# Date 2008-01-16 Time 03:22:00 PST -0800 (1200482520.27 s)
#phil __OFF__

Command line arguments: "../1214.param" "adp.set_b_iso=10" "sites.shake=0.5" "main.number_of_macro_cycles=5" "--overwrite"

HOST = idle.lbl.gov
HOSTTYPE = x86_64-linux
USER = phzwart
PID = 21584
JOB_ID = 5158
SGE_ARCH = lx24-amd64
SGE_TASK_FIRST = 1
SGE_TASK_LAST = 1330
SGE_TASK_ID = 1214

-------------------------------------------------------------------------------
  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: (72.0062, 45.7567, 85.9581, 90, 90, 90)
  Space group: P 21 21 21 (No. 19)

/net/cci-filer1/vol1/tmp/phzwart/tassos/trial/model.pdb
  Monomer Library directory:
    "/net/rosie/scratch3/phzwart/CCTBX/Sources/mon_lib"
  Total number of atoms: 2823
  Number of models: 1
  Model: 0
    Number of conformers: 2
    Conformer: "A"
      Number of atoms: 2769
      Number of chains: 2
        Number of residues, atoms: 302, 2333
          Classifications: {'peptide': 302}
          Modifications used: {'COO': 1}
          Link IDs: {'PTRANS': 7, 'CIS': 1, 'TRANS': 293}
        Number of residues, atoms: 436, 436
          Classifications: {'water': 436}
          Link IDs: {None: 435}
    Conformer: "B"
      Number of atoms: 2771
      Common with "A": 2717
      Number of chains: 2
        Number of residues, atoms: 302, 2333
          Classifications: {'peptide': 302}
          Modifications used: {'COO': 1}
          Link IDs: {'PTRANS': 7, 'CIS': 1, 'TRANS': 293}
          bond proxies already assigned to first conformer: 2332
        Number of residues, atoms: 438, 438
          Classifications: {'water': 438}
          Link IDs: {None: 437}
  Time building chain proxies: 3.23, per 1000 atoms: 1.14


================================== 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: (72.0062, 45.7567, 85.9581, 90, 90, 90)
Space group: P 21 21 21 (No. 19)
Systematic absences: 0
Centric reflections: 2427
Resolution range: 15.2429 1.95451
Completeness in resolution range: 0.926632
Completeness with d_max=infinity: 0.924009

Number of F-obs in resolution range:                   19589
Number of F-obs <= 0:                                  0
Refinement resolution range: d_max =  15.2429
                             d_min =   1.9545

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: (72.0062, 45.7567, 85.9581, 90, 90, 90)
Space group: P 21 21 21 (No. 19)
Systematic absences: 0
Centric reflections: 2427
Resolution range: 15.2429 1.95451
Completeness in resolution range: 0.926632
Completeness with d_max=infinity: 0.924009

Test (R-free flags) flag value: 1

Number of work/free reflections by resolution:
                                         work  free  %free
  bin  1: 15.2433 -  4.1846 [2223/2250]  2002   221   9.9%
  bin  2:  4.1846 -  3.3328 [2140/2160]  1928   212   9.9%
  bin  3:  3.3328 -  2.9149 [2114/2133]  1898   216  10.2%
  bin  4:  2.9149 -  2.6499 [2074/2104]  1866   208  10.0%
  bin  5:  2.6499 -  2.4608 [2077/2096]  1875   202   9.7%
  bin  6:  2.4608 -  2.3162 [2060/2085]  1847   213  10.3%
  bin  7:  2.3162 -  2.2006 [2054/2082]  1839   215  10.5%
  bin  8:  2.2006 -  2.1051 [2063/2099]  1865   198   9.6%
  bin  9:  2.1051 -  2.0242 [1958/2070]  1769   189   9.7%
  bin 10:  2.0242 -  1.9545 [ 826/2061]   741    85  10.3%
                                overall 17630  1959  10.0%
Writing MTZ file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/trial/run_1214/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: 0.13 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:
        1.48 -     2.17: 21
        2.17 -     2.85: 1121
        2.85 -     3.53: 4459
        3.53 -     4.22: 9348
        4.22 -     4.90: 13507
  Nonbonded interactions sorted by model distance:
             atom i - atom j             model   vdw sym.op. j
  " O   HOH Z 201 " - " O   HOH Z 349 "  1.483 3.040 -x+1/2,-y+1,z+1/2
  " O   HOH Z 204 " - " O   HOH Z 296 "  1.644 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
  " OG BSER A 216 " - " O   HOH Z 113 "  1.718 3.040 -x+1/2,-y+1,z-1/2
  " O   HOH Z  61 " - " O   HOH Z 246 "  1.742 3.040 x,y+1,z
  ... (remaining 28451 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_1214/model_refine_001.eff

Writing geometry restraints to file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/trial/run_1214/model_refine_001.geo

CPU time processing inputs: 8.72


============================ 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 = 72.00625 45.75675 85.95805 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 - 15.24 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.5157   r_free= 0.5127   ksol= 0.00   Bsol= 0.00   scale= 0.765    |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (0.00,0.00,0.00,0.00,0.00,0.00); trace/3= 0.00                              |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.90 A                  |
| x-ray target function (ml) for work reflections: 6.313646                   |
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
| Bin     Resolution   Compl.  No. Refl.    R-factors          Targets        |
|number     range              work test   work   test        work        test|
|  1: 15.2433 -  4.6684 0.99   1437  163 0.4448 0.4645      6.6683      6.7245|
|  2:  4.6684 -  3.7232 0.99   1392  152 0.4589 0.4506      6.8806      6.8671|
|  3:  3.7232 -  3.2578 0.99   1364  147 0.4903 0.4738      6.7207      6.7184|
|  4:  3.2578 -  2.9623 0.99   1347  158 0.5133 0.5327      6.5608      6.5497|
|  5:  2.9623 -  2.7513 0.99   1356  144 0.5373 0.5322      6.3921      6.3929|
|  6:  2.7513 -  2.5899 0.99   1327  154 0.5526 0.5360      6.3059      6.2402|
|  7:  2.5899 -  2.4608 0.99   1346  141 0.5554 0.5017      6.2465      6.1697|
|  8:  2.4608 -  2.3541 0.98   1334  154 0.5438 0.5326      6.1763      6.2305|
|  9:  2.3541 -  2.2638 0.98   1302  145 0.5531 0.5220      6.1449      6.1346|
| 10:  2.2638 -  2.1859 1.00   1326  154 0.5456 0.5571      6.0911       6.073|
| 11:  2.1859 -  2.1177 0.98   1304  137 0.5318 0.5426       6.033      6.0495|
| 12:  2.1177 -  2.0573 0.98   1318  149 0.5384 0.5878      5.9415      5.9554|
| 13:  2.0573 -  2.0033 0.84   1115  123 0.5564 0.4926      5.8773      5.8274|
| 14:  2.0033 -  1.9545 0.27    362   38 0.5730 0.5418      5.8945       5.845|
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
|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: 15.2433 -  4.6684  1437   163  0.59  43.32   0.76     0.67     109899.40|
|  2:  4.6684 -  3.7232  1392   152  0.60  43.40   0.83     0.69     151742.19|
|  3:  3.7232 -  3.2578  1364   147  0.45  55.86   0.81     0.58     159771.29|
|  4:  3.2578 -  2.9623  1347   158  0.32  65.51   0.76     0.43     143006.53|
|  5:  2.9623 -  2.7513  1356   144  0.22  73.64   0.71     0.28     111059.53|
|  6:  2.7513 -  2.5899  1327   154  0.22  73.20   0.70     0.28      89796.50|
|  7:  2.5899 -  2.4608  1346   141  0.25  71.46   0.72     0.30      73900.76|
|  8:  2.4608 -  2.3541  1334   154  0.28  69.15   0.71     0.34      64057.72|
|  9:  2.3541 -  2.2638  1302   145  0.28  69.04   0.72     0.34      58578.38|
| 10:  2.2638 -  2.1859  1326   154  0.27  69.77   0.73     0.34      54021.57|
| 11:  2.1859 -  2.1177  1304   137  0.24  72.40   0.75     0.31      53185.42|
| 12:  2.1177 -  2.0573  1318   149  0.21  74.62   0.74     0.28      48675.54|
| 13:  2.0573 -  2.0033  1115   123  0.22  73.86   0.70     0.29      41106.59|
| 14:  2.0033 -  1.9545   362    38  0.34  64.99   0.73     0.39      30085.30|
|alpha:            min =        0.28 max =            0.69 mean =         0.40|
|beta:             min =    30085.30 max =       159771.29 mean =     89195.86|
|figures of merit: min =        0.00 max =            1.00 mean =         0.32|
|phase err.(work): min =        0.00 max =           89.98 mean =        65.43|
|phase err.(test): min =        0.00 max =           89.90 mean =        65.65|
|-----------------------------------------------------------------------------|

