# Date 2008-01-16 Time 01:37:20 PST -0800 (1200476240.12 s)
#phil __OFF__

Command line arguments: "../492.param" "adp.set_b_iso=10" "sites.shake=0.5" "main.number_of_macro_cycles=5" "--overwrite"

HOST = blackbird.lbl.gov
HOSTTYPE = x86_64-linux
USER = phzwart
PID = 10230
JOB_ID = 5158
SGE_ARCH = lx24-amd64
SGE_TASK_FIRST = 1
SGE_TASK_LAST = 1330
SGE_TASK_ID = 492

-------------------------------------------------------------------------------
  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: (69.8988, 45.7567, 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: 2.76, per 1000 atoms: 0.98


================================== 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: (69.8988, 45.7567, 87.6859, 90, 90, 90)
Space group: P 21 21 21 (No. 19)
Systematic absences: 0
Centric reflections: 2427
Resolution range: 14.9985 1.95324
Completeness in resolution range: 0.933343
Completeness with d_max=infinity: 0.930594

Number of F-obs in resolution range:                   19589
Number of F-obs <= 0:                                  0
Refinement resolution range: d_max =  14.9985
                             d_min =   1.9532

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: (69.8988, 45.7567, 87.6859, 90, 90, 90)
Space group: P 21 21 21 (No. 19)
Systematic absences: 0
Centric reflections: 2427
Resolution range: 14.9985 1.95324
Completeness in resolution range: 0.933343
Completeness with d_max=infinity: 0.930594

Test (R-free flags) flag value: 1

Number of work/free reflections by resolution:
                                         work  free  %free
  bin  1: 14.9990 -  4.1806 [2205/2230]  1982   223  10.1%
  bin  2:  4.1806 -  3.3302 [2124/2144]  1917   207   9.7%
  bin  3:  3.3302 -  2.9128 [2084/2103]  1874   210  10.1%
  bin  4:  2.9128 -  2.6480 [2071/2101]  1856   215  10.4%
  bin  5:  2.6480 -  2.4591 [2065/2084]  1867   198   9.6%
  bin  6:  2.4591 -  2.3147 [2052/2077]  1845   207  10.1%
  bin  7:  2.3147 -  2.1991 [2013/2041]  1809   204  10.1%
  bin  8:  2.1991 -  2.1037 [2043/2079]  1834   209  10.2%
  bin  9:  2.1037 -  2.0229 [2028/2077]  1838   190   9.4%
  bin 10:  2.0229 -  1.9532 [ 904/2052]   808    96  10.6%
                                overall 17630  1959  10.0%
Writing MTZ file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/trial/run_492/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: 0.12 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:
        1.55 -     2.22: 27
        2.22 -     2.89: 1347
        2.89 -     3.56: 4527
        3.56 -     4.23: 9287
        4.23 -     4.90: 13363
  Nonbonded interactions sorted by model distance:
             atom i - atom j             model   vdw sym.op. j
  " OE1 GLN A  55 " - " O   HOH Z 403 "  1.545 3.040 -x+1,y-1/2,-z+1/2
  " O   HOH Z  70 " - " O   HOH Z 302 "  1.587 3.040 -x+1/2,-y+1,z+1/2
  " OG1 THR A  29 " - " O   HOH Z 245 "  1.681 3.040 x,y+1,z
  " O   HOH Z  61 " - " O   HOH Z 246 "  1.742 3.040 x,y+1,z
  " N   ASN A 148 " - " O   HOH Z 138 "  1.794 3.120 x,y-1,z
  ... (remaining 28546 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_492/model_refine_001.eff

Writing geometry restraints to file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/trial/run_492/model_refine_001.geo

CPU time processing inputs: 7.94


============================ 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 = 69.89875 45.75675 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: 1.95 - 15.00 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.5047   r_free= 0.4966   ksol= 0.00   Bsol= 0.00   scale= 0.777    |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (0.00,0.00,0.00,0.00,0.00,0.00); trace/3= 0.00                              |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.86 A                  |
| x-ray target function (ml) for work reflections: 6.306685                   |
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
| Bin     Resolution   Compl.  No. Refl.    R-factors          Targets        |
|number     range              work test   work   test        work        test|
|  1: 14.9990 -  4.6634 0.99   1429  157 0.4344 0.4296      6.6598      6.6875|
|  2:  4.6634 -  3.7200 0.99   1381  157 0.4454 0.4316      6.8626      6.8239|
|  3:  3.7200 -  3.2553 0.99   1355  149 0.4700 0.4038      6.7119      6.6643|
|  4:  3.2553 -  2.9601 0.99   1340  151 0.4999 0.4813      6.5628      6.5189|
|  5:  2.9601 -  2.7494 0.99   1332  145 0.5446 0.5405      6.3755      6.4196|
|  6:  2.7494 -  2.5881 0.99   1328  147 0.5340 0.5438      6.2903       6.214|
|  7:  2.5881 -  2.4591 0.99   1331  147 0.5239 0.5202      6.2523      6.2034|
|  8:  2.4591 -  2.3525 0.98   1318  152 0.5568 0.5196      6.1844      6.1826|
|  9:  2.3525 -  2.2622 0.98   1291  140 0.5403 0.5711      6.1298      6.1946|
| 10:  2.2622 -  2.1844 1.00   1328  147 0.5346 0.5593      6.0875      6.1177|
| 11:  2.1844 -  2.1163 0.98   1307  146 0.5179 0.5199      6.0416      6.0144|
| 12:  2.1163 -  2.0560 0.98   1298  137 0.5340 0.5778      5.9467       5.983|
| 13:  2.0560 -  2.0020 0.92   1222  141 0.5569 0.5339       5.891      5.8097|
| 14:  2.0020 -  1.9532 0.28    370   43 0.5460 0.4593      5.8745      5.8526|
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
|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: 14.9990 -  4.6634  1429   157  0.64  39.56   0.77     0.70      92173.52|
|  2:  4.6634 -  3.7200  1381   157  0.66  38.81   0.84     0.75     127087.05|
|  3:  3.7200 -  3.2553  1355   149  0.54  48.62   0.83     0.68     132681.40|
|  4:  3.2553 -  2.9601  1340   151  0.44  56.71   0.77     0.54     118048.34|
|  5:  2.9601 -  2.7494  1332   145  0.31  66.43   0.71     0.40      95047.95|
|  6:  2.7494 -  2.5881  1328   147  0.27  69.87   0.70     0.32      84043.25|
|  7:  2.5881 -  2.4591  1331   147  0.21  74.60   0.74     0.24      77661.07|
|  8:  2.4591 -  2.3525  1318   152  0.20  74.86   0.71     0.25      70403.03|
|  9:  2.3525 -  2.2622  1291   140  0.19  75.94   0.73     0.23      64599.08|
| 10:  2.2622 -  2.1844  1328   147  0.22  73.48   0.74     0.27      55692.01|
| 11:  2.1844 -  2.1163  1307   146  0.21  74.07   0.77     0.27      53731.56|
| 12:  2.1163 -  2.0560  1298   137  0.22  73.49   0.75     0.30      47541.16|
| 13:  2.0560 -  2.0020  1222   141  0.22  73.39   0.70     0.30      42225.08|
| 14:  2.0020 -  1.9532   370    43  0.28  69.44   0.73     0.32      33115.88|
|alpha:            min =        0.23 max =            0.75 mean =         0.41|
|beta:             min =    33115.88 max =       132681.40 mean =     81265.26|
|figures of merit: min =        0.00 max =            1.00 mean =         0.34|
|phase err.(work): min =        0.00 max =           90.00 mean =        64.35|
|phase err.(test): min =        0.00 max =           89.97 mean =        64.61|
|-----------------------------------------------------------------------------|

============================== 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 = 24.135665             wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 83.854   (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 2.034846              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 79.179   (deg)                 |
|-----------------------------------------------------------------------------|


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

|-Geometry statistics: start--------------------------------------------------|
|            Histogram of deviations from ideal values for                    |
| Bonds                | Angles                   |  Nonbonded contacts       |
| 0.000 - 0.140:   597 |   0.009 -   7.457:   713 |  1.196 -  1.566:        7 |
| 0.140 - 0.280:   585 |   7.457 -  14.906:   711 |  1.566 -  1.937:       35 |
| 0.280 - 0.420:   441 |  14.906 -  22.354:   630 |  1.937 -  2.307:      181 |
| 0.420 - 0.560:   366 |  22.354 -  29.802:   474 |  2.307 -  2.677:      713 |
| 0.560 - 0.700:   237 |  29.802 -  37.251:   338 |  2.677 -  3.048:     1511 |
| 0.700 - 0.840:   127 |  37.251 -  44.699:   241 |  3.048 -  3.418:     2671 |
| 0.840 - 0.980:    59 |  44.699 -  52.147:   125 |  3.418 -  3.789:     3955 |
| 0.980 - 1.120:    17 |  52.147 -  59.595:    51 |  3.789 -  4.159:     5124 |
| 1.120 - 1.260:     9 |  59.595 -  67.044:    13 |  4.159 -  4.530:     6622 |
| 1.260 - 1.400:     1 |  67.044 -  74.492:     3 |  4.530 -  4.900:     7775 |
|-----------------------------------------------------------------------------|
|-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 |       53.362 |
| planarity |      436 |   0.145    0.405  0.000 |     250.485 |              |
|  dihedral |      870 |  33.790  144.062  0.019 |      20.704 |              |
| nonbonded |     2439 |   4.088    4.900  1.196 |       2.428 |              |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 11.628)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      10.00   10.00   10.00    None  None   None       |
|    all(noH): 2823   0      10.00   10.00   10.00    None  None   None       |
|    Sol.    : 438    0      10.00   10.00   10.00    None  None   None       |
|    Mac.    : 2385   0      10.00   10.00   10.00    None  None   None       |
|    Hyd.    : 0      0      None    None    None     None  None   None       |
|    - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -      |
|       Distribution of isotropic (or equivalent) ADP for non-H atoms:        |
|    Bin#      value range     #atoms | Bin#      value range     #atoms      |
|      0:    10.000 -  10.000: 2823   |   5:    10.000 -  10.000:    0        |
|      1:    10.000 -  10.000:    0   |   6:    10.000 -  10.000:    0        |
|      2:    10.000 -  10.000:    0   |   7:    10.000 -  10.000:    0        |
|      3:    10.000 -  10.000:    0   |   8:    10.000 -  10.000:    0        |
|      4:    10.000 -  10.000:    0   |   9:    10.000 -  10.000:    0        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|

|-Occupancies statistics------------------------------------------------------|
| occupancies: max = 1.00   min = 0.30   number of occupancies < 0.1 = 0      |
|-----------------------------------------------------------------------------|

