| 10:  2.2592 -  2.1815 0.98   1265  139 0.1170 0.1650      4.9933      5.1819|
| 11:  2.1815 -  2.1135 0.99   1279  140 0.1176 0.1904      4.9622      5.3522|
| 12:  2.1135 -  2.0532 0.97   1260  138 0.1195 0.1644      4.9295      5.1761|
| 13:  2.0532 -  1.9993 0.99   1264  139 0.1122 0.1871      4.7984      5.0854|
| 14:  1.9993 -  1.9506 0.65    819   95 0.0984 0.1661      4.6343      4.9107|
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
|R-free likelihood based estimates for figures of merit, absolute phase error,|
|and distribution parameters alpha and beta (Acta Cryst. (1995). A51, 880-887)|
|                                                                             |
| Bin     Resolution      No. Refl.   FOM  Phase Scale    Alpha        Beta   |
|  #        range        work  test        error factor                       |
|  1: 14.6795 -  4.6544  1390   153  0.94   9.39   0.99     0.97       7659.02|
|  2:  4.6544 -  3.7141  1327   151  0.95   8.29   1.04     1.02       9565.77|
|  3:  3.7141 -  3.2504  1316   146  0.93  12.12   1.05     1.04      11218.05|
|  4:  3.2504 -  2.9559  1300   137  0.92  13.65   1.02     1.02      10563.41|
|  5:  2.9559 -  2.7455  1296   146  0.90  16.25   1.00     0.97       8655.31|
|  6:  2.7455 -  2.5845  1283   148  0.90  16.13   0.99     0.96       7076.66|
|  7:  2.5845 -  2.4557  1286   144  0.90  16.00   1.00     0.96       6210.95|
|  8:  2.4557 -  2.3493  1287   136  0.91  15.18   1.01     0.99       5494.17|
|  9:  2.3493 -  2.2592  1258   147  0.91  15.72   1.01     0.99       5128.82|
| 10:  2.2592 -  2.1815  1265   139  0.90  16.22   1.01     0.97       4657.83|
| 11:  2.1815 -  2.1135  1279   140  0.90  16.62   1.02     0.98       4651.09|
| 12:  2.1135 -  2.0532  1260   138  0.90  16.58   1.03     1.02       4413.46|
| 13:  2.0532 -  1.9993  1264   139  0.90  15.89   1.02     1.01       3422.19|
| 14:  1.9993 -  1.9506   819    95  0.92  13.59   1.00     0.97       2360.17|
|alpha:            min =        0.96 max =            1.04 mean =         0.99|
|beta:             min =     2360.17 max =        11218.05 mean =      6653.58|
|figures of merit: min =        0.00 max =            1.00 mean =         0.91|
|phase err.(work): min =        0.00 max =           89.96 mean =        14.37|
|phase err.(test): min =        0.00 max =           89.92 mean =        13.86|
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.95 - 14.68 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1168   r_free= 0.1616   ksol= 0.32   Bsol= 34.61   scale= 1.016   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-0.75,-0.19,0.94,0.00,0.00,0.00); trace/3= 0.00                            |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.14 A                  |
| x-ray target function (ml) for work reflections: 5.170370                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.95 - 14.68 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1168   r_free= 0.1616   ksol= 0.32   Bsol= 34.61   scale= 1.016   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-0.75,-0.19,0.94,0.00,0.00,0.00); trace/3= 0.00                            |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.14 A                  |
| x-ray target function (ml) for work reflections: 5.170370                   |
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
| Bin     Resolution   Compl.  No. Refl.    R-factors          Targets        |
|number     range              work test   work   test        work        test|
|  1: 14.6795 -  4.6544 0.99   1390  153 0.1045 0.1311      5.4194      5.5536|
|  2:  4.6544 -  3.7141 0.99   1327  151 0.0913 0.1212      5.4865      5.6999|
|  3:  3.7141 -  3.2504 0.99   1316  146 0.1131 0.1431      5.5263      5.8151|
|  4:  3.2504 -  2.9559 0.99   1300  137 0.1264 0.1727      5.4824      5.6639|
|  5:  2.9559 -  2.7455 0.99   1296  146 0.1358 0.1743      5.3546      5.5386|
|  6:  2.7455 -  2.5845 0.99   1283  148 0.1259 0.1967      5.2271       5.491|
|  7:  2.5845 -  2.4557 0.99   1286  144 0.1267 0.1615       5.171      5.3387|
|  8:  2.4557 -  2.3493 0.98   1287  136 0.1206 0.1638      5.0998      5.3327|
|  9:  2.3493 -  2.2592 0.98   1258  147 0.1225 0.1815      5.0462      5.3437|
| 10:  2.2592 -  2.1815 0.98   1265  139 0.1169 0.1649       4.993      5.1815|
| 11:  2.1815 -  2.1135 0.99   1279  140 0.1175 0.1903      4.9619       5.352|
| 12:  2.1135 -  2.0532 0.97   1260  138 0.1195 0.1644      4.9294      5.1768|
| 13:  2.0532 -  1.9993 0.99   1264  139 0.1122 0.1869      4.7981      5.0843|
| 14:  1.9993 -  1.9506 0.65    819   95 0.0983 0.1660      4.6335      4.9103|
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
|R-free likelihood based estimates for figures of merit, absolute phase error,|
|and distribution parameters alpha and beta (Acta Cryst. (1995). A51, 880-887)|
|                                                                             |
| Bin     Resolution      No. Refl.   FOM  Phase Scale    Alpha        Beta   |
|  #        range        work  test        error factor                       |
|  1: 14.6795 -  4.6544  1390   153  0.94   9.38   0.99     0.97       7633.07|
|  2:  4.6544 -  3.7141  1327   151  0.95   8.29   1.04     1.02       9568.78|
|  3:  3.7141 -  3.2504  1316   146  0.93  12.14   1.05     1.04      11241.17|
|  4:  3.2504 -  2.9559  1300   137  0.92  13.65   1.02     1.02      10566.71|
|  5:  2.9559 -  2.7455  1296   146  0.90  16.25   1.00     0.97       8646.25|
|  6:  2.7455 -  2.5845  1283   148  0.90  16.12   0.99     0.96       7071.09|
|  7:  2.5845 -  2.4557  1286   144  0.90  15.99   1.00     0.96       6202.41|
|  8:  2.4557 -  2.3493  1287   136  0.91  15.17   1.01     1.00       5487.08|
|  9:  2.3493 -  2.2592  1258   147  0.91  15.72   1.01     0.99       5123.24|
| 10:  2.2592 -  2.1815  1265   139  0.90  16.22   1.01     0.97       4657.52|
| 11:  2.1815 -  2.1135  1279   140  0.90  16.62   1.02     0.98       4651.32|
| 12:  2.1135 -  2.0532  1260   138  0.90  16.57   1.03     1.02       4412.81|
| 13:  2.0532 -  1.9993  1264   139  0.90  15.89   1.02     1.01       3420.08|
| 14:  1.9993 -  1.9506   819    95  0.92  13.58   1.00     0.97       2357.40|
|alpha:            min =        0.96 max =            1.04 mean =         0.99|
|beta:             min =     2357.40 max =        11241.17 mean =      6650.79|
|figures of merit: min =        0.00 max =            1.00 mean =         0.91|
|phase err.(work): min =        0.00 max =           89.93 mean =        14.36|
|phase err.(test): min =        0.00 max =           89.94 mean =        13.86|
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 11.264)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      1.18    92.94   14.98    None  None   None       |
|    all(noH): 2823   0      1.18    92.94   14.98    None  None   None       |
|    Sol.    : 438    0      4.21    82.13   38.37    None  None   None       |
|    Mac.    : 2385   0      1.18    92.94   10.68    None  None   None       |
|    Hyd.    : 0      0      None    None    None     None  None   None       |
|    - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -      |
|       Distribution of isotropic (or equivalent) ADP for non-H atoms:        |
|    Bin#      value range     #atoms | Bin#      value range     #atoms      |
|      0:     1.178 -  10.354: 1588   |   5:    47.059 -  56.235:   93        |
|      1:    10.354 -  19.531:  672   |   6:    56.235 -  65.412:   51        |
|      2:    19.531 -  28.707:  157   |   7:    65.412 -  74.588:   12        |
|      3:    28.707 -  37.883:  123   |   8:    74.588 -  83.764:    6        |
|      4:    37.883 -  47.059:  119   |   9:    83.764 -  92.940:    2        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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