============================== 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 = 28.531499             wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 83.580   (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 2.391593              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 78.297   (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:        4 |
| 0.140 - 0.280:   585 |   7.457 -  14.906:   711 |  1.566 -  1.937:       33 |
| 0.280 - 0.420:   441 |  14.906 -  22.354:   630 |  1.937 -  2.307:      175 |
| 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:     1521 |
| 0.700 - 0.840:   127 |  37.251 -  44.699:   241 |  3.048 -  3.418:     2656 |
| 0.840 - 0.980:    59 |  44.699 -  52.147:   125 |  3.418 -  3.789:     3950 |
| 0.980 - 1.120:    17 |  52.147 -  59.595:    51 |  3.789 -  4.159:     5109 |
| 1.120 - 1.260:     9 |  59.595 -  67.044:    13 |  4.159 -  4.530:     6541 |
| 1.260 - 1.400:     1 |  67.044 -  74.492:     3 |  4.530 -  4.900:     7778 |
|-----------------------------------------------------------------------------|
|-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 |       53.523 |
| 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 |       2.301 |              |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 11.775)------------------------------------------|
|    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 = 11.775)------------------------------------------|
|    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 - 15.24 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.5175   r_free= 0.5148   ksol= 0.00   Bsol= 0.00   scale= 0.738    |
|                                                                             |
| 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:   0.90 A                  |
| x-ray target function (ml) for work reflections: 6.314200                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.95 - 15.24 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.5071   r_free= 0.5021   ksol= 0.37   Bsol= 20.00   scale= 0.944   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (8.64,8.41,6.32,0.00,0.00,0.00); trace/3= 7.79                              |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.91 A                  |
| x-ray target function (ml) for work reflections: 6.310965                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 23.162242             wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 84.549   (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 2.169218              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 76.268   (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.5071      final r-factor (work) = 0.4558          |
| start r-factor (free) = 0.5021      final r-factor (free) = 0.4843          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 126.5764 = 23.16 * 0.50 * 6.3080 + 1.00 * 53.5230                           |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 72.7989 = 23.16 * 0.50 * 6.2727 + 1.00 * 0.1542                             |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 26     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.4558      final r-factor (work) = 0.4214          |
| start r-factor (free) = 0.4843      final r-factor (free) = 0.4818          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 13.6212 = 2.17 * 1.00 * 6.2727 + 1.00 * 0.0144                              |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 13.5497 = 2.17 * 1.00 * 6.2362 + 1.00 * 0.0219                              |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 29     |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 11.775)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.00    80.96   16.66    None  None   None       |
|    all(noH): 2823   0      0.00    80.96   16.66    None  None   None       |
|    Sol.    : 438    0      0.00    80.96   22.69    None  None   None       |
|    Mac.    : 2385   0      0.00    78.94   15.55    None  None   None       |
|    Hyd.    : 0      0      None    None    None     None  None   None       |
|    - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -      |
|       Distribution of isotropic (or equivalent) ADP for non-H atoms:        |
|    Bin#      value range     #atoms | Bin#      value range     #atoms      |
|      0:     0.000 -   8.096:  813   |   5:    40.478 -  48.574:   98        |
|      1:     8.096 -  16.191:  815   |   6:    48.574 -  56.669:   45        |
|      2:    16.191 -  24.287:  577   |   7:    56.669 -  64.765:   14        |
|      3:    24.287 -  32.382:  292   |   8:    64.765 -  72.860:   14        |
|      4:    32.382 -  40.478:  147   |   9:    72.860 -  80.956:    8        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.4214 r_free = 0.4818             target_work(ml) = 6.235         |
| occupancies: max = 1.00  min = 0.30   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.4211 r_free = 0.4817             target_work(ml) = 6.235         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:       15 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.95 - 15.24 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.4211   r_free= 0.4817   ksol= 0.37   Bsol= 20.00   scale= 1.093   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (8.64,8.41,6.32,0.00,0.00,0.00); trace/3= 7.79                              |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.83 A                  |
| x-ray target function (ml) for work reflections: 6.234672                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.95 - 15.24 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.4193   r_free= 0.4795   ksol= 0.34   Bsol= 37.25   scale= 1.004   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (4.93,4.53,3.31,0.00,0.00,0.00); trace/3= 4.26                              |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.83 A                  |
| x-ray target function (ml) for work reflections: 6.234725                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 17.857225             wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 103.809  (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 1.020080              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 148.655  (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.4193      final r-factor (work) = 0.3743          |
| start r-factor (free) = 0.4795      final r-factor (free) = 0.4545          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 55.8049 = 17.86 * 0.50 * 6.2328 + 1.00 * 0.1542                             |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 55.4120 = 17.86 * 0.50 * 6.1938 + 1.00 * 0.1101                             |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 28     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.3743      final r-factor (work) = 0.3621          |
| start r-factor (free) = 0.4545      final r-factor (free) = 0.4475          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 6.3401 = 1.02 * 1.00 * 6.1938 + 1.00 * 0.0219                               |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 6.2886 = 1.02 * 1.00 * 6.1490 + 1.00 * 0.0162                               |
|-----------------------------------------------------------------------------|
| number of iterations = 9       |    number of function evaluations = 10     |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 11.775)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.00    81.34   16.41    None  None   None       |
|    all(noH): 2823   0      0.00    81.34   16.41    None  None   None       |
|    Sol.    : 438    0      0.00    81.34   23.55    None  None   None       |
|    Mac.    : 2385   0      0.00    78.27   15.10    None  None   None       |
|    Hyd.    : 0      0      None    None    None     None  None   None       |
|    - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -      |
|       Distribution of isotropic (or equivalent) ADP for non-H atoms:        |
|    Bin#      value range     #atoms | Bin#      value range     #atoms      |
|      0:     0.000 -   8.134:  751   |   5:    40.672 -  48.806:   87        |
|      1:     8.134 -  16.269:  892   |   6:    48.806 -  56.941:   29        |
|      2:    16.269 -  24.403:  613   |   7:    56.941 -  65.075:   15        |
|      3:    24.403 -  32.537:  286   |   8:    65.075 -  73.209:    9        |
|      4:    32.537 -  40.672:  136   |   9:    73.209 -  81.344:    5        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.3621 r_free = 0.4475             target_work(ml) = 6.141         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:       15 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.3619 r_free = 0.4470             target_work(ml) = 6.141         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:       24 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.95 - 15.24 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.3619   r_free= 0.4470   ksol= 0.34   Bsol= 37.25   scale= 1.041   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (4.93,4.53,3.31,0.00,0.00,0.00); trace/3= 4.26                              |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.66 A                  |
| x-ray target function (ml) for work reflections: 6.140584                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.95 - 15.24 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.3623   r_free= 0.4455   ksol= 0.32   Bsol= 44.65   scale= 1.016   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (3.77,2.87,3.21,0.00,0.00,0.00); trace/3= 3.28                              |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.67 A                  |
| x-ray target function (ml) for work reflections: 6.141243                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 10.032396             wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 105.344  (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 1.265497              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 128.794  (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.3623      final r-factor (work) = 0.3243          |
| start r-factor (free) = 0.4455      final r-factor (free) = 0.4063          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 30.9563 = 10.03 * 0.50 * 6.1493 + 1.00 * 0.1102                             |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 30.7203 = 10.03 * 0.50 * 6.1078 + 1.00 * 0.0826                             |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 28     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.3243      final r-factor (work) = 0.3095          |
| start r-factor (free) = 0.4063      final r-factor (free) = 0.3996          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 7.7466 = 1.27 * 1.00 * 6.1078 + 1.00 * 0.0173                               |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 7.8518 = 1.27 * 1.00 * 6.0433 + 1.00 * 0.2041                               |
|-----------------------------------------------------------------------------|
| number of iterations = 6       |    number of function evaluations = 6      |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 11.775)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.00    92.32   16.61    None  None   None       |
|    all(noH): 2823   0      0.00    92.32   16.61    None  None   None       |
|    Sol.    : 438    0      0.00    79.98   26.32    None  None   None       |
|    Mac.    : 2385   0      0.00    92.32   14.83    None  None   None       |
|    Hyd.    : 0      0      None    None    None     None  None   None       |
|    - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -      |
|       Distribution of isotropic (or equivalent) ADP for non-H atoms:        |
|    Bin#      value range     #atoms | Bin#      value range     #atoms      |
|      0:     0.000 -   9.232:  893   |   5:    46.160 -  55.392:   55        |
|      1:     9.232 -  18.464:  885   |   6:    55.392 -  64.624:   18        |
|      2:    18.464 -  27.696:  598   |   7:    64.624 -  73.856:   11        |
|      3:    27.696 -  36.928:  247   |   8:    73.856 -  83.088:    4        |
|      4:    36.928 -  46.160:  111   |   9:    83.088 -  92.320:    1        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.3095 r_free = 0.3996             target_work(ml) = 6.035         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:       24 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.3092 r_free = 0.3993             target_work(ml) = 6.035         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:       22 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.95 - 15.24 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.3092   r_free= 0.3993   ksol= 0.32   Bsol= 44.65   scale= 1.050   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (3.77,2.87,3.21,0.00,0.00,0.00); trace/3= 3.28                              |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.53 A                  |
| x-ray target function (ml) for work reflections: 6.034617                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.95 - 15.24 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.3092   r_free= 0.3988   ksol= 0.33   Bsol= 44.65   scale= 1.024   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (2.63,1.72,2.54,0.00,0.00,0.00); trace/3= 2.30                              |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.53 A                  |
| x-ray target function (ml) for work reflections: 6.034686                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 12.647528             wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 106.700  (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 4.689130              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 91.096   (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.3092      final r-factor (work) = 0.2563          |
