# Date 2008-01-16 Time 00:57:31 PST -0800 (1200473851.30 s)
#phil __OFF__

Command line arguments: "../222.param" "adp.set_b_iso=10" "sites.shake=0.5" "main.number_of_macro_cycles=5" "--overwrite"

HOST = moonbird.lbl.gov
HOSTTYPE = x86_64-linux
USER = phzwart
PID = 25293
JOB_ID = 5158
SGE_ARCH = lx24-amd64
SGE_TASK_FIRST = 1
SGE_TASK_LAST = 1330
SGE_TASK_ID = 222

-------------------------------------------------------------------------------
  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: (68.845, 47.8686, 85.0941, 90, 90, 90)
  Space group: P 21 21 21 (No. 19)

/net/cci-filer1/vol1/tmp/phzwart/tassos/trial/model.pdb
  Monomer Library directory:
    "/net/rosie/scratch3/phzwart/CCTBX/Sources/mon_lib"
  Total number of atoms: 2823
  Number of models: 1
  Model: 0
    Number of conformers: 2
    Conformer: "A"
      Number of atoms: 2769
      Number of chains: 2
        Number of residues, atoms: 302, 2333
          Classifications: {'peptide': 302}
          Modifications used: {'COO': 1}
          Link IDs: {'PTRANS': 7, 'CIS': 1, 'TRANS': 293}
        Number of residues, atoms: 436, 436
          Classifications: {'water': 436}
          Link IDs: {None: 435}
    Conformer: "B"
      Number of atoms: 2771
      Common with "A": 2717
      Number of chains: 2
        Number of residues, atoms: 302, 2333
          Classifications: {'peptide': 302}
          Modifications used: {'COO': 1}
          Link IDs: {'PTRANS': 7, 'CIS': 1, 'TRANS': 293}
          bond proxies already assigned to first conformer: 2332
        Number of residues, atoms: 438, 438
          Classifications: {'water': 438}
          Link IDs: {None: 437}
  Time building chain proxies: 3.24, per 1000 atoms: 1.15


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

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

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

Miller array info: /net/cci-filer1/vol1/tmp/phzwart/tassos/trial/1e0w.cns:FOBS,SIGMA
Observation type: xray.amplitude
Type of data: double, size=19589
Type of sigmas: double, size=19589
Number of Miller indices: 19589
Anomalous flag: False
Unit cell: (68.845, 47.8686, 85.0941, 90, 90, 90)
Space group: P 21 21 21 (No. 19)
Systematic absences: 0
Centric reflections: 2427
Resolution range: 14.9401 1.96064
Completeness in resolution range: 0.944503
Completeness with d_max=infinity: 0.941643

Number of F-obs in resolution range:                   19589
Number of F-obs <= 0:                                  0
Refinement resolution range: d_max =  14.9401
                             d_min =   1.9606

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: (68.845, 47.8686, 85.0941, 90, 90, 90)
Space group: P 21 21 21 (No. 19)
Systematic absences: 0
Centric reflections: 2427
Resolution range: 14.9401 1.96064
Completeness in resolution range: 0.944503
Completeness with d_max=infinity: 0.941643

Test (R-free flags) flag value: 1

Number of work/free reflections by resolution:
                                         work  free  %free
  bin  1: 14.9406 -  4.1958 [2180/2209]  1960   220  10.1%
  bin  2:  4.1958 -  3.3426 [2090/2113]  1882   208  10.0%
  bin  3:  3.3426 -  2.9237 [2065/2090]  1857   208  10.1%
  bin  4:  2.9237 -  2.6580 [2027/2045]  1831   196   9.7%
  bin  5:  2.6580 -  2.4684 [2034/2076]  1822   212  10.4%
  bin  6:  2.4684 -  2.3234 [2027/2055]  1834   193   9.5%
  bin  7:  2.3234 -  2.2075 [2005/2041]  1800   205  10.2%
  bin  8:  2.2075 -  2.1116 [1994/2036]  1803   191   9.6%
  bin  9:  2.1116 -  2.0306 [1987/2045]  1783   204  10.3%
  bin 10:  2.0306 -  1.9606 [1180/2030]  1058   122  10.3%
                                overall 17630  1959  10.0%
Writing MTZ file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/trial/run_222/model_refine_data.mtz


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

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

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

  Number of disulfides: simple=3, symmetry=0
    Simple disulfide: " SG  CYS A 168 " - " SG ACYS A 201 " distance=2.08
    Simple disulfide: " SG  CYS A 168 " - " SG BCYS A 201 " distance=1.98
    Simple disulfide: " SG  CYS A 254 " - " SG  CYS A 260 " distance=2.05
  Time building geometry restraints manager: 0.14 seconds
  Histogram of bond lengths:
        1.21 -     1.38: 943
        1.38 -     1.56: 1465
        1.56 -     1.73: 7
        1.73 -     1.90: 21
        1.90 -     2.08: 3
  Bond restraints sorted by residual:
             atom i - atom j            ideal  model  delta   weight residual
  " SG  CYS A 168 " - " SG BCYS A 201 " 2.031  1.983  0.048 2.50e+03 5.87e+00
  " C   GLN A  88 " - " N   GLN A  89 " 1.329  1.360 -0.031 5.10e+03 4.97e+00
  " SG  CYS A 168 " - " SG ACYS A 201 " 2.031  2.075 -0.044 2.50e+03 4.89e+00
  " CB  CYS A 201 " - " SG ACYS A 201 " 1.808  1.738  0.070 9.18e+02 4.46e+00
  " C   PRO A 198 " - " N   ILE A 199 " 1.329  1.301  0.028 5.10e+03 4.10e+00
  ... (remaining 2434 not shown)
  Histogram of nonbonded interaction distances:
        1.21 -     1.95: 15
        1.95 -     2.69: 165
        2.69 -     3.43: 4525
        3.43 -     4.16: 9447
        4.16 -     4.90: 14475
  Nonbonded interactions sorted by model distance:
             atom i - atom j             model   vdw sym.op. j
  " O   HOH Z  18 " - " O   HOH Z 102 "  1.215 3.040 -x+1,y+1/2,-z+1/2
  " OD2 ASP A 107 " - " OG BSER A 216 "  1.436 3.040 -x+1/2,-y+1,z+1/2
  " O   HOH Z  52 " - " O   HOH Z 183 "  1.609 3.040 -x+1,y+1/2,-z+1/2
  " O   HOH Z  69 " - " O   HOH Z 357 "  1.617 3.040 -x+1/2,-y+1,z+1/2
  " C   GLY A  91 " - " O   HOH Z 401 "  1.666 3.270 -x+1,y-1/2,-z+1/2
  ... (remaining 28622 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_222/model_refine_001.eff

Writing geometry restraints to file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/trial/run_222/model_refine_001.geo

CPU time processing inputs: 9.08


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

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

#phil __ON__
refinement {
  crystal_symmetry {
    unit_cell = 68.845 47.8686 85.09415 90 90 90
    space_group = "P 21 21 21"
  }
  input {
    pdb {
      file_name = "/net/cci-filer1/vol1/tmp/phzwart/tassos/trial/model.pdb"
    }
    xray_data {
      file_name = "/net/cci-filer1/vol1/tmp/phzwart/tassos/trial/1e0w.cns"
      labels = "FOBS,SIGMA"
      r_free_flags {
        file_name = "/net/cci-filer1/vol1/tmp/phzwart/tassos/trial/1e0w.cns"
        label = "TEST"
        test_flag_value = 1
      }
    }
  }
  output {
    prefix = "model_refine"
    serial = 1
  }
  main {
    number_of_macro_cycles = 5
  }
  modify_start_model {
    adp {
      set_b_iso = 10
    }
    sites {
      shake = 0.5
    }
  }
}
#phil __OFF__


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


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


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

|--(resolution: 1.96 - 14.94 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.5101   r_free= 0.4977   ksol= 0.00   Bsol= 0.00   scale= 0.778    |
|                                                                             |
| 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:   0.88 A                  |
| x-ray target function (ml) for work reflections: 6.304412                   |
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
| Bin     Resolution   Compl.  No. Refl.    R-factors          Targets        |
|number     range              work test   work   test        work        test|
|  1: 14.9406 -  4.6800 0.99   1414  159 0.4235 0.4210      6.6384      6.6837|
|  2:  4.6800 -  3.7338 0.99   1360  151 0.4484 0.4312      6.8524      6.8611|
|  3:  3.7338 -  3.2674 0.99   1335  147 0.4803 0.4519      6.7161      6.7427|
|  4:  3.2674 -  2.9712 0.99   1323  139 0.4903 0.4722      6.5464      6.5053|
|  5:  2.9712 -  2.7597 0.99   1316  151 0.5465 0.5431      6.3939      6.4052|
|  6:  2.7597 -  2.5979 0.99   1307  148 0.5321 0.5196      6.2883       6.191|
|  7:  2.5979 -  2.4684 0.98   1297  149 0.5436 0.5052      6.2764      6.2019|
|  8:  2.4684 -  2.3614 0.98   1321  136 0.5437 0.5346      6.1838      6.2106|
|  9:  2.3614 -  2.2708 0.99   1289  144 0.5551 0.5672      6.1357       6.155|
| 10:  2.2708 -  2.1927 0.98   1297  145 0.5517 0.5758      6.1202      6.1389|
| 11:  2.1927 -  2.1243 0.97   1268  145 0.5545 0.5720      6.0331      6.0398|
| 12:  2.1243 -  2.0638 0.98   1285  148 0.5516 0.5116      5.9684      6.0059|
| 13:  2.0638 -  2.0096 0.92   1220  128 0.5534 0.5560      5.8977      5.8816|
| 14:  2.0096 -  1.9606 0.46    598   69 0.5690 0.4468        5.87      5.6773|
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
|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: 14.9406 -  4.6800  1414   159  0.62  41.17   0.79     0.64      94466.85|
|  2:  4.6800 -  3.7338  1360   151  0.63  41.13   0.86     0.69     133019.46|
|  3:  3.7338 -  3.2674  1335   147  0.52  50.01   0.83     0.65     138392.10|
|  4:  3.2674 -  2.9712  1323   139  0.44  56.32   0.79     0.54     115668.49|
|  5:  2.9712 -  2.7597  1316   151  0.32  65.74   0.71     0.41      96184.55|
|  6:  2.7597 -  2.5979  1307   148  0.28  68.64   0.71     0.33      81283.26|
|  7:  2.5979 -  2.4684  1297   149  0.26  70.27   0.72     0.31      73976.18|
|  8:  2.4684 -  2.3614  1321   136  0.27  69.75   0.72     0.32      65051.35|
|  9:  2.3614 -  2.2708  1289   144  0.26  70.90   0.71     0.32      61407.98|
| 10:  2.2708 -  2.1927  1297   145  0.23  73.21   0.75     0.27      56051.44|
| 11:  2.1927 -  2.1243  1268   145  0.18  76.90   0.73     0.23      54816.71|
| 12:  2.1243 -  2.0638  1285   148  0.18  76.90   0.73     0.24      50447.26|
| 13:  2.0638 -  2.0096  1220   128  0.23  72.78   0.74     0.30      41243.93|
| 14:  2.0096 -  1.9606   598    69  0.37  62.40   0.70     0.42      27455.64|
|alpha:            min =        0.23 max =            0.69 mean =         0.41|
|beta:             min =    27455.64 max =       138392.10 mean =     80537.92|
|figures of merit: min =        0.00 max =            1.00 mean =         0.35|
|phase err.(work): min =        0.00 max =           89.97 mean =        63.74|
|phase err.(test): min =        0.00 max =           89.99 mean =        63.85|
|-----------------------------------------------------------------------------|