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

Number of peaks found at mFobs-DFmodel map (map cutoff=3.00 sigma)= 323         
Filter by distance & map next to the model:
   mapped sites are within: 0.694 - 5.709
   number of sites selected in [dist_min= 0.70, dist_max= 6.00]: 322 from: 323
   mapped sites are within: 0.801 - 5.709

peak=   11.061 closest distance to " CB  VAL A 296 " =    1.557
peak=   10.722 closest distance to " CB  VAL A 230 " =    1.396
peak=    7.537 closest distance to " O   HOH Z 130 " =    1.484
peak=    6.084 closest distance to " O   HOH Z 236 " =    1.609
peak=    5.854 closest distance to " CD2 LEU A   5 " =    1.231
peak=    5.715 closest distance to " O   HOH Z 193 " =    1.755
peak=    5.704 closest distance to " O   HOH Z 142 " =    1.973
peak=    5.660 closest distance to " CG  LEU A   5 " =    1.188
peak=    5.636 closest distance to " CB  ARG A 275 " =    1.021
peak=    5.565 closest distance to " NE2 GLN A  11 " =    1.145
peak=    5.548 closest distance to " O   HOH Z 375 " =    1.172
peak=    5.501 closest distance to " O   HOH Z   9 " =    1.363
peak=    5.235 closest distance to " O   HOH Z  78 " =    1.667
peak=    5.221 closest distance to " O   HOH Z 124 " =    1.533
peak=    5.214 closest distance to " O   HOH Z  65 " =    1.076
peak=    5.171 closest distance to " O   HOH Z  28 " =    1.381
peak=    5.050 closest distance to " O   HOH Z 272 " =    1.866
peak=    5.017 closest distance to " O   HOH Z 414 " =    1.479
peak=    4.912 closest distance to " O   HOH Z 380 " =    1.874
peak=    4.906 closest distance to " O   HOH Z 427 " =    2.461
peak=    4.854 closest distance to " CG  PRO A  54 " =    1.331
peak=    4.838 closest distance to " O   HOH Z 403 " =    1.892
peak=    4.806 closest distance to " O   HOH Z 126 " =    1.927
peak=    4.799 closest distance to " O   HOH Z 424 " =    1.210
peak=    4.782 closest distance to " CG  LEU A 228 " =    1.124
peak=    4.780 closest distance to " CB  VAL A 230 " =    1.152
peak=    4.762 closest distance to " O   HOH Z 369 " =    2.636
peak=    4.755 closest distance to " CB  PRO A  54 " =    1.070
peak=    4.664 closest distance to " O   HOH Z 423 " =    1.539
peak=    4.631 closest distance to " CD1AILE A 234 " =    0.872
peak=    4.620 closest distance to " NH2 ARG A  56 " =    1.921
peak=    4.616 closest distance to " O   HOH Z 250 " =    2.386
peak=    4.598 closest distance to " O   HOH Z  85 " =    1.493
peak=    4.578 closest distance to " CB  VAL A 202 " =    1.642
peak=    4.558 closest distance to " CG  PRO A 213 " =    1.248
peak=    4.547 closest distance to " O   HOH Z 209 " =    2.272
peak=    4.494 closest distance to " CB  GLN A 183 " =    1.278
peak=    4.447 closest distance to " O   SER A  87 " =    2.338
peak=    4.413 closest distance to " CB  SER A   3 " =    1.235
peak=    4.406 closest distance to " CB  GLN A 223 " =    1.657
peak=    4.399 closest distance to " O   HOH Z 352 " =    1.408
peak=    4.295 closest distance to " NZ  LYS A 117 " =    3.161
peak=    4.286 closest distance to " O   HOH Z 344 " =    1.338
peak=    4.269 closest distance to " O   HOH Z  43 " =    1.275
peak=    4.247 closest distance to " O   HOH Z  44 " =    1.821
peak=    4.243 closest distance to " O   HOH Z  11 " =    1.706
peak=    4.240 closest distance to " O   HOH Z 126 " =    1.541
peak=    4.239 closest distance to " O   HOH Z 278 " =    1.021
peak=    4.236 closest distance to " O   HOH Z  97 " =    2.056
peak=    4.236 closest distance to " O   HOH Z  97 " =    1.609
peak=    4.233 closest distance to " O   HOH Z   3 " =    2.162
peak=    4.229 closest distance to " O   HOH Z  69 " =    1.241
peak=    4.191 closest distance to " O   HOH Z 130 " =    1.818
peak=    4.187 closest distance to " O   HOH Z 346 " =    1.663
peak=    4.182 closest distance to " CB  ARG A  79 " =    1.420
peak=    4.165 closest distance to " O   HOH Z 146 " =    1.715
peak=    4.158 closest distance to " CB  SER A  26 " =    1.629
peak=    4.128 closest distance to " O   HOH Z 148 " =    1.640
peak=    4.125 closest distance to " O   HOH Z 422 " =    2.276
peak=    4.104 closest distance to " O   HOH Z 250 " =    1.493
peak=    4.100 closest distance to " O   HOH Z 263 " =    1.552
peak=    4.089 closest distance to " CG  PRO A 243 " =    1.180
peak=    4.065 closest distance to " CB  VAL A 265 " =    1.264
peak=    4.040 closest distance to " O   HOH Z 112 " =    1.250
peak=    4.022 closest distance to " CG2 VAL A 257 " =    0.892
peak=    4.018 closest distance to " O   HOH Z 371 " =    1.724
peak=    4.013 closest distance to " OE1 GLU A   2 " =    2.070
peak=    4.007 closest distance to " O   HOH Z 411 " =    3.744
peak=    4.001 closest distance to " CB  SER A  63 " =    1.225
peak=    3.998 closest distance to " O   HOH Z 423 " =    1.946
peak=    3.973 closest distance to " CA  TYR A  30 " =    1.026
peak=    3.973 closest distance to " O   HOH Z  61 " =    1.676
peak=    3.970 closest distance to " O   HOH Z 261 " =    2.201
peak=    3.961 closest distance to " O   HOH Z 189 " =    2.546
peak=    3.960 closest distance to " O   HOH Z 234 " =    3.371
peak=    3.942 closest distance to " CB BVAL A  41 " =    1.170
peak=    3.940 closest distance to " O   HOH Z 130 " =    1.789
peak=    3.939 closest distance to " O   HOH Z 406 " =    1.278
peak=    3.939 closest distance to " O   HOH Z 425 " =    2.161
peak=    3.938 closest distance to " O   HOH Z 249 " =    1.158
peak=    3.936 closest distance to " O   HOH Z 316 " =    2.893
peak=    3.932 closest distance to " O   HOH Z  66 " =    2.047
peak=    3.913 closest distance to " O   HOH Z 137 " =    1.581
peak=    3.891 closest distance to " O   HOH Z 203 " =    1.476
peak=    3.879 closest distance to " CD2 LEU A 228 " =    1.199
peak=    3.856 closest distance to " CB  ASN A 148 " =    1.398
peak=    3.848 closest distance to " CG  GLN A  88 " =    0.993
peak=    3.848 closest distance to " C   PRO A 198 " =    1.497
peak=    3.847 closest distance to " CA  ASN A 127 " =    1.070
peak=    3.845 closest distance to " O   HOH Z 337 " =    1.678
peak=    3.841 closest distance to " O   HOH Z 192 " =    1.313
peak=    3.832 closest distance to " O   HOH Z 143 " =    1.444
peak=    3.803 closest distance to " O   HOH Z  59 " =    1.598
peak=    3.800 closest distance to " NH2AARG A 190 " =    1.841
peak=    3.792 closest distance to " O   HOH Z 334 " =    1.418
peak=    3.787 closest distance to " CB  ALA A 114 " =    1.483
peak=    3.778 closest distance to " CB  GLU A 152 " =    1.250
peak=    3.778 closest distance to " CA  PHE A 283 " =    1.193
peak=    3.775 closest distance to " CB  GLN A 278 " =    0.908
peak=    3.771 closest distance to " O   HOH Z 114 " =    1.927
peak=    3.770 closest distance to " O   HOH Z 123 " =    1.183
peak=    3.758 closest distance to " N   PHE A 130 " =    1.286
peak=    3.757 closest distance to " O   HOH Z 145 " =    1.713
peak=    3.756 closest distance to " NE1 TRP A 274 " =    1.014
