# Date 2008-01-16 Time 00:56:58 PST -0800 (1200473818.32 s)
#phil __OFF__

Command line arguments: "../206.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 = 11511
JOB_ID = 5158
SGE_ARCH = lx24-amd64
SGE_TASK_FIRST = 1
SGE_TASK_LAST = 1330
SGE_TASK_ID = 206

-------------------------------------------------------------------------------
  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, 47.3993, 87.6859, 90, 90, 90)
  Space group: P 21 21 21 (No. 19)

/net/cci-filer1/vol1/tmp/phzwart/tassos/trial/model.pdb
  Monomer Library directory:
    "/net/rosie/scratch3/phzwart/CCTBX/Sources/mon_lib"
  Total number of atoms: 2823
  Number of models: 1
  Model: 0
    Number of conformers: 2
    Conformer: "A"
      Number of atoms: 2769
      Number of chains: 2
        Number of residues, atoms: 302, 2333
          Classifications: {'peptide': 302}
          Modifications used: {'COO': 1}
          Link IDs: {'PTRANS': 7, 'CIS': 1, 'TRANS': 293}
        Number of residues, atoms: 436, 436
          Classifications: {'water': 436}
          Link IDs: {None: 435}
    Conformer: "B"
      Number of atoms: 2771
      Common with "A": 2717
      Number of chains: 2
        Number of residues, atoms: 302, 2333
          Classifications: {'peptide': 302}
          Modifications used: {'COO': 1}
          Link IDs: {'PTRANS': 7, 'CIS': 1, 'TRANS': 293}
          bond proxies already assigned to first conformer: 2332
        Number of residues, atoms: 438, 438
          Classifications: {'water': 438}
          Link IDs: {None: 437}
  Time building chain proxies: 3.27, per 1000 atoms: 1.16


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

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

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

Miller array info: /net/cci-filer1/vol1/tmp/phzwart/tassos/trial/1e0w.cns:FOBS,SIGMA
Observation type: xray.amplitude
Type of data: double, size=19589
Type of sigmas: double, size=19589
Number of Miller indices: 19589
Anomalous flag: False
Unit cell: (68.845, 47.3993, 87.6859, 90, 90, 90)
Space group: P 21 21 21 (No. 19)
Systematic absences: 0
Centric reflections: 2427
Resolution range: 14.864 1.96088
Completeness in resolution range: 0.9258
Completeness with d_max=infinity: 0.923008

Number of F-obs in resolution range:                   19589
Number of F-obs <= 0:                                  0
Refinement resolution range: d_max =  14.8640
                             d_min =   1.9609

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, 47.3993, 87.6859, 90, 90, 90)
Space group: P 21 21 21 (No. 19)
Systematic absences: 0
Centric reflections: 2427
Resolution range: 14.864 1.96088
Completeness in resolution range: 0.9258
Completeness with d_max=infinity: 0.923008

Test (R-free flags) flag value: 1

Number of work/free reflections by resolution:
                                         work  free  %free
  bin  1: 14.8645 -  4.1959 [2220/2248]  1997   223  10.0%
  bin  2:  4.1959 -  3.3429 [2129/2152]  1912   217  10.2%
  bin  3:  3.3429 -  2.9240 [2105/2130]  1901   204   9.7%
  bin  4:  2.9240 -  2.6583 [2087/2103]  1875   212  10.2%
  bin  5:  2.6583 -  2.4687 [2066/2105]  1854   212  10.3%
  bin  6:  2.4687 -  2.3237 [2056/2088]  1852   204   9.9%
  bin  7:  2.3237 -  2.2077 [2057/2094]  1860   197   9.6%
  bin  8:  2.2077 -  2.1119 [2050/2092]  1840   210  10.2%
  bin  9:  2.1119 -  2.0308 [2030/2069]  1834   196   9.7%
  bin 10:  2.0308 -  1.9609 [ 789/2078]   705    84  10.6%
                                overall 17630  1959  10.0%
Writing MTZ file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/trial/run_206/model_refine_data.mtz


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

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

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

  Number of disulfides: simple=3, symmetry=0
    Simple disulfide: " SG  CYS A 168 " - " SG ACYS A 201 " distance=2.08
    Simple disulfide: " SG  CYS A 168 " - " SG BCYS A 201 " distance=1.98
    Simple disulfide: " SG  CYS A 254 " - " SG  CYS A 260 " distance=2.05
  Time building geometry restraints manager: 0.14 seconds
  Histogram of bond lengths:
        1.21 -     1.38: 943
        1.38 -     1.56: 1465
        1.56 -     1.73: 7
        1.73 -     1.90: 21
        1.90 -     2.08: 3
  Bond restraints sorted by residual:
             atom i - atom j            ideal  model  delta   weight residual
  " SG  CYS A 168 " - " SG BCYS A 201 " 2.031  1.983  0.048 2.50e+03 5.87e+00
  " C   GLN A  88 " - " N   GLN A  89 " 1.329  1.360 -0.031 5.10e+03 4.97e+00
  " SG  CYS A 168 " - " SG ACYS A 201 " 2.031  2.075 -0.044 2.50e+03 4.89e+00
  " CB  CYS A 201 " - " SG ACYS A 201 " 1.808  1.738  0.070 9.18e+02 4.46e+00
  " C   PRO A 198 " - " N   ILE A 199 " 1.329  1.301  0.028 5.10e+03 4.10e+00
  ... (remaining 2434 not shown)
  Histogram of nonbonded interaction distances:
        1.34 -     2.05: 12
        2.05 -     2.76: 424
        2.76 -     3.47: 4573
        3.47 -     4.19: 9360
        4.19 -     4.90: 13948
  Nonbonded interactions sorted by model distance:
             atom i - atom j             model   vdw sym.op. j
  " O   HOH Z 109 " - " O   HOH Z 417 "  1.335 3.040 -x+1,y-1/2,-z+1/2
  " O   HOH Z  43 " - " O   HOH Z 169 "  1.446 3.040 -x+1,y+1/2,-z+1/2
  " O   HOH Z  81 " - " O   HOH Z 186 "  1.553 3.040 -x+1,y+1/2,-z+1/2
  " NH1 ARG A  24 " - " O   GLY A  91 "  1.599 3.120 -x+1,y+1/2,-z+1/2
  " O   HOH Z  18 " - " O   HOH Z 102 "  1.632 3.040 -x+1,y+1/2,-z+1/2
  ... (remaining 28312 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_206/model_refine_001.eff

Writing geometry restraints to file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/trial/run_206/model_refine_001.geo

CPU time processing inputs: 9.17


============================ 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 47.3993 87.68585 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 - 14.86 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.4851   r_free= 0.4707   ksol= 0.00   Bsol= 0.00   scale= 0.790    |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (0.00,0.00,0.00,0.00,0.00,0.00); trace/3= 0.00                              |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.74 A                  |
| x-ray target function (ml) for work reflections: 6.283979                   |
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
| Bin     Resolution   Compl.  No. Refl.    R-factors          Targets        |
|number     range              work test   work   test        work        test|
|  1: 14.8645 -  4.6799 0.99   1442  160 0.3855 0.3777      6.5883      6.6229|
|  2:  4.6799 -  3.7340 0.99   1395  154 0.3939 0.4369      6.7601      6.8531|
|  3:  3.7340 -  3.2677 0.99   1360  153 0.4578 0.4130      6.6721      6.6481|
|  4:  3.2677 -  2.9715 0.99   1351  143 0.4763 0.4645      6.5019      6.4936|
|  5:  2.9715 -  2.7600 0.98   1335  153 0.5164 0.4739      6.3624      6.3874|
|  6:  2.7600 -  2.5982 0.99   1341  149 0.5112 0.5478      6.2829      6.2155|
|  7:  2.5982 -  2.4687 0.99   1315  156 0.5137 0.4701      6.2301      6.1471|
|  8:  2.4687 -  2.3616 0.99   1341  137 0.5348 0.4732      6.1814      6.1396|
|  9:  2.3616 -  2.2711 0.99   1329  147 0.5441 0.5246      6.1276      6.1775|
| 10:  2.2711 -  2.1929 0.98   1319  146 0.5389 0.4908      6.0975      6.0972|
| 11:  2.1929 -  2.1246 0.98   1282  155 0.5335 0.5707      6.0269      6.0166|
| 12:  2.1246 -  2.0640 1.00   1343  144 0.5448 0.4916       5.945      5.9302|
| 13:  2.0640 -  2.0098 0.87   1187  124 0.5360 0.5362      5.8772      5.8595|
| 14:  2.0098 -  1.9609 0.22    290   38 0.5415 0.4573       5.944      5.6935|
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
|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: 14.8645 -  4.6799  1442   160  0.69  35.51   0.80     0.70      73841.99|
|  2:  4.6799 -  3.7340  1395   154  0.69  36.45   0.89     0.74     110484.99|
|  3:  3.7340 -  3.2677  1360   153  0.59  44.93   0.82     0.70     115607.14|
|  4:  3.2677 -  2.9715  1351   143  0.50  51.94   0.79     0.60      99293.70|
|  5:  2.9715 -  2.7600  1335   153  0.42  58.56   0.72     0.51      81372.58|
|  6:  2.7600 -  2.5982  1341   149  0.39  60.90   0.72     0.45      72337.78|
|  7:  2.5982 -  2.4687  1315   156  0.37  61.76   0.75     0.44      65523.89|
|  8:  2.4687 -  2.3616  1341   137  0.39  60.60   0.71     0.46      55828.89|
|  9:  2.3616 -  2.2711  1329   147  0.40  60.34   0.71     0.49      52009.89|
| 10:  2.2711 -  2.1929  1319   146  0.38  61.50   0.73     0.45      46265.48|
| 11:  2.1929 -  2.1246  1282   155  0.32  65.94   0.74     0.41      48181.28|
| 12:  2.1246 -  2.0640  1343   144  0.29  68.11   0.74     0.39      44177.01|
| 13:  2.0640 -  2.0098  1187   124  0.30  67.78   0.71     0.39      38770.09|
| 14:  2.0098 -  1.9609   290    38  0.38  61.25   0.78     0.40      27963.18|
|alpha:            min =        0.39 max =            0.74 mean =         0.52|
|beta:             min =    27963.18 max =       115607.14 mean =     69428.18|
|figures of merit: min =        0.00 max =            1.00 mean =         0.44|
|phase err.(work): min =        0.00 max =           89.97 mean =        56.22|
|phase err.(test): min =        0.00 max =           89.98 mean =        56.52|
|-----------------------------------------------------------------------------|

============================== 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 = 14.050306             wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 80.281   (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 1.208927              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 76.643   (deg)                 |
|-----------------------------------------------------------------------------|


