# Date 2008-01-16 Time 06:48:40 PST -0800 (1200494920.26 s)
#phil __OFF__

Command line arguments: "../1298.param" "main.number_of_macro_cycles=5" "--overwrite"

HOST = thunderbird.lbl.gov
HOSTTYPE = x86_64-linux
USER = phzwart
PID = 16077
JOB_ID = 5159
SGE_ARCH = lx24-amd64
SGE_TASK_FIRST = 1
SGE_TASK_LAST = 1330
SGE_TASK_ID = 1298

-------------------------------------------------------------------------------
  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.main.number_of_macro_cycles = 5

Working crystal symmetry after inspecting all inputs:
  Unit cell: (72.0062, 47.6339, 84.2302, 90, 90, 90)
  Space group: P 21 21 21 (No. 19)

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


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

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

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

Miller array info: /net/cci-filer1/vol1/tmp/phzwart/tassos/trial/1e0w.cns:FOBS,SIGMA
Observation type: xray.amplitude
Type of data: double, size=19589
Type of sigmas: double, size=19589
Number of Miller indices: 19589
Anomalous flag: False
Unit cell: (72.0062, 47.6339, 84.2302, 90, 90, 90)
Space group: P 21 21 21 (No. 19)
Systematic absences: 0
Centric reflections: 2427
Resolution range: 15.1542 1.95153
Completeness in resolution range: 0.904762
Completeness with d_max=infinity: 0.902137

Number of F-obs in resolution range:                   19589
Number of F-obs <= 0:                                  0
Refinement resolution range: d_max =  15.1542
                             d_min =   1.9515

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, 47.6339, 84.2302, 90, 90, 90)
Space group: P 21 21 21 (No. 19)
Systematic absences: 0
Centric reflections: 2427
Resolution range: 15.1542 1.95153
Completeness in resolution range: 0.904762
Completeness with d_max=infinity: 0.902137

Test (R-free flags) flag value: 1

Number of work/free reflections by resolution:
                                         work  free  %free
  bin  1: 15.1547 -  4.1779 [2278/2307]  2052   226   9.9%
  bin  2:  4.1779 -  3.3276 [2165/2188]  1947   218  10.1%
  bin  3:  3.3276 -  2.9104 [2154/2179]  1932   222  10.3%
  bin  4:  2.9104 -  2.6458 [2147/2164]  1940   207   9.6%
  bin  5:  2.6458 -  2.4570 [2108/2151]  1903   205   9.7%
  bin  6:  2.4570 -  2.3127 [2125/2153]  1902   223  10.5%
  bin  7:  2.3127 -  2.1972 [2110/2146]  1902   208   9.9%
  bin  8:  2.1972 -  2.1019 [2081/2123]  1875   206   9.9%
  bin  9:  2.1019 -  2.0211 [1903/2120]  1709   194  10.2%
  bin 10:  2.0211 -  1.9515 [ 518/2120]   468    50   9.7%
                                overall 17630  1959  10.0%
Writing MTZ file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/noshake/run_1298/model_refine_data.mtz


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

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

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

  Number of disulfides: simple=3, symmetry=0
    Simple disulfide: " SG  CYS A 168 " - " SG ACYS A 201 " distance=2.08
    Simple disulfide: " SG  CYS A 168 " - " SG BCYS A 201 " distance=1.98
    Simple disulfide: " SG  CYS A 254 " - " SG  CYS A 260 " distance=2.05
  Time building geometry restraints manager: 0.15 seconds
  Histogram of bond lengths:
        1.21 -     1.38: 943
        1.38 -     1.56: 1465
        1.56 -     1.73: 7
        1.73 -     1.90: 21
        1.90 -     2.08: 3
  Bond restraints sorted by residual:
             atom i - atom j            ideal  model  delta   weight residual
  " SG  CYS A 168 " - " SG BCYS A 201 " 2.031  1.983  0.048 2.50e+03 5.87e+00
  " C   GLN A  88 " - " N   GLN A  89 " 1.329  1.360 -0.031 5.10e+03 4.97e+00
  " SG  CYS A 168 " - " SG ACYS A 201 " 2.031  2.075 -0.044 2.50e+03 4.89e+00
  " CB  CYS A 201 " - " SG ACYS A 201 " 1.808  1.738  0.070 9.18e+02 4.46e+00
  " C   PRO A 198 " - " N   ILE A 199 " 1.329  1.301  0.028 5.10e+03 4.10e+00
  ... (remaining 2434 not shown)
  Histogram of nonbonded interaction distances:
        1.53 -     2.21: 28
        2.21 -     2.88: 1276
        2.88 -     3.55: 4439
        3.55 -     4.23: 9197
        4.23 -     4.90: 13310
  Nonbonded interactions sorted by model distance:
             atom i - atom j             model   vdw sym.op. j
  " ND2 ASN A 215 " - " O   HOH Z 203 "  1.532 3.120 -x+1/2,-y+1,z-1/2
  " O   HOH Z 100 " - " O   HOH Z 352 "  1.614 3.040 -x+1/2,-y+1,z+1/2
  " O   HOH Z 113 " - " O   HOH Z 350 "  1.652 3.040 -x+1/2,-y+1,z+1/2
  " O   HOH Z 207 " - " O   HOH Z 341 "  1.671 3.040 -x+1/2,-y+1,z+1/2
  " O   HOH Z 209 " - " O   HOH Z 301 "  1.693 3.040 -x+1/2,-y+1,z+1/2
  ... (remaining 28245 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 =====================