| start r-factor (free) = 0.3988      final r-factor (free) = 0.3416          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 38.2939 = 12.65 * 0.50 * 6.0425 + 1.00 * 0.0826                             |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 37.8645 = 12.65 * 0.50 * 5.9707 + 1.00 * 0.1070                             |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 28     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.2563      final r-factor (work) = 0.2247          |
| start r-factor (free) = 0.3416      final r-factor (free) = 0.3105          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 28.0182 = 4.69 * 1.00 * 5.9707 + 1.00 * 0.0207                              |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 27.3815 = 4.69 * 1.00 * 5.8341 + 1.00 * 0.0246                              |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 27     |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 11.775)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.00    99.90   17.55    None  None   None       |
|    all(noH): 2823   0      0.00    99.90   17.55    None  None   None       |
|    Sol.    : 438    0      0.00    99.90   40.96    None  None   None       |
|    Mac.    : 2385   0      0.00    94.24   13.25    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 -   9.990: 1243   |   5:    49.948 -  59.937:  105        |
|      1:     9.990 -  19.979:  740   |   6:    59.937 -  69.927:   58        |
|      2:    19.979 -  29.969:  316   |   7:    69.927 -  79.916:   30        |
|      3:    29.969 -  39.958:  170   |   8:    79.916 -  89.906:    8        |
|      4:    39.958 -  49.948:  148   |   9:    89.906 -  99.895:    5        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.2247 r_free = 0.3105             target_work(ml) = 5.780         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:       22 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.2244 r_free = 0.3102             target_work(ml) = 5.779         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:       18 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.95 - 15.24 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.2244   r_free= 0.3102   ksol= 0.33   Bsol= 44.65   scale= 1.042   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (2.63,1.72,2.54,0.00,0.00,0.00); trace/3= 2.30                              |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.35 A                  |
| x-ray target function (ml) for work reflections: 5.778873                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.95 - 15.24 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.2243   r_free= 0.3099   ksol= 0.34   Bsol= 59.07   scale= 1.026   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (2.05,0.94,2.26,0.00,0.00,0.00); trace/3= 1.75                              |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.35 A                  |
| x-ray target function (ml) for work reflections: 5.777759                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 6.683427              wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 103.499  (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 0.174542              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 132.038  (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.2243      final r-factor (work) = 0.1858          |
| start r-factor (free) = 0.3099      final r-factor (free) = 0.2647          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 19.6034 = 6.68 * 0.50 * 5.8343 + 1.00 * 0.1070                              |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 19.1587 = 6.68 * 0.50 * 5.7103 + 1.00 * 0.0765                              |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 29     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1858      final r-factor (work) = 0.1763          |
| start r-factor (free) = 0.2647      final r-factor (free) = 0.2371          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 1.0211 = 0.17 * 1.00 * 5.7103 + 1.00 * 0.0244                               |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 0.9973 = 0.17 * 1.00 * 5.6073 + 1.00 * 0.0186                               |
|-----------------------------------------------------------------------------|
| number of iterations = 7       |    number of function evaluations = 10     |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 11.775)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.00    95.73   16.92    None  None   None       |
|    all(noH): 2823   0      0.00    95.73   16.92    None  None   None       |
|    Sol.    : 438    0      2.52    95.73   40.02    None  None   None       |
|    Mac.    : 2385   0      0.00    92.80   12.68    None  None   None       |
|    Hyd.    : 0      0      None    None    None     None  None   None       |
|    - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -      |
|       Distribution of isotropic (or equivalent) ADP for non-H atoms:        |
|    Bin#      value range     #atoms | Bin#      value range     #atoms      |
|      0:     0.000 -   9.573: 1231   |   5:    47.864 -  57.436:   98        |
|      1:     9.573 -  19.145:  839   |   6:    57.436 -  67.009:   53        |
|      2:    19.145 -  28.718:  273   |   7:    67.009 -  76.582:   33        |
|      3:    28.718 -  38.291:  151   |   8:    76.582 -  86.154:    7        |
|      4:    38.291 -  47.864:  134   |   9:    86.154 -  95.727:    4        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.1763 r_free = 0.2371             target_work(ml) = 5.545         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:       18 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.1760 r_free = 0.2361             target_work(ml) = 5.542         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:       16 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.95 - 15.24 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1760   r_free= 0.2361   ksol= 0.34   Bsol= 59.07   scale= 1.049   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (2.05,0.94,2.26,0.00,0.00,0.00); trace/3= 1.75                              |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.22 A                  |
| x-ray target function (ml) for work reflections: 5.542224                   |
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
| Bin     Resolution   Compl.  No. Refl.    R-factors          Targets        |
|number     range              work test   work   test        work        test|
|  1: 15.2433 -  4.6684 0.99   1437  163 0.1144 0.1679      5.5354      5.8312|
|  2:  4.6684 -  3.7232 0.99   1392  152 0.1170 0.1651      5.7476      6.0744|
|  3:  3.7232 -  3.2578 0.99   1364  147 0.1638 0.2314      5.8502      6.1132|
|  4:  3.2578 -  2.9623 0.99   1347  158 0.1937 0.2459      5.8382      5.9873|
|  5:  2.9623 -  2.7513 0.99   1356  144 0.1989 0.2696      5.7042      5.9258|
|  6:  2.7513 -  2.5899 0.99   1327  154 0.1942 0.2727       5.607      5.7919|
|  7:  2.5899 -  2.4608 0.99   1346  141 0.2013 0.2584      5.5526       5.731|
|  8:  2.4608 -  2.3541 0.98   1334  154 0.2072 0.2678      5.5158      5.7341|
|  9:  2.3541 -  2.2638 0.98   1302  145 0.1923 0.2508       5.435       5.605|
| 10:  2.2638 -  2.1859 1.00   1326  154 0.1904 0.2619      5.3712      5.5361|
| 11:  2.1859 -  2.1177 0.98   1304  137 0.1957 0.2733      5.3593      5.6947|
| 12:  2.1177 -  2.0573 0.98   1318  149 0.1977 0.2654      5.3051         5.5|
| 13:  2.0573 -  2.0033 0.84   1115  123 0.2196 0.2696      5.2484      5.3997|
| 14:  2.0033 -  1.9545 0.27    362   38 0.1973 0.2329      5.1715      5.2697|
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
|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: 15.2433 -  4.6684  1437   163  0.91  12.56   0.98     0.97      11066.74|
|  2:  4.6684 -  3.7232  1392   152  0.92  12.75   1.06     1.06      17359.11|
|  3:  3.7232 -  3.2578  1364   147  0.86  19.95   1.09     1.08      23934.76|
|  4:  3.2578 -  2.9623  1347   158  0.82  23.91   1.05     1.02      24264.51|
|  5:  2.9623 -  2.7513  1356   144  0.80  26.18   1.06     1.00      20017.54|
|  6:  2.7513 -  2.5899  1327   154  0.80  26.53   1.04     0.98      16840.98|
|  7:  2.5899 -  2.4608  1346   141  0.80  26.85   1.05     0.97      14842.78|
|  8:  2.4608 -  2.3541  1334   154  0.80  26.39   1.05     1.00      13453.23|
|  9:  2.3541 -  2.2638  1302   145  0.81  25.74   1.06     0.98      11425.41|
| 10:  2.2638 -  2.1859  1326   154  0.81  25.71   1.07     1.00      10169.56|
| 11:  2.1859 -  2.1177  1304   137  0.80  26.36   1.09     1.02      10312.49|
| 12:  2.1177 -  2.0573  1318   149  0.79  27.58   1.08     1.06      10011.61|
| 13:  2.0573 -  2.0033  1115   123  0.79  27.92   1.08     1.02       7948.97|
| 14:  2.0033 -  1.9545   362    38  0.84  23.12   1.07     1.02       6057.27|
|alpha:            min =        0.97 max =            1.08 mean =         1.01|
|beta:             min =     6057.27 max =        24264.51 mean =     14683.73|
|figures of merit: min =        0.00 max =            1.00 mean =         0.83|
|phase err.(work): min =        0.00 max =           89.98 mean =        23.55|
|phase err.(test): min =        0.00 max =           89.68 mean =        22.24|
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.95 - 15.24 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1754   r_free= 0.2353   ksol= 0.33   Bsol= 47.73   scale= 1.018   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (0.26,-0.85,0.59,-0.00,0.00,0.00); trace/3= 0.00                            |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.21 A                  |
| x-ray target function (ml) for work reflections: 5.541520                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.95 - 15.24 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1754   r_free= 0.2353   ksol= 0.33   Bsol= 47.73   scale= 1.018   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (0.26,-0.85,0.59,-0.00,0.00,0.00); trace/3= 0.00                            |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.21 A                  |
| x-ray target function (ml) for work reflections: 5.541520                   |
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
| Bin     Resolution   Compl.  No. Refl.    R-factors          Targets        |
|number     range              work test   work   test        work        test|
|  1: 15.2433 -  4.6684 0.99   1437  163 0.1143 0.1656      5.5267      5.8201|
|  2:  4.6684 -  3.7232 0.99   1392  152 0.1169 0.1626      5.7443      6.0655|
|  3:  3.7232 -  3.2578 0.99   1364  147 0.1636 0.2319      5.8487       6.113|
|  4:  3.2578 -  2.9623 0.99   1347  158 0.1939 0.2459       5.838      5.9854|
|  5:  2.9623 -  2.7513 0.99   1356  144 0.1987 0.2697      5.7037      5.9278|
|  6:  2.7513 -  2.5899 0.99   1327  154 0.1940 0.2725      5.6068      5.7928|
|  7:  2.5899 -  2.4608 0.99   1346  141 0.2013 0.2595      5.5528       5.734|
|  8:  2.4608 -  2.3541 0.98   1334  154 0.2074 0.2685      5.5174      5.7373|
|  9:  2.3541 -  2.2638 0.98   1302  145 0.1924 0.2508      5.4358      5.6041|
| 10:  2.2638 -  2.1859 1.00   1326  154 0.1907 0.2622      5.3715      5.5368|
| 11:  2.1859 -  2.1177 0.98   1304  137 0.1959 0.2735      5.3598      5.6951|
| 12:  2.1177 -  2.0573 0.98   1318  149 0.1979 0.2661      5.3069      5.5029|
| 13:  2.0573 -  2.0033 0.84   1115  123 0.2198 0.2701      5.2494      5.4007|
| 14:  2.0033 -  1.9545 0.27    362   38 0.1973 0.2331      5.1719      5.2698|
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
|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: 15.2433 -  4.6684  1437   163  0.91  12.29   0.97     0.96      10629.42|
|  2:  4.6684 -  3.7232  1392   152  0.92  12.51   1.04     1.04      16916.84|
|  3:  3.7232 -  3.2578  1364   147  0.86  19.77   1.06     1.06      23639.16|
|  4:  3.2578 -  2.9623  1347   158  0.82  23.85   1.02     0.99      24168.75|
|  5:  2.9623 -  2.7513  1356   144  0.80  26.10   1.02     0.97      19966.67|
|  6:  2.7513 -  2.5899  1327   154  0.80  26.48   1.00     0.94      16840.58|
|  7:  2.5899 -  2.4608  1346   141  0.79  26.87   1.00     0.93      14876.66|
|  8:  2.4608 -  2.3541  1334   154  0.80  26.43   1.00     0.96      13521.61|
|  9:  2.3541 -  2.2638  1302   145  0.81  25.76   1.01     0.93      11476.39|
| 10:  2.2638 -  2.1859  1326   154  0.81  25.70   1.01     0.95      10182.18|
| 11:  2.1859 -  2.1177  1304   137  0.80  26.35   1.03     0.97      10334.79|
| 12:  2.1177 -  2.0573  1318   149  0.79  27.59   1.02     1.00      10040.77|
| 13:  2.0573 -  2.0033  1115   123  0.79  27.94   1.01     0.96       7971.18|
| 14:  2.0033 -  1.9545   362    38  0.84  23.09   1.00     0.95       6058.75|
|alpha:            min =        0.93 max =            1.06 mean =         0.97|
|beta:             min =     6058.75 max =        24168.75 mean =     14596.78|
|figures of merit: min =        0.00 max =            1.00 mean =         0.83|
|phase err.(work): min =        0.00 max =           89.91 mean =        23.48|
|phase err.(test): min =        0.00 max =           89.28 mean =        22.19|
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 11.775)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.62    96.35   17.55    None  None   None       |
|    all(noH): 2823   0      0.62    96.35   17.55    None  None   None       |
|    Sol.    : 438    0      3.14    96.35   40.64    None  None   None       |
|    Mac.    : 2385   0      0.62    93.42   13.31    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:     0.623 -  10.196: 1231   |   5:    48.486 -  58.059:   98        |
|      1:    10.196 -  19.768:  839   |   6:    58.059 -  67.632:   53        |
|      2:    19.768 -  29.341:  273   |   7:    67.632 -  77.204:   33        |
|      3:    29.341 -  38.914:  151   |   8:    77.204 -  86.777:    7        |
|      4:    38.914 -  48.486:  134   |   9:    86.777 -  96.350:    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)= 377         
Filter by distance & map next to the model:
   mapped sites are within: 0.282 - 5.963
   number of sites selected in [dist_min= 0.70, dist_max= 6.00]: 361 from: 377
   mapped sites are within: 0.701 - 5.963