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

|-Geometry statistics: start--------------------------------------------------|
|            Histogram of deviations from ideal values for                    |
| Bonds                | Angles                   |  Nonbonded contacts       |
| 0.000 - 0.140:   597 |   0.009 -   7.457:   713 |  1.044 -  1.430:        4 |
| 0.140 - 0.280:   585 |   7.457 -  14.906:   711 |  1.430 -  1.815:       12 |
| 0.280 - 0.420:   441 |  14.906 -  22.354:   630 |  1.815 -  2.201:      109 |
| 0.420 - 0.560:   366 |  22.354 -  29.802:   474 |  2.201 -  2.586:      548 |
| 0.560 - 0.700:   237 |  29.802 -  37.251:   338 |  2.586 -  2.972:     1350 |
| 0.700 - 0.840:   127 |  37.251 -  44.699:   241 |  2.972 -  3.358:     2490 |
| 0.840 - 0.980:    59 |  44.699 -  52.147:   125 |  3.358 -  3.743:     3912 |
| 0.980 - 1.120:    17 |  52.147 -  59.595:    51 |  3.743 -  4.129:     5170 |
| 1.120 - 1.260:     9 |  59.595 -  67.044:    13 |  4.129 -  4.514:     6739 |
| 1.260 - 1.400:     1 |  67.044 -  74.492:     3 |  4.514 -  4.900:     8006 |
|-----------------------------------------------------------------------------|
|-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 |       53.740 |
| planarity |      436 |   0.145    0.405  0.000 |     250.485 |              |
|  dihedral |      870 |  33.790  144.062  0.019 |      20.704 |              |
| nonbonded |     2439 |   4.089    4.900  1.044 |       2.407 |              |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 11.837)------------------------------------------|
|    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 = 11.837)------------------------------------------|
|    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 - 14.86 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.4909   r_free= 0.4728   ksol= 0.00   Bsol= 0.00   scale= 0.760    |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (0.00,0.00,0.00,0.00,0.00,0.00); trace/3= 0.00                              |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.75 A                  |
| x-ray target function (ml) for work reflections: 6.285368                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.96 - 14.86 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.4768   r_free= 0.4649   ksol= 0.34   Bsol= 20.00   scale= 0.995   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (7.58,8.87,9.86,0.00,0.00,0.00); trace/3= 8.77                              |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.74 A                  |
| x-ray target function (ml) for work reflections: 6.276098                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 12.966572             wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 81.584   (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 1.165383              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 76.190   (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.4768      final r-factor (work) = 0.3884          |
| start r-factor (free) = 0.4649      final r-factor (free) = 0.4091          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 94.4755 = 12.97 * 0.50 * 6.2832 + 1.00 * 53.7400                            |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 40.2789 = 12.97 * 0.50 * 6.1896 + 1.00 * 0.1500                             |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 26     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.3884      final r-factor (work) = 0.3410          |
| start r-factor (free) = 0.4091      final r-factor (free) = 0.3967          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 7.2277 = 1.17 * 1.00 * 6.1896 + 1.00 * 0.0144                               |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 7.1135 = 1.17 * 1.00 * 6.0894 + 1.00 * 0.0170                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 26     |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 11.837)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.00    76.11   13.44    None  None   None       |
|    all(noH): 2823   0      0.00    76.11   13.44    None  None   None       |
|    Sol.    : 438    0      0.00    72.76   27.36    None  None   None       |
|    Mac.    : 2385   0      0.00    76.11   10.88    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 -   7.611: 1132   |   5:    38.055 -  45.666:   68        |
|      1:     7.611 -  15.222:  760   |   6:    45.666 -  53.277:   33        |
|      2:    15.222 -  22.833:  421   |   7:    53.277 -  60.888:   33        |
|      3:    22.833 -  30.444:  234   |   8:    60.888 -  68.498:   12        |
|      4:    30.444 -  38.055:  127   |   9:    68.498 -  76.109:    3        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.3410 r_free = 0.3967             target_work(ml) = 6.071         |
| occupancies: max = 1.00  min = 0.30   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.3406 r_free = 0.3972             target_work(ml) = 6.070         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        6 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.96 - 14.86 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.3406   r_free= 0.3972   ksol= 0.34   Bsol= 20.00   scale= 1.107   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (7.58,8.87,9.86,0.00,0.00,0.00); trace/3= 8.77                              |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.50 A                  |
| x-ray target function (ml) for work reflections: 6.070400                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.96 - 14.86 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.3370   r_free= 0.3939   ksol= 0.33   Bsol= 43.34   scale= 1.004   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (3.63,4.69,5.92,0.00,0.00,0.00); trace/3= 4.75                              |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.51 A                  |
| x-ray target function (ml) for work reflections: 6.071589                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 5.222477              wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 98.760   (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 0.470238              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 135.206  (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.3370      final r-factor (work) = 0.2496          |
| start r-factor (free) = 0.3939      final r-factor (free) = 0.2995          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 16.0474 = 5.22 * 0.50 * 6.0881 + 1.00 * 0.1500                              |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 15.6194 = 5.22 * 0.50 * 5.9516 + 1.00 * 0.0784                              |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 28     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.2496      final r-factor (work) = 0.2285          |
| start r-factor (free) = 0.2995      final r-factor (free) = 0.2803          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 2.8188 = 0.47 * 1.00 * 5.9516 + 1.00 * 0.0202                               |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 2.7458 = 0.47 * 1.00 * 5.7783 + 1.00 * 0.0287                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 33     |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 11.837)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.00    82.23   13.34    None  None   None       |
|    all(noH): 2823   0      0.00    82.23   13.34    None  None   None       |
|    Sol.    : 438    0      1.99    74.01   32.79    None  None   None       |
|    Mac.    : 2385   0      0.00    82.23   9.77     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 -   8.223: 1355   |   5:    41.113 -  49.336:   96        |
|      1:     8.223 -  16.445:  747   |   6:    49.336 -  57.558:   38        |
|      2:    16.445 -  24.668:  283   |   7:    57.558 -  65.781:   24        |
|      3:    24.668 -  32.891:  150   |   8:    65.781 -  74.004:    7        |
|      4:    32.891 -  41.113:  121   |   9:    74.004 -  82.226:    2        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.2285 r_free = 0.2803             target_work(ml) = 5.748         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        6 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.2281 r_free = 0.2804             target_work(ml) = 5.748         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        6 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.96 - 14.86 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.2281   r_free= 0.2804   ksol= 0.33   Bsol= 43.34   scale= 1.050   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (3.63,4.69,5.92,0.00,0.00,0.00); trace/3= 4.75                              |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.30 A                  |
| x-ray target function (ml) for work reflections: 5.748264                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.96 - 14.86 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.2265   r_free= 0.2801   ksol= 0.31   Bsol= 52.66   scale= 1.001   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (1.68,3.11,3.98,0.00,0.00,0.00); trace/3= 2.92                              |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.31 A                  |
| x-ray target function (ml) for work reflections: 5.748523                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 3.948051              wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 97.615   (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 0.426360              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 94.587   (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.2265      final r-factor (work) = 0.1612          |
| start r-factor (free) = 0.2801      final r-factor (free) = 0.2047          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 11.4935 = 3.95 * 0.50 * 5.7827 + 1.00 * 0.0784                              |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 11.1603 = 3.95 * 0.50 * 5.6180 + 1.00 * 0.0702                              |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 28     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1612      final r-factor (work) = 0.1465          |
| start r-factor (free) = 0.2047      final r-factor (free) = 0.1893          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 2.4138 = 0.43 * 1.00 * 5.6180 + 1.00 * 0.0185                               |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 2.3170 = 0.43 * 1.00 * 5.3990 + 1.00 * 0.0151                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 26     |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 11.837)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.00    77.51   13.56    None  None   None       |
|    all(noH): 2823   0      0.00    77.51   13.56    None  None   None       |
|    Sol.    : 438    0      2.09    73.65   36.90    None  None   None       |
|    Mac.    : 2385   0      0.00    77.51   9.28     None  None   None       |
|    Hyd.    : 0      0      None    None    None     None  None   None       |
|    - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -      |
|       Distribution of isotropic (or equivalent) ADP for non-H atoms:        |
|    Bin#      value range     #atoms | Bin#      value range     #atoms      |
|      0:     0.000 -   7.751: 1342   |   5:    38.754 -  46.504:  102        |
|      1:     7.751 -  15.501:  789   |   6:    46.504 -  54.255:   71        |
|      2:    15.501 -  23.252:  218   |   7:    54.255 -  62.006:   54        |
|      3:    23.252 -  31.003:  111   |   8:    62.006 -  69.756:   25        |
|      4:    31.003 -  38.754:  106   |   9:    69.756 -  77.507:    5        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.1465 r_free = 0.1893             target_work(ml) = 5.362         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        6 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.1462 r_free = 0.1895             target_work(ml) = 5.361         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        8 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.96 - 14.86 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1462   r_free= 0.1895   ksol= 0.31   Bsol= 52.66   scale= 1.022   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (1.68,3.11,3.98,0.00,0.00,0.00); trace/3= 2.92                              |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.18 A                  |
| x-ray target function (ml) for work reflections: 5.361097                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.96 - 14.86 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1458   r_free= 0.1890   ksol= 0.33   Bsol= 52.66   scale= 0.999   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (0.83,2.13,3.21,0.00,0.00,0.00); trace/3= 2.06                              |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.18 A                  |
| x-ray target function (ml) for work reflections: 5.359695                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 1.992506              wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 110.511  (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 0.316242              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 101.891  (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1458      final r-factor (work) = 0.1290          |
| start r-factor (free) = 0.1890      final r-factor (free) = 0.1711          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 5.4545 = 1.99 * 0.50 * 5.4046 + 1.00 * 0.0702                               |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 5.3486 = 1.99 * 0.50 * 5.3092 + 1.00 * 0.0594                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 29     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1290      final r-factor (work) = 0.1262          |