============================== 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 = 23.356962             wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 83.023   (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 1.924190              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 84.130   (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 |  0.906 -  1.306:        5 |
| 0.140 - 0.280:   585 |   7.457 -  14.906:   711 |  1.306 -  1.705:        8 |
| 0.280 - 0.420:   441 |  14.906 -  22.354:   630 |  1.705 -  2.105:       67 |
| 0.420 - 0.560:   366 |  22.354 -  29.802:   474 |  2.105 -  2.504:      454 |
| 0.560 - 0.700:   237 |  29.802 -  37.251:   338 |  2.504 -  2.903:     1201 |
| 0.700 - 0.840:   127 |  37.251 -  44.699:   241 |  2.903 -  3.303:     2392 |
| 0.840 - 0.980:    59 |  44.699 -  52.147:   125 |  3.303 -  3.702:     3943 |
| 0.980 - 1.120:    17 |  52.147 -  59.595:    51 |  3.702 -  4.101:     5273 |
| 1.120 - 1.260:     9 |  59.595 -  67.044:    13 |  4.101 -  4.501:     6961 |
| 1.260 - 1.400:     1 |  67.044 -  74.492:     3 |  4.501 -  4.900:     8340 |
|-----------------------------------------------------------------------------|
|-Geometry statistics: start--------------------------------------------------|
|      Type |    Count |    Deviation from ideal |     Targets | Target (sum) |
|           |          |    rmsd      max    min |             |              |
|      bond |     2439 |   0.414    1.400  0.000 |     454.651 |              |
|     angle |     3299 |  24.226   74.492  0.009 |     193.752 |              |
| chirality |      348 |   2.119    6.404  0.009 |     112.240 |       53.308 |
| planarity |      436 |   0.145    0.405  0.000 |     250.485 |              |
|  dihedral |      870 |  33.790  144.062  0.019 |      20.704 |              |
| nonbonded |     2439 |   4.088    4.900  0.906 |       2.727 |              |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 11.628)------------------------------------------|
|    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 = 11.628)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.01    19.99   9.86     None  None   None       |
|    all(noH): 2823   0      0.01    19.99   9.86     None  None   None       |
|    Sol.    : 438    0      0.06    19.99   10.10    None  None   None       |
|    Mac.    : 2385   0      0.01    19.98   9.82     None  None   None       |
|    Hyd.    : 0      0      None    None    None     None  None   None       |
|    - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -      |
|       Distribution of isotropic (or equivalent) ADP for non-H atoms:        |
|    Bin#      value range     #atoms | Bin#      value range     #atoms      |
|      0:     0.008 -   2.007:  301   |   5:    10.002 -  12.000:  285        |
|      1:     2.007 -   4.006:  276   |   6:    12.000 -  13.999:  292        |
|      2:     4.006 -   6.004:  309   |   7:    13.999 -  15.998:  289        |
|      3:     6.004 -   8.003:  285   |   8:    15.998 -  17.996:  266        |
|      4:     8.003 -  10.002:  251   |   9:    17.996 -  19.995:  269        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.96 - 14.94 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.5138   r_free= 0.5037   ksol= 0.00   Bsol= 0.00   scale= 0.749    |
|                                                                             |
| 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:   0.92 A                  |
| x-ray target function (ml) for work reflections: 6.304530                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.96 - 14.94 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.5028   r_free= 0.4914   ksol= 0.34   Bsol= 4.50   scale= 0.974    |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (7.25,11.00,7.61,0.00,0.00,0.00); trace/3= 8.62                             |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.91 A                  |
| x-ray target function (ml) for work reflections: 6.299028                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 20.856375             wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 84.500   (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 1.870480              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 82.091   (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.5028      final r-factor (work) = 0.4375          |
| start r-factor (free) = 0.4914      final r-factor (free) = 0.4589          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 119.0389 = 20.86 * 0.50 * 6.3032 + 1.00 * 53.3082                           |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 65.3011 = 20.86 * 0.50 * 6.2453 + 1.00 * 0.1744                             |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 26     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.4375      final r-factor (work) = 0.3983          |
| start r-factor (free) = 0.4589      final r-factor (free) = 0.4509          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 11.6959 = 1.87 * 1.00 * 6.2453 + 1.00 * 0.0143                              |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 11.6149 = 1.87 * 1.00 * 6.1978 + 1.00 * 0.0222                              |
|-----------------------------------------------------------------------------|
| number of iterations = 17      |    number of function evaluations = 20     |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 11.628)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.00    84.71   15.46    None  None   None       |
|    all(noH): 2823   0      0.00    84.71   15.46    None  None   None       |
|    Sol.    : 438    0      0.00    84.71   24.86    None  None   None       |
|    Mac.    : 2385   0      0.00    66.85   13.74    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 -   8.471:  998   |   5:    42.353 -  50.823:   66        |
|      1:     8.471 -  16.941:  811   |   6:    50.823 -  59.294:   31        |
|      2:    16.941 -  25.412:  465   |   7:    59.294 -  67.764:   15        |
|      3:    25.412 -  33.882:  270   |   8:    67.764 -  76.235:    7        |
|      4:    33.882 -  42.353:  159   |   9:    76.235 -  84.705:    1        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.3983 r_free = 0.4509             target_work(ml) = 6.185         |
| occupancies: max = 1.00  min = 0.30   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.3974 r_free = 0.4507             target_work(ml) = 6.184         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:       12 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.96 - 14.94 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.3974   r_free= 0.4507   ksol= 0.34   Bsol= 4.50   scale= 1.113    |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (7.25,11.00,7.61,0.00,0.00,0.00); trace/3= 8.62                             |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.67 A                  |
| x-ray target function (ml) for work reflections: 6.184256                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.96 - 14.94 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.3960   r_free= 0.4437   ksol= 0.30   Bsol= 20.00   scale= 1.023   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (3.64,6.57,4.71,0.00,0.00,0.00); trace/3= 4.97                              |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.68 A                  |
| x-ray target function (ml) for work reflections: 6.184600                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 13.761443             wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 101.088  (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 0.732701              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 121.577  (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.3960      final r-factor (work) = 0.3231          |
| start r-factor (free) = 0.4437      final r-factor (free) = 0.3780          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 42.7964 = 13.76 * 0.50 * 6.1944 + 1.00 * 0.1744                             |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 42.1334 = 13.76 * 0.50 * 6.1070 + 1.00 * 0.1128                             |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 27     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.3231      final r-factor (work) = 0.2992          |
| start r-factor (free) = 0.3780      final r-factor (free) = 0.3590          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 4.4960 = 0.73 * 1.00 * 6.1070 + 1.00 * 0.0214                               |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 4.4108 = 0.73 * 1.00 * 6.0007 + 1.00 * 0.0141                               |
|-----------------------------------------------------------------------------|
| number of iterations = 17      |    number of function evaluations = 19     |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 11.628)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.00    94.43   15.36    None  None   None       |
|    all(noH): 2823   0      0.00    94.43   15.36    None  None   None       |
|    Sol.    : 438    0      0.00    94.43   30.69    None  None   None       |
|    Mac.    : 2385   0      0.00    71.08   12.54    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 -   9.443: 1185   |   5:    47.216 -  56.659:   56        |
|      1:     9.443 -  18.886:  817   |   6:    56.659 -  66.102:   19        |
|      2:    18.886 -  28.330:  408   |   7:    66.102 -  75.545:   14        |
|      3:    28.330 -  37.773:  202   |   8:    75.545 -  84.989:    1        |
|      4:    37.773 -  47.216:  119   |   9:    84.989 -  94.432:    2        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.2992 r_free = 0.3590             target_work(ml) = 5.980         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:       12 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.2990 r_free = 0.3585             target_work(ml) = 5.979         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:       11 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.96 - 14.94 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.2990   r_free= 0.3585   ksol= 0.30   Bsol= 20.00   scale= 1.079   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (3.64,6.57,4.71,0.00,0.00,0.00); trace/3= 4.97                              |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.43 A                  |
| x-ray target function (ml) for work reflections: 5.979155                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.96 - 14.94 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.2963   r_free= 0.3569   ksol= 0.32   Bsol= 44.90   scale= 1.018   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (1.41,3.76,2.56,0.00,0.00,0.00); trace/3= 2.57                              |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.44 A                  |
| x-ray target function (ml) for work reflections: 5.977554                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 8.584115              wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 103.066  (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 0.275136              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 112.210  (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.2963      final r-factor (work) = 0.2143          |
| start r-factor (free) = 0.3569      final r-factor (free) = 0.2689          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 25.8723 = 8.58 * 0.50 * 6.0016 + 1.00 * 0.1128                              |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 25.2540 = 8.58 * 0.50 * 5.8625 + 1.00 * 0.0919                              |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 27     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.2143      final r-factor (work) = 0.1923          |
| start r-factor (free) = 0.2689      final r-factor (free) = 0.2416          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 1.6269 = 0.28 * 1.00 * 5.8625 + 1.00 * 0.0139                               |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 1.6186 = 0.28 * 1.00 * 5.6487 + 1.00 * 0.0644                               |
|-----------------------------------------------------------------------------|
| number of iterations = 8       |    number of function evaluations = 8      |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 11.628)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.00    141.45  15.01    None  None   None       |
|    all(noH): 2823   0      0.00    141.45  15.01    None  None   None       |
|    Sol.    : 438    0      3.94    92.27   33.73    None  None   None       |
|    Mac.    : 2385   0      0.00    141.45  11.58    None  None   None       |
|    Hyd.    : 0      0      None    None    None     None  None   None       |
|    - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -      |
|       Distribution of isotropic (or equivalent) ADP for non-H atoms:        |
|    Bin#      value range     #atoms | Bin#      value range     #atoms      |
|      0:     0.000 -  14.145: 1837   |   5:    70.727 -  84.872:    5        |
|      1:    14.145 -  28.291:  556   |   6:    84.872 -  99.017:    2        |
|      2:    28.291 -  42.436:  287   |   7:    99.017 - 113.163:    0        |
|      3:    42.436 -  56.581:  111   |   8:   113.163 - 127.308:    0        |
|      4:    56.581 -  70.727:   24   |   9:   127.308 - 141.454:    1        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.1923 r_free = 0.2416             target_work(ml) = 5.600         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:       11 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.1919 r_free = 0.2417             target_work(ml) = 5.599         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:       10 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.96 - 14.94 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1919   r_free= 0.2417   ksol= 0.32   Bsol= 44.90   scale= 1.056   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (1.41,3.76,2.56,0.00,0.00,0.00); trace/3= 2.57                              |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.22 A                  |