==================== 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/noshake/run_1298/model_refine_001.eff

Writing geometry restraints to file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/noshake/run_1298/model_refine_001.geo

CPU time processing inputs: 9.13


============================ 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 47.63395 84.23025 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
  }
}
#phil __OFF__


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


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


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

|--(resolution: 1.95 - 15.15 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.4827   r_free= 0.4797   ksol= 0.00   Bsol= 0.00   scale= 0.878    |
|                                                                             |
| 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:   0.91 A                  |
| x-ray target function (ml) for work reflections: 6.288598                   |
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
| Bin     Resolution   Compl.  No. Refl.    R-factors          Targets        |
|number     range              work test   work   test        work        test|
|  1: 15.1547 -  4.6607 0.99   1479  167 0.3741 0.3810      6.5618       6.565|
|  2:  4.6607 -  3.7173 0.99   1415  156 0.4140 0.4004      6.8288      6.8523|
|  3:  3.7173 -  3.2527 0.99   1396  149 0.4636 0.4347      6.6731      6.6588|
|  4:  3.2527 -  2.9577 0.99   1381  160 0.4766 0.4598      6.4999      6.5038|
|  5:  2.9577 -  2.7471 0.99   1377  150 0.5059 0.5072       6.357      6.3442|
|  6:  2.7471 -  2.5860 0.99   1360  159 0.5249 0.5279      6.2805      6.2119|
|  7:  2.5860 -  2.4570 0.98   1366  137 0.5282 0.4967      6.2335      6.2035|
|  8:  2.4570 -  2.3505 0.98   1354  154 0.5280 0.5320       6.143      6.2005|
|  9:  2.3505 -  2.2603 0.99   1358  152 0.5452 0.5169      6.1503      6.1276|
| 10:  2.2603 -  2.1825 0.98   1347  158 0.5426 0.5733       6.084      6.1178|
| 11:  2.1825 -  2.1145 0.97   1335  145 0.5330 0.6148      6.0134      5.9839|
| 12:  2.1145 -  2.0542 0.98   1337  143 0.5292 0.5588      5.9324      5.9558|
| 13:  2.0542 -  2.0002 0.66    901  108 0.5417 0.4841      5.8601      5.8348|
| 14:  2.0002 -  1.9515 0.16    224   21 0.5868 0.4063      5.7766      5.8188|
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
|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: 15.1547 -  4.6607  1479   167  0.71  33.27   0.82     0.74      67245.28|
|  2:  4.6607 -  3.7173  1415   156  0.69  35.77   0.90     0.79     106177.30|
|  3:  3.7173 -  3.2527  1396   149  0.56  46.91   0.88     0.73     118870.98|
|  4:  3.2527 -  2.9577  1381   160  0.44  56.44   0.89     0.63     112202.36|
|  5:  2.9577 -  2.7471  1377   150  0.36  63.08   0.86     0.52      89928.67|
|  6:  2.7471 -  2.5860  1360   159  0.34  64.78   0.88     0.50      77456.09|
|  7:  2.5860 -  2.4570  1366   137  0.33  65.22   0.88     0.46      65669.56|
|  8:  2.4570 -  2.3505  1354   154  0.29  68.28   0.88     0.44      63836.01|
|  9:  2.3505 -  2.2603  1358   152  0.23  73.10   0.91     0.34      60710.67|
| 10:  2.2603 -  2.1825  1347   158  0.16  78.13   0.91     0.25      61039.31|
| 11:  2.1825 -  2.1145  1335   145  0.07  84.51   0.91     0.12      57461.66|
| 12:  2.1145 -  2.0542  1337   143  0.06  85.33   0.90     0.11      52472.33|
| 13:  2.0542 -  2.0002   901   108  0.12  81.34   0.90     0.19      42961.02|
| 14:  2.0002 -  1.9515   224    21  0.24  72.21   0.85     0.40      32742.88|
|alpha:            min =        0.11 max =            0.79 mean =         0.46|
|beta:             min =    32742.88 max =       118870.98 mean =     75636.80|
|figures of merit: min =        0.00 max =            1.00 mean =         0.35|
|phase err.(work): min =        0.00 max =           90.00 mean =        63.56|
|phase err.(test): min =        0.00 max =           89.93 mean =        63.51|
|-----------------------------------------------------------------------------|