peak=    3.752 closest distance to " O   HOH Z 128 " =    2.007
peak=    3.733 closest distance to " CG AARG A 275 " =    1.192
peak=    3.727 closest distance to " CG  PRO A 198 " =    1.266
peak=    3.722 closest distance to " O   HOH Z 366 " =    2.743
peak=    3.717 closest distance to " CB  ALA A 248 " =    1.442
peak=    3.709 closest distance to " O   HOH Z 368 " =    2.124
peak=    3.704 closest distance to " O   HOH Z 419 " =    1.916
peak=    3.698 closest distance to " NH2BARG A 190 " =    1.554
peak=    3.682 closest distance to " O   HOH Z 193 " =    1.931
peak=    3.680 closest distance to " O   HOH Z 222 " =    2.220
peak=    3.680 closest distance to " O   HOH Z  10 " =    1.720
peak=    3.664 closest distance to " OD2 ASP A 286 " =    2.429
peak=    3.659 closest distance to " CG  LYS A  76 " =    1.365
peak=    3.657 closest distance to " CB  TRP A 266 " =    1.129
peak=    3.635 closest distance to " O   HOH Z 392 " =    2.960
peak=    3.631 closest distance to " O   HOH Z  88 " =    2.720
peak=    3.628 closest distance to " O   HOH Z 287 " =    1.642
peak=    3.626 closest distance to " O   HOH Z  61 " =    1.507
peak=    3.618 closest distance to " OG BSER A 210 " =    1.497
peak=    3.612 closest distance to " O   HOH Z  80 " =    1.662
peak=    3.608 closest distance to " O   HOH Z 132 " =    1.157
peak=    3.602 closest distance to " CA  ASN A 215 " =    1.057
peak=    3.600 closest distance to " O   HOH Z 389 " =    1.355
peak=    3.598 closest distance to " O   HOH Z 251 " =    1.703
peak=    3.597 closest distance to " O   HOH Z  58 " =    1.811
peak=    3.596 closest distance to " CB  GLU A 277 " =    3.437
peak=    3.595 closest distance to " O   HOH Z   9 " =    1.937
peak=    3.592 closest distance to " O   HOH Z 291 " =    1.524
peak=    3.592 closest distance to " O   HOH Z 176 " =    1.613
peak=    3.592 closest distance to " O   HOH Z 343 " =    3.150
peak=    3.589 closest distance to " OG BSER A 164 " =    2.128
peak=    3.587 closest distance to " O   HOH Z 353 " =    2.442
peak=    3.583 closest distance to " NH1 ARG A 138 " =    1.155
peak=    3.581 closest distance to " O   HOH Z 402 " =    1.388
peak=    3.581 closest distance to " O   HOH Z 245 " =    1.404
peak=    3.565 closest distance to " CB  ARG A 139 " =    0.995
peak=    3.564 closest distance to " CD  GLN A 194 " =    1.370
peak=    3.563 closest distance to " CG  TRP A 179 " =    2.265
peak=    3.563 closest distance to " NH1BARG A 190 " =    1.906
peak=    3.551 closest distance to " O   HOH Z 194 " =    1.981
peak=    3.548 closest distance to " O   HOH Z 322 " =    2.115
peak=    3.546 closest distance to " O   HOH Z 128 " =    2.118
peak=    3.536 closest distance to " CD2 TRP A 179 " =    1.416
peak=    3.533 closest distance to " O   GLN A  58 " =    1.406
peak=    3.533 closest distance to " O   HOH Z  89 " =    1.753
peak=    3.529 closest distance to " O   HOH Z 410 " =    1.277
peak=    3.526 closest distance to " O   HOH Z  59 " =    1.955
peak=    3.525 closest distance to " CB  ASN A 215 " =    1.047
peak=    3.524 closest distance to " NE2 GLN A  55 " =    1.282
peak=    3.520 closest distance to " OG1 THR A 294 " =    2.379
peak=    3.518 closest distance to " CD  ARG A 269 " =    1.067
peak=    3.516 closest distance to " NH1 ARG A  14 " =    0.985
peak=    3.499 closest distance to " O   HOH Z 365 " =    1.809
peak=    3.498 closest distance to " O   HOH Z 227 " =    2.198
peak=    3.494 closest distance to " N   ARG A 156 " =    1.275
peak=    3.491 closest distance to " O   HOH Z 106 " =    2.547
peak=    3.484 closest distance to " CB  ALA A   9 " =    1.502
peak=    3.484 closest distance to " O   HOH Z 188 " =    1.264
peak=    3.475 closest distance to " O   HOH Z  80 " =    2.118
peak=    3.474 closest distance to " C   LYS A 290 " =    1.243
peak=    3.469 closest distance to " NH2BARG A 145 " =    1.222
peak=    3.465 closest distance to " CE1 HIS A 108 " =    1.291
peak=    3.463 closest distance to " CB  SER A 276 " =    1.341
peak=    3.463 closest distance to " O   HOH Z 261 " =    1.731
peak=    3.461 closest distance to " CE AMET A  47 " =    1.213
peak=    3.460 closest distance to " CB  LEU A 255 " =    0.801
peak=    3.457 closest distance to " O   HOH Z 156 " =    2.917
peak=    3.455 closest distance to " O   HOH Z  59 " =    2.102
peak=    3.455 closest distance to " O   HOH Z 435 " =    1.986
peak=    3.454 closest distance to " CB  GLU A 128 " =    1.007
peak=    3.451 closest distance to " O   HOH Z   1 " =    4.476
peak=    3.449 closest distance to " O   HOH Z 227 " =    2.016
peak=    3.443 closest distance to " O   HOH Z 284 " =    2.632
peak=    3.443 closest distance to " CG2 ILE A  20 " =    1.685
peak=    3.440 closest distance to " O   HOH Z 298 " =    1.774
peak=    3.436 closest distance to " O   HOH Z  47 " =    1.734
peak=    3.436 closest distance to " CE BMET A  47 " =    1.320
peak=    3.435 closest distance to " CB  GLN A  88 " =    1.316
peak=    3.431 closest distance to " O   HOH Z 193 " =    1.873
peak=    3.431 closest distance to " CB  TYR A  30 " =    1.750
peak=    3.428 closest distance to " O   HOH Z  39 " =    1.330
peak=    3.425 closest distance to " O   HOH Z 383 " =    1.843
peak=    3.425 closest distance to " ND1 HIS A  81 " =    1.488
peak=    3.416 closest distance to " O   HOH Z 196 " =    1.400
peak=    3.416 closest distance to " CB  TRP A 179 " =    1.182
peak=    3.416 closest distance to " O   HOH Z  71 " =    1.164
peak=    3.416 closest distance to " O   HOH Z 152 " =    2.568
peak=    3.412 closest distance to " O   HOH Z 153 " =    3.476
peak=    3.409 closest distance to " CB  HIS A 108 " =    0.883
peak=    3.408 closest distance to " C   ALA A 299 " =    0.969
peak=    3.399 closest distance to " O   HOH Z 407 " =    2.235
peak=    3.399 closest distance to " NE  ARG A  56 " =    3.392
peak=    3.396 closest distance to " O   HOH Z 213 " =    1.689
peak=    3.395 closest distance to " CB  THR A  31 " =    1.626
peak=    3.390 closest distance to " O   HOH Z 130 " =    2.597
peak=    3.389 closest distance to " NE BARG A 275 " =    1.174
peak=    3.388 closest distance to " O   HOH Z 248 " =    1.687
peak=    3.385 closest distance to " O   HOH Z  51 " =    1.438
peak=    3.378 closest distance to " O   HOH Z 109 " =    2.127
peak=    3.374 closest distance to " O   HOH Z 215 " =    1.494
peak=    3.366 closest distance to " ND2 ASN A 187 " =    1.623
peak=    3.365 closest distance to " CB  THR A  52 " =    1.110
peak=    3.363 closest distance to " CB  TYR A 169 " =    1.046
peak=    3.363 closest distance to " O   HOH Z 344 " =    2.584
peak=    3.362 closest distance to " CG1BVAL A  72 " =    1.288
peak=    3.360 closest distance to " O   HOH Z 280 " =    2.533
peak=    3.354 closest distance to " O   HOH Z 273 " =    2.829
peak=    3.354 closest distance to " CB  ALA A  21 " =    1.963
peak=    3.354 closest distance to " CB  ASN A 187 " =    1.186