| x-ray target function (ml) for work reflections: 5.598661                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.96 - 14.94 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1902   r_free= 0.2399   ksol= 0.32   Bsol= 37.88   scale= 1.011   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-0.28,1.77,1.13,0.00,0.00,0.00); trace/3= 0.87                             |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.24 A                  |
| x-ray target function (ml) for work reflections: 5.597303                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 3.598777              wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 102.101  (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 0.287701              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 90.835   (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1902      final r-factor (work) = 0.1530          |
| start r-factor (free) = 0.2399      final r-factor (free) = 0.1980          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 10.2696 = 3.60 * 0.50 * 5.6562 + 1.00 * 0.0919                              |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 9.9748 = 3.60 * 0.50 * 5.5054 + 1.00 * 0.0685                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 27     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1530      final r-factor (work) = 0.1395          |
| start r-factor (free) = 0.1980      final r-factor (free) = 0.1842          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 1.6040 = 0.29 * 1.00 * 5.5054 + 1.00 * 0.0201                               |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 1.5524 = 0.29 * 1.00 * 5.3629 + 1.00 * 0.0095                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 30     |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 11.628)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.00    81.92   15.25    None  None   None       |
|    all(noH): 2823   0      0.00    81.92   15.25    None  None   None       |
|    Sol.    : 438    0      3.80    77.43   38.45    None  None   None       |
|    Mac.    : 2385   0      0.00    81.92   11.00    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:     0.000 -   8.192: 1084   |   5:    40.960 -  49.152:   98        |
|      1:     8.192 -  16.384: 1005   |   6:    49.152 -  57.344:   75        |
|      2:    16.384 -  24.576:  262   |   7:    57.344 -  65.536:   46        |
|      3:    24.576 -  32.768:  120   |   8:    65.536 -  73.728:   13        |
|      4:    32.768 -  40.960:  110   |   9:    73.728 -  81.920:   10        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.1395 r_free = 0.1842             target_work(ml) = 5.323         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:       10 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.1394 r_free = 0.1841             target_work(ml) = 5.322         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        9 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.96 - 14.94 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1394   r_free= 0.1841   ksol= 0.32   Bsol= 37.88   scale= 1.023   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-0.28,1.77,1.13,0.00,0.00,0.00); trace/3= 0.87                             |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.17 A                  |
| x-ray target function (ml) for work reflections: 5.322256                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.96 - 14.94 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1394   r_free= 0.1849   ksol= 0.32   Bsol= 43.82   scale= 1.004   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-0.93,0.85,0.59,0.00,0.00,0.00); trace/3= 0.17                             |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.17 A                  |
| x-ray target function (ml) for work reflections: 5.325292                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 3.261746              wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 118.909  (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 0.213614              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 144.165  (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1394      final r-factor (work) = 0.1230          |
| start r-factor (free) = 0.1849      final r-factor (free) = 0.1701          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 8.8223 = 3.26 * 0.50 * 5.3676 + 1.00 * 0.0685                               |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 8.6723 = 3.26 * 0.50 * 5.2726 + 1.00 * 0.0733                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 28     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1230      final r-factor (work) = 0.1210          |
| start r-factor (free) = 0.1701      final r-factor (free) = 0.1670          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 1.1357 = 0.21 * 1.00 * 5.2726 + 1.00 * 0.0094                               |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 1.1237 = 0.21 * 1.00 * 5.2202 + 1.00 * 0.0086                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 29     |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 11.628)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.72    82.96   14.93    None  None   None       |
|    all(noH): 2823   0      0.72    82.96   14.93    None  None   None       |
|    Sol.    : 438    0      3.78    80.16   37.61    None  None   None       |
|    Mac.    : 2385   0      0.72    82.96   10.76    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:     0.717 -   8.941: 1250   |   5:    41.838 -  50.063:   93        |
|      1:     8.941 -  17.165:  923   |   6:    50.063 -  58.287:   66        |
|      2:    17.165 -  25.390:  208   |   7:    58.287 -  66.511:   37        |
|      3:    25.390 -  33.614:  120   |   8:    66.511 -  74.736:   12        |
|      4:    33.614 -  41.838:  107   |   9:    74.736 -  82.960:    7        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.1210 r_free = 0.1670             target_work(ml) = 5.210         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        9 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.1208 r_free = 0.1670             target_work(ml) = 5.210         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:       11 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.96 - 14.94 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1208   r_free= 0.1670   ksol= 0.32   Bsol= 43.82   scale= 1.006   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-0.93,0.85,0.59,0.00,0.00,0.00); trace/3= 0.17                             |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.16 A                  |
| x-ray target function (ml) for work reflections: 5.209658                   |
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
| Bin     Resolution   Compl.  No. Refl.    R-factors          Targets        |
|number     range              work test   work   test        work        test|
|  1: 14.9406 -  4.6800 0.99   1414  159 0.1016 0.1340      5.4175      5.5768|
|  2:  4.6800 -  3.7338 0.99   1360  151 0.0901 0.1145      5.4895      5.6968|
|  3:  3.7338 -  3.2674 0.99   1335  147 0.1149 0.1667      5.5507       5.925|
|  4:  3.2674 -  2.9712 0.99   1323  139 0.1346 0.1707      5.5274      5.7379|
|  5:  2.9712 -  2.7597 0.99   1316  151 0.1476 0.1728      5.4071      5.5296|
|  6:  2.7597 -  2.5979 0.99   1307  148 0.1385 0.2186      5.3006      5.5753|
|  7:  2.5979 -  2.4684 0.98   1297  149 0.1280 0.1681      5.2095       5.394|
|  8:  2.4684 -  2.3614 0.98   1321  136 0.1274 0.1719      5.1341      5.3609|
|  9:  2.3614 -  2.2708 0.99   1289  144 0.1259 0.1955      5.0767      5.3767|
| 10:  2.2708 -  2.1927 0.98   1297  145 0.1269 0.1854      5.0577      5.2975|
| 11:  2.1927 -  2.1243 0.97   1268  145 0.1232 0.1826      4.9794      5.2378|
| 12:  2.1243 -  2.0638 0.98   1285  148 0.1235 0.1787      4.9126      5.1729|
| 13:  2.0638 -  2.0096 0.92   1220  128 0.1203 0.1799      4.8196      5.0862|
| 14:  2.0096 -  1.9606 0.46    598   69 0.1096 0.1681      4.6902      4.9094|
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
|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: 14.9406 -  4.6800  1414   159  0.93   9.82   0.98     0.96       8057.77|
|  2:  4.6800 -  3.7338  1360   151  0.95   8.82   1.02     1.01      10333.65|
|  3:  3.7338 -  3.2674  1335   147  0.92  12.91   1.03     1.01      12376.77|
|  4:  3.2674 -  2.9712  1323   139  0.91  15.30   1.02     1.00      12075.82|
|  5:  2.9712 -  2.7597  1316   151  0.88  17.98   1.00     0.96       9846.10|
|  6:  2.7597 -  2.5979  1307   148  0.89  17.64   0.98     0.94       8158.04|
|  7:  2.5979 -  2.4684  1297   149  0.90  16.53   0.99     0.95       6843.57|
|  8:  2.4684 -  2.3614  1321   136  0.90  16.49   1.01     0.99       6158.57|
|  9:  2.3614 -  2.2708  1289   144  0.89  17.38   1.01     0.98       5693.17|
| 10:  2.2708 -  2.1927  1297   145  0.89  17.15   1.01     0.97       5314.21|
| 11:  2.1927 -  2.1243  1268   145  0.89  17.14   1.01     0.98       4782.80|
| 12:  2.1243 -  2.0638  1285   148  0.90  16.19   1.01     0.98       4085.11|
| 13:  2.0638 -  2.0096  1220   128  0.90  16.57   1.01     1.01       3464.92|
| 14:  2.0096 -  1.9606   598    69  0.91  15.45   0.99     0.95       2679.19|
|alpha:            min =        0.94 max =            1.01 mean =         0.98|
|beta:             min =     2679.19 max =        12376.77 mean =      7371.11|
|figures of merit: min =        0.00 max =            1.00 mean =         0.90|
|phase err.(work): min =        0.00 max =           89.92 mean =        15.31|
|phase err.(test): min =        0.00 max =           89.43 mean =        14.71|
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.96 - 14.94 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1208   r_free= 0.1670   ksol= 0.32   Bsol= 43.91   scale= 1.004   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-1.05,0.59,0.46,0.00,0.00,0.00); trace/3= -0.00                            |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.16 A                  |
| x-ray target function (ml) for work reflections: 5.209681                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.96 - 14.94 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1208   r_free= 0.1670   ksol= 0.32   Bsol= 43.91   scale= 1.004   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-1.05,0.59,0.46,0.00,0.00,0.00); trace/3= -0.00                            |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.16 A                  |
| x-ray target function (ml) for work reflections: 5.209681                   |
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
| Bin     Resolution   Compl.  No. Refl.    R-factors          Targets        |
|number     range              work test   work   test        work        test|
|  1: 14.9406 -  4.6800 0.99   1414  159 0.1016 0.1340      5.4172      5.5766|
|  2:  4.6800 -  3.7338 0.99   1360  151 0.0901 0.1146      5.4897      5.6973|
|  3:  3.7338 -  3.2674 0.99   1335  147 0.1150 0.1668      5.5511      5.9259|
|  4:  3.2674 -  2.9712 0.99   1323  139 0.1345 0.1706      5.5274      5.7378|
|  5:  2.9712 -  2.7597 0.99   1316  151 0.1476 0.1726      5.4068      5.5291|
|  6:  2.7597 -  2.5979 0.99   1307  148 0.1384 0.2183      5.3002      5.5749|
|  7:  2.5979 -  2.4684 0.98   1297  149 0.1280 0.1682      5.2092       5.394|
|  8:  2.4684 -  2.3614 0.98   1321  136 0.1273 0.1718       5.134      5.3608|
|  9:  2.3614 -  2.2708 0.99   1289  144 0.1257 0.1957      5.0766      5.3776|
| 10:  2.2708 -  2.1927 0.98   1297  145 0.1269 0.1856      5.0578      5.2986|
| 11:  2.1927 -  2.1243 0.97   1268  145 0.1232 0.1826      4.9796      5.2377|
| 12:  2.1243 -  2.0638 0.98   1285  148 0.1235 0.1790       4.913      5.1733|
| 13:  2.0638 -  2.0096 0.92   1220  128 0.1204 0.1797        4.82      5.0854|
| 14:  2.0096 -  1.9606 0.46    598   69 0.1095 0.1682      4.6899        4.91|
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
|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: 14.9406 -  4.6800  1414   159  0.93   9.82   0.98     0.96       8053.45|
|  2:  4.6800 -  3.7338  1360   151  0.95   8.82   1.02     1.01      10336.74|
|  3:  3.7338 -  3.2674  1335   147  0.92  12.92   1.03     1.01      12390.42|
|  4:  3.2674 -  2.9712  1323   139  0.91  15.31   1.01     1.00      12081.04|
|  5:  2.9712 -  2.7597  1316   151  0.88  17.97   1.00     0.96       9835.62|
|  6:  2.7597 -  2.5979  1307   148  0.89  17.63   0.98     0.94       8153.03|
|  7:  2.5979 -  2.4684  1297   149  0.90  16.52   0.98     0.95       6839.95|
|  8:  2.4684 -  2.3614  1321   136  0.90  16.49   1.01     0.99       6161.28|
|  9:  2.3614 -  2.2708  1289   144  0.89  17.38   1.01     0.98       5698.14|
| 10:  2.2708 -  2.1927  1297   145  0.89  17.16   1.00     0.96       5317.63|
| 11:  2.1927 -  2.1243  1268   145  0.89  17.15   1.00     0.98       4786.79|
| 12:  2.1243 -  2.0638  1285   148  0.90  16.20   1.01     0.98       4090.25|
| 13:  2.0638 -  2.0096  1220   128  0.90  16.57   1.00     1.00       3464.30|
| 14:  2.0096 -  1.9606   598    69  0.91  15.44   0.98     0.95       2674.31|
|alpha:            min =        0.94 max =            1.01 mean =         0.98|
|beta:             min =     2674.31 max =        12390.42 mean =      7372.28|
|figures of merit: min =        0.00 max =            1.00 mean =         0.90|
|phase err.(work): min =        0.00 max =           89.92 mean =        15.31|
|phase err.(test): min =        0.00 max =           89.43 mean =        14.71|
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 11.628)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.80    83.05   15.01    None  None   None       |
|    all(noH): 2823   0      0.80    83.05   15.01    None  None   None       |
|    Sol.    : 438    0      3.87    80.25   37.70    None  None   None       |
|    Mac.    : 2385   0      0.80    83.05   10.85    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:     0.804 -   9.028: 1250   |   5:    41.926 -  50.150:   93        |
|      1:     9.028 -  17.253:  923   |   6:    50.150 -  58.374:   66        |
|      2:    17.253 -  25.477:  208   |   7:    58.374 -  66.599:   37        |
|      3:    25.477 -  33.701:  120   |   8:    66.599 -  74.823:   12        |
|      4:    33.701 -  41.926:  107   |   9:    74.823 -  83.047:    7        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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