| start r-factor (free) = 0.1711      final r-factor (free) = 0.1682          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 1.7226 = 0.32 * 1.00 * 5.3092 + 1.00 * 0.0436                               |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 1.6715 = 0.32 * 1.00 * 5.2512 + 1.00 * 0.0109                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 29     |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 11.837)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.00    78.58   13.39    None  None   None       |
|    all(noH): 2823   0      0.00    78.58   13.39    None  None   None       |
|    Sol.    : 438    0      2.24    74.57   36.70    None  None   None       |
|    Mac.    : 2385   0      0.00    78.58   9.11     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 -   7.858: 1390   |   5:    39.288 -  47.145:   97        |
|      1:     7.858 -  15.715:  780   |   6:    47.145 -  55.003:   70        |
|      2:    15.715 -  23.573:  190   |   7:    55.003 -  62.860:   48        |
|      3:    23.573 -  31.430:  114   |   8:    62.860 -  70.718:   21        |
|      4:    31.430 -  39.288:  108   |   9:    70.718 -  78.575:    5        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.1262 r_free = 0.1682             target_work(ml) = 5.242         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        8 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.1261 r_free = 0.1682             target_work(ml) = 5.241         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        7 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.96 - 14.86 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1261   r_free= 0.1682   ksol= 0.33   Bsol= 52.66   scale= 1.001   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (0.83,2.13,3.21,0.00,0.00,0.00); trace/3= 2.06                              |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.17 A                  |
| x-ray target function (ml) for work reflections: 5.241476                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.96 - 14.86 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1261   r_free= 0.1682   ksol= 0.33   Bsol= 52.66   scale= 1.001   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (0.83,2.13,3.21,0.00,0.00,0.00); trace/3= 2.06                              |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.17 A                  |
| x-ray target function (ml) for work reflections: 5.241476                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 1.817781              wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 135.318  (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 1.039811              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 152.475  (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1261      final r-factor (work) = 0.1204          |
| start r-factor (free) = 0.1682      final r-factor (free) = 0.1624          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 4.8319 = 1.82 * 0.50 * 5.2510 + 1.00 * 0.0594                               |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 4.8058 = 1.82 * 0.50 * 5.2207 + 1.00 * 0.0608                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 29     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1204      final r-factor (work) = 0.1188          |
| start r-factor (free) = 0.1624      final r-factor (free) = 0.1630          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 5.4394 = 1.04 * 1.00 * 5.2207 + 1.00 * 0.0108                               |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 5.4173 = 1.04 * 1.00 * 5.1977 + 1.00 * 0.0127                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 28     |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 11.837)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.00    86.19   13.54    None  None   None       |
|    all(noH): 2823   0      0.00    86.19   13.54    None  None   None       |
|    Sol.    : 438    0      1.94    80.59   37.74    None  None   None       |
|    Mac.    : 2385   0      0.00    86.19   9.10     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 -   8.620: 1551   |   5:    43.097 -  51.717:   87        |
|      1:     8.620 -  17.239:  675   |   6:    51.717 -  60.336:   63        |
|      2:    17.239 -  25.859:  165   |   7:    60.336 -  68.956:   38        |
|      3:    25.859 -  34.478:  112   |   8:    68.956 -  77.575:   16        |
|      4:    34.478 -  43.097:  111   |   9:    77.575 -  86.195:    5        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.1188 r_free = 0.1630             target_work(ml) = 5.201         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        7 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.1188 r_free = 0.1631             target_work(ml) = 5.201         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        6 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.96 - 14.86 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1188   r_free= 0.1631   ksol= 0.33   Bsol= 52.66   scale= 1.000   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (0.83,2.13,3.21,0.00,0.00,0.00); trace/3= 2.06                              |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.16 A                  |
| x-ray target function (ml) for work reflections: 5.200645                   |
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
| Bin     Resolution   Compl.  No. Refl.    R-factors          Targets        |
|number     range              work test   work   test        work        test|
|  1: 14.8645 -  4.6799 0.99   1442  160 0.1019 0.1329      5.4164      5.5835|
|  2:  4.6799 -  3.7340 0.99   1395  154 0.0868 0.1055      5.4453      5.6352|
|  3:  3.7340 -  3.2677 0.99   1360  153 0.1110 0.1545      5.4969      5.8462|
|  4:  3.2677 -  2.9715 0.99   1351  143 0.1312 0.1681      5.4878      5.6626|
|  5:  2.9715 -  2.7600 0.98   1335  153 0.1417 0.1628      5.3798      5.5219|
|  6:  2.7600 -  2.5982 0.99   1341  149 0.1342 0.2274      5.2722      5.5748|
|  7:  2.5982 -  2.4687 0.99   1315  156 0.1337 0.1625      5.2252      5.3677|
|  8:  2.4687 -  2.3616 0.99   1341  137 0.1266 0.1825      5.1388      5.3493|
|  9:  2.3616 -  2.2711 0.99   1329  147 0.1247 0.1898      5.0607      5.3597|
| 10:  2.2711 -  2.1929 0.98   1319  146 0.1210 0.1719      4.9988      5.2029|
| 11:  2.1929 -  2.1246 0.98   1282  155 0.1218 0.1991      4.9572      5.3194|
| 12:  2.1246 -  2.0640 1.00   1343  144 0.1203 0.1613        4.91      5.1154|
| 13:  2.0640 -  2.0098 0.87   1187  124 0.1192 0.1911      4.8217      5.0812|
| 14:  2.0098 -  1.9609 0.22    290   38 0.1079 0.1625      4.7757      4.9201|
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
|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: 14.8645 -  4.6799  1442   160  0.94   9.52   0.97     0.95       7793.35|
|  2:  4.6799 -  3.7340  1395   154  0.95   8.27   1.02     1.00       9233.85|
|  3:  3.7340 -  3.2677  1360   153  0.93  11.58   1.03     1.02      10651.75|
|  4:  3.2677 -  2.9715  1351   143  0.91  14.70   1.01     1.00      10970.21|
|  5:  2.9715 -  2.7600  1335   153  0.89  16.90   1.00     0.98       9300.57|
|  6:  2.7600 -  2.5982  1341   149  0.88  17.78   0.98     0.94       7946.67|
|  7:  2.5982 -  2.4687  1315   156  0.90  16.55   0.98     0.94       6872.54|
|  8:  2.4687 -  2.3616  1341   137  0.89  16.88   1.00     0.97       6224.42|
|  9:  2.3616 -  2.2711  1329   147  0.90  16.81   1.00     0.96       5305.13|
| 10:  2.2711 -  2.1929  1319   146  0.89  16.93   1.00     0.96       4882.88|
| 11:  2.1929 -  2.1246  1282   155  0.90  16.77   1.00     0.95       4541.20|
| 12:  2.1246 -  2.0640  1343   144  0.90  17.02   1.00     1.00       4291.83|
| 13:  2.0640 -  2.0098  1187   124  0.89  17.51   0.98     0.96       3681.21|
| 14:  2.0098 -  1.9609   290    38  0.91  15.12   0.97     0.93       3108.67|
|alpha:            min =        0.93 max =            1.02 mean =         0.97|
|beta:             min =     3108.67 max =        10970.21 mean =      7046.59|
|figures of merit: min =        0.00 max =            1.00 mean =         0.91|
|phase err.(work): min =        0.00 max =           89.77 mean =        15.08|
|phase err.(test): min =        0.00 max =           89.53 mean =        14.53|
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.96 - 14.86 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1188   r_free= 0.1634   ksol= 0.33   Bsol= 54.75   scale= 1.000   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-1.19,0.01,1.17,0.00,0.00,0.00); trace/3= 0.00                             |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.17 A                  |
| x-ray target function (ml) for work reflections: 5.201946                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.96 - 14.86 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1188   r_free= 0.1634   ksol= 0.33   Bsol= 54.75   scale= 1.000   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-1.19,0.01,1.17,0.00,0.00,0.00); trace/3= 0.00                             |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.17 A                  |
| x-ray target function (ml) for work reflections: 5.201946                   |
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
| Bin     Resolution   Compl.  No. Refl.    R-factors          Targets        |
|number     range              work test   work   test        work        test|
|  1: 14.8645 -  4.6799 0.99   1442  160 0.1005 0.1357       5.426      5.5998|
|  2:  4.6799 -  3.7340 0.99   1395  154 0.0878 0.1055      5.4563      5.6347|
|  3:  3.7340 -  3.2677 0.99   1360  153 0.1113 0.1546      5.4991      5.8449|
|  4:  3.2677 -  2.9715 0.99   1351  143 0.1314 0.1677      5.4866      5.6603|
|  5:  2.9715 -  2.7600 0.98   1335  153 0.1418 0.1620      5.3783      5.5161|
|  6:  2.7600 -  2.5982 0.99   1341  149 0.1340 0.2277      5.2704       5.575|
|  7:  2.5982 -  2.4687 0.99   1315  156 0.1337 0.1628      5.2253       5.368|
|  8:  2.4687 -  2.3616 0.99   1341  137 0.1265 0.1823      5.1386       5.349|
|  9:  2.3616 -  2.2711 0.99   1329  147 0.1245 0.1896      5.0603      5.3593|
| 10:  2.2711 -  2.1929 0.98   1319  146 0.1208 0.1719      4.9985      5.2034|
| 11:  2.1929 -  2.1246 0.98   1282  155 0.1218 0.1990      4.9569      5.3187|
| 12:  2.1246 -  2.0640 1.00   1343  144 0.1202 0.1613      4.9092      5.1147|
| 13:  2.0640 -  2.0098 0.87   1187  124 0.1192 0.1906       4.821      5.0799|
| 14:  2.0098 -  1.9609 0.22    290   38 0.1079 0.1627      4.7753      4.9197|
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
|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: 14.8645 -  4.6799  1442   160  0.93   9.92   0.97     0.95       8237.49|
|  2:  4.6799 -  3.7340  1395   154  0.95   8.39   1.02     1.00       9455.55|
|  3:  3.7340 -  3.2677  1360   153  0.93  11.59   1.03     1.02      10670.27|
|  4:  3.2677 -  2.9715  1351   143  0.91  14.64   1.01     1.00      10893.51|
|  5:  2.9715 -  2.7600  1335   153  0.89  16.82   1.00     0.98       9224.61|
|  6:  2.7600 -  2.5982  1341   149  0.89  17.74   0.98     0.94       7916.68|
|  7:  2.5982 -  2.4687  1315   156  0.90  16.56   0.99     0.95       6880.81|
|  8:  2.4687 -  2.3616  1341   137  0.89  16.88   1.00     0.97       6223.96|
|  9:  2.3616 -  2.2711  1329   147  0.90  16.82   1.00     0.96       5310.13|
| 10:  2.2711 -  2.1929  1319   146  0.89  16.93   1.00     0.96       4879.99|
| 11:  2.1929 -  2.1246  1282   155  0.90  16.76   1.00     0.95       4535.36|
| 12:  2.1246 -  2.0640  1343   144  0.90  17.01   1.01     1.00       4286.58|
| 13:  2.0640 -  2.0098  1187   124  0.89  17.48   0.99     0.96       3673.09|
| 14:  2.0098 -  1.9609   290    38  0.91  15.11   0.98     0.93       3100.92|
|alpha:            min =        0.93 max =            1.02 mean =         0.97|
|beta:             min =     3100.92 max =        10893.51 mean =      7087.22|
|figures of merit: min =        0.00 max =            1.00 mean =         0.91|
|phase err.(work): min =        0.00 max =           89.99 mean =        15.11|
|phase err.(test): min =        0.00 max =           88.70 mean =        14.59|
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 11.837)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      2.09    88.29   15.63    None  None   None       |
|    all(noH): 2823   0      2.09    88.29   15.63    None  None   None       |
|    Sol.    : 438    0      4.03    82.68   39.83    None  None   None       |
|    Mac.    : 2385   0      2.09    88.29   11.19    None  None   None       |
|    Hyd.    : 0      0      None    None    None     None  None   None       |
|    - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -      |
|       Distribution of isotropic (or equivalent) ADP for non-H atoms:        |
|    Bin#      value range     #atoms | Bin#      value range     #atoms      |
|      0:     2.092 -  10.711: 1551   |   5:    45.189 -  53.808:   87        |
|      1:    10.711 -  19.331:  675   |   6:    53.808 -  62.428:   63        |
|      2:    19.331 -  27.950:  165   |   7:    62.428 -  71.047:   38        |
|      3:    27.950 -  36.569:  112   |   8:    71.047 -  79.667:   16        |
|      4:    36.569 -  45.189:  111   |   9:    79.667 -  88.286:    5        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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