============================== 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 = 20.675898             wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 90.157   (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 3.990369              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 89.898   (deg)                 |
|-----------------------------------------------------------------------------|


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

|-Geometry statistics: start--------------------------------------------------|
|            Histogram of deviations from ideal values for                    |
| Bonds                | Angles                   |  Nonbonded contacts       |
| 0.000 - 0.007:  1367 |   0.001 -   0.989:  1519 |  1.532 -  1.869:       10 |
| 0.007 - 0.014:   729 |   0.989 -   1.976:   994 |  1.869 -  2.205:       18 |
| 0.014 - 0.021:   262 |   1.976 -   2.963:   470 |  2.205 -  2.542:       39 |
| 0.021 - 0.028:    63 |   2.963 -   3.950:   196 |  2.542 -  2.879:     1237 |
| 0.028 - 0.035:    15 |   3.950 -   4.938:    66 |  2.879 -  3.216:     1901 |
| 0.035 - 0.042:     0 |   4.938 -   5.925:    29 |  3.216 -  3.553:     2538 |
| 0.042 - 0.049:     2 |   5.925 -   6.912:    16 |  3.553 -  3.890:     4652 |
| 0.049 - 0.056:     0 |   6.912 -   7.899:     2 |  3.890 -  4.226:     4545 |
| 0.056 - 0.063:     0 |   7.899 -   8.887:     3 |  4.226 -  4.563:     6063 |
| 0.063 - 0.070:     1 |   8.887 -   9.874:     4 |  4.563 -  4.900:     7247 |
|-----------------------------------------------------------------------------|
|-Geometry statistics: start--------------------------------------------------|
|      Type |    Count |    Deviation from ideal |     Targets | Target (sum) |
|           |          |    rmsd      max    min |             |              |
|      bond |     2439 |   0.010    0.070  0.000 |       0.254 |              |
|     angle |     3299 |   1.822    9.874  0.001 |       1.000 |              |
| chirality |      348 |   0.101    0.314  0.000 |       0.257 |        0.193 |
| planarity |      436 |   0.009    0.055  0.000 |       0.973 |              |
|  dihedral |      870 |  15.968   85.889  0.013 |       1.071 |              |
| nonbonded |     2439 |   4.110    4.900  1.532 |       0.629 |              |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 12.016)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      5.09    63.06   16.02    None  None   None       |
|    all(noH): 2823   0      5.09    63.06   16.02    None  None   None       |
|    Sol.    : 438    0      6.19    63.06   36.87    None  None   None       |
|    Mac.    : 2385   0      5.09    49.51   12.19    None  None   None       |
|    Hyd.    : 0      0      None    None    None     None  None   None       |
|    - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -      |
|       Distribution of isotropic (or equivalent) ADP for non-H atoms:        |
|    Bin#      value range     #atoms | Bin#      value range     #atoms      |
|      0:     5.090 -  10.887: 1254   |   5:    34.075 -  39.872:   81        |
|      1:    10.887 -  16.684:  844   |   6:    39.872 -  45.669:   78        |
|      2:    16.684 -  22.481:  225   |   7:    45.669 -  51.466:   64        |
|      3:    22.481 -  28.278:  122   |   8:    51.466 -  57.263:   37        |
|      4:    28.278 -  34.075:   94   |   9:    57.263 -  63.060:   24        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|