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

Number of peaks found at mFobs-DFmodel map (map cutoff=3.00 sigma)= 332         
Filter by distance & map next to the model:
   mapped sites are within: 0.412 - 5.026
   number of sites selected in [dist_min= 0.70, dist_max= 6.00]: 328 from: 332
   mapped sites are within: 0.770 - 5.026

peak=    9.700 closest distance to " CG2 VAL A 230 " =    1.438
peak=    7.835 closest distance to " O   HOH Z 120 " =    1.636
peak=    7.118 closest distance to " CG1 ILE A 234 " =    1.489
peak=    6.456 closest distance to " O   HOH Z 316 " =    1.266
peak=    6.201 closest distance to " O   HOH Z 402 " =    1.681
peak=    6.033 closest distance to " CB  VAL A 296 " =    1.113
peak=    5.501 closest distance to " O   HOH Z 247 " =    1.516
peak=    5.430 closest distance to " CG  LEU A   5 " =    1.386
peak=    5.344 closest distance to " O   HOH Z 142 " =    1.705
peak=    5.275 closest distance to " O   HOH Z 278 " =    1.380
peak=    5.236 closest distance to " O   HOH Z 403 " =    1.974
peak=    5.173 closest distance to " O   HOH Z 236 " =    1.484
peak=    4.989 closest distance to " O   HOH Z 272 " =    1.976
peak=    4.977 closest distance to " O   HOH Z 124 " =    1.652
peak=    4.960 closest distance to " O   HOH Z 193 " =    1.762
peak=    4.952 closest distance to " NH2 ARG A  56 " =    2.284
peak=    4.931 closest distance to " O   HOH Z 154 " =    1.893
peak=    4.905 closest distance to " O   HOH Z 209 " =    2.297
peak=    4.864 closest distance to " CB  SER A  63 " =    1.119
peak=    4.862 closest distance to " CG2 VAL A 296 " =    1.057
peak=    4.771 closest distance to " O   HOH Z  46 " =    1.129
peak=    4.737 closest distance to " CB  ARG A 275 " =    0.953
peak=    4.733 closest distance to " CD2 LEU A   5 " =    1.290
peak=    4.638 closest distance to " O   HOH Z  80 " =    2.094
peak=    4.546 closest distance to " O   HOH Z 128 " =    1.638
peak=    4.544 closest distance to " O   HOH Z  43 " =    1.737
peak=    4.507 closest distance to " O   HOH Z 134 " =    2.014
peak=    4.503 closest distance to " O   HOH Z 357 " =    1.998
peak=    4.478 closest distance to " O   HOH Z 155 " =    1.739
peak=    4.476 closest distance to " O   HOH Z 327 " =    1.751
peak=    4.476 closest distance to " CG  PRO A 213 " =    1.216
peak=    4.457 closest distance to " CB  GLN A 223 " =    1.392
peak=    4.446 closest distance to " O   HOH Z  68 " =    2.020
peak=    4.426 closest distance to " NE2 GLN A  11 " =    1.021
peak=    4.424 closest distance to " O   HOH Z 249 " =    1.138
peak=    4.417 closest distance to " O   HOH Z 279 " =    1.278
peak=    4.413 closest distance to " CB  VAL A 230 " =    1.236
peak=    4.413 closest distance to " C   PRO A 198 " =    1.480
peak=    4.397 closest distance to " O   HOH Z 414 " =    2.469
peak=    4.385 closest distance to " O   HOH Z  11 " =    1.348
peak=    4.380 closest distance to " O   HOH Z  85 " =    1.835
peak=    4.372 closest distance to " O   HOH Z 102 " =    1.414
peak=    4.371 closest distance to " O   HOH Z 316 " =    2.023
peak=    4.361 closest distance to " O   HOH Z  49 " =    1.223
peak=    4.320 closest distance to " CA  VAL A  41 " =    0.842
peak=    4.302 closest distance to " O   SER A  87 " =    2.284
peak=    4.298 closest distance to " CA  TYR A  30 " =    1.004
peak=    4.267 closest distance to " O   HOH Z  63 " =    2.682
peak=    4.240 closest distance to " O   HOH Z 234 " =    3.490
peak=    4.222 closest distance to " O   HOH Z 404 " =    1.339
peak=    4.204 closest distance to " O   HOH Z 232 " =    2.381
peak=    4.199 closest distance to " O   HOH Z 156 " =    3.043
peak=    4.181 closest distance to " OE1 GLU A   2 " =    2.153
peak=    4.174 closest distance to " CB  GLN A 183 " =    1.288
peak=    4.167 closest distance to " O   HOH Z 263 " =    1.533
peak=    4.166 closest distance to " O   HOH Z 389 " =    1.890
peak=    4.147 closest distance to " O   HOH Z 423 " =    1.910
peak=    4.145 closest distance to " CG  ARG A  66 " =    1.123
peak=    4.143 closest distance to " O   HOH Z 245 " =    1.438
peak=    4.092 closest distance to " O   HOH Z 411 " =    3.214
peak=    4.092 closest distance to " CG2 THR A 221 " =    1.202
peak=    4.085 closest distance to " O   HOH Z 394 " =    1.617
peak=    4.076 closest distance to " O   HOH Z  40 " =    1.883
peak=    4.066 closest distance to " CB  SER A   3 " =    1.356
peak=    4.064 closest distance to " NH2BARG A 145 " =    2.168
peak=    4.053 closest distance to " O   GLY A  91 " =    1.347
peak=    4.052 closest distance to " CG  LEU A 228 " =    1.297
peak=    4.045 closest distance to " O   HOH Z 163 " =    1.488
peak=    4.009 closest distance to " O   HOH Z 130 " =    2.688
peak=    3.990 closest distance to " CB  ASN A 187 " =    1.607
peak=    3.989 closest distance to " O   HOH Z  39 " =    1.573
peak=    3.989 closest distance to " OD1 ASN A  60 " =    1.530
peak=    3.979 closest distance to " O   HOH Z 116 " =    1.174
peak=    3.975 closest distance to " O   HOH Z 265 " =    2.323
peak=    3.974 closest distance to " O   HOH Z 136 " =    1.281
peak=    3.963 closest distance to " CG1 ILE A  33 " =    1.277
peak=    3.961 closest distance to " CB  TRP A 179 " =    1.123
peak=    3.960 closest distance to " O   HOH Z 248 " =    1.673
peak=    3.956 closest distance to " CB  SER A  26 " =    1.716
peak=    3.956 closest distance to " NZ  LYS A 117 " =    3.100
peak=    3.956 closest distance to " O   HOH Z 303 " =    2.386
peak=    3.953 closest distance to " O   HOH Z 345 " =    2.334
peak=    3.939 closest distance to " CA  ALA A  21 " =    1.212
peak=    3.938 closest distance to " O   HOH Z 189 " =    2.461
peak=    3.932 closest distance to " O   HOH Z 403 " =    1.483
peak=    3.926 closest distance to " CD2 LEU A 228 " =    1.220
peak=    3.908 closest distance to " CG1 VAL A 296 " =    1.094
peak=    3.907 closest distance to " CB  GLU A 152 " =    1.118
peak=    3.896 closest distance to " O   HOH Z   4 " =    1.540
peak=    3.881 closest distance to " O   HOH Z   9 " =    2.384
peak=    3.869 closest distance to " O   HOH Z 361 " =    2.848
peak=    3.867 closest distance to " O   HOH Z 408 " =    1.640
peak=    3.863 closest distance to " CB  ALA A 100 " =    1.199
peak=    3.858 closest distance to " O   HOH Z  97 " =    1.881
peak=    3.855 closest distance to " OE1 GLN A  11 " =    1.799
peak=    3.855 closest distance to " O   HOH Z 346 " =    1.435
peak=    3.853 closest distance to " CE1 HIS A 108 " =    1.137
peak=    3.841 closest distance to " O   HOH Z  42 " =    2.330
peak=    3.838 closest distance to " N   ASN A  39 " =    1.273
peak=    3.838 closest distance to " CE  LYS A 119 " =    1.055
peak=    3.835 closest distance to " CB  PRO A 198 " =    1.102
peak=    3.830 closest distance to " O   HOH Z 250 " =    1.628
peak=    3.826 closest distance to " O   HOH Z 406 " =    1.578
peak=    3.826 closest distance to " O   HOH Z  15 " =    2.238
peak=    3.811 closest distance to " O   HOH Z  48 " =    1.812
peak=    3.807 closest distance to " O   HOH Z 126 " =    1.827
peak=    3.804 closest distance to " O   ASP A 124 " =    1.522
peak=    3.802 closest distance to " O   HOH Z 345 " =    1.999
peak=    3.797 closest distance to " O   HOH Z  54 " =    1.607
peak=    3.797 closest distance to " O   HOH Z 126 " =    1.449
peak=    3.796 closest distance to " O   HOH Z 368 " =    2.083
peak=    3.796 closest distance to " O   HOH Z 426 " =    1.591
peak=    3.794 closest distance to " O   HOH Z 412 " =    3.618
peak=    3.789 closest distance to " O   HOH Z  47 " =    1.601
peak=    3.789 closest distance to " O   HOH Z 433 " =    1.560
peak=    3.787 closest distance to " NH1BARG A 190 " =    2.099
peak=    3.785 closest distance to " O   HOH Z 315 " =    1.741
peak=    3.779 closest distance to " O   HOH Z 203 " =    1.531
peak=    3.773 closest distance to " CD2 TRP A 179 " =    1.411
peak=    3.768 closest distance to " O   HOH Z 425 " =    1.504
peak=    3.755 closest distance to " O   HOH Z 409 " =    3.119
peak=    3.730 closest distance to " CG  PRO A 198 " =    1.200
peak=    3.722 closest distance to " O   HOH Z 146 " =    1.388
peak=    3.719 closest distance to " O   HOH Z  66 " =    2.170
peak=    3.714 closest distance to " CB  SER A 141 " =    0.997
peak=    3.711 closest distance to " CG  PRO A 243 " =    1.198
peak=    3.706 closest distance to " O   HOH Z  78 " =    1.577
peak=    3.702 closest distance to " O   HOH Z 146 " =    1.454
peak=    3.700 closest distance to " CD  ARG A 159 " =    0.770
peak=    3.693 closest distance to " O   HOH Z 334 " =    1.491
peak=    3.692 closest distance to " O   HOH Z  59 " =    2.220
peak=    3.686 closest distance to " OG  SER A  62 " =    2.950
peak=    3.684 closest distance to " OG BSER A 210 " =    1.228
peak=    3.680 closest distance to " CD  ARG A 195 " =    1.029
peak=    3.680 closest distance to " O   HOH Z 273 " =    2.623
peak=    3.679 closest distance to " CD  ARG A 269 " =    1.203
peak=    3.677 closest distance to " CB  ARG A 139 " =    1.002
peak=    3.654 closest distance to " CD  LYS A 166 " =    1.474
peak=    3.654 closest distance to " O   HOH Z 130 " =    1.175
peak=    3.647 closest distance to " O   HOH Z 421 " =    2.088
peak=    3.637 closest distance to " CG2 THR A 220 " =    0.785
peak=    3.633 closest distance to " O   HOH Z  97 " =    2.176
peak=    3.630 closest distance to " ND2 ASN A 187 " =    1.843
peak=    3.628 closest distance to " O   HOH Z 132 " =    2.412
peak=    3.626 closest distance to " CD  PRO A  54 " =    0.865
peak=    3.622 closest distance to " O   HOH Z 395 " =    1.438
peak=    3.622 closest distance to " O   HOH Z 380 " =    2.059
peak=    3.617 closest distance to " O   HOH Z 236 " =    1.827
peak=    3.617 closest distance to " CB  VAL A 265 " =    1.294
peak=    3.610 closest distance to " CG1BVAL A  72 " =    1.723
peak=    3.609 closest distance to " O   HOH Z 423 " =    3.038
peak=    3.609 closest distance to " CB  TRP A 266 " =    1.245
peak=    3.607 closest distance to " O   HOH Z 197 " =    2.208
peak=    3.605 closest distance to " O   HOH Z 313 " =    1.784
peak=    3.601 closest distance to " CB  ASN A 148 " =    1.293
peak=    3.599 closest distance to " CG2 THR A 294 " =    1.387
peak=    3.592 closest distance to " O   HOH Z  88 " =    3.741
peak=    3.590 closest distance to " O   HOH Z 253 " =    2.014
peak=    3.586 closest distance to " CA  ARG A 195 " =    1.262
peak=    3.583 closest distance to " ND1 HIS A  81 " =    1.438
peak=    3.582 closest distance to " O   HOH Z 271 " =    2.243
