# Date 2008-01-16 Time 00:57:16 PST -0800 (1200473836.43 s)
#phil __OFF__

Command line arguments: "../215.param" "adp.set_b_iso=10" "sites.shake=0.5" "main.number_of_macro_cycles=5" "--overwrite"

HOST = thunderbird.lbl.gov
HOSTTYPE = x86_64-linux
USER = phzwart
PID = 11889
JOB_ID = 5158
SGE_ARCH = lx24-amd64
SGE_TASK_FIRST = 1
SGE_TASK_LAST = 1330
SGE_TASK_ID = 215

-------------------------------------------------------------------------------
  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, 47.6339, 86.822, 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: 3.30, per 1000 atoms: 1.17


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

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

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

Miller array info: /net/cci-filer1/vol1/tmp/phzwart/tassos/trial/1e0w.cns:FOBS,SIGMA
Observation type: xray.amplitude
Type of data: double, size=19589
Type of sigmas: double, size=19589
Number of Miller indices: 19589
Anomalous flag: False
Unit cell: (68.845, 47.6339, 86.822, 90, 90, 90)
Space group: P 21 21 21 (No. 19)
Systematic absences: 0
Centric reflections: 2427
Resolution range: 14.9118 1.96081
Completeness in resolution range: 0.929931
Completeness with d_max=infinity: 0.927114

Number of F-obs in resolution range:                   19589
Number of F-obs <= 0:                                  0
Refinement resolution range: d_max =  14.9118
                             d_min =   1.9608

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, 47.6339, 86.822, 90, 90, 90)
Space group: P 21 21 21 (No. 19)
Systematic absences: 0
Centric reflections: 2427
Resolution range: 14.9118 1.96081
Completeness in resolution range: 0.929931
Completeness with d_max=infinity: 0.927114

Test (R-free flags) flag value: 1

Number of work/free reflections by resolution:
                                         work  free  %free
  bin  1: 14.9123 -  4.1960 [2212/2240]  1988   224  10.1%
  bin  2:  4.1960 -  3.3428 [2117/2140]  1906   211  10.0%
  bin  3:  3.3428 -  2.9239 [2091/2116]  1882   209  10.0%
  bin  4:  2.9239 -  2.6582 [2085/2101]  1877   208  10.0%
  bin  5:  2.6582 -  2.4686 [2037/2081]  1831   206  10.1%
  bin  6:  2.4686 -  2.3236 [2063/2091]  1861   202   9.8%
  bin  7:  2.3236 -  2.2076 [2040/2076]  1837   203  10.0%
  bin  8:  2.2076 -  2.1118 [2041/2083]  1836   205  10.0%
  bin  9:  2.1118 -  2.0307 [2009/2056]  1814   195   9.7%
  bin 10:  2.0307 -  1.9608 [ 894/2081]   798    96  10.7%
                                overall 17630  1959  10.0%
Writing MTZ file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/trial/run_215/model_refine_data.mtz


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

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

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

  Number of disulfides: simple=3, symmetry=0
    Simple disulfide: " SG  CYS A 168 " - " SG ACYS A 201 " distance=2.08
    Simple disulfide: " SG  CYS A 168 " - " SG BCYS A 201 " distance=1.98
    Simple disulfide: " SG  CYS A 254 " - " SG  CYS A 260 " distance=2.05
  Time building geometry restraints manager: 0.15 seconds
  Histogram of bond lengths:
        1.21 -     1.38: 943
        1.38 -     1.56: 1465
        1.56 -     1.73: 7
        1.73 -     1.90: 21
        1.90 -     2.08: 3
  Bond restraints sorted by residual:
             atom i - atom j            ideal  model  delta   weight residual
  " SG  CYS A 168 " - " SG BCYS A 201 " 2.031  1.983  0.048 2.50e+03 5.87e+00
  " C   GLN A  88 " - " N   GLN A  89 " 1.329  1.360 -0.031 5.10e+03 4.97e+00
  " SG  CYS A 168 " - " SG ACYS A 201 " 2.031  2.075 -0.044 2.50e+03 4.89e+00
  " CB  CYS A 201 " - " SG ACYS A 201 " 1.808  1.738  0.070 9.18e+02 4.46e+00
  " C   PRO A 198 " - " N   ILE A 199 " 1.329  1.301  0.028 5.10e+03 4.10e+00
  ... (remaining 2434 not shown)
  Histogram of nonbonded interaction distances:
        1.31 -     2.03: 10
        2.03 -     2.75: 299
        2.75 -     3.46: 4627
        3.46 -     4.18: 9377
        4.18 -     4.90: 14045
  Nonbonded interactions sorted by model distance:
             atom i - atom j             model   vdw sym.op. j
  " O   HOH Z 109 " - " O   HOH Z 417 "  1.309 3.040 -x+1,y-1/2,-z+1/2
  " O   HOH Z  18 " - " O   HOH Z 102 "  1.355 3.040 -x+1,y+1/2,-z+1/2
  " O   HOH Z  81 " - " O   HOH Z 186 "  1.483 3.040 -x+1,y+1/2,-z+1/2
  " O   HOH Z  70 " - " O   HOH Z 296 "  1.713 3.040 -x+1/2,-y+1,z+1/2
  " CE BMET A  47 " - " O  BHOH Z  74 "  1.806 3.460
  ... (remaining 28353 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_215/model_refine_001.eff

Writing geometry restraints to file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/trial/run_215/model_refine_001.geo

CPU time processing inputs: 9.25


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

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

#phil __ON__
refinement {
  crystal_symmetry {
    unit_cell = 68.845 47.63395 86.82195 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 - 14.91 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.4851   r_free= 0.4719   ksol= 0.00   Bsol= 0.00   scale= 0.791    |
|                                                                             |
| 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:   0.75 A                  |
| x-ray target function (ml) for work reflections: 6.285740                   |
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
| Bin     Resolution   Compl.  No. Refl.    R-factors          Targets        |
|number     range              work test   work   test        work        test|
|  1: 14.9123 -  4.6802 0.99   1438  159 0.3919 0.3881      6.5965      6.6386|
|  2:  4.6802 -  3.7340 0.99   1384  155 0.4000 0.4158      6.7734      6.8216|
|  3:  3.7340 -  3.2677 0.99   1349  149 0.4533 0.4129      6.6717      6.6671|
|  4:  3.2677 -  2.9715 0.99   1350  145 0.4738 0.4515      6.5085      6.4744|
|  5:  2.9715 -  2.7599 0.98   1332  152 0.5184 0.4818      6.3697      6.3888|
|  6:  2.7599 -  2.5981 0.99   1338  148 0.5136 0.5596      6.2829      6.1964|
|  7:  2.5981 -  2.4686 0.98   1293  150 0.5080 0.4818      6.2322      6.1626|
|  8:  2.4686 -  2.3616 0.99   1333  138 0.5300 0.4718      6.1852      6.1533|
|  9:  2.3616 -  2.2710 0.99   1329  152 0.5335 0.5509      6.1156       6.181|
| 10:  2.2710 -  2.1929 0.98   1319  142 0.5382 0.5000      6.1057      6.0839|
| 11:  2.1929 -  2.1245 0.97   1297  147 0.5591 0.5358       6.041      6.0389|
| 12:  2.1245 -  2.0639 0.99   1297  153 0.5316 0.5231      5.9513      5.9583|
| 13:  2.0639 -  2.0097 0.91   1226  126 0.5402 0.5631      5.8715      5.8469|
| 14:  2.0097 -  1.9608 0.26    345   43 0.5706 0.4656      5.9223      5.7157|
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
|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: 14.9123 -  4.6802  1438   159  0.67  37.20   0.80     0.68      80084.98|
|  2:  4.6802 -  3.7340  1384   155  0.68  37.07   0.89     0.73     112241.40|
|  3:  3.7340 -  3.2677  1349   149  0.59  44.68   0.83     0.70     115157.61|
|  4:  3.2677 -  2.9715  1350   145  0.52  50.33   0.79     0.61      95166.80|
|  5:  2.9715 -  2.7599  1332   152  0.43  57.72   0.73     0.52      79894.42|
|  6:  2.7599 -  2.5981  1338   148  0.39  60.38   0.71     0.45      70517.07|
|  7:  2.5981 -  2.4686  1293   150  0.36  62.93   0.75     0.42      66866.18|
|  8:  2.4686 -  2.3616  1333   138  0.37  62.11   0.73     0.44      57415.06|
|  9:  2.3616 -  2.2710  1329   152  0.37  62.09   0.72     0.46      53770.12|
| 10:  2.2710 -  2.1929  1319   142  0.38  61.66   0.73     0.45      47015.09|
| 11:  2.1929 -  2.1245  1297   147  0.33  65.62   0.73     0.43      47333.36|
| 12:  2.1245 -  2.0639  1297   153  0.30  67.38   0.75     0.40      44277.64|
| 13:  2.0639 -  2.0097  1226   126  0.28  69.48   0.71     0.36      39396.82|
| 14:  2.0097 -  1.9608   345    43  0.30  67.95   0.75     0.31      30118.25|
|alpha:            min =        0.31 max =            0.73 mean =         0.51|
|beta:             min =    30118.25 max =       115157.61 mean =     69714.96|
|figures of merit: min =        0.00 max =            1.00 mean =         0.44|
|phase err.(work): min =        0.00 max =           89.98 mean =        56.71|
|phase err.(test): min =        0.00 max =           89.90 mean =        56.88|
|-----------------------------------------------------------------------------|