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

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

|--(resolution: 1.95 - 15.15 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.4827   r_free= 0.4797   ksol= 0.00   Bsol= 0.00   scale= 0.878    |
|                                                                             |
| 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:   0.91 A                  |
| x-ray target function (ml) for work reflections: 6.288598                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.95 - 15.15 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.4766   r_free= 0.4743   ksol= 0.29   Bsol= 31.02   scale= 0.923   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (0.89,0.89,1.00,0.00,0.00,0.00); trace/3= 0.93                              |
|                                                                             |
| maximum likelihood estimate for coordinate error:   1.04 A                  |
| x-ray target function (ml) for work reflections: 5.837466                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 15.637377             wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 90.325   (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 1.648588              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 89.443   (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.4766      final r-factor (work) = 0.3664          |
| start r-factor (free) = 0.4743      final r-factor (free) = 0.4093          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 49.3147 = 15.64 * 0.50 * 6.2825 + 1.00 * 0.1935                             |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 44.9401 = 15.64 * 0.50 * 5.7273 + 1.00 * 0.1603                             |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 27     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.3664      final r-factor (work) = 0.3321          |
| start r-factor (free) = 0.4093      final r-factor (free) = 0.4148          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 9.4483 = 1.65 * 1.00 * 5.7273 + 1.00 * 0.0064                               |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 10.0243 = 1.65 * 1.00 * 6.0671 + 1.00 * 0.0221                              |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 28     |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 12.016)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.00    104.55  19.40    None  None   None       |
|    all(noH): 2823   0      0.00    104.55  19.40    None  None   None       |
|    Sol.    : 438    0      0.00    104.55  40.62    None  None   None       |
|    Mac.    : 2385   0      0.00    98.70   15.50    None  None   None       |
|    Hyd.    : 0      0      None    None    None     None  None   None       |
|    - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -      |
|       Distribution of isotropic (or equivalent) ADP for non-H atoms:        |
|    Bin#      value range     #atoms | Bin#      value range     #atoms      |
|      0:     0.000 -  10.455:  967   |   5:    52.273 -  62.728:   90        |
|      1:    10.455 -  20.909:  886   |   6:    62.728 -  73.182:   42        |
|      2:    20.909 -  31.364:  445   |   7:    73.182 -  83.637:   21        |
|      3:    31.364 -  41.819:  241   |   8:    83.637 -  94.092:    5        |
|      4:    41.819 -  52.273:  124   |   9:    94.092 - 104.546:    2        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.3321 r_free = 0.4148             target_work(ml) = 6.072         |
| occupancies: max = 1.00  min = 0.30   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.3319 r_free = 0.4151             target_work(ml) = 6.072         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        3 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.95 - 15.15 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.3319   r_free= 0.4151   ksol= 0.29   Bsol= 31.02   scale= 1.014   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (0.89,0.89,1.00,0.00,0.00,0.00); trace/3= 0.93                              |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.59 A                  |
| x-ray target function (ml) for work reflections: 6.071558                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.95 - 15.15 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.3308   r_free= 0.4131   ksol= 0.34   Bsol= 72.89   scale= 1.004   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (0.19,0.54,0.38,0.00,0.00,0.00); trace/3= 0.37                              |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.59 A                  |
| x-ray target function (ml) for work reflections: 6.070584                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 13.022625             wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 98.332   (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 1.126165              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 150.624  (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.3308      final r-factor (work) = 0.2503          |
| start r-factor (free) = 0.4131      final r-factor (free) = 0.3206          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 39.6646 = 13.02 * 0.50 * 6.0669 + 1.00 * 0.1610                             |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 39.1129 = 13.02 * 0.50 * 5.9908 + 1.00 * 0.1052                             |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 28     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.2503      final r-factor (work) = 0.2272          |