peak=    3.352 closest distance to " CB  ASN A 142 " =    1.035
peak=    3.352 closest distance to " OD1 ASN A  69 " =    2.712
peak=    3.350 closest distance to " CA  ALA A  51 " =    1.016
peak=    3.350 closest distance to " CA  LYS A 117 " =    1.203
peak=    3.349 closest distance to " CZ AARG A 102 " =    1.775
peak=    3.349 closest distance to " CG1 ILE A  33 " =    1.391
peak=    3.347 closest distance to " N   VAL A 257 " =    1.627
peak=    3.345 closest distance to " O   HOH Z 426 " =    1.606
peak=    3.343 closest distance to " CA  ASN A 284 " =    0.964
peak=    3.342 closest distance to " O   HOH Z 145 " =    2.244
peak=    3.338 closest distance to " O   HOH Z 425 " =    1.444
peak=    3.333 closest distance to " O   HOH Z 128 " =    2.519
peak=    3.330 closest distance to " CG  LYS A 119 " =    1.055
peak=    3.315 closest distance to " O   ARG A 145 " =    1.876
peak=    3.314 closest distance to " CD1 ILE A 263 " =    1.425
peak=    3.313 closest distance to " CE ALYS A 290 " =    1.083
peak=    3.313 closest distance to " O   HOH Z 234 " =    2.097
peak=    3.310 closest distance to " O   HOH Z  97 " =    0.901
peak=    3.310 closest distance to " CB  ASN A 110 " =    1.046
peak=    3.307 closest distance to " O   HOH Z 272 " =    2.072
peak=    3.305 closest distance to " CB  ASN A  69 " =    1.519
peak=    3.305 closest distance to " CG  MET A 185 " =    1.383
peak=    3.304 closest distance to " O   HOH Z 181 " =    2.124
peak=    3.302 closest distance to " O   HOH Z 437 " =    2.257
peak=    3.298 closest distance to " O   HOH Z 423 " =    2.038
peak=    3.298 closest distance to " CG2 THR A 221 " =    1.191
peak=    3.293 closest distance to " O   HOH Z 258 " =    2.230
peak=    3.293 closest distance to " O   GLN A 194 " =    1.693
peak=    3.291 closest distance to " O   HOH Z 392 " =    1.287
peak=    3.291 closest distance to " OH  TYR A 116 " =    1.098
peak=    3.285 closest distance to " O   HOH Z 276 " =    1.229
peak=    3.284 closest distance to " O   HOH Z 213 " =    1.752
peak=    3.283 closest distance to " CG1 ILE A 120 " =    1.384
peak=    3.282 closest distance to " O   HOH Z 113 " =    1.822
peak=    3.281 closest distance to " CG  LYS A  76 " =    0.943
peak=    3.280 closest distance to " O   HOH Z 326 " =    1.994
peak=    3.279 closest distance to " O   HOH Z 424 " =    2.256
peak=    3.278 closest distance to " NH1BARG A 145 " =    1.595
peak=    3.277 closest distance to " OG BSER A  99 " =    2.242
peak=    3.276 closest distance to " N   GLN A 278 " =    0.960
peak=    3.272 closest distance to " CG  LYS A 166 " =    1.409
peak=    3.271 closest distance to " O   HOH Z 355 " =    1.879
peak=    3.266 closest distance to " O   HOH Z 357 " =    1.689
peak=    3.265 closest distance to " SD  MET A 185 " =    1.491
peak=    3.263 closest distance to " N   ASN A  39 " =    1.167
peak=    3.262 closest distance to " OD1 ASN A 148 " =    2.015
peak=    3.261 closest distance to " O   HOH Z 147 " =    1.405
peak=    3.261 closest distance to " CB  ALA A  10 " =    1.466
peak=    3.260 closest distance to " O   ASP A 124 " =    1.226
peak=    3.260 closest distance to " CE  LYS A 119 " =    1.165
peak=    3.259 closest distance to " O   HOH Z 410 " =    3.132
peak=    3.252 closest distance to " O   HOH Z 244 " =    1.733
peak=    3.250 closest distance to " O   HOH Z 233 " =    1.649
peak=    3.250 closest distance to " O   HOH Z 303 " =    1.701
peak=    3.249 closest distance to " O   PRO A 198 " =    1.275
peak=    3.246 closest distance to " CD1 ILE A 106 " =    1.136
peak=    3.241 closest distance to " CG  LEU A 281 " =    1.035
peak=    3.233 closest distance to " NE2 GLN A  58 " =    5.709
peak=    3.230 closest distance to " CG2 ILE A 234 " =    0.891
peak=    3.227 closest distance to " O   HOH Z 212 " =    1.498
peak=    3.226 closest distance to " CD1 LEU A 228 " =    1.790
peak=    3.222 closest distance to " O   HOH Z 188 " =    2.265
peak=    3.221 closest distance to " O   HOH Z 366 " =    1.970
peak=    3.219 closest distance to " CG  ARG A  66 " =    0.952
peak=    3.219 closest distance to " O   HOH Z   1 " =    1.630
peak=    3.214 closest distance to " O   HOH Z 305 " =    3.435
peak=    3.212 closest distance to " O   HOH Z  39 " =    2.749
peak=    3.207 closest distance to " O   HOH Z 156 " =    2.851
peak=    3.205 closest distance to " O   HOH Z  30 " =    1.592
peak=    3.202 closest distance to " O   HOH Z  66 " =    2.154
peak=    3.199 closest distance to " CE  MET A  93 " =    1.785
peak=    3.199 closest distance to " CA  ASN A 176 " =    1.300
peak=    3.198 closest distance to " CG1 VAL A 153 " =    0.847
peak=    3.196 closest distance to " OE2 GLU A   2 " =    1.824
peak=    3.195 closest distance to " O   HOH Z 134 " =    1.924
peak=    3.190 closest distance to " O   HOH Z 211 " =    0.958
peak=    3.184 closest distance to " CB  VAL A 268 " =    0.892
peak=    3.181 closest distance to " O   HOH Z 408 " =    1.658
peak=    3.175 closest distance to " CE1 PHE A  38 " =    1.274
peak=    3.175 closest distance to " O   HOH Z 180 " =    2.153
peak=    3.173 closest distance to " O   HOH Z 368 " =    3.632
peak=    3.173 closest distance to " O   HOH Z 375 " =    2.277
peak=    3.172 closest distance to " CA  LEU A 300 " =    1.077
peak=    3.170 closest distance to " CA  LEU A 282 " =    1.304
peak=    3.166 closest distance to " CB  GLN A 205 " =    1.214
peak=    3.157 closest distance to " C   GLU A 277 " =    1.356
peak=    3.150 closest distance to " N   ASN A 148 " =    1.007
peak=    3.149 closest distance to " CG2 ILE A 120 " =    1.282
peak=    3.146 closest distance to " O   HOH Z 406 " =    0.990
peak=    3.141 closest distance to " CB  THR A 157 " =    1.170
peak=    3.140 closest distance to " CB  PRO A  90 " =    1.246
peak=    3.138 closest distance to " O   SER A 164 " =    1.114
peak=    3.133 closest distance to " CD1 ILE A  33 " =    1.762
peak=    3.129 closest distance to " N   ASP A 162 " =    1.164
peak=    3.116 closest distance to " O   HOH Z 356 " =    1.284
peak=    3.109 closest distance to " CB  VAL A 126 " =    1.137
peak=    3.098 closest distance to " O   HOH Z 218 " =    2.246
peak=    3.090 closest distance to " O   HOH Z 191 " =    1.946
peak=    3.081 closest distance to " CB  PHE A 204 " =    1.019
peak=    3.081 closest distance to " CG2 ILE A  20 " =    1.152
peak=    3.080 closest distance to " CB  GLU A 175 " =    1.095
peak=    3.077 closest distance to " CD  LYS A 119 " =    1.716
peak=    3.076 closest distance to " O   HOH Z 334 " =    1.196
peak=    3.064 closest distance to " CG2 ILE A 106 " =    0.917
peak=    3.064 closest distance to " ND2 ASN A 249 " =    0.848
peak=    3.061 closest distance to " N   TYR A  15 " =    1.101
peak=    3.028 closest distance to " O  BHOH Z  74 " =    1.357
peak=    3.028 closest distance to " CG  LYS A 289 " =    1.266
peak=    3.022 closest distance to " O   HOH Z 433 " =    1.908