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

Number of peaks found at mFobs-DFmodel map (map cutoff=3.00 sigma)= 312         
Filter by distance & map next to the model:
   mapped sites are within: 0.501 - 4.778
   number of sites selected in [dist_min= 0.70, dist_max= 6.00]: 306 from: 312
   mapped sites are within: 0.711 - 4.778

peak=   10.652 closest distance to " CB  VAL A 230 " =    1.461
peak=    5.748 closest distance to " CG  LEU A   5 " =    1.230
peak=    5.579 closest distance to " NH2 ARG A  56 " =    2.240
peak=    5.520 closest distance to " CB  VAL A 296 " =    1.119
peak=    5.510 closest distance to " CG1 VAL A 296 " =    1.202
peak=    5.498 closest distance to " O   HOH Z 248 " =    1.418
peak=    5.481 closest distance to " CD2 LEU A   5 " =    1.181
peak=    5.404 closest distance to " CG  PRO A  54 " =    1.329
peak=    5.398 closest distance to " O   HOH Z 403 " =    1.786
peak=    5.336 closest distance to " CD1AILE A 234 " =    0.995
peak=    5.204 closest distance to " CB  ARG A 275 " =    0.969
peak=    5.130 closest distance to " CG  LEU A 228 " =    1.177
peak=    5.127 closest distance to " CB  GLN A 223 " =    1.454
peak=    5.074 closest distance to " CG2 VAL A 296 " =    1.042
peak=    4.983 closest distance to " O   HOH Z 124 " =    1.360
peak=    4.793 closest distance to " O   HOH Z 128 " =    1.531
peak=    4.785 closest distance to " NE2 GLN A  11 " =    1.057
peak=    4.735 closest distance to " O   HOH Z 232 " =    2.333
peak=    4.706 closest distance to " O   HOH Z 130 " =    1.191
peak=    4.697 closest distance to " O   HOH Z 193 " =    1.879
peak=    4.606 closest distance to " CB  PRO A  54 " =    1.006
peak=    4.597 closest distance to " O   HOH Z 238 " =    1.290
peak=    4.595 closest distance to " O   HOH Z  85 " =    1.690
peak=    4.525 closest distance to " O   HOH Z 402 " =    1.435
peak=    4.476 closest distance to " CG  PRO A 198 " =    1.203
peak=    4.454 closest distance to " CG  PRO A 243 " =    1.172
peak=    4.442 closest distance to " CB  SER A  63 " =    1.163
peak=    4.427 closest distance to " O   HOH Z 209 " =    2.324
peak=    4.426 closest distance to " O   HOH Z 251 " =    1.539
peak=    4.404 closest distance to " O   HOH Z 346 " =    1.528
peak=    4.389 closest distance to " CD2 TRP A 179 " =    1.332
peak=    4.385 closest distance to " O   HOH Z 130 " =    2.413
peak=    4.376 closest distance to " CB  ARG A  79 " =    1.477
peak=    4.363 closest distance to " O   HOH Z 265 " =    2.056
peak=    4.358 closest distance to " CD2 LEU A 228 " =    1.291
peak=    4.349 closest distance to " O   HOH Z 142 " =    1.634
peak=    4.340 closest distance to " O   HOH Z 247 " =    1.339
peak=    4.330 closest distance to " CB  VAL A 230 " =    1.154
peak=    4.318 closest distance to " O   HOH Z  49 " =    1.224
peak=    4.288 closest distance to " CZ  PHE A 218 " =    1.154
peak=    4.283 closest distance to " O   HOH Z 406 " =    1.467
peak=    4.271 closest distance to " O   HOH Z 368 " =    2.354
peak=    4.256 closest distance to " O   HOH Z  63 " =    1.961
peak=    4.248 closest distance to " CA  ALA A  51 " =    1.011
peak=    4.246 closest distance to " CB  GLN A 183 " =    1.323
peak=    4.246 closest distance to " O   HOH Z  43 " =    1.241
peak=    4.243 closest distance to " O   HOH Z 272 " =    1.911
peak=    4.233 closest distance to " O   HOH Z 404 " =    1.420
peak=    4.224 closest distance to " O   HOH Z 126 " =    1.502
peak=    4.221 closest distance to " O   SER A  87 " =    2.337
peak=    4.216 closest distance to " O   HOH Z 359 " =    1.675
peak=    4.195 closest distance to " O   HOH Z 188 " =    2.845
peak=    4.194 closest distance to " CB  GLU A 277 " =    3.640
peak=    4.174 closest distance to " O   HOH Z 188 " =    1.330
peak=    4.173 closest distance to " CA  TYR A  30 " =    0.938
peak=    4.149 closest distance to " O   HOH Z 313 " =    1.837
peak=    4.149 closest distance to " O   HOH Z 394 " =    1.508
peak=    4.147 closest distance to " O   HOH Z 154 " =    1.724
peak=    4.144 closest distance to " O   HOH Z  40 " =    1.919
peak=    4.120 closest distance to " O   HOH Z 369 " =    2.359
peak=    4.110 closest distance to " CG  PRO A 213 " =    1.205
peak=    4.098 closest distance to " O   HOH Z  80 " =    1.890
peak=    4.075 closest distance to " O   HOH Z 287 " =    1.682
peak=    4.057 closest distance to " O   HOH Z  76 " =    1.013
peak=    4.050 closest distance to " C   PRO A 198 " =    1.527
peak=    4.007 closest distance to " O   HOH Z   4 " =    1.557
peak=    4.005 closest distance to " O   HOH Z  59 " =    2.170
peak=    3.998 closest distance to " O   HOH Z 411 " =    3.918
peak=    3.998 closest distance to " CB  GLU A 152 " =    1.156
peak=    3.990 closest distance to " O   HOH Z 214 " =    1.312
peak=    3.976 closest distance to " O   HOH Z 126 " =    1.807
peak=    3.968 closest distance to " O   HOH Z 236 " =    1.603
peak=    3.966 closest distance to " CB  SER A  26 " =    1.865
peak=    3.952 closest distance to " CB  ARG A 190 " =    1.788
peak=    3.945 closest distance to " O   HOH Z 234 " =    3.678
peak=    3.931 closest distance to " O   HOH Z 422 " =    2.532
peak=    3.928 closest distance to " N   ASN A  39 " =    1.257
peak=    3.925 closest distance to " CB  ASN A 148 " =    1.308
peak=    3.918 closest distance to " O   HOH Z 261 " =    2.410
peak=    3.914 closest distance to " CD  ARG A 159 " =    0.761
peak=    3.913 closest distance to " O   HOH Z 414 " =    1.492
peak=    3.911 closest distance to " O   HOH Z 427 " =    2.716
peak=    3.901 closest distance to " O   HOH Z 214 " =    2.790
peak=    3.898 closest distance to " CZ  PHE A  38 " =    1.167
peak=    3.882 closest distance to " ND2 ASN A 249 " =    0.916
peak=    3.876 closest distance to " CB  ASN A 142 " =    1.189
peak=    3.875 closest distance to " CA  ARG A  36 " =    1.049
peak=    3.873 closest distance to " O   HOH Z  43 " =    2.262
peak=    3.835 closest distance to " CD  LYS A  76 " =    2.030
peak=    3.832 closest distance to " CB  THR A  52 " =    0.851
peak=    3.829 closest distance to " CD  ARG A 269 " =    1.040
peak=    3.822 closest distance to " CB  TRP A 179 " =    1.341
peak=    3.810 closest distance to " O   HOH Z 423 " =    1.807
peak=    3.805 closest distance to " O   HOH Z 298 " =    1.720
peak=    3.791 closest distance to " ND2 ASN A 187 " =    1.651
peak=    3.790 closest distance to " CG2 ILE A  20 " =    1.402
peak=    3.784 closest distance to " CG  GLN A  58 " =    0.945
peak=    3.765 closest distance to " CD  LYS A 166 " =    1.404
peak=    3.755 closest distance to " O   HOH Z  78 " =    1.697
peak=    3.723 closest distance to " O   HOH Z 280 " =    2.994
peak=    3.722 closest distance to " CB  SER A   3 " =    1.233
peak=    3.714 closest distance to " CD1 LEU A  96 " =    0.768
peak=    3.697 closest distance to " O   HOH Z 303 " =    2.166
peak=    3.683 closest distance to " O   HOH Z 365 " =    2.706
peak=    3.678 closest distance to " CG AARG A 275 " =    1.190
peak=    3.673 closest distance to " O   HOH Z 316 " =    3.040
peak=    3.671 closest distance to " O   HOH Z 371 " =    3.055
peak=    3.661 closest distance to " CB BVAL A  41 " =    1.211
peak=    3.659 closest distance to " O   HOH Z 258 " =    2.236
peak=    3.638 closest distance to " CB  TRP A 266 " =    1.120
peak=    3.635 closest distance to " O   HOH Z 173 " =    2.367
peak=    3.631 closest distance to " OG BSER A 164 " =    2.190
peak=    3.612 closest distance to " O   HOH Z 421 " =    2.003
peak=    3.612 closest distance to " O   HOH Z 327 " =    1.576
peak=    3.602 closest distance to " CA  VAL A  41 " =    0.829
peak=    3.596 closest distance to " O   ASN A  74 " =    1.707
peak=    3.593 closest distance to " O   HOH Z 128 " =    2.187
peak=    3.591 closest distance to " O   HOH Z 162 " =    1.729
peak=    3.587 closest distance to " O   HOH Z 389 " =    1.845
peak=    3.586 closest distance to " CB  PHE A 204 " =    0.924
peak=    3.585 closest distance to " CB  ALA A 248 " =    1.329
peak=    3.584 closest distance to " O   HOH Z  44 " =    2.166
peak=    3.582 closest distance to " O   ASP A 124 " =    1.373
peak=    3.581 closest distance to " CB  VAL A 265 " =    1.241
peak=    3.575 closest distance to " CG  LEU A 167 " =    1.208
peak=    3.575 closest distance to " CB  PRO A  90 " =    1.129
peak=    3.570 closest distance to " O   HOH Z 425 " =    1.376
peak=    3.567 closest distance to " O   HOH Z 295 " =    1.493
peak=    3.559 closest distance to " CG2 ILE A 234 " =    1.138
peak=    3.558 closest distance to " NZ  LYS A 117 " =    2.907
peak=    3.555 closest distance to " O   HOH Z 227 " =    1.569
peak=    3.553 closest distance to " O   HOH Z 337 " =    1.820
peak=    3.552 closest distance to " CA  VAL A 125 " =    1.176
peak=    3.546 closest distance to " O   HOH Z 383 " =    1.920
peak=    3.543 closest distance to " O   HOH Z 345 " =    2.950
peak=    3.542 closest distance to " CG  ARG A 138 " =    1.305
peak=    3.541 closest distance to " NH1AARG A 145 " =    1.330
peak=    3.540 closest distance to " O   HOH Z 301 " =    1.803
peak=    3.533 closest distance to " O   HOH Z 357 " =    1.978
peak=    3.525 closest distance to " CA  TYR A 116 " =    1.520
peak=    3.524 closest distance to " O   HOH Z 352 " =    1.826
peak=    3.510 closest distance to " CG1 ILE A  33 " =    1.225
peak=    3.510 closest distance to " CD2 LEU A 297 " =    0.969
peak=    3.507 closest distance to " CG2AVAL A 121 " =    2.156
peak=    3.503 closest distance to " O   HOH Z 102 " =    1.322
peak=    3.503 closest distance to " CG  PHE A 204 " =    0.937
peak=    3.500 closest distance to " CB  THR A  31 " =    1.438
peak=    3.494 closest distance to " CB  ALA A 114 " =    1.018
peak=    3.489 closest distance to " CE  LYS A  76 " =    0.895
peak=    3.486 closest distance to " CE  LYS A 119 " =    1.030