============================== 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 = 14.464901             wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 80.159   (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 1.215693              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 77.204   (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 |  0.928 -  1.325:        4 |
| 0.140 - 0.280:   585 |   7.457 -  14.906:   711 |  1.325 -  1.723:        6 |
| 0.280 - 0.420:   441 |  14.906 -  22.354:   630 |  1.723 -  2.120:       73 |
| 0.420 - 0.560:   366 |  22.354 -  29.802:   474 |  2.120 -  2.517:      445 |
| 0.560 - 0.700:   237 |  29.802 -  37.251:   338 |  2.517 -  2.914:     1222 |
| 0.700 - 0.840:   127 |  37.251 -  44.699:   241 |  2.914 -  3.311:     2383 |
| 0.840 - 0.980:    59 |  44.699 -  52.147:   125 |  3.311 -  3.708:     3922 |
| 0.980 - 1.120:    17 |  52.147 -  59.595:    51 |  3.708 -  4.106:     5217 |
| 1.120 - 1.260:     9 |  59.595 -  67.044:    13 |  4.106 -  4.503:     6917 |
| 1.260 - 1.400:     1 |  67.044 -  74.492:     3 |  4.503 -  4.900:     8236 |
|-----------------------------------------------------------------------------|
|-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 |       53.617 |
| planarity |      436 |   0.145    0.405  0.000 |     250.485 |              |
|  dihedral |      870 |  33.790  144.062  0.019 |      20.704 |              |
| nonbonded |     2439 |   4.090    4.900  0.928 |       2.470 |              |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 11.797)------------------------------------------|
|    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 = 11.797)------------------------------------------|
|    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 - 14.91 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.4900   r_free= 0.4774   ksol= 0.00   Bsol= 0.00   scale= 0.761    |
|                                                                             |
| 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:   0.76 A                  |
| x-ray target function (ml) for work reflections: 6.286866                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.96 - 14.91 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.4774   r_free= 0.4669   ksol= 0.34   Bsol= 9.57   scale= 0.999    |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (7.85,10.66,8.30,0.00,0.00,0.00); trace/3= 8.94                             |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.75 A                  |
| x-ray target function (ml) for work reflections: 6.277411                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 13.717347             wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 81.560   (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 1.201623              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 77.142   (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.4774      final r-factor (work) = 0.3896          |
| start r-factor (free) = 0.4669      final r-factor (free) = 0.4099          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 96.7303 = 13.72 * 0.50 * 6.2860 + 1.00 * 53.6167                            |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 42.6320 = 13.72 * 0.50 * 6.1936 + 1.00 * 0.1522                             |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 26     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.3896      final r-factor (work) = 0.3424          |
| start r-factor (free) = 0.4099      final r-factor (free) = 0.3934          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 7.4567 = 1.20 * 1.00 * 6.1936 + 1.00 * 0.0143                               |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 7.3463 = 1.20 * 1.00 * 6.0988 + 1.00 * 0.0177                               |
|-----------------------------------------------------------------------------|
| number of iterations = 19      |    number of function evaluations = 24     |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 11.797)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.00    66.78   13.25    None  None   None       |
|    all(noH): 2823   0      0.00    66.78   13.25    None  None   None       |
|    Sol.    : 438    0      0.00    66.78   26.00    None  None   None       |
|    Mac.    : 2385   0      0.00    66.11   10.91    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 -   6.678: 1010   |   5:    33.390 -  40.068:   96        |
|      1:     6.678 -  13.356:  726   |   6:    40.068 -  46.746:   57        |
|      2:    13.356 -  20.034:  457   |   7:    46.746 -  53.424:   36        |
|      3:    20.034 -  26.712:  268   |   8:    53.424 -  60.102:   14        |
|      4:    26.712 -  33.390:  150   |   9:    60.102 -  66.780:    9        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.3424 r_free = 0.3934             target_work(ml) = 6.080         |
| occupancies: max = 1.00  min = 0.30   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.3421 r_free = 0.3938             target_work(ml) = 6.079         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        5 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.96 - 14.91 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.3421   r_free= 0.3938   ksol= 0.34   Bsol= 9.57   scale= 1.109    |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (7.85,10.66,8.30,0.00,0.00,0.00); trace/3= 8.94                             |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.50 A                  |
| x-ray target function (ml) for work reflections: 6.078828                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.96 - 14.91 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.3391   r_free= 0.3878   ksol= 0.30   Bsol= 20.00   scale= 1.014   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (4.18,6.31,5.08,0.00,0.00,0.00); trace/3= 5.19                              |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.51 A                  |
| x-ray target function (ml) for work reflections: 6.079007                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 5.270480              wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 98.953   (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 0.472923              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 122.398  (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.3391      final r-factor (work) = 0.2597          |
| start r-factor (free) = 0.3878      final r-factor (free) = 0.3105          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 16.2199 = 5.27 * 0.50 * 6.0972 + 1.00 * 0.1522                              |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 15.7894 = 5.27 * 0.50 * 5.9628 + 1.00 * 0.0759                              |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 27     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.2597      final r-factor (work) = 0.2404          |
| start r-factor (free) = 0.3105      final r-factor (free) = 0.2942          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 2.8375 = 0.47 * 1.00 * 5.9628 + 1.00 * 0.0176                               |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 2.7640 = 0.47 * 1.00 * 5.8209 + 1.00 * 0.0111                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 29     |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 11.797)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.00    71.32   13.08    None  None   None       |
|    all(noH): 2823   0      0.00    71.32   13.08    None  None   None       |
|    Sol.    : 438    0      1.31    68.89   30.78    None  None   None       |
|    Mac.    : 2385   0      0.00    71.32   9.83     None  None   None       |
|    Hyd.    : 0      0      None    None    None     None  None   None       |
|    - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -      |
|       Distribution of isotropic (or equivalent) ADP for non-H atoms:        |
|    Bin#      value range     #atoms | Bin#      value range     #atoms      |
|      0:     0.000 -   7.132: 1169   |   5:    35.661 -  42.793:  108        |
|      1:     7.132 -  14.264:  796   |   6:    42.793 -  49.925:   63        |
|      2:    14.264 -  21.396:  326   |   7:    49.925 -  57.057:   32        |
|      3:    21.396 -  28.528:  197   |   8:    57.057 -  64.189:   19        |
|      4:    28.528 -  35.661:  105   |   9:    64.189 -  71.321:    8        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.2404 r_free = 0.2942             target_work(ml) = 5.797         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        5 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.2403 r_free = 0.2940             target_work(ml) = 5.797         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        4 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.96 - 14.91 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.2403   r_free= 0.2940   ksol= 0.30   Bsol= 20.00   scale= 1.057   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (4.18,6.31,5.08,0.00,0.00,0.00); trace/3= 5.19                              |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.32 A                  |
| x-ray target function (ml) for work reflections: 5.796578                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.96 - 14.91 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.2382   r_free= 0.2925   ksol= 0.32   Bsol= 43.60   scale= 1.001   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (1.82,3.95,3.43,0.00,0.00,0.00); trace/3= 3.07                              |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.33 A                  |
| x-ray target function (ml) for work reflections: 5.794954                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 4.690957              wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 100.729  (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 0.267639              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 141.537  (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.2382      final r-factor (work) = 0.1666          |
| start r-factor (free) = 0.2925      final r-factor (free) = 0.2091          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 13.7427 = 4.69 * 0.50 * 5.8268 + 1.00 * 0.0760                              |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 13.3487 = 4.69 * 0.50 * 5.6606 + 1.00 * 0.0718                              |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 28     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1666      final r-factor (work) = 0.1504          |
| start r-factor (free) = 0.2091      final r-factor (free) = 0.1899          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 1.5261 = 0.27 * 1.00 * 5.6606 + 1.00 * 0.0111                               |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 1.4761 = 0.27 * 1.00 * 5.4250 + 1.00 * 0.0241                               |
|-----------------------------------------------------------------------------|
| number of iterations = 23      |    number of function evaluations = 24     |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 11.797)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.00    71.83   12.97    None  None   None       |
|    all(noH): 2823   0      0.00    71.83   12.97    None  None   None       |
|    Sol.    : 438    0      2.20    67.66   34.22    None  None   None       |
|    Mac.    : 2385   0      0.00    71.83   9.07     None  None   None       |
|    Hyd.    : 0      0      None    None    None     None  None   None       |
|    - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -      |
|       Distribution of isotropic (or equivalent) ADP for non-H atoms:        |
|    Bin#      value range     #atoms | Bin#      value range     #atoms      |
|      0:     0.000 -   7.183: 1261   |   5:    35.915 -  43.099:   93        |
|      1:     7.183 -  14.366:  847   |   6:    43.099 -  50.282:   82        |
|      2:    14.366 -  21.549:  226   |   7:    50.282 -  57.465:   48        |
|      3:    21.549 -  28.732:  123   |   8:    57.465 -  64.648:   17        |
|      4:    28.732 -  35.915:  115   |   9:    64.648 -  71.831:   11        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.1504 r_free = 0.1899             target_work(ml) = 5.378         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        4 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.1502 r_free = 0.1899             target_work(ml) = 5.377         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        3 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.96 - 14.91 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1502   r_free= 0.1899   ksol= 0.32   Bsol= 43.60   scale= 1.023   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (1.82,3.95,3.43,0.00,0.00,0.00); trace/3= 3.07                              |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.18 A                  |
| x-ray target function (ml) for work reflections: 5.376969                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.96 - 14.91 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1496   r_free= 0.1893   ksol= 0.32   Bsol= 43.60   scale= 0.999   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (0.93,2.58,2.92,0.00,0.00,0.00); trace/3= 2.14                              |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.18 A                  |
| x-ray target function (ml) for work reflections: 5.375101                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 1.804426              wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 111.621  (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 0.559245              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 91.294   (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1496      final r-factor (work) = 0.1312          |