peak=    7.944 closest distance to " O  BHOH Z  74 " =    0.711
peak=    6.917 closest distance to " O   HOH Z 390 " =    1.527
peak=    6.201 closest distance to " CB  VAL A 230 " =    1.592
peak=    6.074 closest distance to " O   HOH Z 103 " =    0.829
peak=    6.039 closest distance to " O   HOH Z 415 " =    1.503
peak=    5.739 closest distance to " OD2 ASP A 270 " =    1.017
peak=    5.715 closest distance to " ND2 ASN A 285 " =    1.090
peak=    5.667 closest distance to " O   HOH Z 130 " =    1.514
peak=    5.630 closest distance to " CG  LEU A   5 " =    1.531
peak=    5.616 closest distance to " O   HOH Z  81 " =    1.116
peak=    5.592 closest distance to " O   HOH Z 255 " =    1.355
peak=    5.570 closest distance to " OD2 ASP A 140 " =    0.951
peak=    5.547 closest distance to " O   HOH Z 138 " =    1.048
peak=    5.543 closest distance to " O   HOH Z  41 " =    1.576
peak=    5.499 closest distance to " CD1 LEU A   5 " =    1.043
peak=    5.494 closest distance to " CE2 PHE A  16 " =    1.248
peak=    5.454 closest distance to " O   HOH Z 117 " =    1.560
peak=    5.445 closest distance to " O   HOH Z 381 " =    0.971
peak=    5.377 closest distance to " O   HOH Z 268 " =    1.232
peak=    5.189 closest distance to " O   HOH Z 159 " =    1.265
peak=    5.129 closest distance to " NZ ALYS A 290 " =    1.369
peak=    5.107 closest distance to " OG  SER A 276 " =    1.046
peak=    5.042 closest distance to " O   HOH Z 424 " =    2.293
peak=    5.039 closest distance to " CD  ARG A 138 " =    1.124
peak=    4.972 closest distance to " O   HOH Z 226 " =    1.317
peak=    4.965 closest distance to " OD2 ASP A  50 " =    0.806
peak=    4.949 closest distance to " O   HOH Z 178 " =    1.305
peak=    4.902 closest distance to " O   HOH Z 375 " =    1.591
peak=    4.861 closest distance to " CB  ASN A 284 " =    0.878
peak=    4.850 closest distance to " O   HOH Z 120 " =    1.737
peak=    4.731 closest distance to " O   PRO A 198 " =    1.516
peak=    4.715 closest distance to " O   HOH Z 410 " =    2.090
peak=    4.695 closest distance to " CG  PRO A 198 " =    1.594
peak=    4.690 closest distance to " O   HOH Z   9 " =    2.116
peak=    4.683 closest distance to " O   HOH Z 401 " =    1.843
peak=    4.681 closest distance to " O   HOH Z 350 " =    1.871
peak=    4.659 closest distance to " O   HOH Z 374 " =    1.585
peak=    4.635 closest distance to " O   HOH Z  46 " =    1.819
peak=    4.633 closest distance to " NH1 ARG A 138 " =    1.058
peak=    4.585 closest distance to " CZ  PHE A  16 " =    0.958
peak=    4.563 closest distance to " O   HOH Z  63 " =    1.900
peak=    4.496 closest distance to " O   HOH Z 183 " =    1.603
peak=    4.491 closest distance to " CB  LYS A 290 " =    0.813
peak=    4.490 closest distance to " O   HOH Z  72 " =    0.912
peak=    4.476 closest distance to " O   HOH Z 116 " =    1.712
peak=    4.427 closest distance to " O   HOH Z 215 " =    1.830
peak=    4.377 closest distance to " CG2 VAL A 296 " =    1.216
peak=    4.343 closest distance to " CA  TRP A  92 " =    1.591
peak=    4.309 closest distance to " O   HOH Z 353 " =    2.151
peak=    4.292 closest distance to " ND2 ASN A  74 " =    0.790
peak=    4.283 closest distance to " O   HOH Z 133 " =    1.763
peak=    4.280 closest distance to " O   HOH Z 403 " =    1.759
peak=    4.275 closest distance to " O   HOH Z  61 " =    1.168
peak=    4.265 closest distance to " O   HOH Z 105 " =    1.724
peak=    4.264 closest distance to " NH1 ARG A  56 " =    1.538
peak=    4.255 closest distance to " O   HOH Z 147 " =    1.894
peak=    4.250 closest distance to " N   SER A  63 " =    0.903
peak=    4.249 closest distance to " CE AMET A  47 " =    1.235
peak=    4.239 closest distance to " CA  VAL A 230 " =    1.247
peak=    4.234 closest distance to " CD  LYS A  76 " =    1.771
peak=    4.230 closest distance to " O   ASN A 285 " =    0.766
peak=    4.230 closest distance to " CA  PRO A  54 " =    0.913
peak=    4.229 closest distance to " CG  ARG A 138 " =    1.260
peak=    4.224 closest distance to " CD2 LEU A 297 " =    0.982
peak=    4.221 closest distance to " O   HOH Z 417 " =    1.663
peak=    4.212 closest distance to " CD BLYS A 290 " =    1.018
peak=    4.212 closest distance to " O   HOH Z  97 " =    1.456
peak=    4.211 closest distance to " C   SER A  62 " =    0.837
peak=    4.192 closest distance to " CB  ASP A  50 " =    0.811
peak=    4.178 closest distance to " CB  PRO A  54 " =    1.250
peak=    4.163 closest distance to " CG2 ILE A 151 " =    0.997
peak=    4.147 closest distance to " ND2 ASN A 284 " =    0.908
peak=    4.137 closest distance to " O   HOH Z 359 " =    1.459
peak=    4.109 closest distance to " O   HOH Z 424 " =    1.822
peak=    4.092 closest distance to " CB  ASN A 148 " =    1.352
peak=    4.091 closest distance to " O   HOH Z 416 " =    1.889
peak=    4.076 closest distance to " O   HOH Z  30 " =    1.422
peak=    4.073 closest distance to " CB  ARG A 275 " =    1.334
peak=    4.070 closest distance to " O   HOH Z 111 " =    1.322
peak=    4.058 closest distance to " O   HOH Z 357 " =    1.802
peak=    4.040 closest distance to " CB  GLU A   2 " =    1.119
peak=    4.025 closest distance to " CD1AILE A 234 " =    1.189
peak=    4.018 closest distance to " N   GLY A 302 " =    1.090
peak=    4.000 closest distance to " CG1BVAL A 121 " =    2.032
peak=    3.982 closest distance to " O   HOH Z  37 " =    1.438
peak=    3.975 closest distance to " O   HOH Z 411 " =    3.233
peak=    3.971 closest distance to " CG1 VAL A 296 " =    1.057
peak=    3.968 closest distance to " OG BSER A 258 " =    1.054
peak=    3.962 closest distance to " CG2 VAL A 232 " =    1.272
peak=    3.957 closest distance to " NH2 ARG A  24 " =    0.900
peak=    3.954 closest distance to " CB  SER A 216 " =    1.110
peak=    3.950 closest distance to " O   HOH Z 102 " =    0.724
peak=    3.949 closest distance to " N   GLN A  73 " =    1.204
peak=    3.947 closest distance to " O   HOH Z 184 " =    2.358
peak=    3.947 closest distance to " O   HOH Z 395 " =    1.423
peak=    3.946 closest distance to " NH1BARG A 190 " =    1.639
peak=    3.917 closest distance to " CE3 TRP A 274 " =    1.587
peak=    3.901 closest distance to " NH2BARG A 102 " =    1.276
peak=    3.893 closest distance to " CB  ASN A  39 " =    0.701
peak=    3.889 closest distance to " O   HOH Z 279 " =    2.791
peak=    3.888 closest distance to " O   HOH Z 383 " =    1.178
peak=    3.885 closest distance to " N   SER A  26 " =    0.803
peak=    3.876 closest distance to " N   CYS A 260 " =    1.492
peak=    3.875 closest distance to " O   HOH Z 363 " =    1.541
peak=    3.874 closest distance to " O   HOH Z 233 " =    1.421
peak=    3.874 closest distance to " O   HOH Z  28 " =    1.793
peak=    3.864 closest distance to " O   HOH Z 316 " =    3.006
peak=    3.859 closest distance to " O   HOH Z  65 " =    1.956
peak=    3.846 closest distance to " O   HOH Z 387 " =    1.325
peak=    3.844 closest distance to " O   HOH Z 225 " =    1.709
peak=    3.838 closest distance to " O   HOH Z 331 " =    1.194
peak=    3.828 closest distance to " CA  GLY A  98 " =    0.961
peak=    3.826 closest distance to " CG2 THR A 279 " =    1.387
peak=    3.820 closest distance to " O   HOH Z 144 " =    1.674
peak=    3.813 closest distance to " CA  VAL A 153 " =    0.885
peak=    3.810 closest distance to " O   HOH Z 139 " =    1.868
peak=    3.808 closest distance to " OD1 ASN A 284 " =    0.971
peak=    3.808 closest distance to " CE  MET A  93 " =    1.503
peak=    3.806 closest distance to " CB  ILE A 234 " =    0.900
peak=    3.804 closest distance to " O   HOH Z  57 " =    1.854
peak=    3.776 closest distance to " CB  ARG A 138 " =    0.909
peak=    3.775 closest distance to " OD1 ASN A  45 " =    1.396
peak=    3.772 closest distance to " CG2 THR A 221 " =    1.321
peak=    3.765 closest distance to " CH2 TRP A 150 " =    0.988
peak=    3.755 closest distance to " CB  ASN A  60 " =    1.017
peak=    3.755 closest distance to " CA  ALA A 295 " =    1.068
peak=    3.742 closest distance to " NZ  LYS A 117 " =    1.538
peak=    3.741 closest distance to " NH2 ARG A 269 " =    0.971
peak=    3.741 closest distance to " CB  GLU A 236 " =    1.096
peak=    3.714 closest distance to " CB  MET A  47 " =    1.229
peak=    3.705 closest distance to " OG ASER A 134 " =    1.245
peak=    3.701 closest distance to " CB  SER A   3 " =    1.441
peak=    3.698 closest distance to " O   HOH Z   1 " =    2.045
peak=    3.693 closest distance to " O   HOH Z  70 " =    0.854
peak=    3.689 closest distance to " O   HOH Z 232 " =    2.045
peak=    3.687 closest distance to " NE2 GLN A  11 " =    1.130
peak=    3.687 closest distance to " O   HOH Z 137 " =    1.118
peak=    3.683 closest distance to " O   THR A  82 " =    1.279
peak=    3.678 closest distance to " OG  SER A  22 " =    1.184
peak=    3.676 closest distance to " N   ASN A 142 " =    1.237
peak=    3.675 closest distance to " OD1 ASP A 286 " =    0.929
peak=    3.673 closest distance to " O   HOH Z 303 " =    2.321
peak=    3.671 closest distance to " CH2 TRP A 123 " =    1.240
peak=    3.667 closest distance to " O   HOH Z 411 " =    1.560
peak=    3.654 closest distance to " N   VAL A  67 " =    1.038
peak=    3.653 closest distance to " O   HOH Z 418 " =    1.247
peak=    3.638 closest distance to " CZ3 TRP A 123 " =    1.768
peak=    3.633 closest distance to " N   GLY A 287 " =    0.852
peak=    3.625 closest distance to " CA  ARG A 102 " =    1.079
peak=    3.622 closest distance to " O   HOH Z  59 " =    1.796
peak=    3.613 closest distance to " O   HOH Z 245 " =    0.836
peak=    3.612 closest distance to " O   HOH Z 132 " =    1.484
peak=    3.610 closest distance to " N   PHE A 130 " =    1.305
peak=    3.595 closest distance to " CB  TYR A 169 " =    0.899
peak=    3.587 closest distance to " O   HOH Z 353 " =    2.292
peak=    3.580 closest distance to " OE1 GLN A  58 " =    5.583
peak=    3.575 closest distance to " O   HOH Z 298 " =    2.082
peak=    3.573 closest distance to " O   HOH Z 380 " =    1.964
peak=    3.558 closest distance to " CB  SER A  63 " =    1.530
peak=    3.551 closest distance to " CB  THR A 235 " =    1.580
peak=    3.547 closest distance to " O   HOH Z 362 " =    2.137
peak=    3.544 closest distance to " O   HOH Z 326 " =    1.934
peak=    3.542 closest distance to " CG2 THR A 294 " =    1.298
peak=    3.540 closest distance to " O   ARG A  14 " =    1.100
peak=    3.538 closest distance to " CG2 THR A 246 " =    1.717
peak=    3.537 closest distance to " O   THR A 220 " =    1.750
peak=    3.535 closest distance to " OE1 GLN A 240 " =    1.771
peak=    3.534 closest distance to " O   HOH Z 271 " =    1.779
peak=    3.532 closest distance to " CG2 ILE A 234 " =    1.452
peak=    3.529 closest distance to " CB  TRP A 179 " =    1.523
peak=    3.526 closest distance to " OG1 THR A 279 " =    2.148
peak=    3.519 closest distance to " CD  ARG A 139 " =    1.277
peak=    3.516 closest distance to " N   TYR A  15 " =    0.938
peak=    3.516 closest distance to " CB  PHE A 225 " =    1.698
peak=    3.514 closest distance to " O   HOH Z 186 " =    1.863
peak=    3.511 closest distance to " CG  LEU A 167 " =    1.349
peak=    3.507 closest distance to " O   HOH Z  43 " =    1.801
peak=    3.500 closest distance to " CA  ARG A  36 " =    1.541
peak=    3.497 closest distance to " CB  ALA A  10 " =    1.263
peak=    3.496 closest distance to " CG1 ILE A 120 " =    1.464
peak=    3.492 closest distance to " O   HOH Z  51 " =    1.976