peak=    3.486 closest distance to " CB  ALA A   9 " =    1.661
peak=    3.483 closest distance to " CG BARG A 102 " =    1.807
peak=    3.481 closest distance to " CA  ARG A 195 " =    1.185
peak=    3.479 closest distance to " CB  SER A  62 " =    1.019
peak=    3.476 closest distance to " O   HOH Z  54 " =    1.567
peak=    3.476 closest distance to " CA  ASN A 217 " =    1.122
peak=    3.476 closest distance to " CG2 ILE A 120 " =    1.349
peak=    3.473 closest distance to " CZ3 TRP A 266 " =    1.096
peak=    3.471 closest distance to " CA  ALA A 160 " =    0.935
peak=    3.463 closest distance to " CG  MET A 185 " =    1.186
peak=    3.462 closest distance to " O   ASP A 191 " =    1.632
peak=    3.460 closest distance to " CD  LYS A 119 " =    1.930
peak=    3.454 closest distance to " O   HOH Z 361 " =    3.442
peak=    3.454 closest distance to " CB  GLU A 128 " =    1.139
peak=    3.445 closest distance to " NH2BARG A 145 " =    2.268
peak=    3.443 closest distance to " O   HOH Z 117 " =    2.030
peak=    3.438 closest distance to " CB  ASN A 187 " =    1.374
peak=    3.438 closest distance to " NE2 GLN A  77 " =    3.226
peak=    3.437 closest distance to " CZ3 TRP A  85 " =    0.912
peak=    3.436 closest distance to " O   HOH Z  88 " =    2.724
peak=    3.431 closest distance to " CG2 VAL A 257 " =    0.771
peak=    3.430 closest distance to " CB  ASN A  39 " =    0.884
peak=    3.427 closest distance to " OH  TYR A 116 " =    1.158
peak=    3.424 closest distance to " OE1 GLU A   2 " =    2.093
peak=    3.423 closest distance to " NH2 ARG A 156 " =    1.026
peak=    3.419 closest distance to " O   HOH Z 141 " =    1.600
peak=    3.417 closest distance to " CB  ASN A 110 " =    1.089
peak=    3.411 closest distance to " O   HOH Z 126 " =    1.744
peak=    3.409 closest distance to " O   HOH Z 132 " =    2.658
peak=    3.404 closest distance to " CB  SER A 141 " =    1.150
peak=    3.402 closest distance to " CB  VAL A 202 " =    1.516
peak=    3.400 closest distance to " O   HOH Z 158 " =    3.096
peak=    3.394 closest distance to " CG2AVAL A  72 " =    1.773
peak=    3.391 closest distance to " O   HOH Z 426 " =    1.355
peak=    3.386 closest distance to " O  BHOH Z  74 " =    1.277
peak=    3.385 closest distance to " CB  PRO A 198 " =    1.022
peak=    3.383 closest distance to " CB  ASN A 215 " =    1.117
peak=    3.375 closest distance to " O   HOH Z 344 " =    2.870
peak=    3.368 closest distance to " O   HOH Z 213 " =    1.612
peak=    3.367 closest distance to " N   PHE A 130 " =    1.348
peak=    3.364 closest distance to " CG1 VAL A 153 " =    0.941
peak=    3.364 closest distance to " O   HOH Z 250 " =    1.327
peak=    3.363 closest distance to " NZ  LYS A  48 " =    1.105
peak=    3.362 closest distance to " O   HOH Z 128 " =    2.749
peak=    3.355 closest distance to " CD1 ILE A 199 " =    1.057
peak=    3.354 closest distance to " CA  LYS A 117 " =    1.242
peak=    3.350 closest distance to " O   HOH Z  61 " =    1.621
peak=    3.348 closest distance to " O   HOH Z 263 " =    1.748
peak=    3.337 closest distance to " O   HOH Z 438 " =    2.860
peak=    3.337 closest distance to " O   HOH Z 438 " =    2.278
peak=    3.332 closest distance to " O   HOH Z  48 " =    1.710
peak=    3.331 closest distance to " CE1 TYR A 186 " =    1.225
peak=    3.326 closest distance to " CB  SER A  62 " =    1.133
peak=    3.324 closest distance to " CB  ASN A  45 " =    1.089
peak=    3.323 closest distance to " CG1 ILE A  49 " =    1.509
peak=    3.323 closest distance to " O   GLY A  91 " =    1.395
peak=    3.321 closest distance to " O   HOH Z  68 " =    1.932
peak=    3.320 closest distance to " O   HOH Z 368 " =    4.778
peak=    3.311 closest distance to " O   ALA A 165 " =    1.411
peak=    3.311 closest distance to " N   ALA A 256 " =    1.158
peak=    3.307 closest distance to " O   THR A 182 " =    1.462
peak=    3.307 closest distance to " CD2 TYR A 186 " =    1.096
peak=    3.304 closest distance to " CB  ASP A 124 " =    0.711
peak=    3.303 closest distance to " CB  ASN A 285 " =    1.002
peak=    3.303 closest distance to " OE1 GLN A  11 " =    1.766
peak=    3.299 closest distance to " CA  ALA A  21 " =    1.156
peak=    3.298 closest distance to " O   HOH Z  97 " =    2.139
peak=    3.297 closest distance to " CA  SER A  32 " =    1.731
peak=    3.296 closest distance to " O   HOH Z 148 " =    3.326
peak=    3.291 closest distance to " O   HOH Z 145 " =    2.476
peak=    3.290 closest distance to " CG  LYS A 119 " =    1.140
peak=    3.287 closest distance to " CA  TRP A  85 " =    1.186
peak=    3.285 closest distance to " O   HOH Z   1 " =    1.955
peak=    3.285 closest distance to " O   SER A 164 " =    1.204
peak=    3.283 closest distance to " CA  ALA A 158 " =    1.519
peak=    3.283 closest distance to " O   HOH Z 417 " =    3.347
peak=    3.282 closest distance to " CB  ALA A 295 " =    1.219
peak=    3.275 closest distance to " CA  ASP A 162 " =    1.022
peak=    3.271 closest distance to " OD1 ASN A  69 " =    2.415
peak=    3.271 closest distance to " O   HOH Z 419 " =    1.753
peak=    3.269 closest distance to " CG  GLU A  37 " =    0.899
peak=    3.269 closest distance to " CZ2 TRP A 150 " =    1.118
peak=    3.268 closest distance to " CG AARG A 102 " =    1.125
peak=    3.267 closest distance to " O   TRP A 274 " =    1.710
peak=    3.267 closest distance to " CB  GLU A 277 " =    0.959
peak=    3.265 closest distance to " CB  PRO A 243 " =    1.062
peak=    3.265 closest distance to " CB  ARG A 138 " =    0.822
peak=    3.262 closest distance to " CE1 HIS A 108 " =    1.173
peak=    3.259 closest distance to " O   ASN A 284 " =    1.831
peak=    3.257 closest distance to " O  BHOH Z 338 " =    2.316
peak=    3.257 closest distance to " CG  GLN A  58 " =    2.936
peak=    3.257 closest distance to " O   HOH Z 253 " =    1.415
peak=    3.253 closest distance to " O   HOH Z 271 " =    2.421
peak=    3.252 closest distance to " CA  ASP A 149 " =    1.133
peak=    3.248 closest distance to " CA  LYS A 290 " =    1.122
peak=    3.246 closest distance to " CA  ASN A 215 " =    1.017
peak=    3.243 closest distance to " OG  SER A  62 " =    2.742
peak=    3.242 closest distance to " O   HOH Z  15 " =    2.136
peak=    3.241 closest distance to " O   HOH Z 109 " =    1.317
peak=    3.240 closest distance to " N   ASP A 162 " =    1.198
peak=    3.238 closest distance to " O   HOH Z 245 " =    1.433
peak=    3.236 closest distance to " CA  ALA A 291 " =    0.829
peak=    3.235 closest distance to " O   HOH Z 199 " =    1.560
peak=    3.234 closest distance to " O   GLN A  88 " =    1.601
peak=    3.229 closest distance to " O   HOH Z 193 " =    1.460
peak=    3.227 closest distance to " O   HOH Z  21 " =    1.858
peak=    3.222 closest distance to " O   LEU A 228 " =    1.730
peak=    3.217 closest distance to " O   HOH Z  85 " =    1.666
peak=    3.216 closest distance to " CB  HIS A 108 " =    0.849
peak=    3.213 closest distance to " O   HOH Z 293 " =    1.931
peak=    3.213 closest distance to " CA  SER A  87 " =    1.004
peak=    3.209 closest distance to " O   HOH Z 336 " =    1.809
peak=    3.202 closest distance to " O   HOH Z 353 " =    2.727
peak=    3.202 closest distance to " N   SER A 135 " =    1.382
peak=    3.198 closest distance to " CB  GLN A  89 " =    1.223
peak=    3.198 closest distance to " O   HOH Z 409 " =    3.723
peak=    3.197 closest distance to " CB  SER A  99 " =    1.416
peak=    3.195 closest distance to " CB  ARG A 139 " =    1.047
peak=    3.188 closest distance to " OD2 ASP A 298 " =    3.842
peak=    3.188 closest distance to " O   HOH Z 337 " =    3.595
peak=    3.184 closest distance to " OD1 ASP A 231 " =    1.942
peak=    3.172 closest distance to " O   HOH Z 361 " =    3.596
peak=    3.172 closest distance to " O   HOH Z 183 " =    1.794
peak=    3.164 closest distance to " CB  ASP A 140 " =    1.173
peak=    3.163 closest distance to " O   HOH Z 329 " =    4.088
peak=    3.162 closest distance to " CB  ARG A 190 " =    1.151
peak=    3.157 closest distance to " CB  ARG A 156 " =    1.172
peak=    3.155 closest distance to " O   HOH Z 345 " =    1.576
peak=    3.151 closest distance to " O   HOH Z  35 " =    2.248
peak=    3.150 closest distance to " O   HOH Z 207 " =    1.129
peak=    3.148 closest distance to " OG1 THR A 221 " =    1.276
peak=    3.147 closest distance to " CB  ASP A 298 " =    1.171
peak=    3.143 closest distance to " N   ASP A 231 " =    1.624
peak=    3.140 closest distance to " CB  ASP A 132 " =    1.051
peak=    3.138 closest distance to " CB  GLU A  46 " =    1.004
peak=    3.138 closest distance to " CB  THR A 235 " =    1.264
peak=    3.136 closest distance to " O   HOH Z 299 " =    2.373
peak=    3.131 closest distance to " O   HOH Z  88 " =    3.518
peak=    3.131 closest distance to " CG  MET A 185 " =    0.914
peak=    3.123 closest distance to " CG2 VAL A 197 " =    1.068
peak=    3.119 closest distance to " CG  ARG A  66 " =    0.954
peak=    3.109 closest distance to " O   HOH Z 151 " =    1.742
peak=    3.107 closest distance to " O   HOH Z 134 " =    1.229
peak=    3.101 closest distance to " CG  ARG A 269 " =    1.554
peak=    3.087 closest distance to " O   HOH Z  47 " =    1.874
peak=    3.084 closest distance to " CA  ASN A 176 " =    1.119
peak=    3.076 closest distance to " CA  LEU A 282 " =    1.374
peak=    3.072 closest distance to " CB  LYS A 117 " =    1.163
peak=    3.068 closest distance to " O   HOH Z 210 " =    0.966
peak=    3.065 closest distance to " CB  PHE A 283 " =    0.798
peak=    3.061 closest distance to " O   HOH Z 421 " =    3.276
peak=    3.054 closest distance to " O   HOH Z 195 " =    4.176
peak=    3.049 closest distance to " O   HOH Z 299 " =    4.278
peak=    3.034 closest distance to " CB  ALA A 104 " =    0.789
peak=    3.032 closest distance to " CA  MET A 105 " =    1.065
peak=    3.009 closest distance to " O   HOH Z 109 " =    1.973