| start r-factor (free) = 0.1893      final r-factor (free) = 0.1703          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 4.9710 = 1.80 * 0.50 * 5.4302 + 1.00 * 0.0718                               |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 4.8546 = 1.80 * 0.50 * 5.3179 + 1.00 * 0.0567                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 27     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1312      final r-factor (work) = 0.1282          |
| start r-factor (free) = 0.1703      final r-factor (free) = 0.1687          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 2.9963 = 0.56 * 1.00 * 5.3179 + 1.00 * 0.0223                               |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 2.9921 = 0.56 * 1.00 * 5.2551 + 1.00 * 0.0532                               |
|-----------------------------------------------------------------------------|
| number of iterations = 4       |    number of function evaluations = 6      |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 11.797)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.00    75.98   13.00    None  None   None       |
|    all(noH): 2823   0      0.00    75.98   13.00    None  None   None       |
|    Sol.    : 438    0      2.42    68.08   34.64    None  None   None       |
|    Mac.    : 2385   0      0.00    75.98   9.02     None  None   None       |
|    Hyd.    : 0      0      None    None    None     None  None   None       |
|    - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -      |
|       Distribution of isotropic (or equivalent) ADP for non-H atoms:        |
|    Bin#      value range     #atoms | Bin#      value range     #atoms      |
|      0:     0.000 -   7.598: 1328   |   5:    37.992 -  45.590:  103        |
|      1:     7.598 -  15.197:  827   |   6:    45.590 -  53.188:   77        |
|      2:    15.197 -  22.795:  198   |   7:    53.188 -  60.787:   35        |
|      3:    22.795 -  30.393:  121   |   8:    60.787 -  68.385:   16        |
|      4:    30.393 -  37.992:  114   |   9:    68.385 -  75.983:    4        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.1282 r_free = 0.1687             target_work(ml) = 5.251         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        3 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.1281 r_free = 0.1688             target_work(ml) = 5.251         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        5 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.96 - 14.91 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1281   r_free= 0.1688   ksol= 0.32   Bsol= 43.60   scale= 1.003   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (0.93,2.58,2.92,0.00,0.00,0.00); trace/3= 2.14                              |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.16 A                  |
| x-ray target function (ml) for work reflections: 5.251121                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.96 - 14.91 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1281   r_free= 0.1688   ksol= 0.32   Bsol= 43.60   scale= 1.000   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (0.88,2.32,2.94,0.00,0.00,0.00); trace/3= 2.05                              |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.16 A                  |
| x-ray target function (ml) for work reflections: 5.251142                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 2.333405              wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 128.441  (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 0.721747              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 90.653   (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1281      final r-factor (work) = 0.1193          |
| start r-factor (free) = 0.1688      final r-factor (free) = 0.1626          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 6.1877 = 2.33 * 0.50 * 5.2550 + 1.00 * 0.0567                               |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 6.1563 = 2.33 * 0.50 * 5.2187 + 1.00 * 0.0677                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 27     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1193      final r-factor (work) = 0.1165          |
| start r-factor (free) = 0.1626      final r-factor (free) = 0.1606          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 3.8035 = 0.72 * 1.00 * 5.2187 + 1.00 * 0.0369                               |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 3.7583 = 0.72 * 1.00 * 5.1897 + 1.00 * 0.0127                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 27     |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 11.797)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.00    86.22   13.33    None  None   None       |
|    all(noH): 2823   0      0.00    86.22   13.33    None  None   None       |
|    Sol.    : 438    0      1.62    75.46   36.96    None  None   None       |
|    Mac.    : 2385   0      0.00    86.22   8.99     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 -   8.622: 1573   |   5:    43.111 -  51.733:   92        |
|      1:     8.622 -  17.244:  668   |   6:    51.733 -  60.355:   60        |
|      2:    17.244 -  25.866:  156   |   7:    60.355 -  68.977:   36        |
|      3:    25.866 -  34.488:  121   |   8:    68.977 -  77.599:   13        |
|      4:    34.488 -  43.111:  101   |   9:    77.599 -  86.221:    3        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.1165 r_free = 0.1606             target_work(ml) = 5.184         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        5 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.1164 r_free = 0.1607             target_work(ml) = 5.184         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        6 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.96 - 14.91 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1164   r_free= 0.1607   ksol= 0.32   Bsol= 43.60   scale= 1.001   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (0.88,2.32,2.94,0.00,0.00,0.00); trace/3= 2.05                              |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.15 A                  |
| x-ray target function (ml) for work reflections: 5.183889                   |
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
| Bin     Resolution   Compl.  No. Refl.    R-factors          Targets        |
|number     range              work test   work   test        work        test|
|  1: 14.9123 -  4.6802 0.99   1438  159 0.0994 0.1268      5.3925      5.5422|
|  2:  4.6802 -  3.7340 0.99   1384  155 0.0851 0.1067      5.4271      5.6235|
|  3:  3.7340 -  3.2677 0.99   1349  149 0.1086 0.1521      5.4812      5.8486|
|  4:  3.2677 -  2.9715 0.99   1350  145 0.1262 0.1684      5.4703      5.6627|
|  5:  2.9715 -  2.7599 0.98   1332  152 0.1405 0.1619      5.3725      5.5081|
|  6:  2.7599 -  2.5981 0.99   1338  148 0.1307 0.2221      5.2563      5.5703|
|  7:  2.5981 -  2.4686 0.98   1293  150 0.1309 0.1650      5.2098      5.3739|
|  8:  2.4686 -  2.3616 0.99   1333  138 0.1218 0.1690      5.1231      5.3219|
|  9:  2.3616 -  2.2710 0.99   1329  152 0.1255 0.1968      5.0694      5.3829|
| 10:  2.2710 -  2.1929 0.98   1319  142 0.1201 0.1740      4.9967      5.2095|
| 11:  2.1929 -  2.1245 0.97   1297  147 0.1217 0.1809       4.956      5.2468|
| 12:  2.1245 -  2.0639 0.99   1297  153 0.1158 0.1629      4.8714      5.1051|
| 13:  2.0639 -  2.0097 0.91   1226  126 0.1175 0.1895      4.7991      5.0776|
| 14:  2.0097 -  1.9608 0.26    345   43 0.1068 0.1682        4.74      4.9531|
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
|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: 14.9123 -  4.6802  1438   159  0.94   8.99   0.98     0.96       7315.55|
|  2:  4.6802 -  3.7340  1384   155  0.95   8.17   1.02     1.00       8890.50|
|  3:  3.7340 -  3.2677  1349   149  0.93  11.49   1.03     1.02      10569.73|
|  4:  3.2677 -  2.9715  1350   145  0.91  14.59   1.01     1.00      10814.45|
|  5:  2.9715 -  2.7599  1332   152  0.89  16.84   0.99     0.96       9097.08|
|  6:  2.7599 -  2.5981  1338   148  0.89  17.44   0.98     0.95       7774.39|
|  7:  2.5981 -  2.4686  1293   150  0.90  16.50   0.98     0.94       6754.17|
|  8:  2.4686 -  2.3616  1333   138  0.90  16.75   1.00     0.97       6184.69|
|  9:  2.3616 -  2.2710  1329   152  0.90  16.63   1.00     0.96       5405.13|
| 10:  2.2710 -  2.1929  1319   142  0.89  16.94   1.00     0.96       4882.28|
| 11:  2.1929 -  2.1245  1297   147  0.90  16.86   1.00     0.96       4549.30|
| 12:  2.1245 -  2.0639  1297   153  0.90  16.09   1.01     1.00       3936.27|
| 13:  2.0639 -  2.0097  1226   126  0.90  16.63   0.99     0.97       3436.56|
| 14:  2.0097 -  1.9608   345    43  0.90  15.83   0.97     0.93       2977.24|
|alpha:            min =        0.93 max =            1.02 mean =         0.97|
|beta:             min =     2977.24 max =        10814.45 mean =      6866.04|
|figures of merit: min =        0.00 max =            1.00 mean =         0.91|
|phase err.(work): min =        0.00 max =           89.73 mean =        14.86|
|phase err.(test): min =        0.00 max =           89.96 mean =        14.26|
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.96 - 14.91 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1164   r_free= 0.1612   ksol= 0.32   Bsol= 50.54   scale= 1.001   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-1.13,0.20,0.93,0.00,0.00,0.00); trace/3= 0.00                             |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.16 A                  |
| x-ray target function (ml) for work reflections: 5.185001                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.96 - 14.91 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1164   r_free= 0.1612   ksol= 0.32   Bsol= 50.54   scale= 1.001   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-1.13,0.20,0.93,0.00,0.00,0.00); trace/3= 0.00                             |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.16 A                  |
| x-ray target function (ml) for work reflections: 5.185001                   |
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
| Bin     Resolution   Compl.  No. Refl.    R-factors          Targets        |
|number     range              work test   work   test        work        test|
|  1: 14.9123 -  4.6802 0.99   1438  159 0.0989 0.1314      5.4076      5.5706|
|  2:  4.6802 -  3.7340 0.99   1384  155 0.0864 0.1050      5.4398      5.6235|
|  3:  3.7340 -  3.2677 0.99   1349  149 0.1086 0.1516      5.4824      5.8402|
|  4:  3.2677 -  2.9715 0.99   1350  145 0.1265 0.1680      5.4688      5.6579|
|  5:  2.9715 -  2.7599 0.98   1332  152 0.1400 0.1616        5.37      5.5048|
|  6:  2.7599 -  2.5981 0.99   1338  148 0.1302 0.2229      5.2547      5.5689|
|  7:  2.5981 -  2.4686 0.98   1293  150 0.1304 0.1650      5.2077      5.3741|
|  8:  2.4686 -  2.3616 0.99   1333  138 0.1216 0.1687      5.1212      5.3209|
|  9:  2.3616 -  2.2710 0.99   1329  152 0.1253 0.1965      5.0673      5.3789|
| 10:  2.2710 -  2.1929 0.98   1319  142 0.1198 0.1740      4.9951      5.2082|
| 11:  2.1929 -  2.1245 0.97   1297  147 0.1214 0.1806      4.9546      5.2457|
| 12:  2.1245 -  2.0639 0.99   1297  153 0.1157 0.1631      4.8713      5.1063|
| 13:  2.0639 -  2.0097 0.91   1226  126 0.1175 0.1893      4.7986      5.0761|
| 14:  2.0097 -  1.9608 0.26    345   43 0.1065 0.1674      4.7374      4.9476|
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
|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: 14.9123 -  4.6802  1438   159  0.94   9.54   0.97     0.95       7873.00|
|  2:  4.6802 -  3.7340  1384   155  0.95   8.37   1.02     1.00       9151.37|
|  3:  3.7340 -  3.2677  1349   149  0.93  11.47   1.03     1.02      10536.31|
|  4:  3.2677 -  2.9715  1350   145  0.91  14.52   1.01     1.00      10703.86|
|  5:  2.9715 -  2.7599  1332   152  0.89  16.78   1.00     0.97       9029.95|
|  6:  2.7599 -  2.5981  1338   148  0.89  17.45   0.98     0.95       7769.24|
|  7:  2.5981 -  2.4686  1293   150  0.90  16.51   0.98     0.94       6757.44|
|  8:  2.4686 -  2.3616  1333   138  0.90  16.72   1.00     0.97       6162.54|
|  9:  2.3616 -  2.2710  1329   152  0.90  16.58   1.00     0.97       5378.09|
| 10:  2.2710 -  2.1929  1319   142  0.89  16.90   1.00     0.97       4860.54|
| 11:  2.1929 -  2.1245  1297   147  0.90  16.84   1.00     0.97       4536.51|
| 12:  2.1245 -  2.0639  1297   153  0.90  16.10   1.01     1.00       3940.47|
| 13:  2.0639 -  2.0097  1226   126  0.90  16.61   0.99     0.98       3429.28|
| 14:  2.0097 -  1.9608   345    43  0.90  15.77   0.98     0.93       2954.82|
|alpha:            min =        0.93 max =            1.02 mean =         0.97|
|beta:             min =     2954.82 max =        10703.86 mean =      6908.83|
|figures of merit: min =        0.00 max =            1.00 mean =         0.91|
|phase err.(work): min =        0.00 max =           89.99 mean =        14.89|
|phase err.(test): min =        0.00 max =           89.82 mean =        14.31|
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 11.797)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      2.09    88.31   15.42    None  None   None       |
|    all(noH): 2823   0      2.09    88.31   15.42    None  None   None       |
|    Sol.    : 438    0      3.71    77.55   39.05    None  None   None       |
|    Mac.    : 2385   0      2.09    88.31   11.08    None  None   None       |
|    Hyd.    : 0      0      None    None    None     None  None   None       |
|    - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -      |
|       Distribution of isotropic (or equivalent) ADP for non-H atoms:        |
|    Bin#      value range     #atoms | Bin#      value range     #atoms      |
|      0:     2.094 -  10.716: 1573   |   5:    45.204 -  53.826:   92        |
|      1:    10.716 -  19.338:  668   |   6:    53.826 -  62.448:   60        |
|      2:    19.338 -  27.960:  156   |   7:    62.448 -  71.070:   36        |
|      3:    27.960 -  36.582:  121   |   8:    71.070 -  79.693:   13        |
|      4:    36.582 -  45.204:  101   |   9:    79.693 -  88.315:    3        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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