peak=    3.582 closest distance to " O   HOH Z 435 " =    1.963
peak=    3.579 closest distance to " OG1 THR A 294 " =    2.228
peak=    3.575 closest distance to " CB  GLU A 128 " =    1.152
peak=    3.569 closest distance to " O   HOH Z 227 " =    1.577
peak=    3.559 closest distance to " O   HOH Z 419 " =    1.609
peak=    3.556 closest distance to " CA  ASP A 191 " =    0.942
peak=    3.545 closest distance to " O   HOH Z 128 " =    1.702
peak=    3.542 closest distance to " O   HOH Z 301 " =    1.815
peak=    3.527 closest distance to " O   HOH Z  44 " =    2.083
peak=    3.526 closest distance to " CB  ALA A 256 " =    0.975
peak=    3.525 closest distance to " O   HOH Z 386 " =    2.197
peak=    3.519 closest distance to " O   HOH Z 155 " =    2.581
peak=    3.516 closest distance to " O   HOH Z 383 " =    1.974
peak=    3.492 closest distance to " CA  ALA A 295 " =    0.975
peak=    3.490 closest distance to " CG2 ILE A  20 " =    1.369
peak=    3.485 closest distance to " O   HOH Z 427 " =    3.031
peak=    3.485 closest distance to " CB  THR A  31 " =    1.455
peak=    3.481 closest distance to " O   HOH Z 210 " =    1.017
peak=    3.475 closest distance to " O   HOH Z 298 " =    5.026
peak=    3.463 closest distance to " O   HOH Z 271 " =    1.438
peak=    3.463 closest distance to " CB  VAL A 202 " =    1.495
peak=    3.459 closest distance to " O   HOH Z  48 " =    1.848
peak=    3.457 closest distance to " O   HOH Z  38 " =    1.724
peak=    3.456 closest distance to " O   HOH Z  19 " =    2.001
peak=    3.454 closest distance to " CB  ARG A  79 " =    0.858
peak=    3.449 closest distance to " CB  ASN A  39 " =    0.938
peak=    3.445 closest distance to " CG  PRO A  54 " =    1.517
peak=    3.441 closest distance to " O   HOH Z 425 " =    2.095
peak=    3.437 closest distance to " O   HOH Z 365 " =    2.920
peak=    3.437 closest distance to " O   HOH Z 344 " =    1.768
peak=    3.433 closest distance to " O   HOH Z 194 " =    2.010
peak=    3.431 closest distance to " O   HOH Z 261 " =    2.273
peak=    3.430 closest distance to " C   VAL A 265 " =    1.390
peak=    3.429 closest distance to " O   HOH Z 280 " =    2.490
peak=    3.426 closest distance to " O   HOH Z 339 " =    1.322
peak=    3.423 closest distance to " O   HOH Z 358 " =    2.215
peak=    3.421 closest distance to " O   HOH Z  48 " =    2.478
peak=    3.419 closest distance to " CA  ASN A 176 " =    0.997
peak=    3.416 closest distance to " CB  GLN A  58 " =    1.061
peak=    3.410 closest distance to " O   HOH Z 257 " =    2.224
peak=    3.404 closest distance to " CB  ARG A  79 " =    1.313
peak=    3.401 closest distance to " O   HOH Z 369 " =    1.980
peak=    3.396 closest distance to " O   HOH Z 326 " =    1.480
peak=    3.394 closest distance to " O   HOH Z 109 " =    1.446
peak=    3.389 closest distance to " CB  ASN A 187 " =    1.066
peak=    3.380 closest distance to " CG2 ILE A 120 " =    1.335
peak=    3.375 closest distance to " O   HOH Z 147 " =    1.838
peak=    3.373 closest distance to " O   HOH Z  71 " =    1.814
peak=    3.372 closest distance to " CB  SER A  62 " =    0.896
peak=    3.369 closest distance to " O   HOH Z 162 " =    1.871
peak=    3.364 closest distance to " O   HOH Z 402 " =    2.560
peak=    3.364 closest distance to " NZ  LYS A  48 " =    2.507
peak=    3.362 closest distance to " NH2 ARG A  79 " =    1.287
peak=    3.357 closest distance to " CB  ARG A  79 " =    0.907
peak=    3.355 closest distance to " O   HOH Z 188 " =    0.907
peak=    3.354 closest distance to " N   ALA A   1 " =    3.054
peak=    3.351 closest distance to " O   HOH Z 332 " =    1.578
peak=    3.346 closest distance to " NZ  LYS A 117 " =    1.401
peak=    3.345 closest distance to " CB  ALA A  71 " =    1.177
peak=    3.343 closest distance to " O   HOH Z 112 " =    1.711
peak=    3.342 closest distance to " CE1 TYR A 186 " =    1.319
peak=    3.341 closest distance to " CD1 LEU A   5 " =    1.486
peak=    3.339 closest distance to " CA  ILE A 263 " =    0.962
peak=    3.332 closest distance to " CA  TYR A 214 " =    1.139
peak=    3.330 closest distance to " O   HOH Z 170 " =    1.665
peak=    3.330 closest distance to " O   HOH Z 197 " =    2.146
peak=    3.328 closest distance to " O   HOH Z 173 " =    2.136
peak=    3.325 closest distance to " CZ2 TRP A 150 " =    1.040
peak=    3.323 closest distance to " CD2 LEU A 297 " =    0.899
peak=    3.322 closest distance to " CE BMET A  47 " =    1.374
peak=    3.319 closest distance to " O   HOH Z 166 " =    1.702
peak=    3.317 closest distance to " CD AARG A 190 " =    1.641
peak=    3.314 closest distance to " CB BVAL A  41 " =    1.110
peak=    3.311 closest distance to " OG1 THR A 294 " =    4.008
peak=    3.308 closest distance to " NH2 ARG A 156 " =    1.077
peak=    3.302 closest distance to " CD  LYS A 119 " =    1.873
peak=    3.300 closest distance to " O   HOH Z 295 " =    1.486
peak=    3.295 closest distance to " CB  ALA A 248 " =    1.361
peak=    3.289 closest distance to " OH  TYR A 116 " =    1.194
peak=    3.289 closest distance to " O   HOH Z  66 " =    1.528
peak=    3.286 closest distance to " O   HOH Z 109 " =    1.896
peak=    3.285 closest distance to " CG2AVAL A  41 " =    0.798
peak=    3.282 closest distance to " CG  LYS A 166 " =    1.528
peak=    3.280 closest distance to " O   HOH Z  35 " =    2.133
peak=    3.277 closest distance to " CD1 LEU A 222 " =    0.845
peak=    3.277 closest distance to " O   HOH Z 431 " =    1.403
peak=    3.276 closest distance to " CG1 VAL A 153 " =    1.100
peak=    3.263 closest distance to " CB  LEU A   5 " =    1.156
peak=    3.261 closest distance to " O   HOH Z  61 " =    1.630
peak=    3.258 closest distance to " O   HOH Z 417 " =    3.256
peak=    3.258 closest distance to " OG BSER A 258 " =    3.061
peak=    3.255 closest distance to " CB  ARG A 269 " =    1.692
peak=    3.254 closest distance to " CG2 THR A 251 " =    1.172
peak=    3.252 closest distance to " CA  VAL A 126 " =    0.891
peak=    3.252 closest distance to " O   HOH Z 261 " =    2.049
peak=    3.250 closest distance to " OG  SER A 245 " =    1.401
peak=    3.249 closest distance to " OH  TYR A  30 " =    1.008
peak=    3.246 closest distance to " O   HOH Z 281 " =    4.169
peak=    3.245 closest distance to " O   HOH Z 183 " =    1.739
peak=    3.245 closest distance to " O   HOH Z 173 " =    1.658
peak=    3.243 closest distance to " O   HOH Z 214 " =    2.399
peak=    3.241 closest distance to " NH2BARG A 190 " =    1.583
peak=    3.240 closest distance to " O   ILE A  33 " =    1.121
peak=    3.240 closest distance to " NH1AARG A 275 " =    1.115
peak=    3.237 closest distance to " O   HOH Z 438 " =    2.599
peak=    3.232 closest distance to " O   ALA A 158 " =    1.201
peak=    3.225 closest distance to " O   HOH Z 132 " =    1.101
peak=    3.223 closest distance to " CG  MET A 185 " =    1.132
peak=    3.219 closest distance to " O   HOH Z 132 " =    2.839
peak=    3.216 closest distance to " O   HOH Z 185 " =    1.664
peak=    3.211 closest distance to " CZ AARG A 102 " =    1.654
peak=    3.203 closest distance to " NH2AARG A 275 " =    3.807
peak=    3.200 closest distance to " O   HOH Z 156 " =    2.057
peak=    3.198 closest distance to " CB  ARG A 259 " =    1.892
peak=    3.197 closest distance to " O   HOH Z 374 " =    2.534
peak=    3.195 closest distance to " O   HOH Z 234 " =    1.894
peak=    3.195 closest distance to " O   ALA A 165 " =    1.294
peak=    3.191 closest distance to " O   HOH Z 250 " =    1.327
peak=    3.188 closest distance to " O   HOH Z 367 " =    3.188
peak=    3.182 closest distance to " O   HOH Z 298 " =    1.863
peak=    3.179 closest distance to " CB  GLN A  73 " =    1.452
peak=    3.177 closest distance to " CA  GLU A 152 " =    0.943
peak=    3.173 closest distance to " O   THR A  82 " =    1.996
peak=    3.172 closest distance to " CB  PRO A 163 " =    3.907
peak=    3.172 closest distance to " O   HOH Z  59 " =    1.775
peak=    3.170 closest distance to " CB  SER A  28 " =    0.848
peak=    3.165 closest distance to " CB  GLN A 278 " =    0.855
peak=    3.163 closest distance to " CD2 HIS A  81 " =    1.214
peak=    3.158 closest distance to " O   HOH Z 343 " =    2.398
peak=    3.150 closest distance to " CB  MET A  47 " =    1.242
peak=    3.147 closest distance to " O  BHOH Z 338 " =    2.281
peak=    3.147 closest distance to " O   HOH Z 121 " =    2.123
peak=    3.147 closest distance to " NH1 ARG A  14 " =    0.987
peak=    3.145 closest distance to " O   HOH Z 278 " =    2.570
peak=    3.144 closest distance to " CD2 LEU A 255 " =    1.186
peak=    3.144 closest distance to " O   HOH Z 261 " =    1.852
peak=    3.143 closest distance to " CB  ALA A   9 " =    1.621
peak=    3.142 closest distance to " OG BSER A 164 " =    2.152
peak=    3.140 closest distance to " O   HOH Z 255 " =    1.556
peak=    3.134 closest distance to " NZ  LYS A  76 " =    0.906
peak=    3.130 closest distance to " O   HOH Z 427 " =    2.561
peak=    3.128 closest distance to " O   HOH Z 355 " =    1.896
peak=    3.124 closest distance to " CD BARG A 275 " =    1.493
peak=    3.120 closest distance to " CB  LEU A 228 " =    1.485
peak=    3.120 closest distance to " O   HOH Z 261 " =    1.688
peak=    3.117 closest distance to " NE  ARG A  14 " =    1.316
peak=    3.114 closest distance to " CA  ARG A  66 " =    0.969
peak=    3.111 closest distance to " CA  TYR A 116 " =    1.507
peak=    3.105 closest distance to " CA  CYS A 260 " =    1.904
peak=    3.094 closest distance to " NZ  LYS A  76 " =    1.860
peak=    3.093 closest distance to " O   HOH Z 145 " =    2.867
peak=    3.091 closest distance to " O   HOH Z 148 " =    2.942
peak=    3.085 closest distance to " CD  GLN A 194 " =    1.588
peak=    3.081 closest distance to " OD2 ASP A 286 " =    2.711
peak=    3.072 closest distance to " CG  MET A 113 " =    1.586
peak=    3.071 closest distance to " NE1 TRP A 274 " =    0.895
peak=    3.069 closest distance to " CB  ILE A 199 " =    0.905
peak=    3.068 closest distance to " OD2 ASP A 298 " =    3.890
peak=    3.064 closest distance to " O   HOH Z 113 " =    1.922
peak=    3.061 closest distance to " O   HOH Z 405 " =    2.005
peak=    3.061 closest distance to " NH1AARG A 145 " =    1.239
peak=    3.059 closest distance to " CH2 TRP A 274 " =    2.290
peak=    3.042 closest distance to " CG  ARG A  66 " =    2.972
peak=    3.037 closest distance to " CA  ARG A  36 " =    0.990
peak=    3.024 closest distance to " O   HOH Z 293 " =    1.660
peak=    3.009 closest distance to " O  BHOH Z  74 " =    1.333
peak=    3.001 closest distance to " CE  LYS A 119 " =    1.664