                ----------Modify initial isotropic ADP----------               

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

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

|--(resolution: 1.95 - 15.00 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.5089   r_free= 0.4952   ksol= 0.00   Bsol= 0.00   scale= 0.748    |
|                                                                             |
| 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:   0.84 A                  |
| x-ray target function (ml) for work reflections: 6.307191                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.95 - 15.00 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.4964   r_free= 0.4838   ksol= 0.35   Bsol= 9.33   scale= 0.960    |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (5.76,8.90,9.07,0.00,0.00,0.00); trace/3= 7.91                              |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.84 A                  |
| x-ray target function (ml) for work reflections: 6.302601                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 17.809294             wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 85.109   (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 1.869299              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 78.041   (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.4964      final r-factor (work) = 0.4350          |
| start r-factor (free) = 0.4838      final r-factor (free) = 0.4634          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 109.4600 = 17.81 * 0.50 * 6.2999 + 1.00 * 53.3620                           |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 55.8425 = 17.81 * 0.50 * 6.2541 + 1.00 * 0.1515                             |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 26     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.4350      final r-factor (work) = 0.3982          |
| start r-factor (free) = 0.4634      final r-factor (free) = 0.4631          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 11.7053 = 1.87 * 1.00 * 6.2541 + 1.00 * 0.0144                              |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 11.6239 = 1.87 * 1.00 * 6.2065 + 1.00 * 0.0221                              |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 28     |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 11.628)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.00    87.41   16.44    None  None   None       |
|    all(noH): 2823   0      0.00    87.41   16.44    None  None   None       |
|    Sol.    : 438    0      0.00    87.41   24.27    None  None   None       |
|    Mac.    : 2385   0      0.00    83.53   15.00    None  None   None       |
|    Hyd.    : 0      0      None    None    None     None  None   None       |
|    - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -      |
|       Distribution of isotropic (or equivalent) ADP for non-H atoms:        |
|    Bin#      value range     #atoms | Bin#      value range     #atoms      |
|      0:     0.000 -   8.742:  902   |   5:    43.707 -  52.449:   84        |
|      1:     8.742 -  17.483:  863   |   6:    52.449 -  61.190:   28        |
|      2:    17.483 -  26.224:  520   |   7:    61.190 -  69.932:   14        |
|      3:    26.224 -  34.966:  267   |   8:    69.932 -  78.673:    8        |
|      4:    34.966 -  43.707:  133   |   9:    78.673 -  87.415:    4        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.3982 r_free = 0.4631             target_work(ml) = 6.079         |
| occupancies: max = 1.00  min = 0.30   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.3977 r_free = 0.4639             target_work(ml) = 6.078         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        9 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.95 - 15.00 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.3977   r_free= 0.4639   ksol= 0.35   Bsol= 9.33   scale= 1.110    |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (5.76,8.90,9.07,0.00,0.00,0.00); trace/3= 7.91                              |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.73 A                  |
| x-ray target function (ml) for work reflections: 6.078360                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.95 - 15.00 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.3966   r_free= 0.4607   ksol= 0.36   Bsol= 40.65   scale= 1.022   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (2.94,5.10,5.35,0.00,0.00,0.00); trace/3= 4.46                              |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.73 A                  |
| x-ray target function (ml) for work reflections: 6.080019                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 17.096713             wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 102.760  (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 0.809634              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 148.575  (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.3966      final r-factor (work) = 0.3423          |
| start r-factor (free) = 0.4607      final r-factor (free) = 0.4259          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 53.1816 = 17.10 * 0.50 * 6.2035 + 1.00 * 0.1515                             |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 51.6015 = 17.10 * 0.50 * 6.0227 + 1.00 * 0.1175                             |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 28     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.3423      final r-factor (work) = 0.3266          |
| start r-factor (free) = 0.4259      final r-factor (free) = 0.4157          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 4.8983 = 0.81 * 1.00 * 6.0227 + 1.00 * 0.0222                               |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 4.9483 = 0.81 * 1.00 * 6.0873 + 1.00 * 0.0198                               |
|-----------------------------------------------------------------------------|
| number of iterations = 16      |    number of function evaluations = 20     |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 11.628)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.00    82.98   16.05    None  None   None       |
|    all(noH): 2823   0      0.00    82.98   16.05    None  None   None       |
|    Sol.    : 438    0      0.00    82.98   26.50    None  None   None       |
|    Mac.    : 2385   0      0.00    73.45   14.12    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 -   8.299:  820   |   5:    41.492 -  49.791:   69        |
|      1:     8.299 -  16.597:  913   |   6:    49.791 -  58.089:   22        |
|      2:    16.597 -  24.895:  553   |   7:    58.089 -  66.388:   18        |
|      3:    24.895 -  33.194:  279   |   8:    66.388 -  74.686:    6        |
|      4:    33.194 -  41.492:  142   |   9:    74.686 -  82.985:    1        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.3266 r_free = 0.4157             target_work(ml) = 6.074         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        9 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.3264 r_free = 0.4161             target_work(ml) = 6.074         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        9 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.95 - 15.00 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.3264   r_free= 0.4161   ksol= 0.36   Bsol= 40.65   scale= 1.074   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (2.94,5.10,5.35,0.00,0.00,0.00); trace/3= 4.46                              |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.56 A                  |
| x-ray target function (ml) for work reflections: 6.073920                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.95 - 15.00 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.3262   r_free= 0.4136   ksol= 0.33   Bsol= 49.21   scale= 1.023   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (1.68,2.62,3.29,0.00,0.00,0.00); trace/3= 2.53                              |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.57 A                  |
| x-ray target function (ml) for work reflections: 6.072852                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 7.148574              wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 112.288  (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 3.012127              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 98.188   (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.3262      final r-factor (work) = 0.2852          |
| start r-factor (free) = 0.4136      final r-factor (free) = 0.3611          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 21.8717 = 7.15 * 0.50 * 6.0863 + 1.00 * 0.1175                              |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 21.6284 = 7.15 * 0.50 * 6.0290 + 1.00 * 0.0790                              |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 28     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.2852      final r-factor (work) = 0.2621          |
| start r-factor (free) = 0.3611      final r-factor (free) = 0.3599          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 18.1801 = 3.01 * 1.00 * 6.0290 + 1.00 * 0.0200                              |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 17.8845 = 3.01 * 1.00 * 5.9288 + 1.00 * 0.0261                              |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 27     |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 11.628)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.00    93.97   18.17    None  None   None       |
|    all(noH): 2823   0      0.00    93.97   18.17    None  None   None       |
|    Sol.    : 438    0      0.00    93.97   36.95    None  None   None       |
|    Mac.    : 2385   0      0.00    92.41   14.72    None  None   None       |
|    Hyd.    : 0      0      None    None    None     None  None   None       |
|    - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -      |
|       Distribution of isotropic (or equivalent) ADP for non-H atoms:        |
|    Bin#      value range     #atoms | Bin#      value range     #atoms      |
|      0:     0.000 -   9.397: 1035   |   5:    46.985 -  56.382:  101        |
|      1:     9.397 -  18.794:  757   |   6:    56.382 -  65.779:   66        |
|      2:    18.794 -  28.191:  424   |   7:    65.779 -  75.177:   26        |
|      3:    28.191 -  37.588:  250   |   8:    75.177 -  84.574:    6        |
|      4:    37.588 -  46.985:  148   |   9:    84.574 -  93.971:   10        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.2621 r_free = 0.3599             target_work(ml) = 5.925         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        9 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.2619 r_free = 0.3597             target_work(ml) = 5.924         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:       11 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.95 - 15.00 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.2619   r_free= 0.3597   ksol= 0.33   Bsol= 49.21   scale= 1.056   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (1.68,2.62,3.29,0.00,0.00,0.00); trace/3= 2.53                              |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.45 A                  |
| x-ray target function (ml) for work reflections: 5.924427                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.95 - 15.00 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.2615   r_free= 0.3602   ksol= 0.35   Bsol= 66.56   scale= 1.031   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (0.93,1.50,2.52,0.00,0.00,0.00); trace/3= 1.65                              |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.45 A                  |
| x-ray target function (ml) for work reflections: 5.924680                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 4.584770              wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 96.399   (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 1.705681              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 141.713  (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.2615      final r-factor (work) = 0.2290          |
| start r-factor (free) = 0.3602      final r-factor (free) = 0.3194          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 13.6674 = 4.58 * 0.50 * 5.9276 + 1.00 * 0.0790                              |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 13.5336 = 4.58 * 0.50 * 5.8742 + 1.00 * 0.0676                              |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 28     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.2290      final r-factor (work) = 0.2140          |
| start r-factor (free) = 0.3194      final r-factor (free) = 0.2942          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 10.0453 = 1.71 * 1.00 * 5.8742 + 1.00 * 0.0257                              |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 9.8802 = 1.71 * 1.00 * 5.7804 + 1.00 * 0.0207                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 26     |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 11.628)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.00    108.56  17.54    None  None   None       |