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

Number of peaks found at mFobs-DFmodel map (map cutoff=3.00 sigma)= 314         
Filter by distance & map next to the model:
   mapped sites are within: 0.401 - 4.847
   number of sites selected in [dist_min= 0.70, dist_max= 6.00]: 307 from: 314
   mapped sites are within: 0.760 - 4.847

peak=   10.379 closest distance to " CB  VAL A 230 " =    1.422
peak=    6.180 closest distance to " CD1AILE A 234 " =    1.143
peak=    6.079 closest distance to " CG  LEU A   5 " =    1.244
peak=    5.834 closest distance to " NH2 ARG A  56 " =    2.203
peak=    5.809 closest distance to " CB  VAL A 296 " =    1.156
peak=    5.557 closest distance to " O   HOH Z 403 " =    1.856
peak=    5.401 closest distance to " O   HOH Z 248 " =    1.442
peak=    5.390 closest distance to " O   HOH Z 124 " =    1.466
peak=    5.200 closest distance to " CG  LEU A 228 " =    1.144
peak=    5.130 closest distance to " CG1 VAL A 296 " =    1.193
peak=    5.089 closest distance to " O   HOH Z 193 " =    1.939
peak=    5.084 closest distance to " CG  PRO A  54 " =    1.267
peak=    5.009 closest distance to " CB  ARG A 275 " =    0.979
peak=    4.986 closest distance to " O   HOH Z  85 " =    1.905
peak=    4.956 closest distance to " CB  SER A  63 " =    1.190
peak=    4.891 closest distance to " O   HOH Z  49 " =    1.273
peak=    4.821 closest distance to " CB  GLN A 183 " =    1.301
peak=    4.810 closest distance to " O   HOH Z 209 " =    2.321
peak=    4.791 closest distance to " O   HOH Z 130 " =    1.135
peak=    4.724 closest distance to " CB  PRO A  54 " =    1.008
peak=    4.721 closest distance to " CD2 LEU A   5 " =    1.188
peak=    4.718 closest distance to " CB  GLN A 223 " =    1.436
peak=    4.692 closest distance to " O   HOH Z 404 " =    1.336
peak=    4.656 closest distance to " O   HOH Z 128 " =    1.591
peak=    4.653 closest distance to " O   HOH Z 232 " =    2.320
peak=    4.643 closest distance to " O   HOH Z 130 " =    2.474
peak=    4.620 closest distance to " O   HOH Z 402 " =    1.505
peak=    4.600 closest distance to " CB  VAL A 230 " =    1.163
peak=    4.593 closest distance to " O   HOH Z 142 " =    1.644
peak=    4.527 closest distance to " NE2 GLN A  11 " =    1.028
peak=    4.519 closest distance to " O   HOH Z  43 " =    1.514
peak=    4.487 closest distance to " CG2 VAL A 296 " =    1.023
peak=    4.483 closest distance to " O   HOH Z 154 " =    1.781
peak=    4.481 closest distance to " O   HOH Z 414 " =    1.918
peak=    4.465 closest distance to " CA  TYR A  30 " =    0.954
peak=    4.463 closest distance to " O   HOH Z 102 " =    1.379
peak=    4.431 closest distance to " O   HOH Z 238 " =    1.194
peak=    4.407 closest distance to " O   HOH Z 406 " =    1.387
peak=    4.407 closest distance to " O   HOH Z 327 " =    1.740
peak=    4.398 closest distance to " O   SER A  87 " =    2.288
peak=    4.383 closest distance to " O   HOH Z  63 " =    2.217
peak=    4.381 closest distance to " O   HOH Z 346 " =    1.576
peak=    4.370 closest distance to " CG  PRO A 243 " =    1.169
peak=    4.369 closest distance to " C   PRO A 198 " =    1.506
peak=    4.340 closest distance to " O   HOH Z 272 " =    1.948
peak=    4.312 closest distance to " O   HOH Z  80 " =    1.960
peak=    4.295 closest distance to " O   HOH Z 247 " =    1.326
peak=    4.266 closest distance to " CB  TRP A 179 " =    1.245
peak=    4.261 closest distance to " O   HOH Z 369 " =    2.367
peak=    4.256 closest distance to " O   HOH Z 234 " =    3.592
peak=    4.255 closest distance to " CD2 LEU A 228 " =    1.323
peak=    4.250 closest distance to " CA  ALA A  51 " =    1.052
peak=    4.223 closest distance to " O   HOH Z 126 " =    1.787
peak=    4.217 closest distance to " CB  SER A  26 " =    1.807
peak=    4.214 closest distance to " O   HOH Z  40 " =    1.977
peak=    4.182 closest distance to " CD2 TRP A 179 " =    1.349
peak=    4.126 closest distance to " O   HOH Z 236 " =    1.592
peak=    4.124 closest distance to " O   HOH Z 368 " =    2.262
peak=    4.108 closest distance to " CG  PRO A 213 " =    1.229
peak=    4.103 closest distance to " CB BVAL A  41 " =    1.062
peak=    4.080 closest distance to " CD  LYS A 166 " =    1.397
peak=    4.069 closest distance to " O   HOH Z 298 " =    1.797
peak=    4.063 closest distance to " CG1 ILE A  33 " =    1.233
peak=    4.040 closest distance to " O   HOH Z 261 " =    2.254
peak=    4.039 closest distance to " O   HOH Z   4 " =    1.585
peak=    4.034 closest distance to " O   HOH Z 189 " =    2.755
peak=    4.006 closest distance to " O   HOH Z  54 " =    1.674
peak=    3.998 closest distance to " O   HOH Z 214 " =    2.561
peak=    3.985 closest distance to " O   HOH Z 162 " =    1.877
peak=    3.954 closest distance to " CB  GLU A 277 " =    3.612
peak=    3.949 closest distance to " O   HOH Z 154 " =    2.212
peak=    3.948 closest distance to " O   HOH Z 423 " =    1.803
peak=    3.931 closest distance to " CZ  PHE A  38 " =    1.206
peak=    3.923 closest distance to " CB  ARG A  79 " =    1.434
peak=    3.921 closest distance to " O   HOH Z 394 " =    1.521
peak=    3.915 closest distance to " O   HOH Z 214 " =    1.440
peak=    3.915 closest distance to " CB  GLU A 152 " =    1.131
peak=    3.905 closest distance to " O   HOH Z 359 " =    1.633
peak=    3.902 closest distance to " O   HOH Z 371 " =    3.281
peak=    3.896 closest distance to " O   HOH Z 245 " =    1.460
peak=    3.891 closest distance to " O   HOH Z 422 " =    2.566
peak=    3.890 closest distance to " O   HOH Z 126 " =    1.523
peak=    3.890 closest distance to " O   HOH Z 411 " =    3.626
peak=    3.859 closest distance to " O   HOH Z 427 " =    2.597
peak=    3.856 closest distance to " O   HOH Z 389 " =    1.912
peak=    3.839 closest distance to " CG  PRO A 198 " =    1.174
peak=    3.839 closest distance to " NH2BARG A 145 " =    2.165
peak=    3.832 closest distance to " CG2 ILE A  20 " =    1.471
peak=    3.820 closest distance to " O   HOH Z 265 " =    2.147
peak=    3.816 closest distance to " O   ASP A 124 " =    1.440
peak=    3.804 closest distance to " OE1 GLU A   2 " =    2.070
peak=    3.801 closest distance to " O   HOH Z 406 " =    1.673
peak=    3.801 closest distance to " O   HOH Z  44 " =    2.067
peak=    3.793 closest distance to " O   HOH Z 301 " =    1.856
peak=    3.765 closest distance to " NZ  LYS A 117 " =    2.906
peak=    3.760 closest distance to " N   ASN A  39 " =    1.282
peak=    3.741 closest distance to " O   HOH Z 287 " =    1.728
peak=    3.733 closest distance to " CB  ARG A 190 " =    1.760
peak=    3.727 closest distance to " CB  SER A   3 " =    1.266
peak=    3.725 closest distance to " CG2AVAL A  72 " =    1.777
peak=    3.724 closest distance to " CD  ARG A 159 " =    0.781
peak=    3.720 closest distance to " O   HOH Z 303 " =    2.251
peak=    3.712 closest distance to " O   HOH Z 173 " =    2.394
peak=    3.712 closest distance to " O   HOH Z  48 " =    1.662
peak=    3.709 closest distance to " CA  VAL A  41 " =    0.872
peak=    3.707 closest distance to " NE2 GLN A  77 " =    3.182
peak=    3.707 closest distance to " O   HOH Z 128 " =    2.101
peak=    3.704 closest distance to " CD  ARG A 269 " =    1.091
peak=    3.702 closest distance to " O   HOH Z  97 " =    2.013
peak=    3.698 closest distance to " O   HOH Z 316 " =    2.810
peak=    3.690 closest distance to " CZ  PHE A 218 " =    1.125
peak=    3.674 closest distance to " O   HOH Z 426 " =    1.391
peak=    3.671 closest distance to " O   HOH Z 203 " =    1.748
peak=    3.669 closest distance to " O   HOH Z 357 " =    1.955
peak=    3.668 closest distance to " CB  ARG A  79 " =    0.913
peak=    3.668 closest distance to " O   HOH Z 134 " =    1.568
peak=    3.660 closest distance to " CG  MET A 185 " =    1.138
peak=    3.655 closest distance to " O   HOH Z 109 " =    1.449
peak=    3.652 closest distance to " CB  TRP A 266 " =    1.119
peak=    3.652 closest distance to " O   HOH Z 250 " =    1.335
peak=    3.650 closest distance to " CB  ASN A  45 " =    1.107
peak=    3.643 closest distance to " CB  GLU A 128 " =    1.110
peak=    3.643 closest distance to " CE  LYS A 119 " =    1.047
peak=    3.640 closest distance to " CB  THR A  52 " =    0.864
peak=    3.635 closest distance to " CB  ASN A 148 " =    1.255
peak=    3.634 closest distance to " ND2 ASN A 187 " =    1.596
peak=    3.626 closest distance to " CD  PRO A  54 " =    1.000
peak=    3.626 closest distance to " O   HOH Z 417 " =    3.249
peak=    3.620 closest distance to " CG2 ILE A 120 " =    1.330
peak=    3.619 closest distance to " O   HOH Z 366 " =    2.576
peak=    3.610 closest distance to " O   HOH Z 345 " =    2.779
peak=    3.608 closest distance to " CG  ARG A  66 " =    0.973
peak=    3.604 closest distance to " NH2 ARG A 156 " =    1.105
peak=    3.603 closest distance to " O   HOH Z 280 " =    3.029
peak=    3.587 closest distance to " O   HOH Z 313 " =    1.703
peak=    3.584 closest distance to " CE1 HIS A 108 " =    1.131
peak=    3.582 closest distance to " CD1 LEU A  96 " =    0.760
peak=    3.578 closest distance to " CG2 ILE A 234 " =    1.111
peak=    3.577 closest distance to " CD  LYS A 119 " =    1.966
peak=    3.573 closest distance to " O   HOH Z 185 " =    1.684
peak=    3.573 closest distance to " CG AARG A 275 " =    1.252
peak=    3.556 closest distance to " CB  ARG A 139 " =    0.992
peak=    3.555 closest distance to " O   HOH Z  68 " =    1.872
peak=    3.536 closest distance to " O   HOH Z 322 " =    2.203
peak=    3.535 closest distance to " O   ALA A 165 " =    1.349
peak=    3.535 closest distance to " OE1 GLN A  11 " =    1.779
peak=    3.534 closest distance to " O   HOH Z  61 " =    1.510
peak=    3.533 closest distance to " OG BSER A 164 " =    2.193
peak=    3.529 closest distance to " O   HOH Z 438 " =    2.603
peak=    3.525 closest distance to " NZ  LYS A  76 " =    1.856
peak=    3.523 closest distance to " CA  ASN A 176 " =    1.098