| start r-factor (free) = 0.3206      final r-factor (free) = 0.2937          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 6.7688 = 1.13 * 1.00 * 5.9908 + 1.00 * 0.0222                               |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 6.5636 = 1.13 * 1.00 * 5.8140 + 1.00 * 0.0160                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 28     |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 12.016)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.00    103.15  19.26    None  None   None       |
|    all(noH): 2823   0      0.00    103.15  19.26    None  None   None       |
|    Sol.    : 438    0      4.65    103.15  45.42    None  None   None       |
|    Mac.    : 2385   0      0.00    99.71   14.46    None  None   None       |
|    Hyd.    : 0      0      None    None    None     None  None   None       |
|    - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -      |
|       Distribution of isotropic (or equivalent) ADP for non-H atoms:        |
|    Bin#      value range     #atoms | Bin#      value range     #atoms      |
|      0:     0.000 -  10.315: 1034   |   5:    51.576 -  61.891:   93        |
|      1:    10.315 -  20.631:  960   |   6:    61.891 -  72.207:   60        |
|      2:    20.631 -  30.946:  323   |   7:    72.207 -  82.522:   35        |
|      3:    30.946 -  41.261:  162   |   8:    82.522 -  92.837:    9        |
|      4:    41.261 -  51.576:  142   |   9:    92.837 - 103.152:    5        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.2272 r_free = 0.2937             target_work(ml) = 5.769         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        3 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.2271 r_free = 0.2936             target_work(ml) = 5.768         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        5 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.95 - 15.15 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.2271   r_free= 0.2936   ksol= 0.34   Bsol= 72.89   scale= 1.040   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (0.19,0.54,0.38,0.00,0.00,0.00); trace/3= 0.37                              |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.32 A                  |
| x-ray target function (ml) for work reflections: 5.768242                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.95 - 15.15 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.2269   r_free= 0.2930   ksol= 0.34   Bsol= 71.75   scale= 1.011   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-0.71,-0.69,-0.74,-0.00,-0.00,-0.00); trace/3= -0.71                       |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.33 A                  |
| x-ray target function (ml) for work reflections: 5.767515                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 7.745370              wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 95.845   (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 1.316644              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 136.123  (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.2269      final r-factor (work) = 0.1724          |
| start r-factor (free) = 0.2930      final r-factor (free) = 0.2280          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 22.6294 = 7.75 * 0.50 * 5.8162 + 1.00 * 0.1052                              |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 22.0575 = 7.75 * 0.50 * 5.6747 + 1.00 * 0.0813                              |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 29     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1724      final r-factor (work) = 0.1538          |
| start r-factor (free) = 0.2280      final r-factor (free) = 0.2090          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 7.4875 = 1.32 * 1.00 * 5.6747 + 1.00 * 0.0159                               |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 7.2212 = 1.32 * 1.00 * 5.4737 + 1.00 * 0.0142                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 26     |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 12.016)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.00    107.36  19.04    None  None   None       |
|    all(noH): 2823   0      0.00    107.36  19.04    None  None   None       |
|    Sol.    : 438    0      4.47    105.47  48.23    None  None   None       |
|    Mac.    : 2385   0      0.00    107.36  13.68    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 -  10.736: 1166   |   5:    53.679 -  64.415:   82        |
|      1:    10.736 -  21.472:  978   |   6:    64.415 -  75.151:   62        |
|      2:    21.472 -  32.207:  224   |   7:    75.151 -  85.886:   36        |
|      3:    32.207 -  42.943:  132   |   8:    85.886 -  96.622:   22        |
|      4:    42.943 -  53.679:  114   |   9:    96.622 - 107.358:    7        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.1538 r_free = 0.2090             target_work(ml) = 5.429         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        5 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.1538 r_free = 0.2089             target_work(ml) = 5.429         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        7 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.95 - 15.15 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1538   r_free= 0.2089   ksol= 0.34   Bsol= 71.75   scale= 1.024   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-0.71,-0.69,-0.74,-0.00,-0.00,-0.00); trace/3= -0.71                       |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.21 A                  |