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

Number of peaks found at mFobs-DFmodel map (map cutoff=3.00 sigma)= 216         
Filter by distance & map next to the model:
   mapped sites are within: 0.522 - 5.875
   number of sites selected in [dist_min= 0.70, dist_max= 6.00]: 214 from: 216
   mapped sites are within: 0.745 - 5.875

peak=   -5.454 closest distance to " CG2 VAL A 230 " =    0.783
peak=   -4.679 closest distance to " O   HOH Z 210 " =    0.779
peak=   -4.633 closest distance to " O   HOH Z 155 " =    1.645
peak=   -4.521 closest distance to " O   PRO A 163 " =    2.048
peak=   -4.429 closest distance to " CD  ARG A 156 " =    2.013
peak=   -4.378 closest distance to " CG2BVAL A  41 " =    2.664
peak=   -4.321 closest distance to " O   HOH Z 290 " =    0.847
peak=   -4.313 closest distance to " C   HIS A 108 " =    1.228
peak=   -4.208 closest distance to " C   THR A 279 " =    1.223
peak=   -4.145 closest distance to " SG  CYS A 254 " =    3.163
peak=   -4.109 closest distance to " O   HOH Z 266 " =    4.368
peak=   -4.090 closest distance to " O   HOH Z 166 " =    1.691
peak=   -4.055 closest distance to " CD1 PHE A  59 " =    1.935
peak=   -4.012 closest distance to " O   HOH Z 312 " =    1.518
peak=   -4.010 closest distance to " OG  SER A  97 " =    2.281
peak=   -3.996 closest distance to " OXT GLY A 302 " =    2.778
peak=   -3.982 closest distance to " O   HOH Z 362 " =    5.875
peak=   -3.936 closest distance to " CG  MET A  93 " =    2.486
peak=   -3.890 closest distance to " CD2 TYR A  30 " =    2.699
peak=   -3.856 closest distance to " N   ALA A 226 " =    1.875
peak=   -3.838 closest distance to " O   HOH Z 166 " =    1.132
peak=   -3.835 closest distance to " CG2 THR A 182 " =    2.355
peak=   -3.832 closest distance to " O   VAL A  67 " =    2.641
peak=   -3.803 closest distance to " CB  ALA A 161 " =    2.355
peak=   -3.777 closest distance to " O   HOH Z 423 " =    2.323
peak=   -3.772 closest distance to " CD1 LEU A 228 " =    2.206
peak=   -3.746 closest distance to " O   HOH Z 196 " =    1.951
peak=   -3.732 closest distance to " CG1 VAL A 112 " =    2.560
peak=   -3.724 closest distance to " O   HOH Z 351 " =    1.478
peak=   -3.680 closest distance to " O   SER A 273 " =    1.177
peak=   -3.679 closest distance to " CD  GLN A  58 " =    1.335
peak=   -3.656 closest distance to " O   HOH Z 174 " =    1.776
peak=   -3.654 closest distance to " O   HOH Z 136 " =    2.055
peak=   -3.647 closest distance to " CG  ARG A 219 " =    2.392
peak=   -3.637 closest distance to " O   HOH Z  71 " =    1.297
peak=   -3.622 closest distance to " C   GLY A  91 " =    1.338
peak=   -3.611 closest distance to " OG BSER A 134 " =    1.590
peak=   -3.608 closest distance to " O   HOH Z 407 " =    3.156
peak=   -3.604 closest distance to " CD2 LEU A 300 " =    2.807
peak=   -3.600 closest distance to " CG1 VAL A 296 " =    1.063
peak=   -3.592 closest distance to " O   VAL A 174 " =    2.169
peak=   -3.591 closest distance to " CZ  TYR A 169 " =    1.824
peak=   -3.586 closest distance to " O   HOH Z 426 " =    1.732
peak=   -3.582 closest distance to " OG BSER A 210 " =    1.441
peak=   -3.581 closest distance to " O   HOH Z   6 " =    1.948
peak=   -3.570 closest distance to " SG  CYS A 254 " =    2.756
peak=   -3.565 closest distance to " O   HOH Z 151 " =    1.144
peak=   -3.561 closest distance to " CZ2 TRP A 179 " =    1.321
peak=   -3.555 closest distance to " CB  ALA A 248 " =    1.949
peak=   -3.553 closest distance to " O   HOH Z 422 " =    1.384
peak=   -3.545 closest distance to " NH2AARG A 275 " =    4.688
peak=   -3.544 closest distance to " O   HOH Z  52 " =    2.094
peak=   -3.543 closest distance to " O   TRP A  92 " =    1.989
peak=   -3.543 closest distance to " CA  SER A 276 " =    1.409
peak=   -3.540 closest distance to " O   HOH Z 426 " =    2.391
peak=   -3.538 closest distance to " O   HOH Z 313 " =    1.436
peak=   -3.530 closest distance to " CD2 LEU A 237 " =    2.583
peak=   -3.526 closest distance to " N   THR A 235 " =    1.278
peak=   -3.521 closest distance to " O   HOH Z 137 " =    1.885
peak=   -3.519 closest distance to " CA  GLY A 133 " =    2.005
peak=   -3.516 closest distance to " N   ARG A  66 " =    1.779
peak=   -3.506 closest distance to " CB  PRO A 163 " =    2.918
peak=   -3.505 closest distance to " OG  SER A   3 " =    1.385
peak=   -3.502 closest distance to " CB  ALA A 248 " =    2.122
peak=   -3.498 closest distance to " N   ALA A 248 " =    1.861
peak=   -3.498 closest distance to " O   HOH Z  92 " =    1.449
peak=   -3.496 closest distance to " O   HOH Z  60 " =    1.616
peak=   -3.495 closest distance to " CD1 TRP A 179 " =    1.116
peak=   -3.495 closest distance to " CG2 VAL A 189 " =    1.972
peak=   -3.493 closest distance to " CD  ARG A 195 " =    5.095
peak=   -3.484 closest distance to " CG1 VAL A  78 " =    2.671
peak=   -3.484 closest distance to " CD2 TYR A 293 " =    1.986
peak=   -3.472 closest distance to " O   HOH Z 126 " =    1.842
peak=   -3.461 closest distance to " CE1 HIS A  81 " =    1.261
peak=   -3.459 closest distance to " O   HOH Z 103 " =    1.939
peak=   -3.457 closest distance to " ND2 ASN A  39 " =    1.084
peak=   -3.455 closest distance to " O   HOH Z 120 " =    1.222
peak=   -3.454 closest distance to " O   HOH Z 424 " =    3.085
peak=   -3.442 closest distance to " O   HOH Z 388 " =    2.075
peak=   -3.441 closest distance to " O   HOH Z 165 " =    2.103
peak=   -3.431 closest distance to " OD1 ASN A  39 " =    2.255
peak=   -3.428 closest distance to " O   ALA A   1 " =    1.956
peak=   -3.417 closest distance to " O   HOH Z  11 " =    1.615
peak=   -3.411 closest distance to " CG  ASP A 231 " =    0.780
peak=   -3.409 closest distance to " O   HOH Z 126 " =    1.408
peak=   -3.409 closest distance to " CB  CYS A 254 " =    2.652
peak=   -3.405 closest distance to " O   HOH Z 411 " =    1.592
peak=   -3.398 closest distance to " O   SER A 146 " =    0.930
peak=   -3.395 closest distance to " O   HOH Z  78 " =    1.642
peak=   -3.392 closest distance to " CD2 LEU A 237 " =    2.837
peak=   -3.392 closest distance to " O   HOH Z 340 " =    1.024
peak=   -3.391 closest distance to " N   GLN A  58 " =    1.956
peak=   -3.389 closest distance to " CD1 PHE A 130 " =    2.268
peak=   -3.388 closest distance to " O   HOH Z 407 " =    1.415
peak=   -3.387 closest distance to " O   PRO A 198 " =    1.262
peak=   -3.382 closest distance to " O  BHOH Z 338 " =    1.553
peak=   -3.379 closest distance to " CD  GLN A  11 " =    1.052
peak=   -3.379 closest distance to " OD2 ASP A  50 " =    1.469
peak=   -3.379 closest distance to " OE2 GLU A   2 " =    1.542
peak=   -3.378 closest distance to " NE2 GLN A 194 " =    1.739
peak=   -3.375 closest distance to " NH2 ARG A  66 " =    1.312
peak=   -3.375 closest distance to " ND2 ASN A  69 " =    1.563
peak=   -3.373 closest distance to " N   SER A 210 " =    1.366
peak=   -3.368 closest distance to " O   HOH Z 120 " =    1.031
peak=   -3.364 closest distance to " CA  GLY A 203 " =    2.342
peak=   -3.355 closest distance to " O   MET A  40 " =    2.843
peak=   -3.350 closest distance to " O   HOH Z  10 " =    1.522
peak=   -3.349 closest distance to " OG1 THR A   4 " =    1.826
peak=   -3.345 closest distance to " O   GLY A 196 " =    1.023
peak=   -3.344 closest distance to " CB  LEU A 167 " =    2.188
peak=   -3.342 closest distance to " SG  CYS A 260 " =    2.519
peak=   -3.342 closest distance to " O   GLY A 241 " =    2.200
peak=   -3.339 closest distance to " O   LEU A 228 " =    2.459
peak=   -3.339 closest distance to " OG BSER A 212 " =    1.570
peak=   -3.338 closest distance to " CB  ASP A 132 " =    2.330
peak=   -3.336 closest distance to " CE  MET A 105 " =    1.985
peak=   -3.335 closest distance to " NH1 ARG A 195 " =    2.540
peak=   -3.331 closest distance to " O   HOH Z 292 " =    2.676
peak=   -3.322 closest distance to " NH2 ARG A  66 " =    4.856
peak=   -3.321 closest distance to " O   HOH Z 244 " =    1.612
peak=   -3.321 closest distance to " CG  GLN A  11 " =    1.661
peak=   -3.320 closest distance to " O   GLY A  80 " =    2.613
peak=   -3.318 closest distance to " NE1 TRP A 266 " =    2.239
peak=   -3.316 closest distance to " NH2 ARG A  79 " =    2.023
peak=   -3.315 closest distance to " CD2 PHE A  59 " =    2.511
peak=   -3.313 closest distance to " C   GLY A  80 " =    2.205
peak=   -3.312 closest distance to " O   HOH Z 311 " =    3.521
peak=   -3.311 closest distance to " O   HOH Z  39 " =    1.396
peak=   -3.310 closest distance to " CD1 TYR A 247 " =    2.230
peak=   -3.306 closest distance to " OD1 ASN A 148 " =    1.575
peak=   -3.306 closest distance to " CA  ASP A 298 " =    1.088
peak=   -3.303 closest distance to " OG  SER A  26 " =    1.489
peak=   -3.297 closest distance to " O   HOH Z 389 " =    1.326
peak=   -3.294 closest distance to " C   ALA A 158 " =    1.236
peak=   -3.292 closest distance to " CD  GLN A  73 " =    0.782
peak=   -3.291 closest distance to " O   HOH Z 313 " =    2.214
peak=   -3.290 closest distance to " C   GLY A 133 " =    1.265
peak=   -3.289 closest distance to " N   SER A 271 " =    1.549
peak=   -3.286 closest distance to " O   HOH Z 250 " =    1.406
peak=   -3.285 closest distance to " OD1 ASN A 249 " =    2.323
peak=   -3.284 closest distance to " O   ASN A  45 " =    1.845
peak=   -3.279 closest distance to " O   ALA A  51 " =    1.449
peak=   -3.279 closest distance to " CB  PHE A 208 " =    2.255
peak=   -3.278 closest distance to " O   HOH Z  48 " =    1.355
peak=   -3.277 closest distance to " O   VAL A 197 " =    1.289
peak=   -3.277 closest distance to " CA  ASP A  27 " =    2.480
peak=   -3.273 closest distance to " CA  ALA A 137 " =    2.473
peak=   -3.270 closest distance to " O   ALA A 161 " =    1.589
peak=   -3.263 closest distance to " O   HOH Z 174 " =    4.429
peak=   -3.260 closest distance to " O   HOH Z 150 " =    1.460
peak=   -3.252 closest distance to " CG2 VAL A 296 " =    1.309
peak=   -3.248 closest distance to " O   HOH Z 377 " =    2.106
peak=   -3.244 closest distance to " O   HOH Z  49 " =    0.847
peak=   -3.244 closest distance to " CB  ALA A 291 " =    2.197
peak=   -3.243 closest distance to " O   HOH Z 166 " =    1.541
peak=   -3.237 closest distance to " O   HOH Z 124 " =    1.583
peak=   -3.236 closest distance to " O   HOH Z 146 " =    0.857
peak=   -3.233 closest distance to " O   HOH Z 177 " =    1.775
peak=   -3.232 closest distance to " O   HOH Z 135 " =    1.605
peak=   -3.230 closest distance to " CB  ASP A 200 " =    2.604
peak=   -3.230 closest distance to " OG BSER A 134 " =    1.642
peak=   -3.229 closest distance to " OXT GLY A 302 " =    3.569
peak=   -3.229 closest distance to " O   ALA A 256 " =    1.464
peak=   -3.226 closest distance to " O   HOH Z  17 " =    0.928
peak=   -3.226 closest distance to " O   HOH Z 196 " =    2.263
peak=   -3.224 closest distance to " N   VAL A 189 " =    1.601
peak=   -3.218 closest distance to " O   HOH Z 171 " =    2.104
peak=   -3.218 closest distance to " N   VAL A 230 " =    1.108
peak=   -3.217 closest distance to " OG ASER A 134 " =    1.400
peak=   -3.215 closest distance to " CD  ARG A  36 " =    1.831
peak=   -3.215 closest distance to " CD  GLN A 223 " =    0.745
peak=   -3.214 closest distance to " O   HOH Z 377 " =    1.140
peak=   -3.214 closest distance to " OG1 THR A  82 " =    1.160
peak=   -3.211 closest distance to " CG  MET A 105 " =    0.860
peak=   -3.210 closest distance to " O   HOH Z 145 " =    2.160
peak=   -3.210 closest distance to " CA  GLY A 133 " =    2.278
peak=   -3.198 closest distance to " CD1 TYR A 169 " =    2.231
peak=   -3.196 closest distance to " CB  ALA A 100 " =    1.841
peak=   -3.192 closest distance to " OG  SER A 206 " =    1.370
peak=   -3.187 closest distance to " CE3 TRP A  70 " =    1.835
peak=   -3.186 closest distance to " O   HOH Z  46 " =    0.750
peak=   -3.186 closest distance to " CG  ASP A 132 " =    2.313
peak=   -3.175 closest distance to " O   HOH Z  97 " =    1.164
peak=   -3.174 closest distance to " O   HOH Z 234 " =    3.983
peak=   -3.172 closest distance to " CD  GLN A  88 " =    1.030
peak=   -3.170 closest distance to " OD2 ASP A 191 " =    1.631
peak=   -3.167 closest distance to " O   HOH Z 221 " =    1.325
peak=   -3.164 closest distance to " O   ASP A 191 " =    1.971
peak=   -3.162 closest distance to " O   ASP A 171 " =    1.786
peak=   -3.156 closest distance to " O   HOH Z 191 " =    5.568
peak=   -3.153 closest distance to " O   MET A 188 " =    1.808
peak=   -3.150 closest distance to " O   HOH Z 301 " =    2.265
peak=   -3.150 closest distance to " C   GLN A 144 " =    0.851
peak=   -3.148 closest distance to " O   HOH Z 219 " =    2.864
peak=   -3.146 closest distance to " O   HOH Z 396 " =    1.440
peak=   -3.138 closest distance to " O   HOH Z 405 " =    1.065
peak=   -3.135 closest distance to " CD1 LEU A  96 " =    2.183
peak=   -3.131 closest distance to " O   PHE A 218 " =    1.473
peak=   -3.121 closest distance to " C   ASN A 285 " =    2.203
peak=   -3.119 closest distance to " O   HOH Z 310 " =    3.462
peak=   -3.112 closest distance to " O   HOH Z 139 " =    3.471
peak=   -3.104 closest distance to " O   HOH Z   1 " =    4.376
peak=   -3.094 closest distance to " O   HOH Z 116 " =    1.149
peak=   -3.093 closest distance to " NH1 ARG A  66 " =    4.878
peak=   -3.093 closest distance to " O   HOH Z 297 " =    2.765
peak=   -3.083 closest distance to " O   ASP A 191 " =    1.446
peak=   -3.078 closest distance to " OG1 THR A  18 " =    1.903
peak=   -3.067 closest distance to " O   HOH Z 360 " =    2.433
peak=   -3.065 closest distance to " CE2 TRP A 274 " =    1.249
peak=   -3.054 closest distance to " O   HOH Z 313 " =    1.423
peak=   -3.051 closest distance to " O   HOH Z 109 " =    3.237
peak=   -3.050 closest distance to " O   ALA A  34 " =    2.431
peak=   -3.041 closest distance to " CG  ARG A 269 " =    2.143
peak=   -3.040 closest distance to " ND2 ASN A  60 " =    1.441