peak=    3.519 closest distance to " O   HOH Z 421 " =    2.071
peak=    3.512 closest distance to " CD2 LEU A 297 " =    0.964
peak=    3.512 closest distance to " O   HOH Z 380 " =    1.801
peak=    3.512 closest distance to " CB  ALA A   9 " =    1.674
peak=    3.508 closest distance to " O   HOH Z  97 " =    2.266
peak=    3.508 closest distance to " OG  SER A  62 " =    2.755
peak=    3.506 closest distance to " CB  SER A 141 " =    1.054
peak=    3.504 closest distance to " O   HOH Z 258 " =    2.293
peak=    3.487 closest distance to " OH  TYR A 116 " =    1.212
peak=    3.485 closest distance to " O   HOH Z 383 " =    2.048
peak=    3.485 closest distance to " CB  ALA A 248 " =    1.365
peak=    3.476 closest distance to " NH1AARG A 275 " =    0.964
peak=    3.470 closest distance to " O   HOH Z 251 " =    1.334
peak=    3.468 closest distance to " CA  ARG A 195 " =    1.192
peak=    3.461 closest distance to " CB  VAL A 265 " =    1.224
peak=    3.458 closest distance to " O   HOH Z 353 " =    2.807
peak=    3.457 closest distance to " CA  ARG A  36 " =    1.042
peak=    3.454 closest distance to " CZ2 TRP A 150 " =    1.073
peak=    3.453 closest distance to " O   HOH Z 158 " =    3.072
peak=    3.450 closest distance to " CB  TRP A 150 " =    1.451
peak=    3.447 closest distance to " CB  ALA A 100 " =    1.174
peak=    3.446 closest distance to " CB  THR A  31 " =    1.473
peak=    3.446 closest distance to " OD1 ASN A  69 " =    2.380
peak=    3.439 closest distance to " O   HOH Z 162 " =    2.062
peak=    3.438 closest distance to " OD1 ASP A 286 " =    1.800
peak=    3.436 closest distance to " CG2AVAL A 121 " =    2.028
peak=    3.430 closest distance to " O   HOH Z 227 " =    1.566
peak=    3.429 closest distance to " NZ  LYS A  48 " =    1.283
peak=    3.429 closest distance to " CG2 THR A 221 " =    1.219
peak=    3.428 closest distance to " O   HOH Z  78 " =    1.597
peak=    3.424 closest distance to " O   HOH Z 412 " =    3.723
peak=    3.423 closest distance to " O   HOH Z 345 " =    1.686
peak=    3.423 closest distance to " O   HOH Z 263 " =    1.728
peak=    3.418 closest distance to " CA  ALA A 295 " =    0.990
peak=    3.406 closest distance to " O   HOH Z 148 " =    3.252
peak=    3.399 closest distance to " O   HOH Z 403 " =    1.510
peak=    3.399 closest distance to " O   HOH Z 253 " =    1.551
peak=    3.397 closest distance to " CB  VAL A 202 " =    1.415
peak=    3.396 closest distance to " O   GLY A  91 " =    1.401
peak=    3.391 closest distance to " O   HOH Z 189 " =    2.460
peak=    3.387 closest distance to " O   HOH Z 132 " =    2.713
peak=    3.382 closest distance to " CZ3 TRP A  85 " =    0.946
peak=    3.379 closest distance to " O   HOH Z 271 " =    2.537
peak=    3.377 closest distance to " CG2 THR A 294 " =    1.571
peak=    3.376 closest distance to " CB  ASN A  39 " =    0.872
peak=    3.375 closest distance to " CA  ALA A  21 " =    1.191
peak=    3.371 closest distance to " O   HOH Z 435 " =    1.900
peak=    3.358 closest distance to " CD2 TYR A 186 " =    1.034
peak=    3.358 closest distance to " O   HOH Z 344 " =    3.000
peak=    3.352 closest distance to " CA  TRP A  85 " =    1.158
peak=    3.345 closest distance to " CA  VAL A 125 " =    1.237
peak=    3.343 closest distance to " ND2 ASN A 249 " =    0.894
peak=    3.342 closest distance to " CD  ARG A  66 " =    2.796
peak=    3.340 closest distance to " CA  ASP A 162 " =    1.064
peak=    3.337 closest distance to " O   HOH Z 336 " =    1.831
peak=    3.333 closest distance to " CA  SER A  32 " =    1.688
peak=    3.326 closest distance to " O   HOH Z  88 " =    3.294
peak=    3.326 closest distance to " OG1 THR A 294 " =    2.317
peak=    3.323 closest distance to " O   HOH Z 273 " =    2.878
peak=    3.322 closest distance to " CG  GLN A  11 " =    1.517
peak=    3.316 closest distance to " O   HOH Z   1 " =    2.019
peak=    3.316 closest distance to " O   HOH Z 197 " =    1.988
peak=    3.313 closest distance to " O   HOH Z 145 " =    2.312
peak=    3.311 closest distance to " CD1 ILE A 199 " =    1.047
peak=    3.310 closest distance to " O   HOH Z 337 " =    1.660
peak=    3.307 closest distance to " CB  PHE A 204 " =    0.880
peak=    3.307 closest distance to " O   HOH Z  21 " =    1.844
peak=    3.306 closest distance to " O   HOH Z  15 " =    2.170
peak=    3.305 closest distance to " CA  ARG A 275 " =    1.813
peak=    3.304 closest distance to " OG BSER A 212 " =    2.682
peak=    3.303 closest distance to " CG BARG A 102 " =    1.762
peak=    3.299 closest distance to " NH1AARG A 145 " =    1.242
peak=    3.297 closest distance to " O   HOH Z 433 " =    1.442
peak=    3.294 closest distance to " O   HOH Z 183 " =    1.764
peak=    3.293 closest distance to " CG  LEU A 167 " =    1.116
peak=    3.289 closest distance to " N   CYS A 260 " =    0.848
peak=    3.289 closest distance to " O   HOH Z 298 " =    4.258
peak=    3.288 closest distance to " CA  TYR A 116 " =    1.418
peak=    3.287 closest distance to " CB  PRO A  90 " =    1.116
peak=    3.284 closest distance to " O   HOH Z 361 " =    3.047
peak=    3.282 closest distance to " CG  GLN A  58 " =    2.739
peak=    3.282 closest distance to " O   HOH Z 193 " =    1.910
peak=    3.280 closest distance to " CB  TYR A 247 " =    1.022
peak=    3.280 closest distance to " CA  ALA A 100 " =    0.957
peak=    3.274 closest distance to " O   HOH Z 419 " =    1.878
peak=    3.274 closest distance to " CG2 VAL A 197 " =    1.095
peak=    3.268 closest distance to " CA  SER A  87 " =    0.995
peak=    3.267 closest distance to " N   ASP A 231 " =    1.625
peak=    3.267 closest distance to " CE1 TYR A 186 " =    1.283
peak=    3.264 closest distance to " CB  GLN A  88 " =    1.204
peak=    3.263 closest distance to " O   HOH Z 406 " =    1.357
peak=    3.263 closest distance to " CB  ASN A 285 " =    0.968
peak=    3.262 closest distance to " O   HOH Z  47 " =    1.598
peak=    3.257 closest distance to " CB  SER A  99 " =    1.479
peak=    3.256 closest distance to " CA  ALA A 291 " =    0.851
peak=    3.253 closest distance to " CB  PRO A 198 " =    1.020
peak=    3.252 closest distance to " O  BHOH Z  74 " =    1.462
peak=    3.251 closest distance to " CA  LYS A 117 " =    1.271
peak=    3.247 closest distance to " OG1 THR A 221 " =    1.247
peak=    3.243 closest distance to " CB  LEU A   5 " =    1.269
peak=    3.238 closest distance to " O   HOH Z 409 " =    1.785
peak=    3.236 closest distance to " O   HOH Z 285 " =    2.908
peak=    3.235 closest distance to " O   HOH Z 295 " =    1.459
peak=    3.234 closest distance to " CA  LYS A 290 " =    1.093
peak=    3.233 closest distance to " CB  ARG A 259 " =    1.925
peak=    3.230 closest distance to " O   HOH Z 420 " =    1.950
peak=    3.229 closest distance to " CB  SER A  62 " =    1.003
peak=    3.226 closest distance to " CG1 VAL A 153 " =    0.997
peak=    3.213 closest distance to " CD1 LEU A 101 " =    1.244
peak=    3.213 closest distance to " O   HOH Z 116 " =    2.634
peak=    3.208 closest distance to " CG  LYS A 119 " =    1.142
peak=    3.208 closest distance to " CG  ARG A 269 " =    1.223
peak=    3.205 closest distance to " O   HOH Z 112 " =    1.811
peak=    3.200 closest distance to " O   HOH Z 427 " =    3.132
peak=    3.198 closest distance to " CA  ASN A 217 " =    1.168
peak=    3.197 closest distance to " O   HOH Z 329 " =    4.010
peak=    3.196 closest distance to " CA  ALA A 160 " =    0.906
peak=    3.196 closest distance to " CB  ALA A 295 " =    1.162
peak=    3.195 closest distance to " CB  ASN A 142 " =    1.195
peak=    3.194 closest distance to " CZ2 TRP A 274 " =    1.601
peak=    3.189 closest distance to " O   THR A  31 " =    1.700
peak=    3.183 closest distance to " CB  ARG A 219 " =    1.240
peak=    3.181 closest distance to " O   HOH Z 355 " =    1.885
peak=    3.179 closest distance to " O   HOH Z   9 " =    2.428
peak=    3.179 closest distance to " O   HOH Z  46 " =    1.330
peak=    3.179 closest distance to " O   HOH Z 337 " =    3.595
peak=    3.176 closest distance to " O   HOH Z 299 " =    4.173
peak=    3.176 closest distance to " O   HOH Z 163 " =    1.332
peak=    3.174 closest distance to " CB  ASP A 140 " =    1.088
peak=    3.173 closest distance to " O   HOH Z 387 " =    1.942
peak=    3.171 closest distance to " CA  ASP A 149 " =    1.159
peak=    3.170 closest distance to " CB  ALA A  71 " =    1.317
peak=    3.163 closest distance to " OD2 ASP A 298 " =    3.952
peak=    3.158 closest distance to " CE  LYS A  76 " =    0.871
peak=    3.157 closest distance to " O   HOH Z 438 " =    1.881
peak=    3.156 closest distance to " O   SER A 164 " =    1.165
peak=    3.151 closest distance to " CB  ALA A 114 " =    1.080
peak=    3.150 closest distance to " CG  GLN A  55 " =    2.450
peak=    3.147 closest distance to " O   HOH Z 281 " =    4.847
peak=    3.141 closest distance to " O   HOH Z 364 " =    2.326
peak=    3.137 closest distance to " O   HOH Z  48 " =    1.697
peak=    3.136 closest distance to " O   HOH Z 280 " =    3.038
peak=    3.136 closest distance to " NH2 ARG A  79 " =    1.323
peak=    3.128 closest distance to " CG  GLN A  58 " =    0.914
peak=    3.126 closest distance to " O   HOH Z 387 " =    2.747
peak=    3.125 closest distance to " CB  SER A  62 " =    1.202
peak=    3.123 closest distance to " CB  THR A  52 " =    0.828
peak=    3.122 closest distance to " O   HOH Z 416 " =    2.830
peak=    3.121 closest distance to " OG  SER A 245 " =    1.474
peak=    3.112 closest distance to " CB  PHE A  16 " =    1.049
peak=    3.105 closest distance to " O   HOH Z 250 " =    1.500
peak=    3.103 closest distance to " CG1 ILE A  20 " =    1.277
peak=    3.086 closest distance to " O   HOH Z 192 " =    1.763
peak=    3.083 closest distance to " O   HOH Z 367 " =    3.522
peak=    3.055 closest distance to " O   HOH Z 423 " =    3.083
peak=    3.046 closest distance to " CB  GLN A 278 " =    0.960