| x-ray target function (ml) for work reflections: 5.428909                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.95 - 15.15 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1540   r_free= 0.2087   ksol= 0.34   Bsol= 71.75   scale= 1.002   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-1.51,-1.47,-1.60,-0.00,-0.00,-0.00); trace/3= -1.53                       |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.20 A                  |
| x-ray target function (ml) for work reflections: 5.429469                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 2.589797              wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 118.445  (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 0.403861              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 130.838  (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1540      final r-factor (work) = 0.1372          |
| start r-factor (free) = 0.2087      final r-factor (free) = 0.1888          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 7.1767 = 2.59 * 0.50 * 5.4796 + 1.00 * 0.0813                               |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 7.0376 = 2.59 * 0.50 * 5.3874 + 1.00 * 0.0614                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 27     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1372      final r-factor (work) = 0.1317          |
| start r-factor (free) = 0.1888      final r-factor (free) = 0.1810          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 2.1898 = 0.40 * 1.00 * 5.3874 + 1.00 * 0.0141                               |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 2.1580 = 0.40 * 1.00 * 5.3161 + 1.00 * 0.0111                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 26     |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 12.016)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      1.57    110.42  18.17    None  None   None       |
|    all(noH): 2823   0      1.57    110.42  18.17    None  None   None       |
|    Sol.    : 438    0      5.12    100.91  45.37    None  None   None       |
|    Mac.    : 2385   0      1.57    110.42  13.18    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:     1.567 -  12.452: 1509   |   5:    55.991 -  66.876:   66        |
|      1:    12.452 -  23.337:  759   |   6:    66.876 -  77.761:   48        |
|      2:    23.337 -  34.222:  168   |   7:    77.761 -  88.646:   26        |
|      3:    34.222 -  45.106:  127   |   8:    88.646 -  99.531:    7        |
|      4:    45.106 -  55.991:  107   |   9:    99.531 - 110.416:    6        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.1317 r_free = 0.1810             target_work(ml) = 5.295         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        7 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.1316 r_free = 0.1808             target_work(ml) = 5.294         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        7 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.95 - 15.15 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1316   r_free= 0.1808   ksol= 0.34   Bsol= 71.75   scale= 1.004   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-1.51,-1.47,-1.60,-0.00,-0.00,-0.00); trace/3= -1.53                       |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.17 A                  |
| x-ray target function (ml) for work reflections: 5.294355                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.95 - 15.15 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1319   r_free= 0.1814   ksol= 0.32   Bsol= 62.82   scale= 0.995   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-1.85,-1.79,-1.91,-0.00,-0.00,-0.00); trace/3= -1.85                       |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.17 A                  |
| x-ray target function (ml) for work reflections: 5.297216                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 2.586293              wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 109.040  (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 0.119478              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 147.956  (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1319      final r-factor (work) = 0.1226          |
| start r-factor (free) = 0.1814      final r-factor (free) = 0.1712          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 6.9381 = 2.59 * 0.50 * 5.3177 + 1.00 * 0.0615                               |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 6.8785 = 2.59 * 0.50 * 5.2680 + 1.00 * 0.0662                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 28     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1226      final r-factor (work) = 0.1244          |