================= 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    :  0.5101 0.4977   6.304412e+00   6.295041e+00
   1_bss:  0.5028 0.4914   6.299028e+00   6.290033e+00
   1_xyz:  0.4375 0.4589   6.231965e+00   6.256563e+00
   1_adp:  0.3983 0.4509   6.185121e+00   6.244451e+00
   1_occ:  0.3974 0.4507   6.184256e+00   6.244422e+00
   2_bss:  0.3960 0.4437   6.184600e+00   6.242625e+00
   2_xyz:  0.3231 0.3780   6.028970e+00   6.141888e+00
   2_adp:  0.2992 0.3590   5.979757e+00   6.111399e+00
   2_occ:  0.2990 0.3585   5.979155e+00   6.110755e+00
   3_bss:  0.2963 0.3569   5.977554e+00   6.109358e+00
   3_xyz:  0.2143 0.2689   5.697720e+00   5.878053e+00
   3_adp:  0.1923 0.2416   5.599578e+00   5.784870e+00
   3_occ:  0.1919 0.2417   5.598661e+00   5.784840e+00
   4_bss:  0.1902 0.2399   5.597303e+00   5.780371e+00
   4_xyz:  0.1530 0.1980   5.404301e+00   5.613861e+00
   4_adp:  0.1395 0.1842   5.322768e+00   5.536695e+00
   4_occ:  0.1394 0.1841   5.322256e+00   5.536659e+00
   5_bss:  0.1394 0.1849   5.325292e+00   5.540643e+00
   5_xyz:  0.1230 0.1701   5.227668e+00   5.462644e+00
   5_adp:  0.1210 0.1670   5.209984e+00   5.444328e+00
   5_occ:  0.1208 0.1670   5.209658e+00   5.444418e+00
   5_bss:  0.1208 0.1670   5.209681e+00   5.444563e+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:  0.339   4.496   7.252  10.999   7.607   0.000   0.000   0.000
   1_xyz:  0.339   4.496   7.252  10.999   7.607   0.000   0.000   0.000
   1_adp:  0.339   4.496   7.252  10.999   7.607   0.000   0.000   0.000
   1_occ:  0.339   4.496   7.252  10.999   7.607   0.000   0.000   0.000
   2_bss:  0.295  20.000   3.639   6.575   4.708   0.000   0.000   0.000
   2_xyz:  0.295  20.000   3.639   6.575   4.708   0.000   0.000   0.000
   2_adp:  0.295  20.000   3.639   6.575   4.708   0.000   0.000   0.000
   2_occ:  0.295  20.000   3.639   6.575   4.708   0.000   0.000   0.000
   3_bss:  0.318  44.905   1.412   3.757   2.556   0.000   0.000   0.000
   3_xyz:  0.318  44.905   1.412   3.757   2.556   0.000   0.000   0.000
   3_adp:  0.318  44.905   1.412   3.757   2.556   0.000   0.000   0.000
   3_occ:  0.318  44.905   1.412   3.757   2.556   0.000   0.000   0.000
   4_bss:  0.318  37.875  -0.279   1.766   1.130   0.000   0.000   0.000
   4_xyz:  0.318  37.875  -0.279   1.766   1.130   0.000   0.000   0.000
   4_adp:  0.318  37.875  -0.279   1.766   1.130   0.000   0.000   0.000
   4_occ:  0.318  37.875  -0.279   1.766   1.130   0.000   0.000   0.000
   5_bss:  0.325  43.821  -0.929   0.848   0.591   0.000   0.000   0.000
   5_xyz:  0.325  43.821  -0.929   0.848   0.591   0.000   0.000   0.000
   5_adp:  0.325  43.821  -0.929   0.848   0.591   0.000   0.000   0.000
   5_occ:  0.325  43.821  -0.929   0.848   0.591   0.000   0.000   0.000
   5_bss:  0.325  43.908  -1.046   0.586   0.460   0.000   0.000   0.000
------------------------------------------------------------------------
 stage     <pher>    fom   alpha         beta
   0    :  63.750 0.3454  0.4090    80524.422
   1_bss:  64.395 0.3354  0.5046    79281.357
   1_xyz:  58.430 0.4112  0.6082    66396.125
   1_adp:  54.670 0.4600  0.7552    62292.675
   1_occ:  54.626 0.4605  0.7543    62112.104
   2_bss:  54.261 0.4649  0.6761    61083.963
   2_xyz:  43.106 0.6035  0.8744    41297.320
   2_adp:  39.796 0.6442  0.9317    36879.988
   2_occ:  39.768 0.6445  0.9316    36819.480
   3_bss:  39.438 0.6483  0.8619    36351.119
   3_xyz:  27.707 0.7817  0.9929    19217.479
   3_adp:  24.154 0.8203  1.0260    15670.615
   3_occ:  24.140 0.8204  1.0264    15671.928
   4_bss:  24.008 0.8216  0.9649    15460.887
   4_xyz:  19.095 0.8702  0.9956    10245.736
   4_adp:  17.254 0.8873  1.0028     8718.539
   4_occ:  17.245 0.8874  1.0029     8720.843
   5_bss:  17.316 0.8869  0.9775     8856.868
   5_xyz:  15.689 0.9011  0.9818     7587.308
   5_adp:  15.258 0.9050  0.9804     7367.315
   5_occ:  15.252 0.9051  0.9803     7369.465
   5_bss:  15.251 0.9051  0.9776     7370.627
------------------------------------------------------------------------
 stage       angl   bond   chir   dihe   plan   repu  geom_target
   0    :  24.226  0.414  2.119 33.790  0.145  4.088   5.3308e+01
   1_bss:  24.226  0.414  2.119 33.790  0.145  4.088   5.3308e+01
   1_xyz:   1.886  0.015  0.114 18.625  0.007  4.105   1.7443e-01
   1_adp:   1.886  0.015  0.114 18.625  0.007  4.105   1.7443e-01
   1_occ:   1.886  0.015  0.114 18.625  0.007  4.105   1.7443e-01
   2_bss:   1.886  0.015  0.114 18.625  0.007  4.105   1.7443e-01
   2_xyz:   1.376  0.010  0.091 17.248  0.006  4.104   1.1284e-01
   2_adp:   1.376  0.010  0.091 17.248  0.006  4.104   1.1284e-01
   2_occ:   1.376  0.010  0.091 17.248  0.006  4.104   1.1284e-01
   3_bss:   1.376  0.010  0.091 17.248  0.006  4.104   1.1284e-01
   3_xyz:   1.270  0.009  0.087 16.405  0.005  4.108   9.1852e-02
   3_adp:   1.270  0.009  0.087 16.405  0.005  4.108   9.1852e-02
   3_occ:   1.270  0.009  0.087 16.405  0.005  4.108   9.1852e-02
   4_bss:   1.270  0.009  0.087 16.405  0.005  4.108   9.1852e-02
   4_xyz:   1.057  0.007  0.076 15.909  0.004  4.120   6.8457e-02
   4_adp:   1.057  0.007  0.076 15.909  0.004  4.120   6.8457e-02
   4_occ:   1.057  0.007  0.076 15.909  0.004  4.120   6.8457e-02
   5_bss:   1.057  0.007  0.076 15.909  0.004  4.120   6.8457e-02
   5_xyz:   1.119  0.008  0.084 15.953  0.005  4.109   7.3339e-02
   5_adp:   1.119  0.008  0.084 15.953  0.005  4.109   7.3339e-02
   5_occ:   1.119  0.008  0.084 15.953  0.005  4.109   7.3339e-02
   5_bss:   1.119  0.008  0.084 15.953  0.005  4.109   7.3339e-02
------------------------------------------------------------------------
                      Maximal deviations:
 stage       angl   bond   chir   dihe   plan   repu       |grad|
   0    :  74.492  1.400  6.404144.062  0.405  0.906   6.9040e+00
   1_bss:  74.492  1.400  6.404144.062  0.405  0.906   6.9040e+00
   1_xyz:  17.034  0.185  0.577 87.070  0.053  2.101   1.1480e-01
   1_adp:  17.034  0.185  0.577 87.070  0.053  2.101   1.1480e-01
   1_occ:  17.034  0.185  0.577 87.070  0.053  2.101   1.1480e-01
   2_bss:  17.034  0.185  0.577 87.070  0.053  2.101   1.1480e-01
   2_xyz:   9.398  0.125  0.306 88.366  0.053  1.973   7.9678e-02
   2_adp:   9.398  0.125  0.306 88.366  0.053  1.973   7.9678e-02
   2_occ:   9.398  0.125  0.306 88.366  0.053  1.973   7.9678e-02
   3_bss:   9.398  0.125  0.306 88.366  0.053  1.973   7.9678e-02
   3_xyz:   7.549  0.053  0.281 88.380  0.042  2.151   8.5495e-02
   3_adp:   7.549  0.053  0.281 88.380  0.042  2.151   8.5495e-02
   3_occ:   7.549  0.053  0.281 88.380  0.042  2.151   8.5495e-02
   4_bss:   7.549  0.053  0.281 88.380  0.042  2.151   8.5495e-02
   4_xyz:   7.552  0.050  0.358 80.371  0.036  2.187   5.4047e-02
   4_adp:   7.552  0.050  0.358 80.371  0.036  2.187   5.4047e-02
   4_occ:   7.552  0.050  0.358 80.371  0.036  2.187   5.4047e-02
   5_bss:   7.552  0.050  0.358 80.371  0.036  2.187   5.4047e-02
   5_xyz:   7.482  0.050  0.481 83.301  0.040  2.230   5.3456e-02
   5_adp:   7.482  0.050  0.481 83.301  0.040  2.230   5.3456e-02
   5_occ:   7.482  0.050  0.481 83.301  0.040  2.230   5.3456e-02
   5_bss:   7.482  0.050  0.481 83.301  0.040  2.230   5.3456e-02
------------------------------------------------------------------------
           |-----overall-----|---macromolecule----|------solvent-------|
  stage    b_max  b_min  b_ave  b_max  b_min  b_ave  b_max  b_min  b_ave
   0    :  10.00  10.00  10.00  10.00  10.00  10.00  10.00  10.00  10.00
   1_bss:  19.99   0.01   9.86  19.98   0.01   9.82  19.99   0.06  10.10
   1_xyz:  19.99   0.01   9.86  19.98   0.01   9.82  19.99   0.06  10.10
   1_adp:  84.71   0.00  15.46  66.85   0.00  13.74  84.71   0.00  24.86
   1_occ:  84.71   0.00  15.46  66.85   0.00  13.74  84.71   0.00  24.86
   2_bss:  84.71   0.00  15.46  66.85   0.00  13.74  84.71   0.00  24.86
   2_xyz:  84.71   0.00  15.46  66.85   0.00  13.74  84.71   0.00  24.86
   2_adp:  94.43   0.00  15.36  71.08   0.00  12.54  94.43   0.00  30.69
   2_occ:  94.43   0.00  15.36  71.08   0.00  12.54  94.43   0.00  30.69
   3_bss:  94.43   0.00  15.36  71.08   0.00  12.54  94.43   0.00  30.69
   3_xyz:  94.43   0.00  15.36  71.08   0.00  12.54  94.43   0.00  30.69
   3_adp: 141.45   0.00  15.01 141.45   0.00  11.58  92.27   3.94  33.73
   3_occ: 141.45   0.00  15.01 141.45   0.00  11.58  92.27   3.94  33.73
   4_bss: 141.45   0.00  15.01 141.45   0.00  11.58  92.27   3.94  33.73
   4_xyz: 141.45   0.00  15.01 141.45   0.00  11.58  92.27   3.94  33.73
   4_adp:  81.92   0.00  15.25  81.92   0.00  11.00  77.43   3.80  38.45
   4_occ:  81.92   0.00  15.25  81.92   0.00  11.00  77.43   3.80  38.45
   5_bss:  81.92   0.00  15.25  81.92   0.00  11.00  77.43   3.80  38.45
   5_xyz:  81.92   0.00  15.25  81.92   0.00  11.00  77.43   3.80  38.45
   5_adp:  82.96   0.72  14.93  82.96   0.72  10.76  80.16   3.78  37.61
   5_occ:  82.96   0.72  14.93  82.96   0.72  10.76  80.16   3.78  37.61
   5_bss:  83.05   0.80  15.01  83.05   0.80  10.85  80.25   3.87  37.70
------------------------------------------------------------------------
 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:    1.168    0.016    0.426
   1_adp:    1.168    0.016    0.426
   1_occ:    1.168    0.016    0.426
   2_bss:    1.168    0.016    0.426
   2_xyz:    1.881    0.054    0.635
   2_adp:    1.881    0.054    0.635
   2_occ:    1.881    0.054    0.635
   3_bss:    1.881    0.054    0.635
   3_xyz:    1.752    0.046    0.789
   3_adp:    1.752    0.046    0.789
   3_occ:    1.752    0.046    0.789
   4_bss:    1.752    0.046    0.789
   4_xyz:    1.824    0.036    0.858
   4_adp:    1.824    0.036    0.858
   4_occ:    1.824    0.036    0.858
   5_bss:    1.824    0.036    0.858
   5_xyz:    1.851    0.102    0.890
   5_adp:    1.851    0.102    0.890
   5_occ:    1.851    0.102    0.890
   5_bss:    1.851    0.102    0.890
------------------------------------------------------------------------