peak=    3.491 closest distance to " O   ALA A 291 " =    1.687
peak=    3.491 closest distance to " O   HOH Z  78 " =    1.769
peak=    3.489 closest distance to " N   ARG A  66 " =    0.764
peak=    3.486 closest distance to " CG  LYS A 166 " =    1.518
peak=    3.485 closest distance to " CA  GLU A  46 " =    0.964
peak=    3.485 closest distance to " N   ARG A 275 " =    0.922
peak=    3.483 closest distance to " O   HOH Z 350 " =    1.067
peak=    3.481 closest distance to " O   ALA A  84 " =    1.239
peak=    3.478 closest distance to " CG1AVAL A  72 " =    1.384
peak=    3.470 closest distance to " N   ASN A 285 " =    0.729
peak=    3.466 closest distance to " CG2 THR A 251 " =    1.545
peak=    3.463 closest distance to " O   SER A 271 " =    1.093
peak=    3.462 closest distance to " CA  ASN A  69 " =    0.747
peak=    3.462 closest distance to " ND2 ASN A 249 " =    0.896
peak=    3.459 closest distance to " O   HOH Z 214 " =    1.744
peak=    3.456 closest distance to " O   HOH Z 216 " =    2.472
peak=    3.456 closest distance to " O   HOH Z 363 " =    2.458
peak=    3.455 closest distance to " O   ALA A  71 " =    1.034
peak=    3.451 closest distance to " C   PRO A  54 " =    0.934
peak=    3.450 closest distance to " O   HOH Z 174 " =    4.199
peak=    3.449 closest distance to " O   HOH Z  97 " =    1.372
peak=    3.444 closest distance to " CG  PRO A 243 " =    1.100
peak=    3.444 closest distance to " OE1 GLN A  94 " =    2.535
peak=    3.442 closest distance to " CA  THR A  42 " =    1.133
peak=    3.438 closest distance to " ND2 ASN A 249 " =    1.839
peak=    3.435 closest distance to " OG1 THR A 221 " =    1.536
peak=    3.434 closest distance to " N   GLN A 278 " =    0.884
peak=    3.433 closest distance to " CB  ASP A 140 " =    1.045
peak=    3.432 closest distance to " O   HOH Z 134 " =    1.740
peak=    3.430 closest distance to " CD  PRO A 243 " =    1.304
peak=    3.427 closest distance to " NE BARG A 275 " =    1.206
peak=    3.423 closest distance to " CA  VAL A 126 " =    1.217
peak=    3.421 closest distance to " O   HOH Z 197 " =    1.577
peak=    3.421 closest distance to " CB  ASP A 124 " =    0.965
peak=    3.419 closest distance to " O   HOH Z 361 " =    1.821
peak=    3.412 closest distance to " CB  THR A  52 " =    0.922
peak=    3.406 closest distance to " CA  SER A  12 " =    1.487
peak=    3.405 closest distance to " OD1 ASN A 249 " =    1.103
peak=    3.403 closest distance to " CB  ALA A 248 " =    1.612
peak=    3.402 closest distance to " O   HOH Z 373 " =    1.839
peak=    3.401 closest distance to " CA  GLY A 136 " =    1.117
peak=    3.400 closest distance to " CA  ALA A 299 " =    0.940
peak=    3.394 closest distance to " CB  LEU A 300 " =    0.983
peak=    3.393 closest distance to " CZ  PHE A 218 " =    1.261
peak=    3.392 closest distance to " O   HOH Z 369 " =    1.383
peak=    3.388 closest distance to " O   SER A 288 " =    0.906
peak=    3.382 closest distance to " N   ARG A  24 " =    0.895
peak=    3.381 closest distance to " N   SER A  97 " =    0.778
peak=    3.376 closest distance to " CG2 ILE A 106 " =    1.156
peak=    3.375 closest distance to " CB  MET A  40 " =    0.915
peak=    3.374 closest distance to " SD  MET A 185 " =    2.142
peak=    3.372 closest distance to " O   HOH Z 172 " =    1.742
peak=    3.372 closest distance to " O   HOH Z  69 " =    1.920
peak=    3.372 closest distance to " CB  THR A  31 " =    1.022
peak=    3.367 closest distance to " NE  ARG A 219 " =    1.445
peak=    3.365 closest distance to " O   HOH Z 244 " =    1.462
peak=    3.361 closest distance to " OE1 GLU A   2 " =    1.768
peak=    3.359 closest distance to " CA  ALA A  51 " =    0.827
peak=    3.358 closest distance to " O   HOH Z 207 " =    1.482
peak=    3.353 closest distance to " O   HOH Z 409 " =    3.839
peak=    3.350 closest distance to " O   MET A 105 " =    1.765
peak=    3.343 closest distance to " CB  PHE A 283 " =    1.066
peak=    3.339 closest distance to " CB  ALA A 256 " =    0.940
peak=    3.339 closest distance to " CE1 TYR A  15 " =    1.348
peak=    3.333 closest distance to " OG BSER A  12 " =    0.902
peak=    3.332 closest distance to " N   LEU A  25 " =    0.849
peak=    3.330 closest distance to " N   ALA A 165 " =    1.515
peak=    3.323 closest distance to " O   HOH Z 143 " =    1.533
peak=    3.320 closest distance to " CB  ALA A 242 " =    1.765
peak=    3.316 closest distance to " CB  GLU A 128 " =    1.095
peak=    3.312 closest distance to " NE AARG A 275 " =    1.803
peak=    3.310 closest distance to " NH1AARG A 145 " =    0.739
peak=    3.309 closest distance to " CZ  PHE A 225 " =    1.425
peak=    3.309 closest distance to " O   HOH Z 364 " =    1.692
peak=    3.303 closest distance to " O   HOH Z   9 " =    2.600
peak=    3.302 closest distance to " N   VAL A 296 " =    1.738
peak=    3.302 closest distance to " CA  ALA A 184 " =    2.143
peak=    3.300 closest distance to " O   HOH Z 368 " =    1.999
peak=    3.295 closest distance to " CZ3 TRP A  70 " =    0.823
peak=    3.293 closest distance to " O   HOH Z  27 " =    1.274
peak=    3.285 closest distance to " CA  SER A  87 " =    0.837
peak=    3.284 closest distance to " O   HOH Z 293 " =    1.189
peak=    3.282 closest distance to " CB  ASP A 132 " =    0.875
peak=    3.281 closest distance to " O   HOH Z 239 " =    1.508
peak=    3.279 closest distance to " N   GLY A 111 " =    1.412
peak=    3.278 closest distance to " CB  SER A  62 " =    1.380
peak=    3.275 closest distance to " CB  GLN A 103 " =    1.299
peak=    3.274 closest distance to " O   HOH Z  55 " =    2.267
peak=    3.272 closest distance to " CB  ASN A 252 " =    0.800
peak=    3.271 closest distance to " O   HOH Z 171 " =    1.936
peak=    3.262 closest distance to " O   HOH Z 400 " =    1.095
peak=    3.261 closest distance to " O   HOH Z 321 " =    1.391
peak=    3.261 closest distance to " CB  ALA A 104 " =    0.761
peak=    3.256 closest distance to " CB  SER A 206 " =    1.497
peak=    3.256 closest distance to " CA  GLU A 152 " =    1.213
peak=    3.254 closest distance to " O   HOH Z 315 " =    1.579
peak=    3.253 closest distance to " O   HOH Z 334 " =    1.913
peak=    3.252 closest distance to " O   ALA A 158 " =    1.371
peak=    3.249 closest distance to " OD2 ASP A 286 " =    2.870
peak=    3.249 closest distance to " CG1 VAL A 153 " =    1.119
peak=    3.249 closest distance to " O   HOH Z 368 " =    1.108
peak=    3.249 closest distance to " CD  GLU A  53 " =    1.257
peak=    3.243 closest distance to " CB  SER A 271 " =    1.170
peak=    3.237 closest distance to " CB  PRO A  90 " =    1.613
peak=    3.232 closest distance to " O   HOH Z 133 " =    2.280
peak=    3.228 closest distance to " CB  VAL A 202 " =    1.445
peak=    3.226 closest distance to " O   HOH Z 164 " =    2.311
peak=    3.222 closest distance to " O   HOH Z 153 " =    3.744
peak=    3.222 closest distance to " NZ  LYS A 119 " =    2.186
peak=    3.221 closest distance to " O   HOH Z 286 " =    1.650
peak=    3.221 closest distance to " CB  MET A  47 " =    1.474
peak=    3.217 closest distance to " CB  ASN A 285 " =    0.899
peak=    3.216 closest distance to " CB  LEU A   5 " =    1.258
peak=    3.213 closest distance to " CE1 PHE A 155 " =    1.336
peak=    3.210 closest distance to " O   HOH Z 409 " =    3.396
peak=    3.209 closest distance to " O   HOH Z 104 " =    1.875
peak=    3.209 closest distance to " O   HOH Z 434 " =    1.618
peak=    3.204 closest distance to " O   HOH Z  11 " =    0.943
peak=    3.203 closest distance to " CD2 PHE A 192 " =    1.530
peak=    3.201 closest distance to " O   HOH Z 424 " =    2.825
peak=    3.199 closest distance to " O   HOH Z  49 " =    1.130
peak=    3.196 closest distance to " O   HOH Z 261 " =    2.204
peak=    3.196 closest distance to " CE  LYS A 166 " =    2.167
peak=    3.195 closest distance to " CB  ALA A 233 " =    1.255
peak=    3.195 closest distance to " OG BSER A  99 " =    2.364
peak=    3.194 closest distance to " O   HOH Z 413 " =    1.384
peak=    3.192 closest distance to " CA  ILE A 234 " =    1.320
peak=    3.191 closest distance to " O   HOH Z  78 " =    2.321
peak=    3.190 closest distance to " CB  PRO A 243 " =    1.166
peak=    3.188 closest distance to " N   SER A  87 " =    1.408
peak=    3.188 closest distance to " NH2 ARG A 219 " =    1.727
peak=    3.186 closest distance to " OE2 GLU A 277 " =    2.252
peak=    3.186 closest distance to " CB  GLN A 183 " =    0.983
peak=    3.186 closest distance to " O   HOH Z 218 " =    3.988
peak=    3.184 closest distance to " CG1 ILE A 263 " =    1.293
peak=    3.181 closest distance to " O   PRO A  90 " =    1.566
peak=    3.175 closest distance to " O   HOH Z 124 " =    1.354
peak=    3.173 closest distance to " CG  PRO A 280 " =    1.041
peak=    3.171 closest distance to " CB  GLU A 152 " =    1.431
peak=    3.166 closest distance to " O   HOH Z 215 " =    2.138
peak=    3.165 closest distance to " CG  PRO A 213 " =    1.289
peak=    3.160 closest distance to " O   HOH Z 246 " =    1.713
peak=    3.159 closest distance to " NZ  LYS A 181 " =    1.137
peak=    3.157 closest distance to " O   HOH Z 354 " =    0.900
peak=    3.156 closest distance to " N   ASP A 238 " =    1.472
peak=    3.151 closest distance to " N   GLU A   2 " =    1.395
peak=    3.150 closest distance to " O   HOH Z  88 " =    3.580
peak=    3.148 closest distance to " O   HOH Z 119 " =    1.590
peak=    3.146 closest distance to " O   HOH Z 421 " =    1.819
peak=    3.146 closest distance to " O   GLY A 118 " =    3.106
peak=    3.145 closest distance to " OD1 ASN A 217 " =    1.586
peak=    3.141 closest distance to " O   HOH Z 170 " =    1.317
peak=    3.139 closest distance to " CD2 LEU A 101 " =    1.464
peak=    3.135 closest distance to " O   HOH Z 433 " =    2.692
peak=    3.131 closest distance to " O   GLY A 302 " =    2.001
peak=    3.131 closest distance to " N   ALA A 154 " =    0.905
peak=    3.125 closest distance to " O   HOH Z 317 " =    2.267
peak=    3.121 closest distance to " CB  SER A 276 " =    1.885
peak=    3.119 closest distance to " CB  ARG A 195 " =    1.953
peak=    3.115 closest distance to " O   HOH Z  48 " =    1.750
peak=    3.114 closest distance to " O   HOH Z 112 " =    1.409
peak=    3.113 closest distance to " CB  ALA A 180 " =    1.273
peak=    3.110 closest distance to " C   GLN A  11 " =    1.388
peak=    3.103 closest distance to " OG  SER A  26 " =    1.331
peak=    3.102 closest distance to " O   HOH Z 238 " =    1.892
peak=    3.100 closest distance to " CG2 ILE A  20 " =    1.564
peak=    3.096 closest distance to " O   ILE A  20 " =    1.928
peak=    3.093 closest distance to " O   HOH Z 284 " =    2.080
peak=    3.091 closest distance to " O   HOH Z 414 " =    2.197
peak=    3.084 closest distance to " CG1 ILE A 106 " =    0.859
peak=    3.080 closest distance to " O   HOH Z 115 " =    1.733
peak=    3.077 closest distance to " OD1 ASN A  69 " =    2.915
peak=    3.077 closest distance to " O   HOH Z 139 " =    5.963
peak=    3.077 closest distance to " CG2 THR A 264 " =    1.137
peak=    3.066 closest distance to " O   HOH Z 389 " =    2.507
peak=    3.065 closest distance to " CA  TYR A  30 " =    1.243
peak=    3.059 closest distance to " ND2 ASN A  60 " =    5.738
peak=    3.040 closest distance to " CA  GLN A 278 " =    1.080
peak=    3.037 closest distance to " O   HOH Z 189 " =    2.960
peak=    3.023 closest distance to " N   ASN A  74 " =    0.720