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

Number of peaks found at mFobs-DFmodel map (map cutoff=3.00 sigma)= 198         
Filter by distance & map next to the model:
   mapped sites are within: 0.569 - 5.639
   number of sites selected in [dist_min= 0.70, dist_max= 6.00]: 197 from: 198
   mapped sites are within: 0.739 - 5.639

peak=   -4.508 closest distance to " CG2 VAL A 230 " =    0.764
peak=   -4.480 closest distance to " OG BSER A 134 " =    1.256
peak=   -4.434 closest distance to " O   HOH Z  69 " =    1.544
peak=   -4.426 closest distance to " O   HOH Z 429 " =    2.046
peak=   -4.348 closest distance to " CD  ARG A 156 " =    1.967
peak=   -4.341 closest distance to " CA  VAL A  67 " =    2.821
peak=   -4.227 closest distance to " C   HIS A 108 " =    1.226
peak=   -4.108 closest distance to " O   HOH Z 164 " =    5.639
peak=   -4.099 closest distance to " O   HOH Z 290 " =    1.075
peak=   -3.998 closest distance to " O   HOH Z 130 " =    1.866
peak=   -3.998 closest distance to " O   PRO A 198 " =    1.224
peak=   -3.963 closest distance to " NH2 ARG A  79 " =    1.848
peak=   -3.958 closest distance to " N   GLN A  58 " =    2.049
peak=   -3.945 closest distance to " CA  GLY A  23 " =    1.759
peak=   -3.933 closest distance to " CD  ARG A  14 " =    3.113
peak=   -3.930 closest distance to " CD1 LEU A 255 " =    2.712
peak=   -3.904 closest distance to " CG2 VAL A 230 " =    0.765
peak=   -3.869 closest distance to " OD2 ASP A 191 " =    1.348
peak=   -3.855 closest distance to " O   ALA A 161 " =    1.642
peak=   -3.854 closest distance to " OG  SER A   3 " =    1.260
peak=   -3.842 closest distance to " CG  PHE A 283 " =    2.531
peak=   -3.803 closest distance to " O   HOH Z 234 " =    3.889
peak=   -3.803 closest distance to " O   HOH Z  65 " =    1.024
peak=   -3.792 closest distance to " O   HOH Z 427 " =    1.583
peak=   -3.792 closest distance to " O   SER A 135 " =    1.508
peak=   -3.787 closest distance to " O   HOH Z 266 " =    4.641
peak=   -3.785 closest distance to " O   HOH Z 100 " =    1.105
peak=   -3.746 closest distance to " CE2 TYR A  30 " =    2.777
peak=   -3.740 closest distance to " O   HOH Z 423 " =    2.340
peak=   -3.737 closest distance to " N   HIS A 115 " =    2.040
peak=   -3.734 closest distance to " CG  GLN A  58 " =    1.007
peak=   -3.724 closest distance to " O   ALA A 292 " =    2.184
peak=   -3.714 closest distance to " CB  ALA A 244 " =    2.069
peak=   -3.706 closest distance to " C   ASN A 285 " =    2.053
peak=   -3.705 closest distance to " O   SER A  22 " =    2.228
peak=   -3.701 closest distance to " CG  ARG A 219 " =    2.305
peak=   -3.691 closest distance to " O   HOH Z  11 " =    1.798
peak=   -3.689 closest distance to " O   HOH Z 426 " =    2.343
peak=   -3.684 closest distance to " OD1 ASN A  39 " =    2.058
peak=   -3.675 closest distance to " O   ILE A  49 " =    1.759
peak=   -3.664 closest distance to " CB  SER A 210 " =    1.270
peak=   -3.659 closest distance to " CD  LYS A 289 " =    2.473
peak=   -3.654 closest distance to " CB  ALA A  43 " =    2.191
peak=   -3.647 closest distance to " OXT GLY A 302 " =    2.816
peak=   -3.646 closest distance to " O   VAL A  67 " =    2.638
peak=   -3.630 closest distance to " O   HOH Z 134 " =    2.904
peak=   -3.628 closest distance to " CE2 PHE A 218 " =    2.466
peak=   -3.626 closest distance to " CD  GLN A  88 " =    1.070
peak=   -3.608 closest distance to " O   ARG A  24 " =    1.741
peak=   -3.608 closest distance to " CG  ARG A 219 " =    2.061
peak=   -3.602 closest distance to " O   PRO A 163 " =    1.918
peak=   -3.602 closest distance to " O   HOH Z 313 " =    1.500
peak=   -3.601 closest distance to " O   HOH Z 185 " =    2.080
peak=   -3.584 closest distance to " O   ASN A 187 " =    1.413
peak=   -3.580 closest distance to " N   ALA A 248 " =    1.659
peak=   -3.578 closest distance to " O   HOH Z 414 " =    2.518
peak=   -3.578 closest distance to " O   HOH Z 351 " =    1.448
peak=   -3.573 closest distance to " CD1 LEU A 101 " =    2.196
peak=   -3.568 closest distance to " CB  TYR A 172 " =    2.404
peak=   -3.566 closest distance to " O   HOH Z 111 " =    4.576
peak=   -3.545 closest distance to " CA  GLY A 203 " =    2.303
peak=   -3.521 closest distance to " CB  PRO A 163 " =    2.525
peak=   -3.520 closest distance to " O   HOH Z 131 " =    4.055
peak=   -3.520 closest distance to " O   HOH Z 389 " =    1.957
peak=   -3.516 closest distance to " O   HOH Z 394 " =    1.488
peak=   -3.515 closest distance to " O   HOH Z  56 " =    2.068
peak=   -3.501 closest distance to " O   HOH Z 102 " =    1.639
peak=   -3.499 closest distance to " OG  SER A  87 " =    1.225
peak=   -3.496 closest distance to " C   LEU A 143 " =    0.960
peak=   -3.492 closest distance to " N   MET A 188 " =    1.799
peak=   -3.492 closest distance to " CE3 TRP A 274 " =    2.157
peak=   -3.476 closest distance to " O   HOH Z 165 " =    2.270
peak=   -3.474 closest distance to " NH1 ARG A  56 " =    2.433
peak=   -3.470 closest distance to " O   HOH Z 211 " =    1.695
peak=   -3.460 closest distance to " O   ALA A  51 " =    1.147
peak=   -3.451 closest distance to " O   HOH Z 191 " =    5.128
peak=   -3.450 closest distance to " O   HOH Z 368 " =    2.446
peak=   -3.449 closest distance to " N   THR A 157 " =    1.471
peak=   -3.446 closest distance to " O   HOH Z 235 " =    1.090
peak=   -3.445 closest distance to " O   HOH Z 377 " =    0.999
peak=   -3.437 closest distance to " O   HOH Z  24 " =    1.174
peak=   -3.437 closest distance to " O   HOH Z  37 " =    1.600
peak=   -3.437 closest distance to " O   HOH Z 137 " =    1.453
peak=   -3.436 closest distance to " C   GLN A 205 " =    1.877
peak=   -3.433 closest distance to " O   HOH Z   9 " =    1.414
peak=   -3.430 closest distance to " O   HOH Z 193 " =    1.613
peak=   -3.429 closest distance to " O   HOH Z 114 " =    3.202
peak=   -3.426 closest distance to " CZ  PHE A  59 " =    1.386
peak=   -3.425 closest distance to " CG1 VAL A 112 " =    2.808
peak=   -3.424 closest distance to " O   HOH Z 308 " =    1.664
peak=   -3.421 closest distance to " O   HOH Z 406 " =    0.773
peak=   -3.420 closest distance to " OD1 ASN A 301 " =    1.922
peak=   -3.419 closest distance to " O   HOH Z 140 " =    1.422
peak=   -3.419 closest distance to " CE  LYS A  76 " =    2.909
peak=   -3.415 closest distance to " CB  PHE A 192 " =    1.868
peak=   -3.413 closest distance to " CG  GLN A 278 " =    1.977