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

Number of peaks found at mFobs-DFmodel map (map cutoff=3.00 sigma)= 195         
Filter by distance & map next to the model:
   mapped sites are within: 0.618 - 5.792
   number of sites selected in [dist_min= 0.70, dist_max= 6.00]: 193 from: 195
   mapped sites are within: 0.748 - 5.792

peak=   -4.837 closest distance to " CG  GLN A  58 " =    1.034
peak=   -4.779 closest distance to " CG2 VAL A 230 " =    0.748
peak=   -4.647 closest distance to " SG  CYS A 254 " =    3.281
peak=   -4.354 closest distance to " OG BSER A 134 " =    1.459
peak=   -4.328 closest distance to " O   HOH Z 193 " =    1.128
peak=   -4.305 closest distance to " CD  ARG A 156 " =    2.047
peak=   -4.304 closest distance to " O   HOH Z 210 " =    0.927
peak=   -4.220 closest distance to " O   HOH Z 266 " =    5.509
peak=   -4.209 closest distance to " OXT GLY A 302 " =    2.930
peak=   -4.174 closest distance to " CE2 TYR A  30 " =    2.779
peak=   -4.159 closest distance to " CZ2 TRP A  92 " =    2.836
peak=   -4.156 closest distance to " CG1 VAL A 112 " =    2.634
peak=   -4.120 closest distance to " C   HIS A 108 " =    1.204
peak=   -4.092 closest distance to " O   PRO A 163 " =    2.166
peak=   -4.072 closest distance to " CD2 LEU A 237 " =    2.633
peak=   -4.049 closest distance to " O   HOH Z 131 " =    4.123
peak=   -4.020 closest distance to " O   HOH Z 351 " =    1.512
peak=   -4.019 closest distance to " CD2 TYR A 293 " =    1.871
peak=   -4.000 closest distance to " O   VAL A  67 " =    2.677
peak=   -3.996 closest distance to " CA  ASP A 298 " =    1.080
peak=   -3.978 closest distance to " CD1 LEU A 101 " =    2.363
peak=   -3.972 closest distance to " O   HOH Z 166 " =    1.643
peak=   -3.964 closest distance to " CB  ALA A 248 " =    2.259
peak=   -3.951 closest distance to " CG1 VAL A 296 " =    1.021
peak=   -3.937 closest distance to " O   ASN A  45 " =    1.899
peak=   -3.887 closest distance to " NE2 GLN A  88 " =    1.122
peak=   -3.864 closest distance to " O   PRO A 198 " =    1.247
peak=   -3.860 closest distance to " O   HOH Z 114 " =    3.265
peak=   -3.811 closest distance to " O   HOH Z 196 " =    2.164
peak=   -3.808 closest distance to " CA  GLY A 241 " =    2.430
peak=   -3.777 closest distance to " O   HOH Z 423 " =    2.392
peak=   -3.762 closest distance to " O   HOH Z 154 " =    1.488
peak=   -3.747 closest distance to " O   HOH Z  13 " =    1.744
peak=   -3.743 closest distance to " NE2 GLN A  11 " =    1.771
peak=   -3.741 closest distance to " CE3 TRP A 150 " =    2.221
peak=   -3.739 closest distance to " OE1 GLN A 223 " =    2.457
peak=   -3.734 closest distance to " O   HOH Z 165 " =    2.011
peak=   -3.733 closest distance to " O   HOH Z 214 " =    2.497
peak=   -3.727 closest distance to " CA  VAL A  67 " =    3.016
peak=   -3.725 closest distance to " O   ALA A 227 " =    1.329
peak=   -3.714 closest distance to " O   HOH Z 231 " =    2.249
peak=   -3.702 closest distance to " CB  ALA A 161 " =    2.493
peak=   -3.698 closest distance to " O   GLY A  80 " =    2.546
peak=   -3.688 closest distance to " CB  PHE A 208 " =    2.344
peak=   -3.673 closest distance to " CG  PRO A 243 " =    1.603
peak=   -3.672 closest distance to " CB  ALA A 248 " =    2.145
peak=   -3.672 closest distance to " CD2 LEU A 167 " =    1.761
peak=   -3.663 closest distance to " CD2 PHE A 192 " =    2.135
peak=   -3.644 closest distance to " O   HOH Z 179 " =    2.179
peak=   -3.642 closest distance to " ND2 ASN A  69 " =    1.850
peak=   -3.642 closest distance to " O   HOH Z 285 " =    1.789
peak=   -3.635 closest distance to " CB  ALA A  43 " =    2.510
peak=   -3.620 closest distance to " OG  SER A  97 " =    2.316
peak=   -3.613 closest distance to " O   HOH Z 128 " =    1.216
peak=   -3.608 closest distance to " CZ  ARG A  66 " =    1.117
peak=   -3.581 closest distance to " O   ARG A  24 " =    2.097
peak=   -3.580 closest distance to " ND2 ASN A 187 " =    1.631
peak=   -3.577 closest distance to " O   PHE A 218 " =    1.523
peak=   -3.567 closest distance to " O   ALA A 256 " =    1.761
peak=   -3.560 closest distance to " ND2 ASN A  45 " =    1.174
peak=   -3.546 closest distance to " CA  GLY A 133 " =    2.320
peak=   -3.540 closest distance to " CD2 HIS A 207 " =    2.469
peak=   -3.535 closest distance to " ND2 ASN A 249 " =    2.260
peak=   -3.532 closest distance to " CD1 LEU A 255 " =    2.683
peak=   -3.531 closest distance to " O   HOH Z  37 " =    1.859
peak=   -3.531 closest distance to " CB  SER A 210 " =    1.097
peak=   -3.526 closest distance to " CD1 PHE A  59 " =    1.946
peak=   -3.516 closest distance to " O   HOH Z 290 " =    1.037
peak=   -3.501 closest distance to " O   HOH Z 191 " =    5.664
peak=   -3.493 closest distance to " N   ALA A 248 " =    2.152
peak=   -3.490 closest distance to " O   HOH Z 407 " =    2.767
peak=   -3.487 closest distance to " CE3 TRP A 274 " =    2.291
peak=   -3.483 closest distance to " CG2 VAL A 296 " =    1.291
peak=   -3.482 closest distance to " CG  GLN A 103 " =    2.507
peak=   -3.473 closest distance to " O   LEU A 282 " =    2.142
peak=   -3.466 closest distance to " CE  MET A 105 " =    2.431
peak=   -3.465 closest distance to " CH2 TRP A 179 " =    1.298
peak=   -3.464 closest distance to " C   THR A 279 " =    1.248
peak=   -3.464 closest distance to " CD1 ILE A 199 " =    2.401
peak=   -3.455 closest distance to " O   HOH Z 431 " =    1.998
peak=   -3.452 closest distance to " N   SER A 276 " =    1.392
peak=   -3.450 closest distance to " O   HOH Z  28 " =    2.376
peak=   -3.450 closest distance to " O   HOH Z 216 " =    1.292
peak=   -3.440 closest distance to " ND2 ASN A  39 " =    1.115
peak=   -3.438 closest distance to " O   TRP A  92 " =    1.974
peak=   -3.435 closest distance to " CG  ARG A 269 " =    2.143
peak=   -3.430 closest distance to " CB  PRO A 243 " =    2.729
peak=   -3.421 closest distance to " O   SER A 210 " =    1.735
peak=   -3.420 closest distance to " CD2 PHE A 225 " =    1.068
peak=   -3.420 closest distance to " O   HOH Z 136 " =    1.416
peak=   -3.415 closest distance to " N   ALA A 226 " =    1.959
peak=   -3.413 closest distance to " O   HOH Z 102 " =    1.644
peak=   -3.411 closest distance to " O   HOH Z 150 " =    1.998
peak=   -3.408 closest distance to " O   SER A 146 " =    1.153
peak=   -3.402 closest distance to " OD2 ASP A 191 " =    1.404
peak=   -3.399 closest distance to " CZ  PHE A  38 " =    2.377
peak=   -3.391 closest distance to " NE  ARG A  66 " =    4.309
peak=   -3.384 closest distance to " CE1 TYR A 247 " =    2.633
peak=   -3.382 closest distance to " O   HOH Z  63 " =    1.170
peak=   -3.367 closest distance to " O   HOH Z 211 " =    1.435
peak=   -3.365 closest distance to " O   HOH Z 137 " =    1.784
peak=   -3.365 closest distance to " O   SER A 276 " =    1.758
peak=   -3.364 closest distance to " CG2 ILE A 263 " =    2.209
peak=   -3.361 closest distance to " O   HOH Z 110 " =    1.465
peak=   -3.359 closest distance to " CD  GLN A 223 " =    1.774
peak=   -3.357 closest distance to " O   HOH Z   6 " =    1.733
peak=   -3.354 closest distance to " CD  LYS A 289 " =    2.509
peak=   -3.350 closest distance to " O   ILE A 106 " =    1.702
peak=   -3.350 closest distance to " O   HOH Z 119 " =    2.140
peak=   -3.343 closest distance to " O   MET A  40 " =    2.794
peak=   -3.342 closest distance to " CG  GLU A  53 " =    1.533
peak=   -3.340 closest distance to " O   HOH Z 174 " =    2.172
peak=   -3.338 closest distance to " CA  GLY A 203 " =    2.362
peak=   -3.334 closest distance to " O   HOH Z 426 " =    1.768
peak=   -3.332 closest distance to " C   SER A 206 " =    1.544
peak=   -3.326 closest distance to " C   ILE A 239 " =    2.114
peak=   -3.322 closest distance to " CG2 VAL A 189 " =    2.067
peak=   -3.320 closest distance to " O   HOH Z 185 " =    2.425
peak=   -3.314 closest distance to " CD  GLN A  73 " =    0.802
peak=   -3.309 closest distance to " O   HOH Z 139 " =    5.098
peak=   -3.309 closest distance to " CG  ASP A 231 " =    0.838
peak=   -3.307 closest distance to " CD  PRO A 243 " =    1.961
peak=   -3.306 closest distance to " OH  TYR A 172 " =    1.877
peak=   -3.303 closest distance to " NE2 GLN A 194 " =    1.934
peak=   -3.297 closest distance to " C   ASN A 285 " =    2.202
peak=   -3.294 closest distance to " OE1 GLN A 183 " =    1.497
peak=   -3.294 closest distance to " O   HOH Z 265 " =    2.378
peak=   -3.292 closest distance to " CG  TRP A 266 " =    1.928
peak=   -3.287 closest distance to " O   HOH Z 301 " =    2.476
peak=   -3.287 closest distance to " O   HOH Z 136 " =    2.637
peak=   -3.284 closest distance to " O   HOH Z 397 " =    1.167
peak=   -3.278 closest distance to " CD2 HIS A 115 " =    1.003
peak=   -3.273 closest distance to " CZ  PHE A  38 " =    2.031
peak=   -3.270 closest distance to " CB  TRP A  85 " =    2.657
peak=   -3.269 closest distance to " O   HOH Z  60 " =    2.064
peak=   -3.268 closest distance to " O   HOH Z 130 " =    2.555
peak=   -3.268 closest distance to " NH2 ARG A  66 " =    5.792
peak=   -3.264 closest distance to " O   HOH Z 107 " =    1.086
peak=   -3.264 closest distance to " CB  TYR A  15 " =    2.190
peak=   -3.261 closest distance to " O   HOH Z 174 " =    3.791
peak=   -3.259 closest distance to " CA  GLY A 133 " =    1.973
peak=   -3.250 closest distance to " CB  ALA A  10 " =    2.235
peak=   -3.248 closest distance to " OXT GLY A 302 " =    3.376
peak=   -3.244 closest distance to " SG  CYS A 260 " =    1.941
peak=   -3.238 closest distance to " N   THR A  52 " =    1.663
peak=   -3.237 closest distance to " CE BMET A  47 " =    1.215
peak=   -3.236 closest distance to " N   ALA A 248 " =    1.614
peak=   -3.234 closest distance to " O   TRP A  70 " =    1.653
peak=   -3.233 closest distance to " O   HOH Z 109 " =    0.946
peak=   -3.233 closest distance to " O   HOH Z 252 " =    3.769
peak=   -3.232 closest distance to " NH2AARG A 275 " =    4.760
peak=   -3.229 closest distance to " O   HOH Z 145 " =    2.647
peak=   -3.228 closest distance to " CH2 TRP A 150 " =    1.082
peak=   -3.225 closest distance to " O   HOH Z 177 " =    1.732
peak=   -3.223 closest distance to " O   HOH Z 345 " =    1.858
peak=   -3.220 closest distance to " O   SER A 273 " =    1.158
peak=   -3.218 closest distance to " CG  ASP A 132 " =    2.308
peak=   -3.214 closest distance to " O   HOH Z 359 " =    2.834
peak=   -3.209 closest distance to " CG  MET A 105 " =    0.893
peak=   -3.208 closest distance to " CG2 THR A 178 " =    2.395
peak=   -3.205 closest distance to " O   HOH Z 421 " =    3.927
peak=   -3.205 closest distance to " O   HOH Z  71 " =    2.498
peak=   -3.204 closest distance to " O   HOH Z 111 " =    4.364
peak=   -3.199 closest distance to " O   HOH Z  19 " =    2.230
peak=   -3.190 closest distance to " CG  LEU A  83 " =    2.090
peak=   -3.189 closest distance to " OG ASER A 134 " =    1.318
peak=   -3.187 closest distance to " O   HOH Z 111 " =    1.780
peak=   -3.184 closest distance to " O   HOH Z 283 " =    2.425
peak=   -3.173 closest distance to " CB  HIS A  86 " =    1.171
peak=   -3.168 closest distance to " O   HOH Z 171 " =    2.265
peak=   -3.167 closest distance to " O   GLY A 203 " =    2.399
peak=   -3.162 closest distance to " CZ  TYR A 169 " =    1.824
peak=   -3.162 closest distance to " O   HOH Z 392 " =    1.871
peak=   -3.156 closest distance to " OD2 ASP A 171 " =    2.218
peak=   -3.156 closest distance to " CD  GLN A  88 " =    0.931
peak=   -3.152 closest distance to " CG  LEU A   5 " =    1.015
peak=   -3.145 closest distance to " CB  PRO A 163 " =    2.513
peak=   -3.134 closest distance to " CB  GLN A  55 " =    1.196
peak=   -3.133 closest distance to " O   ASN A 187 " =    1.589
peak=   -3.129 closest distance to " CE  LYS A 166 " =    3.085
peak=   -3.127 closest distance to " CE1 PHE A 192 " =    1.975
peak=   -3.118 closest distance to " O   SER A   3 " =    1.047
peak=   -3.115 closest distance to " OG BSER A  99 " =    1.043
peak=   -3.110 closest distance to " O   HOH Z  11 " =    1.846
peak=   -3.108 closest distance to " CA  ALA A 299 " =    2.242
peak=   -3.105 closest distance to " O   HOH Z  52 " =    1.723
peak=   -3.099 closest distance to " OG1 THR A  82 " =    1.636
peak=   -3.082 closest distance to " CE  LYS A  76 " =    2.559
peak=   -3.079 closest distance to " N   THR A 235 " =    1.185
peak=   -3.076 closest distance to " CG2 VAL A 197 " =    2.333
peak=   -3.074 closest distance to " O   ASN A 252 " =    1.322
peak=   -3.067 closest distance to " O   HOH Z 139 " =    5.096
peak=   -3.047 closest distance to " O   TYR A 186 " =    1.652