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

Number of peaks found at mFobs-DFmodel map (map cutoff=3.00 sigma)= 207         
Filter by distance & map next to the model:
   mapped sites are within: 0.683 - 5.755
   number of sites selected in [dist_min= 0.70, dist_max= 6.00]: 205 from: 207
   mapped sites are within: 0.842 - 5.755

peak=   -4.839 closest distance to " O   HOH Z 210 " =    0.865
peak=   -4.460 closest distance to " CD  ARG A 156 " =    2.011
peak=   -4.455 closest distance to " O   HOH Z 266 " =    5.140
peak=   -4.401 closest distance to " CD  GLN A  58 " =    1.154
peak=   -4.393 closest distance to " SG  CYS A 254 " =    3.212
peak=   -4.205 closest distance to " OXT GLY A 302 " =    2.887
peak=   -4.175 closest distance to " CD2 LEU A 237 " =    2.630
peak=   -4.158 closest distance to " O   ASN A  45 " =    1.812
peak=   -4.133 closest distance to " C   HIS A 108 " =    1.236
peak=   -4.127 closest distance to " O   HOH Z 351 " =    1.508
peak=   -4.096 closest distance to " CD1 LEU A 101 " =    2.423
peak=   -4.086 closest distance to " OG BSER A 134 " =    1.432
peak=   -4.065 closest distance to " O   HOH Z 166 " =    1.548
peak=   -4.044 closest distance to " CG1 VAL A 112 " =    2.592
peak=   -4.040 closest distance to " CB  ALA A 248 " =    2.235
peak=   -4.014 closest distance to " O   HOH Z  13 " =    1.736
peak=   -4.008 closest distance to " CA  ASP A 298 " =    1.066
peak=   -3.981 closest distance to " O   HOH Z 426 " =    1.804
peak=   -3.946 closest distance to " O   VAL A  67 " =    2.627
peak=   -3.930 closest distance to " CD1 PHE A  59 " =    1.981
peak=   -3.912 closest distance to " CE2 TYR A  30 " =    2.738
peak=   -3.890 closest distance to " O   VAL A  67 " =    2.912
peak=   -3.880 closest distance to " O   HOH Z 193 " =    1.322
peak=   -3.862 closest distance to " CH2 TRP A 179 " =    1.321
peak=   -3.833 closest distance to " CB  PHE A 208 " =    2.306
peak=   -3.828 closest distance to " C   THR A 279 " =    1.122
peak=   -3.813 closest distance to " NE2 GLN A  88 " =    1.040
peak=   -3.803 closest distance to " O   PRO A 163 " =    2.108
peak=   -3.796 closest distance to " N   ALA A 226 " =    1.967
peak=   -3.788 closest distance to " O   PRO A 198 " =    1.290
peak=   -3.773 closest distance to " O   HOH Z 231 " =    2.291
peak=   -3.762 closest distance to " O   HOH Z 435 " =    2.607
peak=   -3.760 closest distance to " CG1 VAL A 296 " =    1.048
peak=   -3.758 closest distance to " CB  SER A 210 " =    1.211
peak=   -3.740 closest distance to " O   HOH Z 165 " =    1.959
peak=   -3.714 closest distance to " ND2 ASN A 187 " =    1.642
peak=   -3.703 closest distance to " O   HOH Z 103 " =    1.774
peak=   -3.691 closest distance to " O   HOH Z 196 " =    2.120
peak=   -3.673 closest distance to " O   PHE A 218 " =    1.513
peak=   -3.670 closest distance to " O   HOH Z 394 " =    1.644
peak=   -3.669 closest distance to " O   GLY A  80 " =    2.533
peak=   -3.667 closest distance to " CB  ALA A 161 " =    2.452
peak=   -3.656 closest distance to " CB  ALA A 248 " =    2.060
peak=   -3.645 closest distance to " CE3 TRP A 150 " =    2.250
peak=   -3.644 closest distance to " ND2 ASN A  45 " =    1.126
peak=   -3.644 closest distance to " O   HOH Z 191 " =    5.755
peak=   -3.631 closest distance to " CG  GLN A 223 " =    2.517
peak=   -3.614 closest distance to " ND2 ASN A  39 " =    1.078
peak=   -3.611 closest distance to " CD2 LEU A 167 " =    1.724
peak=   -3.606 closest distance to " CD2 TYR A 293 " =    1.793
peak=   -3.602 closest distance to " O   VAL A  67 " =    1.867
peak=   -3.593 closest distance to " O   HOH Z 423 " =    2.229
peak=   -3.582 closest distance to " ND2 ASN A  69 " =    1.748
peak=   -3.566 closest distance to " O   HOH Z 139 " =    5.123
peak=   -3.556 closest distance to " CA  GLY A 241 " =    2.409
peak=   -3.543 closest distance to " O   HOH Z 422 " =    1.553
peak=   -3.539 closest distance to " N   SER A 276 " =    1.385
peak=   -3.537 closest distance to " O   HOH Z  92 " =    1.699
peak=   -3.537 closest distance to " O   HOH Z 174 " =    2.147
peak=   -3.537 closest distance to " O   HOH Z 131 " =    4.099
peak=   -3.522 closest distance to " CB  PRO A 163 " =    2.571
peak=   -3.511 closest distance to " CB  PRO A 280 " =    2.200
peak=   -3.510 closest distance to " O   HOH Z 114 " =    3.351
peak=   -3.505 closest distance to " OG BSER A 210 " =    1.352
peak=   -3.500 closest distance to " C   SER A 206 " =    1.571
peak=   -3.497 closest distance to " OG  SER A  97 " =    2.349
peak=   -3.494 closest distance to " NH2AARG A 275 " =    4.723
peak=   -3.493 closest distance to " CZ  TYR A 169 " =    1.778
peak=   -3.491 closest distance to " O   HOH Z  15 " =    1.534
peak=   -3.474 closest distance to " O   MET A  40 " =    2.783
peak=   -3.471 closest distance to " CE1 TYR A 247 " =    2.545
peak=   -3.470 closest distance to " CG  GLU A  53 " =    1.545
peak=   -3.470 closest distance to " O   HOH Z 290 " =    1.054
peak=   -3.463 closest distance to " CG  TRP A 266 " =    2.064
peak=   -3.463 closest distance to " O   TRP A  92 " =    1.976
peak=   -3.460 closest distance to " CB  MET A 188 " =    1.861
peak=   -3.456 closest distance to " CD2 PHE A 192 " =    2.084
peak=   -3.450 closest distance to " O   HOH Z 119 " =    2.048
peak=   -3.447 closest distance to " CD1 LEU A  25 " =    2.521
peak=   -3.444 closest distance to " O   HOH Z 407 " =    1.787
peak=   -3.442 closest distance to " CG2 ILE A  49 " =    2.804
peak=   -3.435 closest distance to " O   HOH Z 154 " =    1.482
peak=   -3.434 closest distance to " C   LYS A  76 " =    1.700
peak=   -3.431 closest distance to " CE  LYS A 166 " =    3.053
peak=   -3.427 closest distance to " OD2 ASP A 171 " =    2.289
peak=   -3.425 closest distance to " CA  GLY A 203 " =    2.384
peak=   -3.421 closest distance to " OD1 ASN A 249 " =    2.446
peak=   -3.419 closest distance to " NE2 GLN A  11 " =    1.882
peak=   -3.417 closest distance to " O   HOH Z 407 " =    2.943
peak=   -3.415 closest distance to " O   ARG A 219 " =    1.789
peak=   -3.408 closest distance to " O   HOH Z 180 " =    2.365
peak=   -3.404 closest distance to " O   HOH Z  60 " =    2.280
peak=   -3.399 closest distance to " O   SER A 210 " =    1.839
peak=   -3.389 closest distance to " CE BMET A  47 " =    1.295
peak=   -3.388 closest distance to " CG  ARG A 269 " =    2.134
peak=   -3.381 closest distance to " O   HOH Z 136 " =    2.474
peak=   -3.364 closest distance to " O   HOH Z 388 " =    2.011
peak=   -3.363 closest distance to " CG  MET A 105 " =    0.895
peak=   -3.362 closest distance to " O   HOH Z   6 " =    1.874
peak=   -3.359 closest distance to " O   HOH Z 377 " =    1.530
peak=   -3.357 closest distance to " C   ASN A 285 " =    2.215
peak=   -3.355 closest distance to " O   HOH Z 244 " =    1.419
peak=   -3.352 closest distance to " CG  ASP A 231 " =    0.842
peak=   -3.347 closest distance to " OD1 ASN A 173 " =    1.688
peak=   -3.346 closest distance to " CE  MET A 105 " =    2.392
peak=   -3.340 closest distance to " N   ALA A 248 " =    1.849
peak=   -3.334 closest distance to " CE3 TRP A 274 " =    2.294
peak=   -3.330 closest distance to " NE2 GLN A 194 " =    1.786
peak=   -3.326 closest distance to " NH2 ARG A  66 " =    1.574
peak=   -3.325 closest distance to " CG  LEU A  83 " =    2.036
peak=   -3.325 closest distance to " O   HOH Z 285 " =    1.597
peak=   -3.324 closest distance to " CG2 THR A 182 " =    2.289
peak=   -3.322 closest distance to " N   THR A 235 " =    1.283
peak=   -3.321 closest distance to " O   HOH Z  78 " =    1.745
peak=   -3.316 closest distance to " CG2 ILE A 263 " =    2.188
peak=   -3.313 closest distance to " CH2 TRP A 150 " =    1.043
peak=   -3.311 closest distance to " O   SER A 271 " =    2.117
peak=   -3.310 closest distance to " CZ  ARG A  66 " =    1.101
peak=   -3.306 closest distance to " CA  GLY A 133 " =    2.275
peak=   -3.306 closest distance to " O   HOH Z  11 " =    1.845
peak=   -3.306 closest distance to " O   GLY A 196 " =    1.020
peak=   -3.304 closest distance to " O   HOH Z 110 " =    1.503
peak=   -3.302 closest distance to " O   HOH Z 166 " =    1.640
peak=   -3.301 closest distance to " CB  ALA A 291 " =    2.224
peak=   -3.295 closest distance to " O   ALA A 227 " =    1.325
peak=   -3.294 closest distance to " OD1 ASN A 148 " =    1.453
peak=   -3.291 closest distance to " CG  ARG A 219 " =    2.680
peak=   -3.290 closest distance to " CD  LYS A 289 " =    2.517
peak=   -3.288 closest distance to " O   SER A 273 " =    1.153
peak=   -3.288 closest distance to " CB  ALA A  10 " =    2.310
peak=   -3.279 closest distance to " O   HOH Z  10 " =    1.528
peak=   -3.277 closest distance to " CD  ARG A 139 " =    1.606
peak=   -3.276 closest distance to " CG  ASP A  50 " =    2.314
peak=   -3.276 closest distance to " OXT GLY A 302 " =    3.375
peak=   -3.276 closest distance to " SG  CYS A 260 " =    1.938
peak=   -3.270 closest distance to " CD  GLN A 223 " =    1.001
peak=   -3.267 closest distance to " O   HOH Z 177 " =    1.736
peak=   -3.267 closest distance to " O   SER A  95 " =    1.621
peak=   -3.264 closest distance to " O   HOH Z 252 " =    3.923
peak=   -3.263 closest distance to " CD2 PHE A 225 " =    1.117
peak=   -3.259 closest distance to " CG  ASP A 132 " =    2.339
peak=   -3.258 closest distance to " O   SER A 146 " =    1.072
peak=   -3.249 closest distance to " CG2 THR A 178 " =    2.204
peak=   -3.246 closest distance to " O   HOH Z 193 " =    1.923
peak=   -3.245 closest distance to " O   VAL A 174 " =    2.168
peak=   -3.242 closest distance to " C   ALA A 158 " =    1.295
peak=   -3.235 closest distance to " O   HOH Z 171 " =    2.334
peak=   -3.235 closest distance to " CG2 VAL A 197 " =    2.278
peak=   -3.234 closest distance to " CD  GLN A  73 " =    0.880
peak=   -3.228 closest distance to " O   HOH Z 123 " =    2.432
peak=   -3.225 closest distance to " OG1 THR A  82 " =    1.469
peak=   -3.225 closest distance to " O   HOH Z 208 " =    1.670
peak=   -3.224 closest distance to " CG2 VAL A 296 " =    1.236
peak=   -3.222 closest distance to " CD1 ILE A 151 " =    2.359
peak=   -3.216 closest distance to " CG  ASP A 286 " =    1.344
peak=   -3.213 closest distance to " C   GLY A  91 " =    1.377
peak=   -3.209 closest distance to " N   THR A 220 " =    2.261
peak=   -3.208 closest distance to " O   HOH Z  11 " =    1.832
peak=   -3.206 closest distance to " O   HOH Z  71 " =    2.127
peak=   -3.205 closest distance to " O   HOH Z 137 " =    1.796
peak=   -3.204 closest distance to " O   HOH Z 340 " =    1.086
peak=   -3.204 closest distance to " O  BHOH Z 338 " =    1.265
peak=   -3.202 closest distance to " O   HOH Z 185 " =    2.330
peak=   -3.201 closest distance to " O   HOH Z 366 " =    1.423
peak=   -3.197 closest distance to " O   ARG A  24 " =    2.053
peak=   -3.196 closest distance to " CD1 TRP A 179 " =    1.147
peak=   -3.194 closest distance to " CG  PRO A 243 " =    1.608
peak=   -3.188 closest distance to " O   GLY A  75 " =    1.864
peak=   -3.188 closest distance to " O   ALA A  34 " =    2.445
peak=   -3.183 closest distance to " CA  GLY A 133 " =    2.011
peak=   -3.177 closest distance to " CD2 HIS A 207 " =    2.420
peak=   -3.174 closest distance to " O   ALA A   1 " =    1.873
peak=   -3.170 closest distance to " CB  ASP A 162 " =    2.550
peak=   -3.167 closest distance to " N   THR A  52 " =    1.681
peak=   -3.160 closest distance to " OE1 GLN A 223 " =    1.591
peak=   -3.160 closest distance to " O   HOH Z 214 " =    2.587
peak=   -3.159 closest distance to " CG2 VAL A 189 " =    2.074
peak=   -3.158 closest distance to " O   HOH Z 250 " =    1.541
peak=   -3.158 closest distance to " O   HOH Z 151 " =    1.357
peak=   -3.155 closest distance to " O   HOH Z 145 " =    2.369
peak=   -3.149 closest distance to " O   LYS A 117 " =    1.623
peak=   -3.134 closest distance to " CB  TYR A  15 " =    2.196
peak=   -3.132 closest distance to " N   ALA A 248 " =    2.269
peak=   -3.132 closest distance to " CZ  PHE A  38 " =    2.098
peak=   -3.123 closest distance to " O   HOH Z 281 " =    2.602
peak=   -3.122 closest distance to " CD  PRO A 243 " =    1.895
peak=   -3.116 closest distance to " N   GLN A  58 " =    1.916
peak=   -3.114 closest distance to " O   HOH Z 215 " =    3.873
peak=   -3.110 closest distance to " CZ  TYR A  68 " =    1.199
peak=   -3.100 closest distance to " O   HOH Z 265 " =    2.272
peak=   -3.099 closest distance to " O   HOH Z  59 " =    3.864
peak=   -3.097 closest distance to " O   HOH Z  56 " =    1.445
peak=   -3.096 closest distance to " O   HOH Z 371 " =    1.993
peak=   -3.089 closest distance to " O   HOH Z 111 " =    2.086
peak=   -3.077 closest distance to " N   SER A 206 " =    1.823
peak=   -3.075 closest distance to " CD2 HIS A 115 " =    1.015
peak=   -3.070 closest distance to " OG ASER A 134 " =    1.305
peak=   -3.042 closest distance to " N   PHE A  59 " =    2.094
peak=   -3.042 closest distance to " O   HOH Z 139 " =    3.247
peak=   -3.041 closest distance to " O   HOH Z 429 " =    2.110
peak=   -3.039 closest distance to " O   HOH Z 150 " =    2.079
peak=   -3.038 closest distance to " OG BSER A 134 " =    1.727
peak=   -3.032 closest distance to " C   GLN A 144 " =    0.882
peak=   -3.031 closest distance to " NH1 ARG A 195 " =    2.577
peak=   -3.005 closest distance to " CD  GLN A 223 " =    1.331