| start r-factor (free) = 0.1712      final r-factor (free) = 0.1690          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 0.6404 = 0.12 * 1.00 * 5.2680 + 1.00 * 0.0110                               |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 0.6339 = 0.12 * 1.00 * 5.2443 + 1.00 * 0.0073                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 30     |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 12.016)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      2.54    97.70   16.95    None  None   None       |
|    all(noH): 2823   0      2.54    97.70   16.95    None  None   None       |
|    Sol.    : 438    0      4.98    83.00   39.50    None  None   None       |
|    Mac.    : 2385   0      2.54    97.70   12.81    None  None   None       |
|    Hyd.    : 0      0      None    None    None     None  None   None       |
|    - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -      |
|       Distribution of isotropic (or equivalent) ADP for non-H atoms:        |
|    Bin#      value range     #atoms | Bin#      value range     #atoms      |
|      0:     2.538 -  12.055: 1482   |   5:    50.121 -  59.637:   66        |
|      1:    12.055 -  21.571:  781   |   6:    59.637 -  69.154:   31        |
|      2:    21.571 -  31.088:  179   |   7:    69.154 -  78.670:   20        |
|      3:    31.088 -  40.604:  155   |   8:    78.670 -  88.187:    6        |
|      4:    40.604 -  50.121:   98   |   9:    88.187 -  97.703:    5        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.1244 r_free = 0.1690             target_work(ml) = 5.238         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        7 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.1243 r_free = 0.1687             target_work(ml) = 5.237         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        7 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.95 - 15.15 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1243   r_free= 0.1687   ksol= 0.32   Bsol= 62.82   scale= 0.994   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-1.85,-1.79,-1.91,-0.00,-0.00,-0.00); trace/3= -1.85                       |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.16 A                  |
| x-ray target function (ml) for work reflections: 5.236957                   |
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
| Bin     Resolution   Compl.  No. Refl.    R-factors          Targets        |
|number     range              work test   work   test        work        test|
|  1: 15.1547 -  4.6607 0.99   1479  167 0.1003 0.1318         5.4      5.5983|
|  2:  4.6607 -  3.7173 0.99   1415  156 0.0919 0.1126      5.4874      5.7021|
|  3:  3.7173 -  3.2527 0.99   1396  149 0.1189 0.1852      5.5446      5.9588|
|  4:  3.2527 -  2.9577 0.99   1381  160 0.1455 0.1723       5.562       5.697|
|  5:  2.9577 -  2.7471 0.99   1377  150 0.1479 0.2012      5.4155      5.5978|
|  6:  2.7471 -  2.5860 0.99   1360  159 0.1404 0.1922      5.2913      5.4675|
|  7:  2.5860 -  2.4570 0.98   1366  137 0.1367 0.1755      5.2249      5.4286|
|  8:  2.4570 -  2.3505 0.98   1354  154 0.1349 0.1743      5.1343       5.331|
|  9:  2.3505 -  2.2603 0.99   1358  152 0.1289 0.2010      5.0935      5.3516|
| 10:  2.2603 -  2.1825 0.98   1347  158 0.1284 0.1837      5.0526      5.3201|
| 11:  2.1825 -  2.1145 0.97   1335  145 0.1249 0.1892      4.9887      5.2668|
| 12:  2.1145 -  2.0542 0.98   1337  143 0.1305 0.1976      4.9475      5.1875|
| 13:  2.0542 -  2.0002 0.66    901  108 0.1284 0.1713      4.8353      5.0205|
| 14:  2.0002 -  1.9515 0.16    224   21 0.1332 0.1731      4.7245      4.9442|
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
|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: 15.1547 -  4.6607  1479   167  0.94   9.49   0.97     0.95       7689.87|
|  2:  4.6607 -  3.7173  1415   156  0.95   8.69   1.00     0.99      10006.18|
|  3:  3.7173 -  3.2527  1396   149  0.92  13.44   1.02     1.02      12201.01|
|  4:  3.2527 -  2.9577  1381   160  0.89  16.82   0.99     0.96      12940.27|
|  5:  2.9577 -  2.7471  1377   150  0.88  18.46   0.99     0.97      10060.43|
|  6:  2.7471 -  2.5860  1360   159  0.89  17.59   0.99     0.96       8079.47|
|  7:  2.5860 -  2.4570  1366   137  0.90  16.68   0.99     0.96       6837.11|
|  8:  2.4570 -  2.3505  1354   154  0.89  17.01   1.00     0.97       6108.43|
|  9:  2.3505 -  2.2603  1358   152  0.88  17.71   1.00     0.95       5597.77|
| 10:  2.2603 -  2.1825  1347   158  0.89  17.16   0.99     0.95       5214.30|
| 11:  2.1825 -  2.1145  1335   145  0.89  17.54   0.99     0.95       4876.39|
| 12:  2.1145 -  2.0542  1337   143  0.89  18.12   1.00     1.00       4606.85|
| 13:  2.0542 -  2.0002   901   108  0.89  17.67   0.99     0.97       3632.98|
| 14:  2.0002 -  1.9515   224    21  0.88  17.98   0.98     0.96       2816.95|
|alpha:            min =        0.95 max =            1.02 mean =         0.97|
|beta:             min =     2816.95 max =        12940.27 mean =      7605.55|
|figures of merit: min =        0.00 max =            1.00 mean =         0.90|
|phase err.(work): min =        0.00 max =           89.99 mean =        15.78|
|phase err.(test): min =        0.00 max =           88.43 mean =        14.99|
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.95 - 15.15 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1242   r_free= 0.1685   ksol= 0.32   Bsol= 52.88   scale= 0.991   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-1.86,-1.83,-1.93,-0.00,-0.00,-0.00); trace/3= -1.87                       |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.16 A                  |