================= 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 0.4707   6.283979e+00   6.274625e+00
   1_bss:  0.4768 0.4649   6.276098e+00   6.271181e+00
   1_xyz:  0.3884 0.4091   6.154964e+00   6.192331e+00
   1_adp:  0.3410 0.3967   6.071067e+00   6.161136e+00
   1_occ:  0.3406 0.3972   6.070400e+00   6.161931e+00
   2_bss:  0.3370 0.3939   6.071589e+00   6.161660e+00
   2_xyz:  0.2496 0.2995   5.818473e+00   5.972735e+00
   2_adp:  0.2285 0.2803   5.748379e+00   5.914467e+00
   2_occ:  0.2281 0.2804   5.748264e+00   5.915114e+00
   3_bss:  0.2265 0.2801   5.748523e+00   5.914735e+00
   3_xyz:  0.1612 0.2047   5.445846e+00   5.641387e+00
   3_adp:  0.1465 0.1893   5.361614e+00   5.569761e+00
   3_occ:  0.1462 0.1895   5.361097e+00   5.569755e+00
   4_bss:  0.1458 0.1890   5.359695e+00   5.566960e+00
   4_xyz:  0.1290 0.1711   5.260764e+00   5.474356e+00
   4_adp:  0.1262 0.1682   5.241786e+00   5.454119e+00
   4_occ:  0.1261 0.1682   5.241476e+00   5.453858e+00
   5_bss:  0.1261 0.1682   5.241476e+00   5.453858e+00
   5_xyz:  0.1204 0.1624   5.204757e+00   5.425922e+00
   5_adp:  0.1188 0.1630   5.200904e+00   5.429952e+00
   5_occ:  0.1188 0.1631   5.200645e+00   5.429697e+00
   5_bss:  0.1188 0.1634   5.201946e+00   5.430086e+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:  0.337  20.001   7.577   8.867   9.860   0.000   0.000   0.000
   1_xyz:  0.337  20.001   7.577   8.867   9.860   0.000   0.000   0.000
   1_adp:  0.337  20.001   7.577   8.867   9.860   0.000   0.000   0.000
   1_occ:  0.337  20.001   7.577   8.867   9.860   0.000   0.000   0.000
   2_bss:  0.332  43.342   3.634   4.686   5.920   0.000   0.000   0.000
   2_xyz:  0.332  43.342   3.634   4.686   5.920   0.000   0.000   0.000
   2_adp:  0.332  43.342   3.634   4.686   5.920   0.000   0.000   0.000
   2_occ:  0.332  43.342   3.634   4.686   5.920   0.000   0.000   0.000
   3_bss:  0.314  52.659   1.680   3.112   3.979   0.000   0.000   0.000
   3_xyz:  0.314  52.659   1.680   3.112   3.979   0.000   0.000   0.000
   3_adp:  0.314  52.659   1.680   3.112   3.979   0.000   0.000   0.000
   3_occ:  0.314  52.659   1.680   3.112   3.979   0.000   0.000   0.000
   4_bss:  0.328  52.659   0.834   2.133   3.206   0.000   0.000   0.000
   4_xyz:  0.328  52.659   0.834   2.133   3.206   0.000   0.000   0.000
   4_adp:  0.328  52.659   0.834   2.133   3.206   0.000   0.000   0.000
   4_occ:  0.328  52.659   0.834   2.133   3.206   0.000   0.000   0.000
   5_bss:  0.328  52.659   0.834   2.133   3.206   0.000   0.000   0.000
   5_xyz:  0.328  52.659   0.834   2.133   3.206   0.000   0.000   0.000
   5_adp:  0.328  52.659   0.834   2.133   3.206   0.000   0.000   0.000
   5_occ:  0.328  52.659   0.834   2.133   3.206   0.000   0.000   0.000
   5_bss:  0.328  54.750  -1.185   0.013   1.173   0.000   0.000   0.000
------------------------------------------------------------------------
 stage     <pher>    fom   alpha         beta
   0    :  56.251 0.4426  0.5193    69423.334
   1_bss:  56.218 0.4417  0.6753    68227.641
   1_xyz:  46.421 0.5639  0.8343    48307.255
   1_adp:  43.239 0.6032  0.9336    43910.419
   1_occ:  43.276 0.6027  0.9315    43974.948
   2_bss:  43.080 0.6051  0.8139    43849.936
   2_xyz:  31.535 0.7399  0.9590    24309.744
   2_adp:  28.576 0.7733  0.9931    20871.368
   2_occ:  28.588 0.7732  0.9930    20901.460
   3_bss:  28.502 0.7742  0.9306    20846.319
   3_xyz:  20.048 0.8608  0.9927    10939.012
   3_adp:  18.166 0.8789  1.0004     9487.636
   3_occ:  18.167 0.8789  1.0003     9485.249
   4_bss:  18.089 0.8795  0.9704     9389.517
   4_xyz:  16.052 0.8978  0.9760     7714.195
   4_adp:  15.608 0.9019  0.9735     7492.385
   4_occ:  15.607 0.9019  0.9734     7491.651
   5_bss:  15.607 0.9019  0.9734     7491.651
   5_xyz:  14.981 0.9071  0.9770     7013.265
   5_adp:  15.030 0.9069  0.9715     7051.971
   5_occ:  15.025 0.9069  0.9715     7045.787
   5_bss:  15.055 0.9067  0.9722     7086.416
------------------------------------------------------------------------
 stage       angl   bond   chir   dihe   plan   repu  geom_target
   0    :  24.226  0.414  2.119 33.790  0.145  4.089   5.3740e+01
   1_bss:  24.226  0.414  2.119 33.790  0.145  4.089   5.3740e+01
   1_xyz:   1.758  0.014  0.111 18.134  0.007  4.108   1.4997e-01
   1_adp:   1.758  0.014  0.111 18.134  0.007  4.108   1.4997e-01
   1_occ:   1.758  0.014  0.111 18.134  0.007  4.108   1.4997e-01
   2_bss:   1.758  0.014  0.111 18.134  0.007  4.108   1.4997e-01
   2_xyz:   1.150  0.009  0.075 16.083  0.005  4.109   7.8444e-02
   2_adp:   1.150  0.009  0.075 16.083  0.005  4.109   7.8444e-02
   2_occ:   1.150  0.009  0.075 16.083  0.005  4.109   7.8444e-02
   3_bss:   1.150  0.009  0.075 16.083  0.005  4.109   7.8444e-02
   3_xyz:   1.098  0.007  0.079 15.916  0.004  4.126   7.0240e-02
   3_adp:   1.098  0.007  0.079 15.916  0.004  4.126   7.0240e-02
   3_occ:   1.098  0.007  0.079 15.916  0.004  4.126   7.0240e-02
   4_bss:   1.098  0.007  0.079 15.916  0.004  4.126   7.0240e-02
   4_xyz:   0.990  0.007  0.077 15.402  0.004  4.112   5.9355e-02
   4_adp:   0.990  0.007  0.077 15.402  0.004  4.112   5.9355e-02
   4_occ:   0.990  0.007  0.077 15.402  0.004  4.112   5.9355e-02
   5_bss:   0.990  0.007  0.077 15.402  0.004  4.112   5.9355e-02
   5_xyz:   1.008  0.007  0.078 15.344  0.003  4.115   6.0773e-02
   5_adp:   1.008  0.007  0.078 15.344  0.003  4.115   6.0773e-02
   5_occ:   1.008  0.007  0.078 15.344  0.003  4.115   6.0773e-02
   5_bss:   1.008  0.007  0.078 15.344  0.003  4.115   6.0773e-02
------------------------------------------------------------------------
                      Maximal deviations:
 stage       angl   bond   chir   dihe   plan   repu       |grad|
   0    :  74.492  1.400  6.404144.062  0.405  1.044   6.9620e+00
   1_bss:  74.492  1.400  6.404144.062  0.405  1.044   6.9620e+00
   1_xyz:  16.296  0.177  0.532 85.656  0.039  2.226   1.0833e-01
   1_adp:  16.296  0.177  0.532 85.656  0.039  2.226   1.0833e-01
   1_occ:  16.296  0.177  0.532 85.656  0.039  2.226   1.0833e-01
   2_bss:  16.296  0.177  0.532 85.656  0.039  2.226   1.0833e-01
   2_xyz:   6.884  0.105  0.268 84.041  0.045  2.293   8.3002e-02
   2_adp:   6.884  0.105  0.268 84.041  0.045  2.293   8.3002e-02
   2_occ:   6.884  0.105  0.268 84.041  0.045  2.293   8.3002e-02
   3_bss:   6.884  0.105  0.268 84.041  0.045  2.293   8.3002e-02
   3_xyz:   8.093  0.052  0.345 84.145  0.038  2.216   5.6155e-02
   3_adp:   8.093  0.052  0.345 84.145  0.038  2.216   5.6155e-02
   3_occ:   8.093  0.052  0.345 84.145  0.038  2.216   5.6155e-02
   4_bss:   8.093  0.052  0.345 84.145  0.038  2.216   5.6155e-02
   4_xyz:   6.529  0.038  0.356 81.200  0.037  2.306   3.6380e-02
   4_adp:   6.529  0.038  0.356 81.200  0.037  2.306   3.6380e-02
   4_occ:   6.529  0.038  0.356 81.200  0.037  2.306   3.6380e-02
   5_bss:   6.529  0.038  0.356 81.200  0.037  2.306   3.6380e-02
   5_xyz:   7.104  0.048  0.404 81.247  0.034  2.326   3.5237e-02
   5_adp:   7.104  0.048  0.404 81.247  0.034  2.326   3.5237e-02
   5_occ:   7.104  0.048  0.404 81.247  0.034  2.326   3.5237e-02
   5_bss:   7.104  0.048  0.404 81.247  0.034  2.326   3.5237e-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:  76.11   0.00  13.44  76.11   0.00  10.88  72.76   0.00  27.36
   1_occ:  76.11   0.00  13.44  76.11   0.00  10.88  72.76   0.00  27.36
   2_bss:  76.11   0.00  13.44  76.11   0.00  10.88  72.76   0.00  27.36
   2_xyz:  76.11   0.00  13.44  76.11   0.00  10.88  72.76   0.00  27.36
   2_adp:  82.23   0.00  13.34  82.23   0.00   9.77  74.01   1.99  32.79
   2_occ:  82.23   0.00  13.34  82.23   0.00   9.77  74.01   1.99  32.79
   3_bss:  82.23   0.00  13.34  82.23   0.00   9.77  74.01   1.99  32.79
   3_xyz:  82.23   0.00  13.34  82.23   0.00   9.77  74.01   1.99  32.79
   3_adp:  77.51   0.00  13.56  77.51   0.00   9.28  73.65   2.09  36.90
   3_occ:  77.51   0.00  13.56  77.51   0.00   9.28  73.65   2.09  36.90
   4_bss:  77.51   0.00  13.56  77.51   0.00   9.28  73.65   2.09  36.90
   4_xyz:  77.51   0.00  13.56  77.51   0.00   9.28  73.65   2.09  36.90
   4_adp:  78.58   0.00  13.39  78.58   0.00   9.11  74.57   2.24  36.70
   4_occ:  78.58   0.00  13.39  78.58   0.00   9.11  74.57   2.24  36.70
   5_bss:  78.58   0.00  13.39  78.58   0.00   9.11  74.57   2.24  36.70
   5_xyz:  78.58   0.00  13.39  78.58   0.00   9.11  74.57   2.24  36.70
   5_adp:  86.19   0.00  13.54  86.19   0.00   9.10  80.59   1.94  37.74
   5_occ:  86.19   0.00  13.54  86.19   0.00   9.10  80.59   1.94  37.74
   5_bss:  88.29   2.09  15.63  88.29   2.09  11.19  82.68   4.03  39.83
------------------------------------------------------------------------
 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:    1.299    0.018    0.419
   1_adp:    1.299    0.018    0.419
   1_occ:    1.299    0.018    0.419
   2_bss:    1.299    0.018    0.419
   2_xyz:    1.863    0.050    0.575
   2_adp:    1.863    0.050    0.575
   2_occ:    1.863    0.050    0.575
   3_bss:    1.863    0.050    0.575
   3_xyz:    1.801    0.049    0.665
   3_adp:    1.801    0.049    0.665
   3_occ:    1.801    0.049    0.665
   4_bss:    1.801    0.049    0.665
   4_xyz:    1.945    0.050    0.700
   4_adp:    1.945    0.050    0.700
   4_occ:    1.945    0.050    0.700
   5_bss:    1.945    0.050    0.700
   5_xyz:    1.982    0.079    0.715
   5_adp:    1.982    0.079    0.715
   5_occ:    1.982    0.079    0.715
   5_bss:    1.982    0.079    0.715
------------------------------------------------------------------------