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

Number of peaks found at mFobs-DFmodel map (map cutoff=3.00 sigma)= 206         
Filter by distance & map next to the model:
   mapped sites are within: 0.361 - 5.564
   number of sites selected in [dist_min= 0.70, dist_max= 6.00]: 190 from: 206
   mapped sites are within: 0.722 - 5.564

peak=   -5.838 closest distance to " CD  ARG A 138 " =    0.975
peak=   -4.517 closest distance to " CZ  ARG A  24 " =    2.062
peak=   -4.431 closest distance to " O   HOH Z 102 " =    1.522
peak=   -4.383 closest distance to " OG  SER A  97 " =    2.210
peak=   -4.292 closest distance to " OD2 ASP A  50 " =    1.293
peak=   -4.279 closest distance to " CD  ARG A  14 " =    3.121
peak=   -4.213 closest distance to " CG1 VAL A 296 " =    1.015
peak=   -4.188 closest distance to " C   ASP A  50 " =    1.325
peak=   -4.185 closest distance to " O   SER A  62 " =    1.207
peak=   -4.169 closest distance to " CB  ASN A 285 " =    1.996
peak=   -4.162 closest distance to " CG2 VAL A 230 " =    0.864
peak=   -4.125 closest distance to " O   HOH Z  28 " =    0.726
peak=   -4.113 closest distance to " O   HOH Z 163 " =    1.080
peak=   -4.108 closest distance to " O   HOH Z 404 " =    0.952
peak=   -4.101 closest distance to " OG  SER A  63 " =    1.307
peak=   -4.030 closest distance to " O   HOH Z  52 " =    1.485
peak=   -3.990 closest distance to " CD2 TYR A 116 " =    2.130
peak=   -3.987 closest distance to " ND2 ASN A  74 " =    0.962
peak=   -3.974 closest distance to " O   HOH Z 290 " =    1.151
peak=   -3.955 closest distance to " O   HOH Z 416 " =    2.637
peak=   -3.942 closest distance to " CD2 TRP A 150 " =    1.433
peak=   -3.940 closest distance to " O   PRO A 198 " =    1.022
peak=   -3.936 closest distance to " O   ALA A 226 " =    1.353
peak=   -3.936 closest distance to " O   HOH Z  39 " =    1.037
peak=   -3.897 closest distance to " C   ARG A  66 " =    1.365
peak=   -3.890 closest distance to " N   ARG A 275 " =    1.238
peak=   -3.889 closest distance to " O   HOH Z 411 " =    4.795
peak=   -3.866 closest distance to " CD  LYS A 289 " =    2.254
peak=   -3.860 closest distance to " O   THR A 178 " =    1.033
peak=   -3.851 closest distance to " CB  PHE A 130 " =    1.206
peak=   -3.822 closest distance to " CD2 LEU A   5 " =    0.722
peak=   -3.815 closest distance to " C   ILE A 234 " =    0.788
peak=   -3.814 closest distance to " CG  PRO A 163 " =    2.482
peak=   -3.778 closest distance to " O   HOH Z 138 " =    1.055
peak=   -3.774 closest distance to " CD2 LEU A 237 " =    2.512
peak=   -3.768 closest distance to " CG  MET A 105 " =    0.931
peak=   -3.751 closest distance to " CG BLYS A 290 " =    0.772
peak=   -3.735 closest distance to " O   HOH Z 286 " =    1.292
peak=   -3.731 closest distance to " CA  ASN A 284 " =    1.030
peak=   -3.725 closest distance to " N   ASP A  65 " =    1.340
peak=   -3.718 closest distance to " ND2 ASN A 285 " =    1.325
peak=   -3.713 closest distance to " O   HOH Z 202 " =    2.335
peak=   -3.697 closest distance to " O   HOH Z 231 " =    0.799
peak=   -3.687 closest distance to " CA  GLY A 241 " =    2.064
peak=   -3.674 closest distance to " CG  GLU A 277 " =    3.724
peak=   -3.667 closest distance to " C   PHE A 155 " =    1.283
peak=   -3.661 closest distance to " O   GLY A  91 " =    1.649
peak=   -3.642 closest distance to " CB  ASP A  27 " =    2.745
peak=   -3.638 closest distance to " CD  GLU A 277 " =    1.078
peak=   -3.634 closest distance to " O   TRP A  70 " =    1.353
peak=   -3.624 closest distance to " C   PHE A  59 " =    0.948
peak=   -3.601 closest distance to " N   SER A 271 " =    1.431
peak=   -3.596 closest distance to " O   HOH Z 350 " =    2.161
peak=   -3.585 closest distance to " O   HOH Z 211 " =    0.927
peak=   -3.579 closest distance to " O   SER A 271 " =    2.219
peak=   -3.579 closest distance to " O   HOH Z  95 " =    1.212
peak=   -3.578 closest distance to " O   MET A  47 " =    2.497
peak=   -3.573 closest distance to " CA  MET A 113 " =    1.135
peak=   -3.558 closest distance to " C   ARG A 156 " =    1.208
peak=   -3.535 closest distance to " N   GLN A  77 " =    1.253
peak=   -3.532 closest distance to " O   SER A  32 " =    0.936
peak=   -3.531 closest distance to " C   ARG A  24 " =    1.148
peak=   -3.531 closest distance to " CA  SER A 288 " =    1.560
peak=   -3.528 closest distance to " O   HOH Z  61 " =    1.236
peak=   -3.520 closest distance to " CA  ARG A  56 " =    1.115
peak=   -3.517 closest distance to " C   SER A 276 " =    1.604
peak=   -3.506 closest distance to " CB  VAL A 296 " =    0.952
peak=   -3.506 closest distance to " O   HOH Z 390 " =    2.164
peak=   -3.504 closest distance to " O   HOH Z 381 " =    1.249
peak=   -3.501 closest distance to " CG  ASP A 140 " =    0.914
peak=   -3.496 closest distance to " CA  GLY A 133 " =    1.989
peak=   -3.491 closest distance to " CA  GLY A  23 " =    2.487
peak=   -3.479 closest distance to " O   HOH Z  86 " =    1.017
peak=   -3.478 closest distance to " CA  ARG A 102 " =    2.016
peak=   -3.475 closest distance to " O   HOH Z  51 " =    1.524
peak=   -3.474 closest distance to " OD1 ASN A 301 " =    1.548
peak=   -3.463 closest distance to " ND2BASN A 224 " =    1.366
peak=   -3.460 closest distance to " NE2 GLN A 122 " =    1.113
peak=   -3.452 closest distance to " O   HOH Z 186 " =    1.644
peak=   -3.446 closest distance to " O   HOH Z 385 " =    0.842
peak=   -3.446 closest distance to " CB  ASN A  39 " =    2.244
peak=   -3.434 closest distance to " CD1 ILE A  33 " =    2.039
peak=   -3.433 closest distance to " CG  HIS A 108 " =    0.994
peak=   -3.431 closest distance to " O   SER A   3 " =    2.227
peak=   -3.430 closest distance to " NE2 GLN A 194 " =    2.268
peak=   -3.423 closest distance to " O   HOH Z 372 " =    1.299
peak=   -3.413 closest distance to " O   ASN A 285 " =    1.382
peak=   -3.402 closest distance to " C   VAL A 265 " =    0.956
peak=   -3.395 closest distance to " O   HOH Z 112 " =    0.898
peak=   -3.393 closest distance to " CG  ASN A 284 " =    1.157
peak=   -3.382 closest distance to " OE1 GLU A  44 " =    1.523
peak=   -3.382 closest distance to " CZ  ARG A  66 " =    2.189
peak=   -3.380 closest distance to " O   HOH Z 389 " =    1.969
peak=   -3.377 closest distance to " OD1 ASP A  27 " =    1.891
peak=   -3.377 closest distance to " N   GLN A  55 " =    1.392
peak=   -3.364 closest distance to " CB  ALA A 291 " =    1.893
peak=   -3.362 closest distance to " CG  ARG A 219 " =    2.304
peak=   -3.361 closest distance to " O   HOH Z 433 " =    1.526
peak=   -3.360 closest distance to " OG ASER A 210 " =    2.329
peak=   -3.352 closest distance to " CG  TRP A 274 " =    1.035
peak=   -3.349 closest distance to " O   VAL A 296 " =    0.743
peak=   -3.348 closest distance to " OG  SER A  87 " =    1.595
peak=   -3.342 closest distance to " N   ALA A 242 " =    1.202
peak=   -3.339 closest distance to " O   ALA A  51 " =    1.385
peak=   -3.336 closest distance to " O   HOH Z  68 " =    2.758
peak=   -3.331 closest distance to " N   SER A  95 " =    1.967
peak=   -3.325 closest distance to " O   HOH Z 191 " =    3.455
peak=   -3.324 closest distance to " CB  ALA A 248 " =    2.108
peak=   -3.314 closest distance to " O   VAL A 153 " =    1.592
peak=   -3.312 closest distance to " O   SER A 273 " =    1.219
peak=   -3.305 closest distance to " O   HOH Z  92 " =    0.944
peak=   -3.304 closest distance to " CG  ASP A 270 " =    0.825
peak=   -3.296 closest distance to " C   ILE A 239 " =    1.958
peak=   -3.292 closest distance to " O   HOH Z  57 " =    1.205
peak=   -3.291 closest distance to " O   GLY A  80 " =    2.518
peak=   -3.290 closest distance to " CD  GLN A 223 " =    1.589
peak=   -3.287 closest distance to " C   SER A  63 " =    1.194
peak=   -3.286 closest distance to " CE2 TYR A  30 " =    2.593
peak=   -3.282 closest distance to " O   ASN A  39 " =    1.280
peak=   -3.281 closest distance to " CB  PHE A 218 " =    1.321
peak=   -3.281 closest distance to " O   HOH Z  72 " =    1.018
peak=   -3.273 closest distance to " N   PHE A 283 " =    1.787
peak=   -3.272 closest distance to " C   PRO A 213 " =    1.260
peak=   -3.271 closest distance to " O   HOH Z 380 " =    5.140
peak=   -3.268 closest distance to " O   ASP A  65 " =    1.321
peak=   -3.261 closest distance to " C   ASN A 301 " =    0.926
peak=   -3.253 closest distance to " OE1 GLN A  55 " =    2.241
peak=   -3.249 closest distance to " CG2 ILE A 120 " =    1.357
peak=   -3.247 closest distance to " O   HOH Z 300 " =    2.137
peak=   -3.239 closest distance to " C   LEU A 101 " =    1.185
peak=   -3.237 closest distance to " CA  SER A  26 " =    1.219
peak=   -3.234 closest distance to " OE1 GLN A 144 " =    1.083
peak=   -3.233 closest distance to " OE1 GLN A 278 " =    1.253
peak=   -3.232 closest distance to " CG2 THR A  18 " =    1.393
peak=   -3.230 closest distance to " O   HOH Z 313 " =    1.282
peak=   -3.229 closest distance to " CE2 TRP A  85 " =    1.122
peak=   -3.222 closest distance to " CB  ALA A 165 " =    2.198
peak=   -3.221 closest distance to " O   GLN A  11 " =    1.406
peak=   -3.220 closest distance to " O   HOH Z 181 " =    0.738
peak=   -3.219 closest distance to " OG  SER A   3 " =    1.566
peak=   -3.218 closest distance to " O   HOH Z 406 " =    1.465
peak=   -3.211 closest distance to " OG BSER A 134 " =    2.267
peak=   -3.206 closest distance to " O   ASP A 191 " =    1.881
peak=   -3.202 closest distance to " O   HOH Z 200 " =    4.266
peak=   -3.200 closest distance to " O   HIS A 115 " =    1.324
peak=   -3.198 closest distance to " O   HOH Z 415 " =    1.992
peak=   -3.195 closest distance to " CG  PRO A 213 " =    2.063
peak=   -3.194 closest distance to " O   ARG A 275 " =    1.048
peak=   -3.190 closest distance to " N   ASN A 285 " =    1.295
peak=   -3.189 closest distance to " O   HOH Z 336 " =    5.564
peak=   -3.185 closest distance to " CB  ALA A 161 " =    1.640
peak=   -3.180 closest distance to " C   ASP A 124 " =    1.386
peak=   -3.174 closest distance to " O   ASP A 286 " =    1.135
peak=   -3.173 closest distance to " O   HOH Z 111 " =    1.016
peak=   -3.170 closest distance to " O   HOH Z 434 " =    4.646
peak=   -3.168 closest distance to " O   HOH Z 197 " =    3.543
peak=   -3.162 closest distance to " CZ3 TRP A 123 " =    1.480
peak=   -3.159 closest distance to " N   HIS A 115 " =    1.966
peak=   -3.155 closest distance to " N   VAL A 125 " =    2.166
peak=   -3.154 closest distance to " CB  ASN A  45 " =    2.586
peak=   -3.153 closest distance to " CZ3 TRP A 266 " =    1.171
peak=   -3.151 closest distance to " O   HOH Z 386 " =    2.043
peak=   -3.151 closest distance to " O   HOH Z 208 " =    1.699
peak=   -3.144 closest distance to " O   HOH Z 207 " =    2.145
peak=   -3.143 closest distance to " O   TYR A  15 " =    2.986
peak=   -3.141 closest distance to " CG2AVAL A  72 " =    1.200
peak=   -3.124 closest distance to " C   ALA A 180 " =    1.109
peak=   -3.124 closest distance to " O   HOH Z 166 " =    2.179
peak=   -3.122 closest distance to " O   HOH Z 352 " =    0.871
peak=   -3.121 closest distance to " CZ  PHE A  16 " =    1.786
peak=   -3.116 closest distance to " OG  SER A  32 " =    1.391
peak=   -3.116 closest distance to " O   HOH Z 117 " =    1.096
peak=   -3.106 closest distance to " O   HOH Z 231 " =    1.882
peak=   -3.106 closest distance to " OG1 THR A  82 " =    1.780
peak=   -3.102 closest distance to " CB  THR A 221 " =    0.801
peak=   -3.100 closest distance to " CA  ARG A  66 " =    1.017
peak=   -3.094 closest distance to " N   LYS A 290 " =    0.952
peak=   -3.088 closest distance to " O   HOH Z 426 " =    2.081
peak=   -3.080 closest distance to " OE1 GLN A  88 " =    0.884
peak=   -3.076 closest distance to " OD1 ASN A 176 " =    1.135
peak=   -3.075 closest distance to " OG  SER A 206 " =    1.467
peak=   -3.069 closest distance to " CA  GLY A  98 " =    2.176
peak=   -3.060 closest distance to " O   HOH Z 124 " =    3.329
peak=   -3.060 closest distance to " O   SER A  26 " =    1.494
peak=   -3.058 closest distance to " O   ALA A  84 " =    1.282
peak=   -3.048 closest distance to " O   HOH Z 285 " =    2.916
peak=   -3.044 closest distance to " O   HOH Z  63 " =    2.408
peak=   -3.040 closest distance to " CG2 THR A  31 " =    2.388
peak=   -3.029 closest distance to " O  BHOH Z  74 " =    2.434
peak=   -3.027 closest distance to " CB  ASN A 284 " =    1.300