================= 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    :  0.4851 0.4719   6.285740e+00   6.274629e+00
   1_bss:  0.4774 0.4669   6.277411e+00   6.271475e+00
   1_xyz:  0.3896 0.4099   6.161909e+00   6.196704e+00
   1_adp:  0.3424 0.3934   6.079610e+00   6.168798e+00
   1_occ:  0.3421 0.3938   6.078828e+00   6.169169e+00
   2_bss:  0.3391 0.3878   6.079007e+00   6.167650e+00
   2_xyz:  0.2597 0.3105   5.855214e+00   6.005293e+00
   2_adp:  0.2404 0.2942   5.797080e+00   5.955846e+00
   2_occ:  0.2403 0.2940   5.796578e+00   5.955907e+00
   3_bss:  0.2382 0.2925   5.794954e+00   5.951916e+00
   3_xyz:  0.1666 0.2091   5.474526e+00   5.665574e+00
   3_adp:  0.1504 0.1899   5.377505e+00   5.570247e+00
   3_occ:  0.1502 0.1899   5.376969e+00   5.570152e+00
   4_bss:  0.1496 0.1893   5.375101e+00   5.566028e+00
   4_xyz:  0.1312 0.1703   5.266702e+00   5.468451e+00
   4_adp:  0.1282 0.1687   5.251178e+00   5.459423e+00
   4_occ:  0.1281 0.1688   5.251121e+00   5.459522e+00
   5_bss:  0.1281 0.1688   5.251142e+00   5.459590e+00
   5_xyz:  0.1193 0.1626   5.200474e+00   5.426640e+00
   5_adp:  0.1165 0.1606   5.184103e+00   5.416406e+00
   5_occ:  0.1164 0.1607   5.183889e+00   5.416343e+00
   5_bss:  0.1164 0.1612   5.185001e+00   5.416626e+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:  0.338   9.574   7.847  10.664   8.296   0.000   0.000   0.000
   1_xyz:  0.338   9.574   7.847  10.664   8.296   0.000   0.000   0.000
   1_adp:  0.338   9.574   7.847  10.664   8.296   0.000   0.000   0.000
   1_occ:  0.338   9.574   7.847  10.664   8.296   0.000   0.000   0.000
   2_bss:  0.302  20.000   4.180   6.306   5.082   0.000   0.000   0.000
   2_xyz:  0.302  20.000   4.180   6.306   5.082   0.000   0.000   0.000
   2_adp:  0.302  20.000   4.180   6.306   5.082   0.000   0.000   0.000
   2_occ:  0.302  20.000   4.180   6.306   5.082   0.000   0.000   0.000
   3_bss:  0.319  43.605   1.822   3.952   3.434   0.000   0.000   0.000
   3_xyz:  0.319  43.605   1.822   3.952   3.434   0.000   0.000   0.000
   3_adp:  0.319  43.605   1.822   3.952   3.434   0.000   0.000   0.000
   3_occ:  0.319  43.605   1.822   3.952   3.434   0.000   0.000   0.000
   4_bss:  0.318  43.605   0.933   2.581   2.917   0.000   0.000   0.000
   4_xyz:  0.318  43.605   0.933   2.581   2.917   0.000   0.000   0.000
   4_adp:  0.318  43.605   0.933   2.581   2.917   0.000   0.000   0.000
   4_occ:  0.318  43.605   0.933   2.581   2.917   0.000   0.000   0.000
   5_bss:  0.320  43.605   0.882   2.325   2.936   0.000   0.000   0.000
   5_xyz:  0.320  43.605   0.882   2.325   2.936   0.000   0.000   0.000
   5_adp:  0.320  43.605   0.882   2.325   2.936   0.000   0.000   0.000
   5_occ:  0.320  43.605   0.882   2.325   2.936   0.000   0.000   0.000
   5_bss:  0.323  50.541  -1.131   0.204   0.927   0.000   0.000   0.000
------------------------------------------------------------------------
 stage     <pher>    fom   alpha         beta
   0    :  56.729 0.4366  0.5113    69709.416
   1_bss:  56.963 0.4322  0.6595    68533.034
   1_xyz:  47.243 0.5534  0.8217    49279.844
   1_adp:  43.395 0.6013  0.9364    44525.632
   1_occ:  43.401 0.6012  0.9352    44508.358
   2_bss:  42.988 0.6063  0.8285    43928.293
   2_xyz:  33.305 0.7195  0.9541    26613.735
   2_adp:  30.698 0.7497  0.9849    23361.334
   2_occ:  30.696 0.7497  0.9848    23334.759
   3_bss:  30.424 0.7527  0.9166    22995.722
   3_xyz:  20.760 0.8536  0.9918    11434.536
   3_adp:  18.273 0.8779  1.0042     9464.645
   3_occ:  18.266 0.8780  1.0042     9463.454
   4_bss:  18.157 0.8788  0.9722     9337.075
   4_xyz:  15.958 0.8985  0.9795     7584.413
   4_adp:  15.742 0.9006  0.9773     7515.399
   4_occ:  15.745 0.9006  0.9772     7520.416
   5_bss:  15.745 0.9006  0.9741     7521.601
   5_xyz:  15.067 0.9062  0.9769     7036.344
   5_adp:  14.802 0.9086  0.9731     6868.505
   5_occ:  14.796 0.9086  0.9730     6865.048
   5_bss:  14.835 0.9084  0.9742     6907.850
------------------------------------------------------------------------
 stage       angl   bond   chir   dihe   plan   repu  geom_target
   0    :  24.226  0.414  2.119 33.790  0.145  4.090   5.3617e+01
   1_bss:  24.226  0.414  2.119 33.790  0.145  4.090   5.3617e+01
   1_xyz:   1.774  0.014  0.113 18.062  0.007  4.108   1.5225e-01
   1_adp:   1.774  0.014  0.113 18.062  0.007  4.108   1.5225e-01
   1_occ:   1.774  0.014  0.113 18.062  0.007  4.108   1.5225e-01
   2_bss:   1.774  0.014  0.113 18.062  0.007  4.108   1.5225e-01
   2_xyz:   1.156  0.008  0.076 16.101  0.004  4.124   7.5933e-02
   2_adp:   1.156  0.008  0.076 16.101  0.004  4.124   7.5933e-02
   2_occ:   1.156  0.008  0.076 16.101  0.004  4.124   7.5933e-02
   3_bss:   1.156  0.008  0.076 16.101  0.004  4.124   7.5933e-02
   3_xyz:   1.110  0.008  0.080 15.805  0.004  4.126   7.1795e-02
   3_adp:   1.110  0.008  0.080 15.805  0.004  4.126   7.1795e-02
   3_occ:   1.110  0.008  0.080 15.805  0.004  4.126   7.1795e-02
   4_bss:   1.110  0.008  0.080 15.805  0.004  4.126   7.1795e-02
   4_xyz:   0.961  0.006  0.074 15.312  0.003  4.112   5.6696e-02
   4_adp:   0.961  0.006  0.074 15.312  0.003  4.112   5.6696e-02
   4_occ:   0.961  0.006  0.074 15.312  0.003  4.112   5.6696e-02
   5_bss:   0.961  0.006  0.074 15.312  0.003  4.112   5.6696e-02
   5_xyz:   1.071  0.008  0.084 15.443  0.004  4.115   6.7660e-02
   5_adp:   1.071  0.008  0.084 15.443  0.004  4.115   6.7660e-02
   5_occ:   1.071  0.008  0.084 15.443  0.004  4.115   6.7660e-02
   5_bss:   1.071  0.008  0.084 15.443  0.004  4.115   6.7660e-02
------------------------------------------------------------------------
                      Maximal deviations:
 stage       angl   bond   chir   dihe   plan   repu       |grad|
   0    :  74.492  1.400  6.404144.062  0.405  0.928   6.9456e+00
   1_bss:  74.492  1.400  6.404144.062  0.405  0.928   6.9456e+00
   1_xyz:  16.904  0.179  0.567 85.688  0.041  2.257   1.0989e-01
   1_adp:  16.904  0.179  0.567 85.688  0.041  2.257   1.0989e-01
   1_occ:  16.904  0.179  0.567 85.688  0.041  2.257   1.0989e-01
   2_bss:  16.904  0.179  0.567 85.688  0.041  2.257   1.0989e-01
   2_xyz:   7.514  0.087  0.261 82.234  0.028  2.176   6.4749e-02
   2_adp:   7.514  0.087  0.261 82.234  0.028  2.176   6.4749e-02
   2_occ:   7.514  0.087  0.261 82.234  0.028  2.176   6.4749e-02
   3_bss:   7.514  0.087  0.261 82.234  0.028  2.176   6.4749e-02
   3_xyz:   6.990  0.058  0.351 81.876  0.038  2.164   5.0900e-02
   3_adp:   6.990  0.058  0.351 81.876  0.038  2.164   5.0900e-02
   3_occ:   6.990  0.058  0.351 81.876  0.038  2.164   5.0900e-02
   4_bss:   6.990  0.058  0.351 81.876  0.038  2.164   5.0900e-02
   4_xyz:   6.861  0.034  0.342 81.105  0.034  2.247   3.7569e-02
   4_adp:   6.861  0.034  0.342 81.105  0.034  2.247   3.7569e-02
   4_occ:   6.861  0.034  0.342 81.105  0.034  2.247   3.7569e-02
   5_bss:   6.861  0.034  0.342 81.105  0.034  2.247   3.7569e-02
   5_xyz:   7.638  0.045  0.463 81.490  0.034  2.258   5.8540e-02
   5_adp:   7.638  0.045  0.463 81.490  0.034  2.258   5.8540e-02
   5_occ:   7.638  0.045  0.463 81.490  0.034  2.258   5.8540e-02
   5_bss:   7.638  0.045  0.463 81.490  0.034  2.258   5.8540e-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:  66.78   0.00  13.25  66.11   0.00  10.91  66.78   0.00  26.00
   1_occ:  66.78   0.00  13.25  66.11   0.00  10.91  66.78   0.00  26.00
   2_bss:  66.78   0.00  13.25  66.11   0.00  10.91  66.78   0.00  26.00
   2_xyz:  66.78   0.00  13.25  66.11   0.00  10.91  66.78   0.00  26.00
   2_adp:  71.32   0.00  13.08  71.32   0.00   9.83  68.89   1.31  30.78
   2_occ:  71.32   0.00  13.08  71.32   0.00   9.83  68.89   1.31  30.78
   3_bss:  71.32   0.00  13.08  71.32   0.00   9.83  68.89   1.31  30.78
   3_xyz:  71.32   0.00  13.08  71.32   0.00   9.83  68.89   1.31  30.78
   3_adp:  71.83   0.00  12.97  71.83   0.00   9.07  67.66   2.20  34.22
   3_occ:  71.83   0.00  12.97  71.83   0.00   9.07  67.66   2.20  34.22
   4_bss:  71.83   0.00  12.97  71.83   0.00   9.07  67.66   2.20  34.22
   4_xyz:  71.83   0.00  12.97  71.83   0.00   9.07  67.66   2.20  34.22
   4_adp:  75.98   0.00  13.00  75.98   0.00   9.02  68.08   2.42  34.64
   4_occ:  75.98   0.00  13.00  75.98   0.00   9.02  68.08   2.42  34.64
   5_bss:  75.98   0.00  13.00  75.98   0.00   9.02  68.08   2.42  34.64
   5_xyz:  75.98   0.00  13.00  75.98   0.00   9.02  68.08   2.42  34.64
   5_adp:  86.22   0.00  13.33  86.22   0.00   8.99  75.46   1.62  36.96
   5_occ:  86.22   0.00  13.33  86.22   0.00   8.99  75.46   1.62  36.96
   5_bss:  88.31   2.09  15.42  88.31   2.09  11.08  77.55   3.71  39.05
------------------------------------------------------------------------
 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:    1.245    0.019    0.420
   1_adp:    1.245    0.019    0.420
   1_occ:    1.245    0.019    0.420
   2_bss:    1.245    0.019    0.420
   2_xyz:    1.837    0.049    0.576
   2_adp:    1.837    0.049    0.576
   2_occ:    1.837    0.049    0.576
   3_bss:    1.837    0.049    0.576
   3_xyz:    1.854    0.058    0.683
   3_adp:    1.854    0.058    0.683
   3_occ:    1.854    0.058    0.683
   4_bss:    1.854    0.058    0.683
   4_xyz:    1.974    0.019    0.722
   4_adp:    1.974    0.019    0.722
   4_occ:    1.974    0.019    0.722
   5_bss:    1.974    0.019    0.722
   5_xyz:    1.971    0.112    0.740
   5_adp:    1.971    0.112    0.740
   5_occ:    1.971    0.112    0.740
   5_bss:    1.971    0.112    0.740
------------------------------------------------------------------------