peak=   -3.412 closest distance to " CB  ALA A  64 " =    2.651
peak=   -3.407 closest distance to " O   HOH Z 407 " =    2.576
peak=   -3.395 closest distance to " O   HOH Z 150 " =    2.170
peak=   -3.379 closest distance to " CG1 VAL A 230 " =    1.835
peak=   -3.376 closest distance to " O   HOH Z 139 " =    3.230
peak=   -3.372 closest distance to " OG  SER A  97 " =    2.204
peak=   -3.371 closest distance to " OG ASER A 134 " =    1.310
peak=   -3.370 closest distance to " N   GLN A  77 " =    1.581
peak=   -3.355 closest distance to " O   HOH Z  16 " =    2.133
peak=   -3.354 closest distance to " N   GLN A  58 " =    1.115
peak=   -3.352 closest distance to " O   HOH Z 364 " =    1.452
peak=   -3.347 closest distance to " N   PRO A 163 " =    1.624
peak=   -3.342 closest distance to " O   ALA A   8 " =    1.781
peak=   -3.341 closest distance to " O   HOH Z 203 " =    1.795
peak=   -3.337 closest distance to " O   HOH Z 397 " =    1.235
peak=   -3.331 closest distance to " CB  ALA A   7 " =    2.017
peak=   -3.331 closest distance to " CB  ALA A 291 " =    2.113
peak=   -3.326 closest distance to " CA  GLY A 133 " =    1.838
peak=   -3.323 closest distance to " CG  ARG A 219 " =    2.675
peak=   -3.322 closest distance to " O   HOH Z 192 " =    1.097
peak=   -3.319 closest distance to " O   HOH Z 210 " =    1.970
peak=   -3.317 closest distance to " CG  ASP A 231 " =    0.753
peak=   -3.313 closest distance to " CG  GLU A 152 " =    1.359
peak=   -3.311 closest distance to " O   HOH Z 281 " =    3.269
peak=   -3.309 closest distance to " O   HOH Z 392 " =    0.739
peak=   -3.305 closest distance to " O   HOH Z  97 " =    1.168
peak=   -3.305 closest distance to " N   VAL A  72 " =    1.869
peak=   -3.305 closest distance to " O   SER A  95 " =    1.406
peak=   -3.304 closest distance to " CD2 LEU A 237 " =    2.645
peak=   -3.303 closest distance to " O   HOH Z 387 " =    2.186
peak=   -3.299 closest distance to " O   HOH Z 125 " =    3.082
peak=   -3.285 closest distance to " ND2 ASN A 173 " =    1.430
peak=   -3.270 closest distance to " CB  ASP A 132 " =    2.293
peak=   -3.270 closest distance to " OE2 GLU A 152 " =    1.269
peak=   -3.266 closest distance to " CZ  TYR A 169 " =    1.770
peak=   -3.266 closest distance to " O   GLN A 240 " =    2.040
peak=   -3.265 closest distance to " CA  TRP A  70 " =    2.381
peak=   -3.257 closest distance to " O   ARG A 145 " =    1.592
peak=   -3.256 closest distance to " C   MET A 188 " =    1.509
peak=   -3.255 closest distance to " O   HOH Z 346 " =    1.661
peak=   -3.254 closest distance to " C   LEU A 222 " =    1.448
peak=   -3.252 closest distance to " O   TRP A 179 " =    1.568
peak=   -3.243 closest distance to " NH2 ARG A  66 " =    2.864
peak=   -3.236 closest distance to " O   ALA A   1 " =    1.584
peak=   -3.235 closest distance to " CG  GLU A 152 " =    2.139
peak=   -3.231 closest distance to " OG  SER A 245 " =    1.300
peak=   -3.228 closest distance to " O   PRO A 243 " =    2.541
peak=   -3.224 closest distance to " ND2 ASN A  45 " =    1.041
peak=   -3.220 closest distance to " O   HOH Z 166 " =    1.464
peak=   -3.220 closest distance to " O   HOH Z 359 " =    1.780
peak=   -3.220 closest distance to " CA  ALA A 299 " =    2.418
peak=   -3.217 closest distance to " OD1 ASP A 171 " =    1.495
peak=   -3.213 closest distance to " O   HOH Z  60 " =    2.448
peak=   -3.213 closest distance to " O   HOH Z 158 " =    1.944
peak=   -3.211 closest distance to " O   HOH Z 175 " =    1.254
peak=   -3.204 closest distance to " CZ3 TRP A 123 " =    1.661
peak=   -3.198 closest distance to " N   ALA A 226 " =    1.902
peak=   -3.194 closest distance to " CA  GLY A  98 " =    1.874
peak=   -3.193 closest distance to " OE2 GLU A   2 " =    1.123
peak=   -3.189 closest distance to " ND2 ASN A 252 " =    1.829
peak=   -3.186 closest distance to " O   SER A 146 " =    0.929
peak=   -3.185 closest distance to " CG  LEU A 228 " =    1.005
peak=   -3.179 closest distance to " ND2 ASN A  39 " =    1.199
peak=   -3.177 closest distance to " O   MET A  40 " =    2.756
peak=   -3.177 closest distance to " CB  ALA A 114 " =    2.304
peak=   -3.175 closest distance to " CD2 HIS A 115 " =    1.008
peak=   -3.175 closest distance to " O   HOH Z  51 " =    0.963
peak=   -3.174 closest distance to " OE1 GLN A  88 " =    1.077
peak=   -3.173 closest distance to " O   TRP A  70 " =    1.424
peak=   -3.170 closest distance to " O   HOH Z 238 " =    0.941
peak=   -3.166 closest distance to " O   HOH Z 231 " =    2.034
peak=   -3.165 closest distance to " O   HOH Z 249 " =    1.263
peak=   -3.165 closest distance to " ND2 ASN A 209 " =    1.996
peak=   -3.155 closest distance to " CD  GLU A 277 " =    0.924
peak=   -3.151 closest distance to " CA  GLY A  35 " =    1.979
peak=   -3.151 closest distance to " O   HOH Z 431 " =    1.471
peak=   -3.149 closest distance to " CB  ASP A 286 " =    2.384
peak=   -3.148 closest distance to " O   HOH Z 197 " =    4.972
peak=   -3.147 closest distance to " O   GLU A 152 " =    1.447
peak=   -3.145 closest distance to " N   SER A 276 " =    1.151
peak=   -3.144 closest distance to " CG2 VAL A 202 " =    2.665
peak=   -3.136 closest distance to " ND2 ASN A  60 " =    1.718
peak=   -3.134 closest distance to " O   ASN A 301 " =    1.583
peak=   -3.130 closest distance to " CD1 ILE A 199 " =    2.305
peak=   -3.127 closest distance to " O   HOH Z 134 " =    3.764
peak=   -3.125 closest distance to " NE  ARG A 259 " =    0.921
peak=   -3.121 closest distance to " O   HOH Z 372 " =    2.370
peak=   -3.115 closest distance to " O   HOH Z  13 " =    1.681
peak=   -3.111 closest distance to " O   HOH Z  88 " =    1.737
peak=   -3.110 closest distance to " O   HOH Z 389 " =    1.446
peak=   -3.101 closest distance to " C   ALA A 158 " =    1.315
peak=   -3.085 closest distance to " CD2 LEU A   5 " =    1.187
peak=   -3.083 closest distance to " O   HOH Z 175 " =    4.224
peak=   -3.076 closest distance to " CZ2 TRP A 274 " =    0.910
peak=   -3.071 closest distance to " O   HOH Z 237 " =    2.318
peak=   -3.059 closest distance to " OD1 ASP A 200 " =    1.455
peak=   -3.054 closest distance to " CG1 VAL A 197 " =    2.228
peak=   -3.053 closest distance to " CB  TRP A 266 " =    1.920
peak=   -3.039 closest distance to " O   LYS A 117 " =    1.518
peak=   -3.033 closest distance to " CD2 TYR A 293 " =    1.989
peak=   -3.030 closest distance to " CB  PHE A  38 " =    2.945