================= 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    :  0.5157 0.5127   6.313646e+00   6.305836e+00
   1_bss:  0.5071 0.5021   6.310965e+00   6.301572e+00
   1_xyz:  0.4558 0.4843   6.263863e+00   6.284033e+00
   1_adp:  0.4214 0.4818   6.235116e+00   6.285905e+00
   1_occ:  0.4211 0.4817   6.234672e+00   6.286124e+00
   2_bss:  0.4193 0.4795   6.234725e+00   6.285237e+00
   2_xyz:  0.3743 0.4545   6.155695e+00   6.250990e+00
   2_adp:  0.3621 0.4475   6.141172e+00   6.242517e+00
   2_occ:  0.3619 0.4470   6.140584e+00   6.242126e+00
   3_bss:  0.3623 0.4455   6.141243e+00   6.241541e+00
   3_xyz:  0.3243 0.4063   6.059031e+00   6.187818e+00
   3_adp:  0.3095 0.3996   6.035312e+00   6.177576e+00
   3_occ:  0.3092 0.3993   6.034617e+00   6.176908e+00
   4_bss:  0.3092 0.3988   6.034686e+00   6.175875e+00
   4_xyz:  0.2563 0.3416   5.883565e+00   6.063212e+00
   4_adp:  0.2247 0.3105   5.779867e+00   5.993419e+00
   4_occ:  0.2244 0.3102   5.778873e+00   5.992844e+00
   5_bss:  0.2243 0.3099   5.777759e+00   5.990903e+00
   5_xyz:  0.1858 0.2647   5.617983e+00   5.856017e+00
   5_adp:  0.1763 0.2371   5.544989e+00   5.763438e+00
   5_occ:  0.1760 0.2361   5.542224e+00   5.760175e+00
   5_bss:  0.1754 0.2353   5.541520e+00   5.759382e+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:  0.369  20.000   8.640   8.410   6.319   0.000   0.000   0.000
   1_xyz:  0.369  20.000   8.640   8.410   6.319   0.000   0.000   0.000
   1_adp:  0.369  20.000   8.640   8.410   6.319   0.000   0.000   0.000
   1_occ:  0.369  20.000   8.640   8.410   6.319   0.000   0.000   0.000
   2_bss:  0.343  37.247   4.933   4.534   3.313   0.000   0.000   0.000
   2_xyz:  0.343  37.247   4.933   4.534   3.313   0.000   0.000   0.000
   2_adp:  0.343  37.247   4.933   4.534   3.313   0.000   0.000   0.000
   2_occ:  0.343  37.247   4.933   4.534   3.313   0.000   0.000   0.000
   3_bss:  0.321  44.652   3.769   2.866   3.214   0.000   0.000   0.000
   3_xyz:  0.321  44.652   3.769   2.866   3.214   0.000   0.000   0.000
   3_adp:  0.321  44.652   3.769   2.866   3.214   0.000   0.000   0.000
   3_occ:  0.321  44.652   3.769   2.866   3.214   0.000   0.000   0.000
   4_bss:  0.330  44.653   2.631   1.718   2.537   0.000   0.000   0.000
   4_xyz:  0.330  44.653   2.631   1.718   2.537   0.000   0.000   0.000
   4_adp:  0.330  44.653   2.631   1.718   2.537   0.000   0.000   0.000
   4_occ:  0.330  44.653   2.631   1.718   2.537   0.000   0.000   0.000
   5_bss:  0.335  59.065   2.048   0.935   2.259   0.000   0.000   0.000
   5_xyz:  0.335  59.065   2.048   0.935   2.259   0.000   0.000   0.000
   5_adp:  0.335  59.065   2.048   0.935   2.259   0.000   0.000   0.000
   5_occ:  0.335  59.065   2.048   0.935   2.259   0.000   0.000   0.000
   5_bss:  0.325  47.732   0.258  -0.850   0.592  -0.000   0.000   0.000
------------------------------------------------------------------------
 stage     <pher>    fom   alpha         beta
   0    :  65.453 0.3237  0.3988    89194.986
   1_bss:  65.001 0.3290  0.5095    87767.328
   1_xyz:  60.958 0.3805  0.5772    78345.777
   1_adp:  61.709 0.3702  0.6217    79220.504
   1_occ:  61.720 0.3701  0.6209    79344.403
   2_bss:  61.391 0.3741  0.5589    78493.785
   2_xyz:  54.618 0.4609  0.6894    65346.028
   2_adp:  52.776 0.4847  0.7284    62633.660
   2_occ:  52.713 0.4854  0.7288    62480.726
   3_bss:  52.553 0.4874  0.7073    62114.752
   3_xyz:  45.806 0.5710  0.8180    48826.863
   3_adp:  44.619 0.5858  0.8434    47355.182
   3_occ:  44.586 0.5862  0.8432    47229.022
   4_bss:  44.501 0.5872  0.8161    47074.217
   4_xyz:  36.887 0.6778  0.9146    32573.976
   4_adp:  32.237 0.7321  0.9404    26057.550
   4_occ:  32.192 0.7326  0.9407    25976.660
   5_bss:  32.101 0.7335  0.9236    25847.401
   5_xyz:  27.090 0.7873  0.9672    18166.351
   5_adp:  23.513 0.8263  1.0127    14836.895
   5_occ:  23.416 0.8271  1.0126    14683.994
   5_bss:  23.352 0.8277  0.9729    14597.073
------------------------------------------------------------------------
 stage       angl   bond   chir   dihe   plan   repu  geom_target
   0    :  24.226  0.414  2.119 33.790  0.145  4.088   5.3523e+01
   1_bss:  24.226  0.414  2.119 33.790  0.145  4.088   5.3523e+01
   1_xyz:   1.736  0.014  0.109 18.579  0.007  4.106   1.5425e-01
   1_adp:   1.736  0.014  0.109 18.579  0.007  4.106   1.5425e-01
   1_occ:   1.736  0.014  0.109 18.579  0.007  4.106   1.5425e-01
   2_bss:   1.736  0.014  0.109 18.579  0.007  4.106   1.5425e-01
   2_xyz:   1.249  0.009  0.088 17.164  0.005  4.101   1.1010e-01
   2_adp:   1.249  0.009  0.088 17.164  0.005  4.101   1.1010e-01
   2_occ:   1.249  0.009  0.088 17.164  0.005  4.101   1.1010e-01
   3_bss:   1.249  0.009  0.088 17.164  0.005  4.101   1.1010e-01
   3_xyz:   1.128  0.008  0.080 16.194  0.005  4.116   8.2594e-02
   3_adp:   1.128  0.008  0.080 16.194  0.005  4.116   8.2594e-02
   3_occ:   1.128  0.008  0.080 16.194  0.005  4.116   8.2594e-02
   4_bss:   1.128  0.008  0.080 16.194  0.005  4.116   8.2594e-02
   4_xyz:   1.312  0.011  0.092 16.397  0.005  4.109   1.0700e-01
   4_adp:   1.312  0.011  0.092 16.397  0.005  4.109   1.0700e-01
   4_occ:   1.312  0.011  0.092 16.397  0.005  4.109   1.0700e-01
   5_bss:   1.312  0.011  0.092 16.397  0.005  4.109   1.0700e-01
   5_xyz:   1.103  0.008  0.079 15.545  0.004  4.105   7.6534e-02
   5_adp:   1.103  0.008  0.079 15.545  0.004  4.105   7.6534e-02
   5_occ:   1.103  0.008  0.079 15.545  0.004  4.105   7.6534e-02
   5_bss:   1.103  0.008  0.079 15.545  0.004  4.105   7.6534e-02
------------------------------------------------------------------------
                      Maximal deviations:
 stage       angl   bond   chir   dihe   plan   repu       |grad|
   0    :  74.492  1.400  6.404144.062  0.405  1.196   6.9351e+00
   1_bss:  74.492  1.400  6.404144.062  0.405  1.196   6.9351e+00
   1_xyz:  13.158  0.174  0.435 89.020  0.046  2.125   1.0301e-01
   1_adp:  13.158  0.174  0.435 89.020  0.046  2.125   1.0301e-01
   1_occ:  13.158  0.174  0.435 89.020  0.046  2.125   1.0301e-01
   2_bss:  13.158  0.174  0.435 89.020  0.046  2.125   1.0301e-01
   2_xyz:   6.911  0.082  0.318 82.545  0.037  2.004   8.8589e-02
   2_adp:   6.911  0.082  0.318 82.545  0.037  2.004   8.8589e-02
   2_occ:   6.911  0.082  0.318 82.545  0.037  2.004   8.8589e-02
   3_bss:   6.911  0.082  0.318 82.545  0.037  2.004   8.8589e-02
   3_xyz:   7.889  0.066  0.315 75.842  0.062  2.120   6.7904e-02
   3_adp:   7.889  0.066  0.315 75.842  0.062  2.120   6.7904e-02
   3_occ:   7.889  0.066  0.315 75.842  0.062  2.120   6.7904e-02
   4_bss:   7.889  0.066  0.315 75.842  0.062  2.120   6.7904e-02
   4_xyz:   9.192  0.056  0.407 79.945  0.032  2.138   9.7296e-02
   4_adp:   9.192  0.056  0.407 79.945  0.032  2.138   9.7296e-02
   4_occ:   9.192  0.056  0.407 79.945  0.032  2.138   9.7296e-02
   5_bss:   9.192  0.056  0.407 79.945  0.032  2.138   9.7296e-02
   5_xyz:   8.494  0.060  0.330 77.625  0.032  2.235   5.8509e-02
   5_adp:   8.494  0.060  0.330 77.625  0.032  2.235   5.8509e-02
   5_occ:   8.494  0.060  0.330 77.625  0.032  2.235   5.8509e-02
   5_bss:   8.494  0.060  0.330 77.625  0.032  2.235   5.8509e-02
------------------------------------------------------------------------
           |-----overall-----|---macromolecule----|------solvent-------|
  stage    b_max  b_min  b_ave  b_max  b_min  b_ave  b_max  b_min  b_ave
   0    :  10.00  10.00  10.00  10.00  10.00  10.00  10.00  10.00  10.00
   1_bss:  19.99   0.01   9.86  19.98   0.01   9.82  19.99   0.06  10.10
   1_xyz:  19.99   0.01   9.86  19.98   0.01   9.82  19.99   0.06  10.10
   1_adp:  80.96   0.00  16.66  78.94   0.00  15.55  80.96   0.00  22.69
   1_occ:  80.96   0.00  16.66  78.94   0.00  15.55  80.96   0.00  22.69
   2_bss:  80.96   0.00  16.66  78.94   0.00  15.55  80.96   0.00  22.69
   2_xyz:  80.96   0.00  16.66  78.94   0.00  15.55  80.96   0.00  22.69
   2_adp:  81.34   0.00  16.41  78.27   0.00  15.10  81.34   0.00  23.55
   2_occ:  81.34   0.00  16.41  78.27   0.00  15.10  81.34   0.00  23.55
   3_bss:  81.34   0.00  16.41  78.27   0.00  15.10  81.34   0.00  23.55
   3_xyz:  81.34   0.00  16.41  78.27   0.00  15.10  81.34   0.00  23.55
   3_adp:  92.32   0.00  16.61  92.32   0.00  14.83  79.98   0.00  26.32
   3_occ:  92.32   0.00  16.61  92.32   0.00  14.83  79.98   0.00  26.32
   4_bss:  92.32   0.00  16.61  92.32   0.00  14.83  79.98   0.00  26.32
   4_xyz:  92.32   0.00  16.61  92.32   0.00  14.83  79.98   0.00  26.32
   4_adp:  99.90   0.00  17.55  94.24   0.00  13.25  99.90   0.00  40.96
   4_occ:  99.90   0.00  17.55  94.24   0.00  13.25  99.90   0.00  40.96
   5_bss:  99.90   0.00  17.55  94.24   0.00  13.25  99.90   0.00  40.96
   5_xyz:  99.90   0.00  17.55  94.24   0.00  13.25  99.90   0.00  40.96
   5_adp:  95.73   0.00  16.92  92.80   0.00  12.68  95.73   2.52  40.02
   5_occ:  95.73   0.00  16.92  92.80   0.00  12.68  95.73   2.52  40.02
   5_bss:  96.35   0.62  17.55  93.42   0.62  13.31  96.35   3.14  40.64
------------------------------------------------------------------------
 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:    1.272    0.017    0.412
   1_adp:    1.272    0.017    0.412
   1_occ:    1.272    0.017    0.412
   2_bss:    1.272    0.017    0.412
   2_xyz:    1.611    0.006    0.580
   2_adp:    1.611    0.006    0.580
   2_occ:    1.611    0.006    0.580
   3_bss:    1.611    0.006    0.580
   3_xyz:    1.689    0.023    0.672
   3_adp:    1.689    0.023    0.672
   3_occ:    1.689    0.023    0.672
   4_bss:    1.689    0.023    0.672
   4_xyz:    2.177    0.061    0.843
   4_adp:    2.177    0.061    0.843
   4_occ:    2.177    0.061    0.843
   5_bss:    2.177    0.061    0.843
   5_xyz:    2.363    0.077    0.929
   5_adp:    2.363    0.077    0.929
   5_occ:    2.363    0.077    0.929
   5_bss:    2.363    0.077    0.929
------------------------------------------------------------------------