CPU time actual refinement: 357.26


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

Writing refined structure to PDB file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/trial/run_215/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_215/model_refine_001_2mFobs-DFmodel.map
Writing mFobs-DFmodel XPLOR map to file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/trial/run_215/model_refine_001_mFobs-DFmodel.map
Writing map coefficients to MTZ file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/trial/run_215/model_refine_001_map_coeffs.mtz

Writing default parameters for subsequent refinement:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/trial/run_215/model_refine_002.def


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

Pure refinement (no I/O, processing, etc)= 357.09 
  Macro-tasks:
    bulk solvent and scale       = 46.96  
    individual site refinement   = 147.94 
    weights calculation          = 32.78  
    collect and process          = 6.64   
    model show statistics        = 0.14   
    TOTAL for macro-tasks        = 234.46 
  Micro-tasks:
    mask                            = 2.39   
    f_calc                          = 110.27 
    alpha_beta                      = 8.35   
    target                          = 1.17   
    gradients_wrt_atomic_parameters = 121.29 
    fmodel                         = 8.46   
    r_factors                      = 0.30   
    phase_errors                   = 10.53  
    foms                           = 0.30   
    TOTAL for micro-tasks          = 263.06 
NUMBER OF MASK CALCS=  5
Time per interpreted Python bytecode instruction: 4.945 micro seconds
Total CPU time: 6.18 minutes
from_scatterers_fft:    663 calls, 109.97 s
gradients_fft:          608 calls, 107.31 s

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

# Date 2008-01-16 Time 01:03:26 PST -0800 (1200474206.44 s)
Start R-work = 0.4851, R-free = 0.4719 (no bulk solvent and anisotropic scale)
Final R-work = 0.1343, R-free = 0.1755 (no bulk solvent and anisotropic scale)

Start R-work = 0.4774, R-free = 0.4669
Final R-work = 0.1164, R-free = 0.1612