|    all(noH): 2823   0      0.00    108.56  17.54    None  None   None       |
|    Sol.    : 438    0      1.09    101.97  42.20    None  None   None       |
|    Mac.    : 2385   0      0.00    108.56  13.02    None  None   None       |
|    Hyd.    : 0      0      None    None    None     None  None   None       |
|    - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -      |
|       Distribution of isotropic (or equivalent) ADP for non-H atoms:        |
|    Bin#      value range     #atoms | Bin#      value range     #atoms      |
|      0:     0.000 -  10.856: 1336   |   5:    54.281 -  65.137:   79        |
|      1:    10.856 -  21.712:  748   |   6:    65.137 -  75.993:   47        |
|      2:    21.712 -  32.568:  279   |   7:    75.993 -  86.849:   13        |
|      3:    32.568 -  43.425:  187   |   8:    86.849 -  97.705:    8        |
|      4:    43.425 -  54.281:  122   |   9:    97.705 - 108.561:    4        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.2140 r_free = 0.2942             target_work(ml) = 5.738         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:       11 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.2140 r_free = 0.2941             target_work(ml) = 5.738         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:       11 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.95 - 15.00 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.2140   r_free= 0.2941   ksol= 0.35   Bsol= 66.56   scale= 1.036   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (0.93,1.50,2.52,0.00,0.00,0.00); trace/3= 1.65                              |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.32 A                  |
| x-ray target function (ml) for work reflections: 5.737969                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.95 - 15.00 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.2142   r_free= 0.2939   ksol= 0.35   Bsol= 66.56   scale= 1.027   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (0.67,0.82,2.42,0.00,0.00,0.00); trace/3= 1.30                              |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.32 A                  |
| x-ray target function (ml) for work reflections: 5.738030                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 4.331242              wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 97.231   (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 0.292976              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 140.391  (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.2142      final r-factor (work) = 0.1772          |
| start r-factor (free) = 0.2939      final r-factor (free) = 0.2436          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 12.5856 = 4.33 * 0.50 * 5.7804 + 1.00 * 0.0676                              |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 12.3301 = 4.33 * 0.50 * 5.6636 + 1.00 * 0.0649                              |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 27     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1772      final r-factor (work) = 0.1646          |
| start r-factor (free) = 0.2436      final r-factor (free) = 0.2190          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 1.6800 = 0.29 * 1.00 * 5.6636 + 1.00 * 0.0208                               |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 1.6331 = 0.29 * 1.00 * 5.5345 + 1.00 * 0.0116                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 29     |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 11.628)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.00    106.69  15.92    None  None   None       |
|    all(noH): 2823   0      0.00    106.69  15.92    None  None   None       |
|    Sol.    : 438    0      3.36    100.71  41.35    None  None   None       |
|    Mac.    : 2385   0      0.00    106.69  11.25    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 -  10.669: 1571   |   5:    53.345 -  64.014:   71        |
|      1:    10.669 -  21.338:  643   |   6:    64.014 -  74.683:   42        |
|      2:    21.338 -  32.007:  196   |   7:    74.683 -  85.351:   11        |
|      3:    32.007 -  42.676:  155   |   8:    85.351 -  96.020:    5        |
|      4:    42.676 -  53.345:  125   |   9:    96.020 - 106.689:    4        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.1646 r_free = 0.2190             target_work(ml) = 5.478         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:       11 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.1644 r_free = 0.2188             target_work(ml) = 5.478         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:       11 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.95 - 15.00 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1644   r_free= 0.2188   ksol= 0.35   Bsol= 66.56   scale= 1.027   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (0.67,0.82,2.42,0.00,0.00,0.00); trace/3= 1.30                              |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.22 A                  |
| x-ray target function (ml) for work reflections: 5.477506                   |
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
| Bin     Resolution   Compl.  No. Refl.    R-factors          Targets        |
|number     range              work test   work   test        work        test|
|  1: 14.9990 -  4.6634 0.99   1429  157 0.1090 0.1509      5.5001       5.748|
|  2:  4.6634 -  3.7200 0.99   1381  157 0.1137 0.1706      5.7048      6.0303|
|  3:  3.7200 -  3.2553 0.99   1355  149 0.1543 0.2055      5.8032      6.0706|
|  4:  3.2553 -  2.9601 0.99   1340  151 0.1844 0.2262      5.7898       5.919|
|  5:  2.9601 -  2.7494 0.99   1332  145 0.1917 0.2511      5.6471      5.8808|
|  6:  2.7494 -  2.5881 0.99   1328  147 0.1810 0.2740       5.528      5.7637|
|  7:  2.5881 -  2.4591 0.99   1331  147 0.1857 0.2288      5.4911      5.6392|
|  8:  2.4591 -  2.3525 0.98   1318  152 0.1903 0.2423      5.4539      5.6636|
|  9:  2.3525 -  2.2622 0.98   1291  140 0.1874 0.2534      5.3851      5.6028|
| 10:  2.2622 -  2.1844 1.00   1328  147 0.1755 0.2365      5.2964      5.4706|
| 11:  2.1844 -  2.1163 0.98   1307  146 0.1799 0.2444      5.2793      5.5865|
| 12:  2.1163 -  2.0560 0.98   1298  137 0.1854 0.2541      5.2417      5.5002|
| 13:  2.0560 -  2.0020 0.92   1222  141 0.1827 0.2092      5.1426      5.2468|
| 14:  2.0020 -  1.9532 0.28    370   43 0.1735 0.2669      5.0678      5.2855|
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
|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: 14.9990 -  4.6634  1429   157  0.92  11.77   0.98     0.96      10503.92|
|  2:  4.6634 -  3.7200  1381   157  0.92  12.14   1.04     1.03      15812.62|
|  3:  3.7200 -  3.2553  1355   149  0.88  18.34   1.06     1.05      21089.75|
|  4:  3.2553 -  2.9601  1340   151  0.84  22.02   1.04     0.99      20855.26|
|  5:  2.9601 -  2.7494  1332   145  0.83  23.17   1.02     0.98      16213.60|
|  6:  2.7494 -  2.5881  1328   147  0.82  24.08   1.00     0.94      13620.27|
|  7:  2.5881 -  2.4591  1331   147  0.82  23.97   1.03     0.99      12572.12|
|  8:  2.4591 -  2.3525  1318   152  0.81  25.08   1.03     0.98      12132.86|
|  9:  2.3525 -  2.2622  1291   140  0.83  23.39   1.02     0.95       9855.45|
| 10:  2.2622 -  2.1844  1328   147  0.83  23.55   1.04     0.98       8642.04|
| 11:  2.1844 -  2.1163  1307   146  0.83  23.84   1.04     0.96       8381.62|
| 12:  2.1163 -  2.0560  1298   137  0.82  24.65   1.04     1.02       8411.84|
| 13:  2.0560 -  2.0020  1222   141  0.81  25.20   1.03     0.98       6686.53|
| 14:  2.0020 -  1.9532   370    43  0.87  19.60   1.03     0.99       4721.95|
|alpha:            min =        0.94 max =            1.05 mean =         0.99|
|beta:             min =     4721.95 max =        21089.75 mean =     12579.14|
|figures of merit: min =        0.00 max =            1.00 mean =         0.85|
|phase err.(work): min =        0.00 max =           89.91 mean =        21.46|
|phase err.(test): min =        0.00 max =           89.12 mean =        20.25|
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.95 - 15.00 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1645   r_free= 0.2183   ksol= 0.32   Bsol= 48.88   scale= 1.012   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-0.59,-0.64,1.23,0.00,0.00,0.00); trace/3= 0.00                            |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.22 A                  |
| x-ray target function (ml) for work reflections: 5.475145                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.95 - 15.00 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1645   r_free= 0.2183   ksol= 0.32   Bsol= 48.88   scale= 1.012   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-0.59,-0.64,1.23,0.00,0.00,0.00); trace/3= 0.00                            |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.22 A                  |
| x-ray target function (ml) for work reflections: 5.475145                   |
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
| Bin     Resolution   Compl.  No. Refl.    R-factors          Targets        |
|number     range              work test   work   test        work        test|
|  1: 14.9990 -  4.6634 0.99   1429  157 0.1082 0.1458       5.478      5.7225|
|  2:  4.6634 -  3.7200 0.99   1381  157 0.1134 0.1672      5.6951      6.0136|
|  3:  3.7200 -  3.2553 0.99   1355  149 0.1542 0.2037      5.7986      6.0607|
|  4:  3.2553 -  2.9601 0.99   1340  151 0.1851 0.2278       5.789      5.9208|
|  5:  2.9601 -  2.7494 0.99   1332  145 0.1916 0.2506      5.6473      5.8817|
|  6:  2.7494 -  2.5881 0.99   1328  147 0.1812 0.2744       5.529       5.765|
|  7:  2.5881 -  2.4591 0.99   1331  147 0.1858 0.2297      5.4932      5.6423|
|  8:  2.4591 -  2.3525 0.98   1318  152 0.1903 0.2432      5.4559      5.6669|
|  9:  2.3525 -  2.2622 0.98   1291  140 0.1874 0.2530      5.3859      5.6013|
| 10:  2.2622 -  2.1844 1.00   1328  147 0.1755 0.2380      5.2969      5.4733|
| 11:  2.1844 -  2.1163 0.98   1307  146 0.1798 0.2445      5.2792      5.5889|
| 12:  2.1163 -  2.0560 0.98   1298  137 0.1856 0.2546      5.2427      5.5019|
| 13:  2.0560 -  2.0020 0.92   1222  141 0.1826 0.2085      5.1429      5.2455|
| 14:  2.0020 -  1.9532 0.28    370   43 0.1737 0.2671      5.0684      5.2868|
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
|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: 14.9990 -  4.6634  1429   157  0.92  11.27   0.97     0.95       9677.51|
|  2:  4.6634 -  3.7200  1381   157  0.93  11.71   1.04     1.03      15006.65|
|  3:  3.7200 -  3.2553  1355   149  0.88  18.10   1.05     1.05      20617.47|
|  4:  3.2553 -  2.9601  1340   151  0.84  21.86   1.03     0.98      20626.91|
|  5:  2.9601 -  2.7494  1332   145  0.83  23.16   1.00     0.96      16248.56|
|  6:  2.7494 -  2.5881  1328   147  0.82  24.14   0.98     0.92      13701.78|
|  7:  2.5881 -  2.4591  1331   147  0.82  24.03   1.01     0.97      12659.63|
|  8:  2.4591 -  2.3525  1318   152  0.81  25.14   1.00     0.96      12208.83|
|  9:  2.3525 -  2.2622  1291   140  0.83  23.42   0.99     0.92       9895.67|
| 10:  2.2622 -  2.1844  1328   147  0.83  23.59   1.01     0.96       8669.31|
| 11:  2.1844 -  2.1163  1307   146  0.83  23.89   1.01     0.94       8420.01|
| 12:  2.1163 -  2.0560  1298   137  0.82  24.69   1.01     0.99       8439.05|
| 13:  2.0560 -  2.0020  1222   141  0.81  25.22   1.00     0.95       6702.17|
| 14:  2.0020 -  1.9532   370    43  0.88  19.55   0.99     0.95       4717.05|
|alpha:            min =        0.92 max =            1.05 mean =         0.97|
|beta:             min =     4717.05 max =        20626.91 mean =     12427.27|
|figures of merit: min =        0.00 max =            1.00 mean =         0.85|
|phase err.(work): min =        0.00 max =           89.99 mean =        21.38|
|phase err.(test): min =        0.00 max =           89.59 mean =        20.19|
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 11.628)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.77    107.46  16.69    None  None   None       |
|    all(noH): 2823   0      0.77    107.46  16.69    None  None   None       |
|    Sol.    : 438    0      4.13    101.48  42.12    None  None   None       |
|    Mac.    : 2385   0      0.77    107.46  12.02    None  None   None       |
|    Hyd.    : 0      0      None    None    None     None  None   None       |
|    - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -      |
|       Distribution of isotropic (or equivalent) ADP for non-H atoms:        |
|    Bin#      value range     #atoms | Bin#      value range     #atoms      |
|      0:     0.771 -  11.440: 1571   |   5:    54.116 -  64.785:   71        |
|      1:    11.440 -  22.109:  643   |   6:    64.785 -  75.454:   42        |
|      2:    22.109 -  32.778:  196   |   7:    75.454 -  86.123:   11        |
|      3:    32.778 -  43.447:  155   |   8:    86.123 -  96.792:    5        |
|      4:    43.447 -  54.116:  125   |   9:    96.792 - 107.461:    4        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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