================= 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    :  0.4995 0.4931   6.294556e+00   6.289418e+00
   1_bss:  0.4900 0.4827   6.286623e+00   6.278381e+00
   1_xyz:  0.4200 0.4429   6.204003e+00   6.233078e+00
   1_adp:  0.3756 0.4217   6.141953e+00   6.213413e+00
   1_occ:  0.3750 0.4211   6.140857e+00   6.213405e+00
   2_bss:  0.3728 0.4152   6.140104e+00   6.210181e+00
   2_xyz:  0.2932 0.3510   5.955208e+00   6.088034e+00
   2_adp:  0.2678 0.3304   5.889348e+00   6.038347e+00
   2_occ:  0.2675 0.3303   5.889064e+00   6.038009e+00
   3_bss:  0.2649 0.3292   5.886196e+00   6.036883e+00
   3_xyz:  0.1938 0.2472   5.605955e+00   5.797561e+00
   3_adp:  0.1738 0.2273   5.513166e+00   5.719184e+00
   3_occ:  0.1731 0.2269   5.511006e+00   5.716864e+00
   4_bss:  0.1719 0.2256   5.508453e+00   5.714295e+00
   4_xyz:  0.1359 0.1813   5.296299e+00   5.515111e+00
   4_adp:  0.1300 0.1731   5.250643e+00   5.467590e+00
   4_occ:  0.1297 0.1730   5.248971e+00   5.465235e+00
   5_bss:  0.1299 0.1723   5.247900e+00   5.463438e+00
   5_xyz:  0.1201 0.1622   5.186407e+00   5.414534e+00
   5_adp:  0.1169 0.1616   5.170928e+00   5.408157e+00
   5_occ:  0.1168 0.1616   5.170580e+00   5.407650e+00
   5_bss:  0.1168 0.1616   5.170370e+00   5.407491e+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:  0.364   0.000   8.044   9.457   7.866   0.000   0.000   0.000
   1_xyz:  0.364   0.000   8.044   9.457   7.866   0.000   0.000   0.000
   1_adp:  0.364   0.000   8.044   9.457   7.866   0.000   0.000   0.000
   1_occ:  0.364   0.000   8.044   9.457   7.866   0.000   0.000   0.000
   2_bss:  0.345  24.897   4.704   5.337   5.046   0.000   0.000   0.000
   2_xyz:  0.345  24.897   4.704   5.337   5.046   0.000   0.000   0.000
   2_adp:  0.345  24.897   4.704   5.337   5.046   0.000   0.000   0.000
   2_occ:  0.345  24.897   4.704   5.337   5.046   0.000   0.000   0.000
   3_bss:  0.337  35.486   2.380   2.913   3.340   0.000   0.000   0.000
   3_xyz:  0.337  35.486   2.380   2.913   3.340   0.000   0.000   0.000
   3_adp:  0.337  35.486   2.380   2.913   3.340   0.000   0.000   0.000
   3_occ:  0.337  35.486   2.380   2.913   3.340   0.000   0.000   0.000
   4_bss:  0.323  31.955   0.872   1.424   2.283   0.000   0.000   0.000
   4_xyz:  0.323  31.955   0.872   1.424   2.283   0.000   0.000   0.000
   4_adp:  0.323  31.955   0.872   1.424   2.283   0.000   0.000   0.000
   4_occ:  0.323  31.955   0.872   1.424   2.283   0.000   0.000   0.000
   5_bss:  0.317  31.955   0.441   1.006   2.065   0.000   0.000   0.000
   5_xyz:  0.317  31.955   0.441   1.006   2.065   0.000   0.000   0.000
   5_adp:  0.317  31.955   0.441   1.006   2.065   0.000   0.000   0.000
   5_occ:  0.317  31.955   0.441   1.006   2.065   0.000   0.000   0.000
   5_bss:  0.317  34.612  -0.749  -0.194   0.944   0.000   0.000   0.000
------------------------------------------------------------------------
 stage     <pher>    fom   alpha         beta
   0    :  64.361 0.3367  0.4034    79071.936
   1_bss:  63.442 0.3470  0.5210    75164.056
   1_xyz:  53.210 0.4786  0.7163    59760.457
   1_adp:  48.203 0.5430  0.8695    54559.124
   1_occ:  48.173 0.5434  0.8681    54422.503
   2_bss:  47.605 0.5503  0.7821    53471.418
   2_xyz:  37.698 0.6697  0.9374    34368.528
   2_adp:  34.391 0.7085  0.9829    29579.911
   2_occ:  34.366 0.7089  0.9831    29566.255
   3_bss:  34.148 0.7112  0.9121    29263.026
   3_xyz:  24.128 0.8201  1.0113    15287.186
   3_adp:  21.557 0.8471  1.0297    13005.360
   3_occ:  21.482 0.8478  1.0301    12915.809
   4_bss:  21.382 0.8486  0.9797    12789.307
   4_xyz:  16.737 0.8920  1.0003     8362.370
   4_adp:  15.606 0.9020  1.0039     7652.324
   4_occ:  15.557 0.9024  1.0040     7608.923
   5_bss:  15.513 0.9027  0.9906     7555.293
   5_xyz:  14.446 0.9116  0.9943     6752.948
   5_adp:  14.319 0.9126  0.9914     6663.648
   5_occ:  14.316 0.9127  0.9913     6652.612
   5_bss:  14.312 0.9127  0.9917     6649.818
------------------------------------------------------------------------
 stage       angl   bond   chir   dihe   plan   repu  geom_target
   0    :  24.226  0.414  2.119 33.790  0.145  4.084   5.2629e+01
   1_bss:  24.226  0.414  2.119 33.790  0.145  4.084   5.2629e+01
   1_xyz:   1.804  0.014  0.110 18.224  0.007  4.104   1.6019e-01
   1_adp:   1.804  0.014  0.110 18.224  0.007  4.104   1.6019e-01
   1_occ:   1.804  0.014  0.110 18.224  0.007  4.104   1.6019e-01
   2_bss:   1.804  0.014  0.110 18.224  0.007  4.104   1.6019e-01
   2_xyz:   1.267  0.010  0.085 16.316  0.005  4.116   9.7711e-02
   2_adp:   1.267  0.010  0.085 16.316  0.005  4.116   9.7711e-02
   2_occ:   1.267  0.010  0.085 16.316  0.005  4.116   9.7711e-02
   3_bss:   1.267  0.010  0.085 16.316  0.005  4.116   9.7711e-02
   3_xyz:   1.099  0.008  0.078 15.867  0.005  4.112   7.5155e-02
   3_adp:   1.099  0.008  0.078 15.867  0.005  4.112   7.5155e-02
   3_occ:   1.099  0.008  0.078 15.867  0.005  4.112   7.5155e-02
   4_bss:   1.099  0.008  0.078 15.867  0.005  4.112   7.5155e-02
   4_xyz:   1.062  0.007  0.073 15.877  0.004  4.107   6.6701e-02
   4_adp:   1.062  0.007  0.073 15.877  0.004  4.107   6.6701e-02
   4_occ:   1.062  0.007  0.073 15.877  0.004  4.107   6.6701e-02
   5_bss:   1.062  0.007  0.073 15.877  0.004  4.107   6.6701e-02
   5_xyz:   0.985  0.006  0.070 15.628  0.004  4.108   5.9614e-02
   5_adp:   0.985  0.006  0.070 15.628  0.004  4.108   5.9614e-02
   5_occ:   0.985  0.006  0.070 15.628  0.004  4.108   5.9614e-02
   5_bss:   0.985  0.006  0.070 15.628  0.004  4.108   5.9614e-02
------------------------------------------------------------------------
                      Maximal deviations:
 stage       angl   bond   chir   dihe   plan   repu       |grad|
   0    :  74.492  1.400  6.404144.062  0.405  1.142   6.8096e+00
   1_bss:  74.492  1.400  6.404144.062  0.405  1.142   6.8096e+00
   1_xyz:  15.729  0.173  0.508 89.154  0.037  2.112   1.0524e-01
   1_adp:  15.729  0.173  0.508 89.154  0.037  2.112   1.0524e-01
   1_occ:  15.729  0.173  0.508 89.154  0.037  2.112   1.0524e-01
   2_bss:  15.729  0.173  0.508 89.154  0.037  2.112   1.0524e-01
   2_xyz:   8.179  0.151  0.408 89.456  0.052  2.186   8.7611e-02
   2_adp:   8.179  0.151  0.408 89.456  0.052  2.186   8.7611e-02
   2_occ:   8.179  0.151  0.408 89.456  0.052  2.186   8.7611e-02
   3_bss:   8.179  0.151  0.408 89.456  0.052  2.186   8.7611e-02
   3_xyz:   7.297  0.080  0.272 87.172  0.031  2.296   6.9911e-02
   3_adp:   7.297  0.080  0.272 87.172  0.031  2.296   6.9911e-02
   3_occ:   7.297  0.080  0.272 87.172  0.031  2.296   6.9911e-02
   4_bss:   7.297  0.080  0.272 87.172  0.031  2.296   6.9911e-02
   4_xyz:   8.266  0.042  0.240 84.933  0.032  2.318   7.1583e-02
   4_adp:   8.266  0.042  0.240 84.933  0.032  2.318   7.1583e-02
   4_occ:   8.266  0.042  0.240 84.933  0.032  2.318   7.1583e-02
   5_bss:   8.266  0.042  0.240 84.933  0.032  2.318   7.1583e-02
   5_xyz:   7.505  0.040  0.207 85.391  0.033  2.330   4.9635e-02
   5_adp:   7.505  0.040  0.207 85.391  0.033  2.330   4.9635e-02
   5_occ:   7.505  0.040  0.207 85.391  0.033  2.330   4.9635e-02
   5_bss:   7.505  0.040  0.207 85.391  0.033  2.330   4.9635e-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:  80.70   0.00  14.82  80.70   0.00  12.74  79.40   0.00  26.18
   1_occ:  80.70   0.00  14.82  80.70   0.00  12.74  79.40   0.00  26.18
   2_bss:  80.70   0.00  14.82  80.70   0.00  12.74  79.40   0.00  26.18
   2_xyz:  80.70   0.00  14.82  80.70   0.00  12.74  79.40   0.00  26.18
   2_adp:  94.75   0.00  14.15  94.75   0.00  10.90  84.36   0.00  31.86
   2_occ:  94.75   0.00  14.15  94.75   0.00  10.90  84.36   0.00  31.86
   3_bss:  94.75   0.00  14.15  94.75   0.00  10.90  84.36   0.00  31.86
   3_xyz:  94.75   0.00  14.15  94.75   0.00  10.90  84.36   0.00  31.86
   3_adp:  92.29   0.00  13.77  92.29   0.00   9.86  76.23   2.49  35.01
   3_occ:  92.29   0.00  13.77  92.29   0.00   9.86  76.23   2.49  35.01
   4_bss:  92.29   0.00  13.77  92.29   0.00   9.86  76.23   2.49  35.01
   4_xyz:  92.29   0.00  13.77  92.29   0.00   9.86  76.23   2.49  35.01
   4_adp:  89.88   0.00  13.57  89.88   0.00   9.55  75.13   2.42  35.47
   4_occ:  89.88   0.00  13.57  89.88   0.00   9.55  75.13   2.42  35.47
   5_bss:  89.88   0.00  13.57  89.88   0.00   9.55  75.13   2.42  35.47
   5_xyz:  89.88   0.00  13.57  89.88   0.00   9.55  75.13   2.42  35.47
   5_adp:  91.76   0.00  13.80  91.76   0.00   9.50  80.95   3.03  37.20
   5_occ:  91.76   0.00  13.80  91.76   0.00   9.50  80.95   3.03  37.20
   5_bss:  92.94   1.18  14.98  92.94   1.18  10.68  82.13   4.21  38.37
------------------------------------------------------------------------
 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:    1.258    0.014    0.422
   1_adp:    1.258    0.014    0.422
   1_occ:    1.258    0.014    0.422
   2_bss:    1.258    0.014    0.422
   2_xyz:    1.541    0.029    0.593
   2_adp:    1.541    0.029    0.593
   2_occ:    1.541    0.029    0.593
   3_bss:    1.541    0.029    0.593
   3_xyz:    1.721    0.052    0.716
   3_adp:    1.721    0.052    0.716
   3_occ:    1.721    0.052    0.716
   4_bss:    1.721    0.052    0.716
   4_xyz:    1.783    0.051    0.778
   4_adp:    1.783    0.051    0.778
   4_occ:    1.783    0.051    0.778
   5_bss:    1.783    0.051    0.778
   5_xyz:    1.787    0.064    0.798
   5_adp:    1.787    0.064    0.798
   5_occ:    1.787    0.064    0.798
   5_bss:    1.787    0.064    0.798
------------------------------------------------------------------------