CPU time actual refinement: 370.35


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

Writing refined structure to PDB file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/trial/run_222/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_222/model_refine_001_2mFobs-DFmodel.map
Writing mFobs-DFmodel XPLOR map to file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/trial/run_222/model_refine_001_mFobs-DFmodel.map
Writing map coefficients to MTZ file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/trial/run_222/model_refine_001_map_coeffs.mtz

Writing default parameters for subsequent refinement:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/trial/run_222/model_refine_002.def


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

Pure refinement (no I/O, processing, etc)= 370.20 
  Macro-tasks:
    bulk solvent and scale       = 46.83  
    individual site refinement   = 163.43 
    weights calculation          = 32.15  
    collect and process          = 6.44   
    model show statistics        = 0.12   
    TOTAL for macro-tasks        = 248.97 
  Micro-tasks:
    mask                            = 2.39   
    f_calc                          = 116.27 
    alpha_beta                      = 8.24   
    target                          = 1.13   
    gradients_wrt_atomic_parameters = 128.98 
    fmodel                         = 8.14   
    r_factors                      = 0.33   
    phase_errors                   = 10.10  
    foms                           = 0.28   
    TOTAL for micro-tasks          = 275.86 
NUMBER OF MASK CALCS=  5
Time per interpreted Python bytecode instruction: 5.035 micro seconds
Total CPU time: 6.40 minutes
from_scatterers_fft:    680 calls, 115.87 s
gradients_fft:          624 calls, 114.43 s

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

# Date 2008-01-16 Time 01:03:54 PST -0800 (1200474234.58 s)
Start R-work = 0.5101, R-free = 0.4977 (no bulk solvent and anisotropic scale)
Final R-work = 0.1385, R-free = 0.1833 (no bulk solvent and anisotropic scale)

Start R-work = 0.5028, R-free = 0.4914
Final R-work = 0.1208, R-free = 0.1670