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

Number of peaks found at mFobs-DFmodel map (map cutoff=3.00 sigma)= 356         
Filter by distance & map next to the model:
   mapped sites are within: 0.524 - 5.667
   number of sites selected in [dist_min= 0.70, dist_max= 6.00]: 346 from: 356
   mapped sites are within: 0.709 - 5.667

peak=    7.392 closest distance to " O   HOH Z 268 " =    1.433
peak=    6.994 closest distance to " O   HOH Z 390 " =    1.308
peak=    6.662 closest distance to " CB  VAL A 230 " =    1.489
peak=    6.474 closest distance to " CG  LEU A   5 " =    1.516
peak=    6.361 closest distance to " CB  VAL A 296 " =    1.535
peak=    6.024 closest distance to " O   HOH Z 130 " =    2.213
peak=    5.966 closest distance to " OD1 ASP A  27 " =    1.006
peak=    5.876 closest distance to " O   HOH Z 159 " =    1.224
peak=    5.856 closest distance to " NH1 ARG A 138 " =    1.115
peak=    5.723 closest distance to " O   HOH Z 103 " =    0.980
peak=    5.718 closest distance to " O  BHOH Z  74 " =    1.078
peak=    5.712 closest distance to " O   HOH Z 375 " =    1.438
peak=    5.517 closest distance to " N   ARG A 275 " =    0.857
peak=    5.368 closest distance to " O   VAL A  72 " =    1.045
peak=    5.298 closest distance to " O   HOH Z 415 " =    1.613
peak=    5.279 closest distance to " CG  ARG A 138 " =    1.233
peak=    5.275 closest distance to " O   HOH Z 139 " =    1.724
peak=    5.240 closest distance to " O   HOH Z 245 " =    1.302
peak=    5.214 closest distance to " OD1 ASN A  69 " =    1.050
peak=    5.122 closest distance to " O   HOH Z 360 " =    1.315
peak=    5.053 closest distance to " O   HOH Z 113 " =    2.217
peak=    5.050 closest distance to " CD1AILE A 234 " =    1.014
peak=    5.046 closest distance to " O   HOH Z 124 " =    1.775
peak=    5.024 closest distance to " O   HOH Z 105 " =    1.257
peak=    4.980 closest distance to " O   HOH Z 359 " =    1.509
peak=    4.959 closest distance to " CZ  PHE A  16 " =    0.962
peak=    4.932 closest distance to " O   HOH Z 416 " =    1.506
peak=    4.901 closest distance to " O   HOH Z  63 " =    1.732
peak=    4.882 closest distance to " CD1 LEU A   5 " =    1.070
peak=    4.880 closest distance to " CZ  PHE A  16 " =    1.094
peak=    4.867 closest distance to " CB  ARG A 275 " =    1.214
peak=    4.858 closest distance to " O   HOH Z 330 " =    1.190
peak=    4.775 closest distance to " O   HOH Z 350 " =    1.681
peak=    4.724 closest distance to " O   HOH Z  77 " =    1.266
peak=    4.713 closest distance to " CD  ARG A 138 " =    0.985
peak=    4.693 closest distance to " O   HOH Z  24 " =    1.852
peak=    4.666 closest distance to " O   HOH Z 422 " =    1.325
peak=    4.647 closest distance to " O   HOH Z 127 " =    1.319
peak=    4.624 closest distance to " O   HOH Z 258 " =    1.773
peak=    4.614 closest distance to " C   GLN A  73 " =    1.052
peak=    4.613 closest distance to " NH2 ARG A 269 " =    0.888
peak=    4.604 closest distance to " NZ  LYS A 289 " =    1.210
peak=    4.600 closest distance to " O   HOH Z  21 " =    1.378
peak=    4.562 closest distance to " NE2 GLN A  11 " =    1.278
peak=    4.515 closest distance to " CG  PRO A 243 " =    1.240
peak=    4.496 closest distance to " O   HOH Z 428 " =    1.347
peak=    4.457 closest distance to " O   HOH Z 403 " =    1.709
peak=    4.439 closest distance to " O   PRO A 198 " =    1.559
peak=    4.439 closest distance to " O   HOH Z  46 " =    1.575
peak=    4.409 closest distance to " CG2 ILE A 120 " =    1.197
peak=    4.397 closest distance to " O   HOH Z 142 " =    2.105
peak=    4.394 closest distance to " O   HOH Z 232 " =    2.124
peak=    4.393 closest distance to " NZ BLYS A 290 " =    1.174
peak=    4.391 closest distance to " O   HOH Z 381 " =    1.076
peak=    4.387 closest distance to " O   HOH Z 331 " =    1.509
peak=    4.372 closest distance to " O   HOH Z 425 " =    1.653
peak=    4.353 closest distance to " O   HOH Z 385 " =    1.695
peak=    4.334 closest distance to " OD2 ASP A 253 " =    1.129
peak=    4.325 closest distance to " O   HOH Z 353 " =    2.199
peak=    4.319 closest distance to " O   HOH Z  59 " =    1.754
peak=    4.292 closest distance to " O   HOH Z  78 " =    1.923
peak=    4.288 closest distance to " CB  GLN A  73 " =    1.178
peak=    4.283 closest distance to " O   HOH Z 225 " =    1.983
peak=    4.275 closest distance to " CB  PRO A  54 " =    1.388
peak=    4.274 closest distance to " OG ASER A 258 " =    2.866
peak=    4.262 closest distance to " OD1 ASP A 272 " =    0.842
peak=    4.243 closest distance to " O   HOH Z 214 " =    1.336
peak=    4.206 closest distance to " O   HOH Z  15 " =    1.104
peak=    4.200 closest distance to " ND2 ASN A 249 " =    0.795
peak=    4.196 closest distance to " O   HOH Z 415 " =    1.555
peak=    4.172 closest distance to " O   HOH Z   9 " =    2.309
peak=    4.166 closest distance to " N   SER A  26 " =    1.070
peak=    4.137 closest distance to " O   HOH Z  65 " =    2.054
peak=    4.126 closest distance to " O   HOH Z 158 " =    2.495
peak=    4.117 closest distance to " CB  ASN A  39 " =    0.838
peak=    4.093 closest distance to " N   GLN A 278 " =    1.033
peak=    4.076 closest distance to " O   HOH Z  45 " =    1.033
peak=    4.057 closest distance to " CB  VAL A 230 " =    1.342
peak=    4.055 closest distance to " O   HOH Z 427 " =    2.044
peak=    4.052 closest distance to " OG BSER A  12 " =    1.101
peak=    4.048 closest distance to " O   SER A 273 " =    0.970
peak=    4.045 closest distance to " O   HOH Z  69 " =    1.690
peak=    4.041 closest distance to " O   HOH Z 287 " =    1.688
peak=    4.039 closest distance to " CB  LYS A 290 " =    1.213
peak=    4.039 closest distance to " O   HOH Z  43 " =    1.674
peak=    4.031 closest distance to " O   HOH Z  66 " =    1.464
peak=    4.029 closest distance to " CE1 PHE A  38 " =    1.002
peak=    4.027 closest distance to " OG  SER A 276 " =    0.981
peak=    4.013 closest distance to " O   HOH Z  53 " =    2.244
peak=    4.000 closest distance to " CA  ILE A 234 " =    1.197
peak=    3.999 closest distance to " CB  TRP A 266 " =    0.955
peak=    3.963 closest distance to " O   ARG A 275 " =    0.869
peak=    3.962 closest distance to " O   HOH Z 417 " =    2.246
peak=    3.961 closest distance to " OD1 ASN A  45 " =    1.303
peak=    3.960 closest distance to " O   HOH Z 148 " =    1.930
peak=    3.941 closest distance to " O   HOH Z  69 " =    1.175
peak=    3.929 closest distance to " N   ARG A 156 " =    1.299
peak=    3.929 closest distance to " OE2 GLU A  53 " =    0.714
peak=    3.923 closest distance to " CB  ALA A 114 " =    1.144
peak=    3.917 closest distance to " O   HOH Z 218 " =    2.238
peak=    3.906 closest distance to " O   HOH Z 293 " =    1.558
peak=    3.874 closest distance to " CE3 TRP A 274 " =    1.362
peak=    3.874 closest distance to " CD2 LEU A 297 " =    1.019
peak=    3.874 closest distance to " N   TYR A  15 " =    1.104
peak=    3.871 closest distance to " NE AARG A 275 " =    1.814
peak=    3.870 closest distance to " CG2 ILE A 234 " =    0.932
peak=    3.868 closest distance to " O   HOH Z 342 " =    1.210
peak=    3.866 closest distance to " O   HOH Z 172 " =    1.572
peak=    3.857 closest distance to " CB  SER A 276 " =    1.289
peak=    3.839 closest distance to " CB  ASN A 187 " =    1.061
peak=    3.839 closest distance to " ND2BASN A 224 " =    0.986
peak=    3.837 closest distance to " O   HOH Z 366 " =    2.944
peak=    3.827 closest distance to " CB  LEU A 300 " =    1.010
peak=    3.823 closest distance to " CG  ARG A 156 " =    1.131
peak=    3.822 closest distance to " O   HOH Z 219 " =    1.913
peak=    3.822 closest distance to " CG2BVAL A  72 " =    1.515
peak=    3.800 closest distance to " N   GLY A 302 " =    0.930
peak=    3.790 closest distance to " CG2AVAL A  72 " =    0.961
peak=    3.788 closest distance to " C   GLN A  11 " =    1.128
peak=    3.785 closest distance to " O   HOH Z   7 " =    1.819
peak=    3.778 closest distance to " CB  SER A   3 " =    1.649
peak=    3.778 closest distance to " CE AMET A  47 " =    1.477
peak=    3.766 closest distance to " O   HOH Z 404 " =    1.148
peak=    3.759 closest distance to " O   HOH Z 154 " =    1.966
peak=    3.758 closest distance to " CZ  PHE A 218 " =    1.232
peak=    3.756 closest distance to " O   HOH Z 153 " =    3.370
peak=    3.755 closest distance to " NH2BARG A 145 " =    1.664
peak=    3.742 closest distance to " CB  ALA A  10 " =    1.084
peak=    3.734 closest distance to " OD1 ASP A  50 " =    0.887
peak=    3.728 closest distance to " O   HOH Z 358 " =    1.439
peak=    3.723 closest distance to " O   HOH Z 181 " =    2.293
peak=    3.718 closest distance to " CA  LEU A 282 " =    0.966
peak=    3.717 closest distance to " N   GLU A   2 " =    1.245
peak=    3.711 closest distance to " CB  ASN A 110 " =    0.968
peak=    3.708 closest distance to " CA  ASN A 284 " =    1.002
peak=    3.700 closest distance to " ND1 HIS A  81 " =    1.447
peak=    3.694 closest distance to " CG2 THR A 246 " =    0.975
peak=    3.693 closest distance to " CA  GLY A 136 " =    0.964
peak=    3.688 closest distance to " O   HOH Z  68 " =    2.108
peak=    3.687 closest distance to " CB  VAL A 202 " =    1.517
peak=    3.683 closest distance to " C   GLN A  11 " =    1.251
peak=    3.681 closest distance to " O   HOH Z 303 " =    1.169
peak=    3.678 closest distance to " CB  ALA A 248 " =    1.567
peak=    3.670 closest distance to " O   HOH Z  47 " =    1.848
peak=    3.669 closest distance to " O   HOH Z  51 " =    2.126
peak=    3.668 closest distance to " O   HOH Z 357 " =    1.703
peak=    3.668 closest distance to " CB  ALA A   8 " =    1.084
peak=    3.665 closest distance to " O   HOH Z 146 " =    1.526
peak=    3.654 closest distance to " O   HOH Z 212 " =    1.434
peak=    3.651 closest distance to " CB  GLN A 223 " =    1.932
peak=    3.650 closest distance to " O   HOH Z  92 " =    1.475
peak=    3.641 closest distance to " O   HOH Z  91 " =    2.242
peak=    3.639 closest distance to " O   HOH Z  99 " =    1.874
peak=    3.632 closest distance to " O   ARG A 275 " =    1.404
peak=    3.622 closest distance to " O   HOH Z 410 " =    1.474
peak=    3.620 closest distance to " O   HOH Z 126 " =    1.968
peak=    3.616 closest distance to " O   HOH Z 422 " =    2.369
peak=    3.615 closest distance to " O   HOH Z 119 " =    1.606
peak=    3.611 closest distance to " CB  PRO A  90 " =    1.242
peak=    3.604 closest distance to " CD1 LEU A 281 " =    1.133
peak=    3.602 closest distance to " O   HOH Z 368 " =    1.918
peak=    3.595 closest distance to " CZ3 TRP A 266 " =    1.167
peak=    3.593 closest distance to " O   HOH Z 389 " =    1.669
peak=    3.591 closest distance to " CG2 THR A 294 " =    1.208
peak=    3.589 closest distance to " O   HOH Z 414 " =    1.927
peak=    3.586 closest distance to " O   HOH Z 194 " =    2.493
peak=    3.584 closest distance to " CG  PRO A 198 " =    1.344
peak=    3.582 closest distance to " CA  THR A  42 " =    1.124
peak=    3.581 closest distance to " OE1 GLU A   2 " =    1.827
peak=    3.580 closest distance to " O   HOH Z 118 " =    2.380