CPU time actual refinement: 354.05


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

Writing refined structure to PDB file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/trial/run_25/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_25/model_refine_001_2mFobs-DFmodel.map
Writing mFobs-DFmodel XPLOR map to file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/trial/run_25/model_refine_001_mFobs-DFmodel.map
Writing map coefficients to MTZ file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/trial/run_25/model_refine_001_map_coeffs.mtz

Writing default parameters for subsequent refinement:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/trial/run_25/model_refine_002.def


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

Pure refinement (no I/O, processing, etc)= 353.90 
  Macro-tasks:
    bulk solvent and scale       = 46.87  
    individual site refinement   = 153.09 
    weights calculation          = 31.82  
    collect and process          = 6.31   
    model show statistics        = 0.12   
    TOTAL for macro-tasks        = 238.21 
  Micro-tasks:
    mask                            = 2.45   
    f_calc                          = 109.29 
    alpha_beta                      = 8.05   
    target                          = 1.13   
    gradients_wrt_atomic_parameters = 121.56 
    fmodel                         = 7.88   
    r_factors                      = 0.32   
    phase_errors                   = 10.05  
    foms                           = 0.22   
    TOTAL for micro-tasks          = 260.95 
NUMBER OF MASK CALCS=  5
Time per interpreted Python bytecode instruction: 4.864 micro seconds
Total CPU time: 6.16 minutes
from_scatterers_fft:    670 calls, 108.89 s
gradients_fft:          614 calls, 107.19 s

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

# Date 2008-01-16 Time 00:33:33 PST -0800 (1200472413.23 s)
Start R-work = 0.4995, R-free = 0.4931 (no bulk solvent and anisotropic scale)
Final R-work = 0.1343, R-free = 0.1775 (no bulk solvent and anisotropic scale)

Start R-work = 0.4900, R-free = 0.4827
Final R-work = 0.1168, R-free = 0.1616