CPU time actual refinement: 354.82


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

Writing refined structure to PDB file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/trial/run_1214/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_1214/model_refine_001_2mFobs-DFmodel.map
Writing mFobs-DFmodel XPLOR map to file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/trial/run_1214/model_refine_001_mFobs-DFmodel.map
Writing map coefficients to MTZ file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/trial/run_1214/model_refine_001_map_coeffs.mtz

Writing default parameters for subsequent refinement:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/trial/run_1214/model_refine_002.def


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

Pure refinement (no I/O, processing, etc)= 354.68 
  Macro-tasks:
    bulk solvent and scale       = 43.23  
    individual site refinement   = 153.93 
    weights calculation          = 32.49  
    collect and process          = 6.20   
    model show statistics        = 0.10   
    TOTAL for macro-tasks        = 235.95 
  Micro-tasks:
    mask                            = 2.88   
    f_calc                          = 114.71 
    alpha_beta                      = 8.62   
    target                          = 1.17   
    gradients_wrt_atomic_parameters = 120.27 
    fmodel                         = 7.29   
    r_factors                      = 0.27   
    phase_errors                   = 9.91   
    foms                           = 0.26   
    TOTAL for micro-tasks          = 265.38 
NUMBER OF MASK CALCS=  6
Time per interpreted Python bytecode instruction: 5.021 micro seconds
Total CPU time: 6.13 minutes
from_scatterers_fft:    611 calls, 114.20 s
gradients_fft:          555 calls, 109.20 s

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

# Date 2008-01-16 Time 03:28:08 PST -0800 (1200482888.97 s)
Start R-work = 0.5157, R-free = 0.5127 (no bulk solvent and anisotropic scale)
Final R-work = 0.1904, R-free = 0.2508 (no bulk solvent and anisotropic scale)

Start R-work = 0.5071, R-free = 0.5021
Final R-work = 0.1754, R-free = 0.2353