peak=    3.574 closest distance to " O   HOH Z 427 " =    1.048
peak=    3.571 closest distance to " CB  ASN A 148 " =    1.433
peak=    3.561 closest distance to " N   CYS A 260 " =    1.171
peak=    3.559 closest distance to " NH2 ARG A  36 " =    1.045
peak=    3.555 closest distance to " O   HOH Z  88 " =    3.409
peak=    3.550 closest distance to " N   ASP A 162 " =    0.976
peak=    3.546 closest distance to " CB  SER A  63 " =    1.310
peak=    3.545 closest distance to " O   HOH Z 419 " =    2.276
peak=    3.541 closest distance to " O   HOH Z 298 " =    1.680
peak=    3.539 closest distance to " CB  SER A 216 " =    1.027
peak=    3.536 closest distance to " CG2 THR A 279 " =    1.077
peak=    3.534 closest distance to " O   HOH Z  57 " =    1.291
peak=    3.531 closest distance to " CG  LYS A 119 " =    0.839
peak=    3.527 closest distance to " N   TYR A  30 " =    1.079
peak=    3.524 closest distance to " O   HOH Z 244 " =    1.592
peak=    3.519 closest distance to " CA  ARG A 159 " =    1.267
peak=    3.505 closest distance to " O   HOH Z 123 " =    1.377
peak=    3.504 closest distance to " O   HOH Z 371 " =    2.571
peak=    3.499 closest distance to " N   ASN A  74 " =    0.798
peak=    3.496 closest distance to " CG1 ILE A 263 " =    1.362
peak=    3.491 closest distance to " O   HOH Z 233 " =    1.804
peak=    3.488 closest distance to " O   HOH Z 246 " =    1.045
peak=    3.477 closest distance to " O   SER A 271 " =    1.077
peak=    3.477 closest distance to " O   HOH Z  89 " =    2.435
peak=    3.470 closest distance to " CB  SER A  26 " =    1.715
peak=    3.468 closest distance to " O   HOH Z 426 " =    1.105
peak=    3.463 closest distance to " CB  LEU A  83 " =    0.764
peak=    3.460 closest distance to " CG2 VAL A 232 " =    1.354
peak=    3.458 closest distance to " O   HOH Z  49 " =    2.714
peak=    3.457 closest distance to " CD  ARG A 139 " =    1.461
peak=    3.449 closest distance to " O   HOH Z 344 " =    1.296
peak=    3.447 closest distance to " CG  LEU A   5 " =    1.127
peak=    3.443 closest distance to " O   HOH Z 196 " =    1.292
peak=    3.442 closest distance to " CB  SER A  62 " =    1.295
peak=    3.440 closest distance to " O   HOH Z 112 " =    1.302
peak=    3.439 closest distance to " CG2 THR A 235 " =    0.948
peak=    3.437 closest distance to " O   HOH Z  30 " =    1.316
peak=    3.437 closest distance to " N   GLN A  73 " =    1.143
peak=    3.435 closest distance to " CB  ARG A  79 " =    1.005
peak=    3.426 closest distance to " OD2 ASP A 140 " =    0.940
peak=    3.422 closest distance to " CA  ARG A  36 " =    0.948
peak=    3.421 closest distance to " CB  GLN A 223 " =    1.876
peak=    3.414 closest distance to " OD1 ASP A 286 " =    1.155
peak=    3.407 closest distance to " O   HOH Z 262 " =    2.370
peak=    3.406 closest distance to " CG2 THR A  29 " =    1.071
peak=    3.403 closest distance to " O   THR A  82 " =    1.112
peak=    3.398 closest distance to " CD2 LEU A 228 " =    1.242
peak=    3.398 closest distance to " CB  PHE A 204 " =    0.987
peak=    3.397 closest distance to " NZ  LYS A 119 " =    1.662
peak=    3.392 closest distance to " O   HOH Z 406 " =    1.416
peak=    3.389 closest distance to " O   HOH Z 428 " =    1.534
peak=    3.388 closest distance to " O   HOH Z 287 " =    1.973
peak=    3.378 closest distance to " CA  SER A  12 " =    1.651
peak=    3.374 closest distance to " CG  GLN A  89 " =    1.670
peak=    3.371 closest distance to " O   HOH Z 147 " =    1.321
peak=    3.371 closest distance to " O   ASN A 301 " =    2.076
peak=    3.367 closest distance to " NE1 TRP A 274 " =    1.122
peak=    3.367 closest distance to " O   HOH Z 423 " =    2.244
peak=    3.366 closest distance to " O   HOH Z 361 " =    1.677
peak=    3.365 closest distance to " O   HOH Z 411 " =    3.136
peak=    3.361 closest distance to " CB  SER A 210 " =    1.071
peak=    3.357 closest distance to " CB  MET A  47 " =    0.950
peak=    3.357 closest distance to " N   GLU A 277 " =    0.948
peak=    3.356 closest distance to " O   HOH Z   7 " =    3.281
peak=    3.355 closest distance to " CD  ARG A  56 " =    1.054
peak=    3.353 closest distance to " O   HOH Z 412 " =    2.834
peak=    3.345 closest distance to " CG  GLN A 205 " =    1.167
peak=    3.338 closest distance to " CG  LEU A 167 " =    1.388
peak=    3.337 closest distance to " N   VAL A  72 " =    0.799
peak=    3.331 closest distance to " O   ASN A 285 " =    0.930
peak=    3.324 closest distance to " CD  ARG A  66 " =    2.131
peak=    3.323 closest distance to " O   HOH Z  27 " =    1.068
peak=    3.320 closest distance to " O   HOH Z 400 " =    0.955
peak=    3.319 closest distance to " O   HOH Z 179 " =    1.177
peak=    3.316 closest distance to " O   HOH Z 143 " =    1.461
peak=    3.315 closest distance to " O   HOH Z 279 " =    2.660
peak=    3.303 closest distance to " O   HOH Z 115 " =    1.706
peak=    3.303 closest distance to " O   HOH Z 362 " =    1.686
peak=    3.303 closest distance to " NH1AARG A 145 " =    1.228
peak=    3.302 closest distance to " O   HOH Z   1 " =    1.944
peak=    3.299 closest distance to " CE AMET A  47 " =    1.377
peak=    3.298 closest distance to " CG2 VAL A 202 " =    1.271
peak=    3.294 closest distance to " NE2 GLN A  73 " =    1.454
peak=    3.289 closest distance to " CA  CYS A 201 " =    1.123
peak=    3.286 closest distance to " CG  LYS A  76 " =    1.843
peak=    3.284 closest distance to " O   HOH Z 430 " =    1.717
peak=    3.284 closest distance to " O   HOH Z  58 " =    1.949
peak=    3.284 closest distance to " CB  GLU A 152 " =    1.320
peak=    3.271 closest distance to " CE BMET A  47 " =    1.509
peak=    3.271 closest distance to " N   SER A  97 " =    0.951
peak=    3.265 closest distance to " O   HOH Z 201 " =    1.951
peak=    3.261 closest distance to " NH2AARG A 145 " =    1.122
peak=    3.261 closest distance to " O   HOH Z 364 " =    1.410
peak=    3.260 closest distance to " O   HOH Z 272 " =    1.882
peak=    3.258 closest distance to " CA  VAL A 153 " =    1.007
peak=    3.258 closest distance to " O   HOH Z 334 " =    1.726
peak=    3.253 closest distance to " NE BARG A 275 " =    1.244
peak=    3.251 closest distance to " O   GLU A   2 " =    0.974
peak=    3.242 closest distance to " O   HOH Z 158 " =    1.372
peak=    3.241 closest distance to " O   HOH Z  28 " =    1.614
peak=    3.241 closest distance to " OXT GLY A 302 " =    3.730
peak=    3.239 closest distance to " CB  ALA A 256 " =    0.892
peak=    3.238 closest distance to " O   HOH Z 145 " =    2.714
peak=    3.234 closest distance to " O   HOH Z 207 " =    1.736
peak=    3.231 closest distance to " O   HOH Z  83 " =    1.103
peak=    3.231 closest distance to " N   PHE A 130 " =    1.355
peak=    3.230 closest distance to " CG2 THR A 221 " =    1.122
peak=    3.228 closest distance to " O   HOH Z 321 " =    1.248
peak=    3.221 closest distance to " O   HOH Z 389 " =    1.451
peak=    3.220 closest distance to " O   HOH Z 303 " =    1.837
peak=    3.220 closest distance to " NH1 ARG A  79 " =    1.041
peak=    3.220 closest distance to " CD2 TYR A 169 " =    1.235
peak=    3.218 closest distance to " O   HOH Z 222 " =    1.870
peak=    3.218 closest distance to " CB  LYS A  76 " =    0.732
peak=    3.218 closest distance to " O   HOH Z   9 " =    2.003
peak=    3.214 closest distance to " N   ASN A 142 " =    1.290
peak=    3.212 closest distance to " O   HOH Z 424 " =    2.183
peak=    3.209 closest distance to " O   HOH Z  39 " =    1.708
peak=    3.209 closest distance to " CB  ASN A 215 " =    1.465
peak=    3.208 closest distance to " CA  MET A  47 " =    1.242
peak=    3.208 closest distance to " O   HOH Z  49 " =    1.306
peak=    3.207 closest distance to " N   GLN A 122 " =    0.709
peak=    3.202 closest distance to " CD2 LEU A 237 " =    0.823
peak=    3.202 closest distance to " CG2 THR A 178 " =    1.312
peak=    3.198 closest distance to " O   HOH Z 249 " =    4.182
peak=    3.197 closest distance to " CZ3 TRP A  70 " =    1.091
peak=    3.195 closest distance to " CB  THR A 235 " =    1.853
peak=    3.193 closest distance to " CG2 ILE A  20 " =    1.352
peak=    3.188 closest distance to " O   HOH Z 211 " =    1.517
peak=    3.185 closest distance to " CZ AARG A 102 " =    2.053
peak=    3.185 closest distance to " O   HOH Z  97 " =    1.627
peak=    3.181 closest distance to " O   HOH Z 371 " =    2.216
peak=    3.179 closest distance to " CG1 VAL A 265 " =    0.970
peak=    3.175 closest distance to " CB  ASN A  74 " =    1.321
peak=    3.174 closest distance to " CB  PRO A  54 " =    1.512
peak=    3.173 closest distance to " CD  GLN A  77 " =    1.418
peak=    3.173 closest distance to " C   ARG A  56 " =    1.097
peak=    3.172 closest distance to " CA  ALA A 160 " =    1.577
peak=    3.171 closest distance to " O   THR A 251 " =    1.034
peak=    3.169 closest distance to " CB  ALA A  43 " =    0.912
peak=    3.167 closest distance to " O   HOH Z 263 " =    1.387
peak=    3.162 closest distance to " CB  ARG A 138 " =    0.875
peak=    3.158 closest distance to " CA  GLY A 287 " =    1.251
peak=    3.148 closest distance to " CA  ASN A 209 " =    1.519
peak=    3.148 closest distance to " O   HOH Z 313 " =    1.754
peak=    3.145 closest distance to " CB  ALA A 131 " =    1.359
peak=    3.144 closest distance to " CD1 LEU A 261 " =    1.350
peak=    3.139 closest distance to " CB  ASP A 124 " =    0.963
peak=    3.138 closest distance to " O   HOH Z  61 " =    2.123
peak=    3.123 closest distance to " CB  GLN A 183 " =    0.969
peak=    3.117 closest distance to " O   HOH Z 125 " =    1.846
peak=    3.115 closest distance to " CB  ALA A 295 " =    1.902
peak=    3.115 closest distance to " CG2BVAL A  72 " =    1.367
peak=    3.113 closest distance to " CG2 VAL A 202 " =    1.050
peak=    3.112 closest distance to " O   HOH Z  52 " =    1.260
peak=    3.111 closest distance to " O   HOH Z  75 " =    1.849
peak=    3.110 closest distance to " CB  ALA A 291 " =    0.951
peak=    3.104 closest distance to " CD  GLN A  58 " =    5.667
peak=    3.102 closest distance to " O   HOH Z 191 " =    3.350
peak=    3.099 closest distance to " CA  MET A  93 " =    1.412
peak=    3.093 closest distance to " CG  GLU A   2 " =    0.844
peak=    3.089 closest distance to " N   ALA A   1 " =    2.987
peak=    3.089 closest distance to " NE2 HIS A  86 " =    1.500
peak=    3.084 closest distance to " CA  ARG A 195 " =    1.259
peak=    3.081 closest distance to " CA  ASP A 124 " =    0.873
peak=    3.075 closest distance to " O   HOH Z 368 " =    2.977
peak=    3.071 closest distance to " N   PHE A  38 " =    1.199
peak=    3.065 closest distance to " CG  GLN A  58 " =    1.202
peak=    3.063 closest distance to " OE2 GLU A 236 " =    1.427
peak=    3.057 closest distance to " N   LYS A  76 " =    1.360
peak=    3.053 closest distance to " NE2 GLN A  73 " =    2.373
peak=    3.050 closest distance to " O   HOH Z 313 " =    2.183
peak=    3.042 closest distance to " CA  ALA A  51 " =    1.047
peak=    3.030 closest distance to " O   HOH Z  89 " =    2.511
peak=    3.019 closest distance to " O   HOH Z  57 " =    2.179
peak=    3.000 closest distance to " C   THR A  29 " =    1.187