CPU time actual refinement: 335.87


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

Writing refined structure to PDB file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/trial/run_206/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_206/model_refine_001_2mFobs-DFmodel.map
Writing mFobs-DFmodel XPLOR map to file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/trial/run_206/model_refine_001_mFobs-DFmodel.map
Writing map coefficients to MTZ file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/trial/run_206/model_refine_001_map_coeffs.mtz

Writing default parameters for subsequent refinement:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/trial/run_206/model_refine_002.def


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

Pure refinement (no I/O, processing, etc)= 335.72 
  Macro-tasks:
    bulk solvent and scale       = 41.22  
    individual site refinement   = 137.41 
    weights calculation          = 32.59  
    collect and process          = 6.71   
    model show statistics        = 0.14   
    TOTAL for macro-tasks        = 218.07 
  Micro-tasks:
    mask                            = 2.42   
    f_calc                          = 103.56 
    alpha_beta                      = 8.29   
    target                          = 1.15   
    gradients_wrt_atomic_parameters = 112.97 
    fmodel                         = 7.62   
    r_factors                      = 0.22   
    phase_errors                   = 10.57  
    foms                           = 0.29   
    TOTAL for micro-tasks          = 247.09 
NUMBER OF MASK CALCS=  5
Time per interpreted Python bytecode instruction: 4.778 micro seconds
Total CPU time: 5.82 minutes
from_scatterers_fft:    632 calls, 103.09 s
gradients_fft:          577 calls, 100.09 s

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

# Date 2008-01-16 Time 01:02:47 PST -0800 (1200474167.41 s)
Start R-work = 0.4851, R-free = 0.4707 (no bulk solvent and anisotropic scale)
Final R-work = 0.1363, R-free = 0.1783 (no bulk solvent and anisotropic scale)

Start R-work = 0.4768, R-free = 0.4649
Final R-work = 0.1188, R-free = 0.1634