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

Number of peaks found at mFobs-DFmodel map (map cutoff=3.00 sigma)= 215         
Filter by distance & map next to the model:
   mapped sites are within: 0.389 - 5.550
   number of sites selected in [dist_min= 0.70, dist_max= 6.00]: 206 from: 215
   mapped sites are within: 0.703 - 5.550

peak=   -6.212 closest distance to " CD  ARG A 138 " =    1.097
peak=   -5.355 closest distance to " OD2 ASP A 253 " =    0.703
peak=   -4.963 closest distance to " CG2 VAL A 230 " =    0.774
peak=   -4.672 closest distance to " O   PRO A 198 " =    1.028
peak=   -4.591 closest distance to " O   ALA A  10 " =    1.360
peak=   -4.413 closest distance to " N   GLU A 277 " =    1.388
peak=   -4.406 closest distance to " O   ALA A  51 " =    1.226
peak=   -4.380 closest distance to " C   GLU A   2 " =    1.789
peak=   -4.344 closest distance to " O   THR A 178 " =    0.930
peak=   -4.233 closest distance to " O   ASP A 191 " =    1.892
peak=   -4.218 closest distance to " O   SER A 273 " =    0.720
peak=   -4.182 closest distance to " OG  SER A  97 " =    2.223
peak=   -4.116 closest distance to " CE BLYS A 290 " =    2.051
peak=   -4.107 closest distance to " N   GLN A  11 " =    0.933
peak=   -4.062 closest distance to " O   HOH Z 131 " =    3.900
peak=   -4.029 closest distance to " O   HOH Z 268 " =    0.847
peak=   -3.976 closest distance to " CB  ASN A 285 " =    1.924
peak=   -3.927 closest distance to " CD2 TYR A 293 " =    1.764
peak=   -3.909 closest distance to " O   HOH Z  28 " =    0.914
peak=   -3.858 closest distance to " O   LYS A  76 " =    1.069
peak=   -3.835 closest distance to " CG  PRO A 213 " =    2.151
peak=   -3.829 closest distance to " CE2 TYR A  30 " =    2.543
peak=   -3.817 closest distance to " O   HOH Z 313 " =    0.834
peak=   -3.817 closest distance to " CD2 LEU A 237 " =    2.202
peak=   -3.796 closest distance to " CG  ASP A  50 " =    0.893
peak=   -3.795 closest distance to " OG BSER A 134 " =    1.888
peak=   -3.792 closest distance to " CG2 ILE A 120 " =    0.886
peak=   -3.785 closest distance to " CD  ARG A  14 " =    2.911
peak=   -3.754 closest distance to " CG1AVAL A  72 " =    2.239
peak=   -3.751 closest distance to " N   GLN A  77 " =    1.156
peak=   -3.737 closest distance to " O   VAL A  72 " =    0.716
peak=   -3.725 closest distance to " CA  GLY A  23 " =    2.584
peak=   -3.713 closest distance to " CA  GLY A 133 " =    1.966
peak=   -3.699 closest distance to " O   HOH Z 300 " =    0.873
peak=   -3.680 closest distance to " CG  ASN A 284 " =    1.235
peak=   -3.667 closest distance to " CG  MET A 105 " =    0.835
peak=   -3.661 closest distance to " O   CYS A 260 " =    1.146
peak=   -3.661 closest distance to " N   VAL A 189 " =    1.664
peak=   -3.656 closest distance to " O   HOH Z  82 " =    1.391
peak=   -3.653 closest distance to " N   ARG A 275 " =    0.732
peak=   -3.633 closest distance to " CA  GLY A  35 " =    1.949
peak=   -3.626 closest distance to " CD  GLU A 277 " =    2.287
peak=   -3.624 closest distance to " C   HIS A 108 " =    1.324
peak=   -3.624 closest distance to " O   HOH Z 390 " =    2.690
peak=   -3.622 closest distance to " O   SER A 135 " =    1.638
peak=   -3.613 closest distance to " CG  TRP A 266 " =    1.594
peak=   -3.611 closest distance to " O   HOH Z 360 " =    0.755
peak=   -3.609 closest distance to " O   HOH Z 385 " =    1.048
peak=   -3.605 closest distance to " CG  ASP A 140 " =    1.104
peak=   -3.596 closest distance to " CA  GLY A  57 " =    2.194
peak=   -3.595 closest distance to " O   HOH Z 428 " =    1.541
peak=   -3.595 closest distance to " O   HOH Z 359 " =    3.281
peak=   -3.585 closest distance to " O   SER A   3 " =    2.299
peak=   -3.584 closest distance to " O   HOH Z  69 " =    1.790
peak=   -3.582 closest distance to " NE2 GLN A  11 " =    1.229
peak=   -3.580 closest distance to " CG2AVAL A  41 " =    2.696
peak=   -3.580 closest distance to " O   HOH Z 402 " =    0.892
peak=   -3.577 closest distance to " CD  LYS A 166 " =    2.598
peak=   -3.564 closest distance to " O   HOH Z 268 " =    1.136
peak=   -3.563 closest distance to " CD1 TRP A 274 " =    1.013
peak=   -3.562 closest distance to " O   LYS A 193 " =    1.342
peak=   -3.561 closest distance to " O   HOH Z  24 " =    1.033
peak=   -3.558 closest distance to " O   HOH Z 315 " =    1.242
peak=   -3.557 closest distance to " O   ILE A  49 " =    1.467
peak=   -3.544 closest distance to " CZ  PHE A  16 " =    0.821
peak=   -3.540 closest distance to " CD1 PHE A  59 " =    1.225
peak=   -3.538 closest distance to " OG  SER A 276 " =    0.864
peak=   -3.537 closest distance to " O   HOH Z 411 " =    4.999
peak=   -3.536 closest distance to " CG  HIS A 108 " =    1.065
peak=   -3.518 closest distance to " CG  GLN A  73 " =    1.165
peak=   -3.510 closest distance to " CB  PHE A 208 " =    2.071
peak=   -3.510 closest distance to " CB  PRO A 243 " =    2.591
peak=   -3.510 closest distance to " N   ALA A 244 " =    1.248
peak=   -3.510 closest distance to " O   HOH Z 216 " =    1.559
peak=   -3.507 closest distance to " N   THR A  29 " =    1.032
peak=   -3.503 closest distance to " O   ARG A 275 " =    0.808
peak=   -3.499 closest distance to " O   HOH Z  95 " =    1.268
peak=   -3.493 closest distance to " O   HOH Z  52 " =    0.711
peak=   -3.491 closest distance to " O   SER A 271 " =    1.640
peak=   -3.490 closest distance to " NE2 GLN A 223 " =    1.351
peak=   -3.488 closest distance to " CG2 ILE A  20 " =    2.677
peak=   -3.480 closest distance to " CB  GLN A  55 " =    1.201
peak=   -3.480 closest distance to " N   THR A 157 " =    1.667
peak=   -3.479 closest distance to " CD1 TRP A 179 " =    1.037
peak=   -3.474 closest distance to " OG  SER A 245 " =    1.824
peak=   -3.474 closest distance to " O   HOH Z 286 " =    1.334
peak=   -3.460 closest distance to " CG BLYS A 290 " =    0.846
peak=   -3.450 closest distance to " O   HOH Z 100 " =    0.829
peak=   -3.441 closest distance to " CD2 LEU A   5 " =    0.755
peak=   -3.434 closest distance to " CE3 TRP A 274 " =    2.113
peak=   -3.430 closest distance to " O   HOH Z 395 " =    0.923
peak=   -3.422 closest distance to " CB  ALA A   7 " =    1.947
peak=   -3.415 closest distance to " O   HOH Z 415 " =    0.768
peak=   -3.414 closest distance to " O   HOH Z 159 " =    1.331
peak=   -3.412 closest distance to " O   HOH Z 197 " =    2.069
peak=   -3.402 closest distance to " CB  ASN A  45 " =    2.030
peak=   -3.401 closest distance to " N   ASN A 127 " =    1.403
peak=   -3.397 closest distance to " O   HOH Z 231 " =    0.835
peak=   -3.395 closest distance to " CB  ASP A  27 " =    1.194
peak=   -3.389 closest distance to " O   HOH Z  60 " =    1.807
peak=   -3.389 closest distance to " O   GLY A 136 " =    1.566
peak=   -3.381 closest distance to " CZ  ARG A  66 " =    2.073
peak=   -3.379 closest distance to " CE2 PHE A 218 " =    2.397
peak=   -3.379 closest distance to " O   HOH Z 256 " =    1.068
peak=   -3.379 closest distance to " O   HOH Z  39 " =    0.746
peak=   -3.377 closest distance to " O   HOH Z 166 " =    2.047
peak=   -3.376 closest distance to " O   THR A  82 " =    1.102
peak=   -3.369 closest distance to " CG  PRO A 163 " =    2.445
peak=   -3.363 closest distance to " O   HOH Z 389 " =    2.410
peak=   -3.357 closest distance to " O   THR A  52 " =    0.960
peak=   -3.356 closest distance to " O   HOH Z  60 " =    2.064
peak=   -3.355 closest distance to " CD  ARG A  79 " =    1.004
peak=   -3.352 closest distance to " O   HOH Z 352 " =    1.673
peak=   -3.350 closest distance to " NH2BARG A 102 " =    0.947
peak=   -3.349 closest distance to " O  BHOH Z  74 " =    0.814
peak=   -3.347 closest distance to " OD2 ASP A 272 " =    1.153
peak=   -3.346 closest distance to " CB  ALA A  10 " =    1.967
peak=   -3.340 closest distance to " N   GLN A  58 " =    1.198
peak=   -3.339 closest distance to " OD1 ASP A  27 " =    1.106
peak=   -3.334 closest distance to " OG BSER A  12 " =    0.717
peak=   -3.331 closest distance to " CB  ALA A 131 " =    1.651
peak=   -3.324 closest distance to " O   HOH Z 189 " =    3.891
peak=   -3.323 closest distance to " CG  ASP A 298 " =    1.099
peak=   -3.308 closest distance to " CG  LEU A   5 " =    1.002
peak=   -3.308 closest distance to " O   HOH Z 174 " =    2.672
peak=   -3.307 closest distance to " CB  SER A 276 " =    1.811
peak=   -3.304 closest distance to " O   HOH Z 298 " =    0.876
peak=   -3.300 closest distance to " O   HOH Z 336 " =    5.057
peak=   -3.299 closest distance to " OD2 ASP A 171 " =    2.464
peak=   -3.297 closest distance to " C   ASP A 124 " =    1.109
peak=   -3.287 closest distance to " N   THR A 235 " =    1.033
peak=   -3.286 closest distance to " N   LYS A 290 " =    1.010
peak=   -3.284 closest distance to " N   PRO A 163 " =    1.465
peak=   -3.282 closest distance to " OE1 GLU A  37 " =    1.465
peak=   -3.281 closest distance to " N   GLN A  55 " =    1.240
peak=   -3.276 closest distance to " OG1 THR A 178 " =    1.209
peak=   -3.276 closest distance to " CG1 VAL A 125 " =    2.044
peak=   -3.273 closest distance to " CD  GLU A  44 " =    1.154
peak=   -3.268 closest distance to " O   HOH Z 140 " =    1.919
peak=   -3.267 closest distance to " NH2 ARG A  24 " =    0.933
peak=   -3.263 closest distance to " CB  VAL A 230 " =    0.795
peak=   -3.255 closest distance to " O   LEU A 222 " =    1.588
peak=   -3.255 closest distance to " O   GLN A  11 " =    1.190
peak=   -3.254 closest distance to " CB  PHE A 130 " =    1.175
peak=   -3.254 closest distance to " ND2 ASN A 249 " =    1.295
peak=   -3.248 closest distance to " OD1 ASP A 298 " =    1.734
peak=   -3.246 closest distance to " CD  PRO A 213 " =    2.167
peak=   -3.241 closest distance to " CA  GLY A 203 " =    2.685
peak=   -3.239 closest distance to " O   ARG A 145 " =    1.744
peak=   -3.238 closest distance to " O   ALA A  84 " =    1.684
peak=   -3.233 closest distance to " OD1 ASP A 107 " =    1.036
peak=   -3.232 closest distance to " CD1 TYR A 169 " =    2.449
peak=   -3.230 closest distance to " O   GLN A  88 " =    1.286
peak=   -3.229 closest distance to " C   ALA A 180 " =    1.154
peak=   -3.227 closest distance to " CA  MET A 113 " =    1.051
peak=   -3.223 closest distance to " CG  GLU A 277 " =    1.129
peak=   -3.220 closest distance to " OD1 ASP A  27 " =    1.802
peak=   -3.219 closest distance to " O   HOH Z 177 " =    2.464
peak=   -3.214 closest distance to " O   ARG A 145 " =    1.090
peak=   -3.214 closest distance to " C   PHE A  59 " =    0.849
peak=   -3.212 closest distance to " OD1 ASN A 249 " =    1.740
peak=   -3.211 closest distance to " NH2 ARG A  24 " =    2.091
peak=   -3.209 closest distance to " O   HOH Z 377 " =    0.995
peak=   -3.202 closest distance to " O   HOH Z 165 " =    1.972
peak=   -3.200 closest distance to " CB  TYR A  68 " =    1.462
peak=   -3.200 closest distance to " O   HOH Z 337 " =    1.767
peak=   -3.199 closest distance to " CG2 VAL A  78 " =    2.460
peak=   -3.199 closest distance to " CD2 TYR A 116 " =    2.235
peak=   -3.198 closest distance to " NH1 ARG A  36 " =    1.613
peak=   -3.195 closest distance to " O   HOH Z 332 " =    1.971
peak=   -3.192 closest distance to " O   HOH Z 347 " =    0.820
peak=   -3.188 closest distance to " CB  ASN A 301 " =    1.741
peak=   -3.185 closest distance to " CD2 PHE A  61 " =    1.378
peak=   -3.178 closest distance to " O   HOH Z 186 " =    1.410
peak=   -3.174 closest distance to " O   HOH Z 245 " =    1.254
peak=   -3.173 closest distance to " O   HOH Z 434 " =    4.205
peak=   -3.172 closest distance to " O   ASN A 301 " =    1.138
peak=   -3.171 closest distance to " NE2 GLN A  55 " =    0.894
peak=   -3.168 closest distance to " O   HOH Z 238 " =    0.789
peak=   -3.166 closest distance to " O   HOH Z  67 " =    3.009
peak=   -3.166 closest distance to " O   HOH Z 235 " =    1.657
peak=   -3.155 closest distance to " CD1 TYR A 214 " =    1.475
peak=   -3.152 closest distance to " CG  ARG A 219 " =    2.205
peak=   -3.151 closest distance to " O   SER A   3 " =    0.963
peak=   -3.149 closest distance to " O   PHE A  61 " =    0.952
peak=   -3.141 closest distance to " C   PHE A 155 " =    0.835
peak=   -3.132 closest distance to " O   HOH Z 412 " =    5.550
peak=   -3.130 closest distance to " O   HOH Z 188 " =    0.858
peak=   -3.128 closest distance to " N   GLN A 122 " =    1.508
peak=   -3.125 closest distance to " O   HOH Z 111 " =    1.831
peak=   -3.116 closest distance to " O   HOH Z 111 " =    1.591
peak=   -3.114 closest distance to " O   HOH Z 435 " =    2.460
peak=   -3.112 closest distance to " O   HOH Z 214 " =    1.162
peak=   -3.112 closest distance to " CA  ASP A  65 " =    1.063
peak=   -3.111 closest distance to " O   HOH Z 244 " =    1.412
peak=   -3.108 closest distance to " NE2 GLN A 122 " =    1.068
peak=   -3.104 closest distance to " CB  TRP A 274 " =    2.756
peak=   -3.104 closest distance to " CB  TRP A  85 " =    1.078
peak=   -3.100 closest distance to " CE BMET A  47 " =    1.225
peak=   -3.094 closest distance to " O   HOH Z  51 " =    0.830
peak=   -3.094 closest distance to " OE1 GLN A 183 " =    1.649
peak=   -3.082 closest distance to " O   HOH Z 398 " =    0.711
peak=   -3.076 closest distance to " O   HOH Z 332 " =    0.975
peak=   -3.073 closest distance to " O   HOH Z  34 " =    2.137
peak=   -3.070 closest distance to " O   PRO A 163 " =    1.776
peak=   -3.066 closest distance to " O   HOH Z 438 " =    2.697

================= 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    :  0.5047 0.4966   6.306685e+00   6.293878e+00
   1_bss:  0.4964 0.4838   6.302601e+00   6.287763e+00
   1_xyz:  0.4350 0.4634   6.240839e+00   6.266049e+00
   1_adp:  0.3982 0.4631   6.078566e+00   6.134607e+00
   1_occ:  0.3977 0.4639   6.078360e+00   6.135374e+00
   2_bss:  0.3966 0.4607   6.080019e+00   6.134785e+00
   2_xyz:  0.3423 0.4259   6.098202e+00   6.216039e+00
   2_adp:  0.3266 0.4157   6.073525e+00   6.200004e+00
   2_occ:  0.3264 0.4161   6.073920e+00   6.200714e+00
   3_bss:  0.3262 0.4136   6.072852e+00   6.199038e+00
   3_xyz:  0.2852 0.3611   5.961039e+00   6.111310e+00
   3_adp:  0.2621 0.3599   5.924866e+00   6.106114e+00
   3_occ:  0.2619 0.3597   5.924427e+00   6.105911e+00
   4_bss:  0.2615 0.3602   5.924680e+00   6.107174e+00
   4_xyz:  0.2290 0.3194   5.803118e+00   6.010351e+00
   4_adp:  0.2140 0.2942   5.738391e+00   5.947765e+00
   4_occ:  0.2140 0.2941   5.737969e+00   5.947512e+00
   5_bss:  0.2142 0.2939   5.738030e+00   5.946835e+00
   5_xyz:  0.1772 0.2436   5.561270e+00   5.789772e+00
   5_adp:  0.1646 0.2190   5.478250e+00   5.698627e+00
   5_occ:  0.1644 0.2188   5.477506e+00   5.697857e+00
   5_bss:  0.1645 0.2183   5.475145e+00   5.694850e+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:  0.355   9.335   5.755   8.897   9.071   0.000   0.000   0.000
   1_xyz:  0.355   9.335   5.755   8.897   9.071   0.000   0.000   0.000
   1_adp:  0.355   9.335   5.755   8.897   9.071   0.000   0.000   0.000
   1_occ:  0.355   9.335   5.755   8.897   9.071   0.000   0.000   0.000
   2_bss:  0.360  40.651   2.940   5.101   5.351   0.000   0.000   0.000
   2_xyz:  0.360  40.651   2.940   5.101   5.351   0.000   0.000   0.000
   2_adp:  0.360  40.651   2.940   5.101   5.351   0.000   0.000   0.000
   2_occ:  0.360  40.651   2.940   5.101   5.351   0.000   0.000   0.000
   3_bss:  0.331  49.207   1.676   2.620   3.294   0.000   0.000   0.000
   3_xyz:  0.331  49.207   1.676   2.620   3.294   0.000   0.000   0.000
   3_adp:  0.331  49.207   1.676   2.620   3.294   0.000   0.000   0.000
   3_occ:  0.331  49.207   1.676   2.620   3.294   0.000   0.000   0.000
   4_bss:  0.348  66.556   0.934   1.500   2.523   0.000   0.000   0.000
   4_xyz:  0.348  66.556   0.934   1.500   2.523   0.000   0.000   0.000
   4_adp:  0.348  66.556   0.934   1.500   2.523   0.000   0.000   0.000
   4_occ:  0.348  66.556   0.934   1.500   2.523   0.000   0.000   0.000
   5_bss:  0.348  66.556   0.673   0.822   2.419   0.000   0.000   0.000
   5_xyz:  0.348  66.556   0.673   0.822   2.419   0.000   0.000   0.000
   5_adp:  0.348  66.556   0.673   0.822   2.419   0.000   0.000   0.000
   5_occ:  0.348  66.556   0.673   0.822   2.419   0.000   0.000   0.000
   5_bss:  0.321  48.876  -0.592  -0.640   1.233   0.000   0.000   0.000
------------------------------------------------------------------------
 stage     <pher>    fom   alpha         beta
   0    :  64.373 0.3365  0.4077    81267.307
   1_bss:  63.842 0.3426  0.5191    79673.095
   1_xyz:  57.456 0.4248  0.6309    69206.184
   1_adp:  57.719 0.4207  0.6879    68887.059
   1_occ:  57.838 0.4192  0.6843    69243.015
   2_bss:  57.380 0.4251  0.6239    68652.821
   2_xyz:  49.597 0.5237  0.7745    54979.526
   2_adp:  47.305 0.5528  0.8300    51613.832
   2_occ:  47.400 0.5516  0.8279    51719.224
   3_bss:  47.103 0.5550  0.7775    51053.124
   3_xyz:  38.950 0.6544  0.9015    37240.478
   3_adp:  38.518 0.6594  0.8981    36708.032
   3_occ:  38.535 0.6591  0.8973    36665.933
   4_bss:  38.523 0.6594  0.8706    36755.100
   4_xyz:  33.538 0.7165  0.9295    27594.830
   4_adp:  30.029 0.7567  0.9464    23124.142
   4_occ:  30.013 0.7569  0.9464    23087.445
   5_bss:  29.982 0.7572  0.9354    23043.146
   5_xyz:  24.504 0.8157  0.9772    15611.169
   5_adp:  21.361 0.8483  0.9866    12630.504
   5_occ:  21.344 0.8484  0.9862    12579.053
   5_bss:  21.264 0.8490  0.9672    12427.116
------------------------------------------------------------------------
 stage       angl   bond   chir   dihe   plan   repu  geom_target
   0    :  24.226  0.414  2.119 33.790  0.145  4.088   5.3362e+01
   1_bss:  24.226  0.414  2.119 33.790  0.145  4.088   5.3362e+01
   1_xyz:   1.738  0.014  0.107 18.542  0.006  4.103   1.5150e-01
   1_adp:   1.738  0.014  0.107 18.542  0.006  4.103   1.5150e-01
   1_occ:   1.738  0.014  0.107 18.542  0.006  4.103   1.5150e-01
   2_bss:   1.738  0.014  0.107 18.542  0.006  4.103   1.5150e-01
   2_xyz:   1.368  0.010  0.089 17.066  0.006  4.103   1.1750e-01
   2_adp:   1.368  0.010  0.089 17.066  0.006  4.103   1.1750e-01
   2_occ:   1.368  0.010  0.089 17.066  0.006  4.103   1.1750e-01
   3_bss:   1.368  0.010  0.089 17.066  0.006  4.103   1.1750e-01
   3_xyz:   1.078  0.008  0.079 15.888  0.004  4.118   7.9027e-02
   3_adp:   1.078  0.008  0.079 15.888  0.004  4.118   7.9027e-02
   3_occ:   1.078  0.008  0.079 15.888  0.004  4.118   7.9027e-02
   4_bss:   1.078  0.008  0.079 15.888  0.004  4.118   7.9027e-02
   4_xyz:   1.016  0.007  0.071 15.612  0.004  4.108   6.7579e-02
   4_adp:   1.016  0.007  0.071 15.612  0.004  4.108   6.7579e-02
   4_occ:   1.016  0.007  0.071 15.612  0.004  4.108   6.7579e-02
   5_bss:   1.016  0.007  0.071 15.612  0.004  4.108   6.7579e-02
   5_xyz:   1.033  0.007  0.076 15.505  0.003  4.116   6.4883e-02
   5_adp:   1.033  0.007  0.076 15.505  0.003  4.116   6.4883e-02
   5_occ:   1.033  0.007  0.076 15.505  0.003  4.116   6.4883e-02
   5_bss:   1.033  0.007  0.076 15.505  0.003  4.116   6.4883e-02
------------------------------------------------------------------------
                      Maximal deviations:
 stage       angl   bond   chir   dihe   plan   repu       |grad|
   0    :  74.492  1.400  6.404144.062  0.405  1.196   6.9132e+00
   1_bss:  74.492  1.400  6.404144.062  0.405  1.196   6.9132e+00
   1_xyz:  13.506  0.191  0.416 89.305  0.034  2.103   1.0055e-01
   1_adp:  13.506  0.191  0.416 89.305  0.034  2.103   1.0055e-01
   1_occ:  13.506  0.191  0.416 89.305  0.034  2.103   1.0055e-01
   2_bss:  13.506  0.191  0.416 89.305  0.034  2.103   1.0055e-01
   2_xyz:   8.693  0.105  0.318 86.341  0.041  1.938   7.4200e-02
   2_adp:   8.693  0.105  0.318 86.341  0.041  1.938   7.4200e-02
   2_occ:   8.693  0.105  0.318 86.341  0.041  1.938   7.4200e-02
   3_bss:   8.693  0.105  0.318 86.341  0.041  1.938   7.4200e-02
   3_xyz:   7.302  0.055  0.276 80.356  0.027  2.209   1.5110e-01
   3_adp:   7.302  0.055  0.276 80.356  0.027  2.209   1.5110e-01
   3_occ:   7.302  0.055  0.276 80.356  0.027  2.209   1.5110e-01
   4_bss:   7.302  0.055  0.276 80.356  0.027  2.209   1.5110e-01
   4_xyz:   6.557  0.044  0.237 85.094  0.028  2.197   1.1150e-01
   4_adp:   6.557  0.044  0.237 85.094  0.028  2.197   1.1150e-01
   4_occ:   6.557  0.044  0.237 85.094  0.028  2.197   1.1150e-01
   5_bss:   6.557  0.044  0.237 85.094  0.028  2.197   1.1150e-01
   5_xyz:   6.902  0.049  0.230 77.531  0.025  2.324   4.5270e-02
   5_adp:   6.902  0.049  0.230 77.531  0.025  2.324   4.5270e-02
   5_occ:   6.902  0.049  0.230 77.531  0.025  2.324   4.5270e-02
   5_bss:   6.902  0.049  0.230 77.531  0.025  2.324   4.5270e-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:  87.41   0.00  16.44  83.53   0.00  15.00  87.41   0.00  24.27
   1_occ:  87.41   0.00  16.44  83.53   0.00  15.00  87.41   0.00  24.27
   2_bss:  87.41   0.00  16.44  83.53   0.00  15.00  87.41   0.00  24.27
   2_xyz:  87.41   0.00  16.44  83.53   0.00  15.00  87.41   0.00  24.27
   2_adp:  82.98   0.00  16.05  73.45   0.00  14.12  82.98   0.00  26.50
   2_occ:  82.98   0.00  16.05  73.45   0.00  14.12  82.98   0.00  26.50
   3_bss:  82.98   0.00  16.05  73.45   0.00  14.12  82.98   0.00  26.50
   3_xyz:  82.98   0.00  16.05  73.45   0.00  14.12  82.98   0.00  26.50
   3_adp:  93.97   0.00  18.17  92.41   0.00  14.72  93.97   0.00  36.95
   3_occ:  93.97   0.00  18.17  92.41   0.00  14.72  93.97   0.00  36.95
   4_bss:  93.97   0.00  18.17  92.41   0.00  14.72  93.97   0.00  36.95
   4_xyz:  93.97   0.00  18.17  92.41   0.00  14.72  93.97   0.00  36.95
   4_adp: 108.56   0.00  17.54 108.56   0.00  13.02 101.97   1.09  42.20
   4_occ: 108.56   0.00  17.54 108.56   0.00  13.02 101.97   1.09  42.20
   5_bss: 108.56   0.00  17.54 108.56   0.00  13.02 101.97   1.09  42.20
   5_xyz: 108.56   0.00  17.54 108.56   0.00  13.02 101.97   1.09  42.20
   5_adp: 106.69   0.00  15.92 106.69   0.00  11.25 100.71   3.36  41.35
   5_occ: 106.69   0.00  15.92 106.69   0.00  11.25 100.71   3.36  41.35
   5_bss: 107.46   0.77  16.69 107.46   0.77  12.02 101.48   4.13  42.12
------------------------------------------------------------------------
 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:    1.311    0.024    0.411
   1_adp:    1.311    0.024    0.411
   1_occ:    1.311    0.024    0.411
   2_bss:    1.311    0.024    0.411
   2_xyz:    1.693    0.022    0.591
   2_adp:    1.693    0.022    0.591
   2_occ:    1.693    0.022    0.591
   3_bss:    1.693    0.022    0.591
   3_xyz:    1.585    0.048    0.676
   3_adp:    1.585    0.048    0.676
   3_occ:    1.585    0.048    0.676
   4_bss:    1.585    0.048    0.676
   4_xyz:    1.733    0.065    0.778
   4_adp:    1.733    0.065    0.778
   4_occ:    1.733    0.065    0.778
   5_bss:    1.733    0.065    0.778
   5_xyz:    1.898    0.058    0.863
   5_adp:    1.898    0.058    0.863
   5_occ:    1.898    0.058    0.863
   5_bss:    1.898    0.058    0.863
------------------------------------------------------------------------

CPU time actual refinement: 292.44


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

Writing refined structure to PDB file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/trial/run_492/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_492/model_refine_001_2mFobs-DFmodel.map
Writing mFobs-DFmodel XPLOR map to file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/trial/run_492/model_refine_001_mFobs-DFmodel.map
Writing map coefficients to MTZ file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/trial/run_492/model_refine_001_map_coeffs.mtz

Writing default parameters for subsequent refinement:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/trial/run_492/model_refine_002.def


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

Pure refinement (no I/O, processing, etc)= 292.30 
  Macro-tasks:
    bulk solvent and scale       = 35.30  
    individual site refinement   = 122.87 
    weights calculation          = 27.38  
    collect and process          = 5.29   
    model show statistics        = 0.11   
    TOTAL for macro-tasks        = 190.95 
  Micro-tasks:
    mask                            = 2.49   
    f_calc                          = 91.52  
    alpha_beta                      = 6.96   
    target                          = 1.01   
    gradients_wrt_atomic_parameters = 99.89  
    fmodel                         = 6.06   
    r_factors                      = 0.20   
    phase_errors                   = 7.99   
    foms                           = 0.25   
    TOTAL for micro-tasks          = 216.37 
NUMBER OF MASK CALCS=  6
Time per interpreted Python bytecode instruction: 4.118 micro seconds
Total CPU time: 5.06 minutes
from_scatterers_fft:    641 calls, 91.25 s
gradients_fft:          585 calls, 88.61 s

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

# Date 2008-01-16 Time 01:42:23 PST -0800 (1200476543.27 s)
Start R-work = 0.5047, R-free = 0.4966 (no bulk solvent and anisotropic scale)
Final R-work = 0.1792, R-free = 0.2335 (no bulk solvent and anisotropic scale)

Start R-work = 0.4964, R-free = 0.4838
Final R-work = 0.1645, R-free = 0.2183