| x-ray target function (ml) for work reflections: 5.236701                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.95 - 15.15 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1242   r_free= 0.1685   ksol= 0.32   Bsol= 52.88   scale= 0.991   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-1.86,-1.83,-1.93,-0.00,-0.00,-0.00); trace/3= -1.87                       |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.16 A                  |
| x-ray target function (ml) for work reflections: 5.236701                   |
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
| Bin     Resolution   Compl.  No. Refl.    R-factors          Targets        |
|number     range              work test   work   test        work        test|
|  1: 15.1547 -  4.6607 0.99   1479  167 0.0999 0.1310      5.3958       5.588|
|  2:  4.6607 -  3.7173 0.99   1415  156 0.0908 0.1113      5.4791      5.6928|
|  3:  3.7173 -  3.2527 0.99   1396  149 0.1185 0.1849      5.5396      5.9579|
|  4:  3.2527 -  2.9577 0.99   1381  160 0.1458 0.1720      5.5619      5.6954|
|  5:  2.9577 -  2.7471 0.99   1377  150 0.1482 0.2016      5.4174      5.5998|
|  6:  2.7471 -  2.5860 0.99   1360  159 0.1407 0.1924      5.2935      5.4704|
|  7:  2.5860 -  2.4570 0.98   1366  137 0.1370 0.1756      5.2274      5.4298|
|  8:  2.4570 -  2.3505 0.98   1354  154 0.1351 0.1748      5.1364      5.3345|
|  9:  2.3505 -  2.2603 0.99   1358  152 0.1291 0.2012      5.0952      5.3532|
| 10:  2.2603 -  2.1825 0.98   1347  158 0.1287 0.1839      5.0543       5.321|
| 11:  2.1825 -  2.1145 0.97   1335  145 0.1250 0.1895      4.9898      5.2678|
| 12:  2.1145 -  2.0542 0.98   1337  143 0.1306 0.1981      4.9489      5.1892|
| 13:  2.0542 -  2.0002 0.66    901  108 0.1284 0.1712       4.836      5.0203|
| 14:  2.0002 -  1.9515 0.16    224   21 0.1333 0.1730      4.7248      4.9439|
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
|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: 15.1547 -  4.6607  1479   167  0.94   9.41   0.97     0.95       7579.12|
|  2:  4.6607 -  3.7173  1415   156  0.95   8.58   1.00     0.99       9830.57|
|  3:  3.7173 -  3.2527  1396   149  0.92  13.29   1.02     1.01      12022.40|
|  4:  3.2527 -  2.9577  1381   160  0.89  16.77   0.99     0.96      12901.20|
|  5:  2.9577 -  2.7471  1377   150  0.88  18.47   0.99     0.97      10081.19|
|  6:  2.7471 -  2.5860  1360   159  0.89  17.64   0.98     0.96       8121.00|
|  7:  2.5860 -  2.4570  1366   137  0.90  16.71   0.98     0.96       6871.77|
|  8:  2.4570 -  2.3505  1354   154  0.89  17.06   0.99     0.96       6140.39|
|  9:  2.3505 -  2.2603  1358   152  0.88  17.76   0.99     0.95       5621.11|
| 10:  2.2603 -  2.1825  1347   158  0.89  17.20   0.98     0.95       5235.01|
| 11:  2.1825 -  2.1145  1335   145  0.89  17.57   0.98     0.94       4890.13|
| 12:  2.1145 -  2.0542  1337   143  0.89  18.14   0.99     0.99       4620.10|
| 13:  2.0542 -  2.0002   901   108  0.89  17.69   0.98     0.96       3638.80|
| 14:  2.0002 -  1.9515   224    21  0.88  17.97   0.97     0.95       2816.00|
|alpha:            min =        0.94 max =            1.01 mean =         0.97|
|beta:             min =     2816.00 max =        12901.20 mean =      7580.64|
|figures of merit: min =        0.00 max =            1.00 mean =         0.90|
|phase err.(work): min =        0.00 max =           89.93 mean =        15.77|
|phase err.(test): min =        0.00 max =           89.99 mean =        14.99|
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 12.016)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      2.45    97.61   16.86    None  None   None       |
|    all(noH): 2823   0      2.45    97.61   16.86    None  None   None       |
|    Sol.    : 438    0      4.89    82.91   39.41    None  None   None       |
|    Mac.    : 2385   0      2.45    97.61   12.72    None  None   None       |
|    Hyd.    : 0      0      None    None    None     None  None   None       |
|    - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -      |
|       Distribution of isotropic (or equivalent) ADP for non-H atoms:        |
|    Bin#      value range     #atoms | Bin#      value range     #atoms      |
|      0:     2.446 -  11.962: 1482   |   5:    50.028 -  59.545:   66        |
|      1:    11.962 -  21.479:  781   |   6:    59.545 -  69.061:   31        |
|      2:    21.479 -  30.995:  179   |   7:    69.061 -  78.578:   20        |
|      3:    30.995 -  40.512:  155   |   8:    78.578 -  88.094:    6        |
|      4:    40.512 -  50.028:   98   |   9:    88.094 -  97.611:    5        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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


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

Number of peaks found at mFobs-DFmodel map (map cutoff=3.00 sigma)= 327         
Filter by distance & map next to the model:
   mapped sites are within: 0.587 - 5.974
   number of sites selected in [dist_min= 0.70, dist_max= 6.00]: 323 from: 327
   mapped sites are within: 0.714 - 5.974

peak=    5.960 closest distance to " NH2BARG A 102 " =    1.042
peak=    5.665 closest distance to " CB  SER A  63 " =    1.361
peak=    5.376 closest distance to " CB  GLN A 223 " =    1.578
peak=    5.070 closest distance to " O   HOH Z 182 " =    1.497
peak=    5.033 closest distance to " O   HOH Z 111 " =    1.964
peak=    5.018 closest distance to " O   HOH Z 126 " =    1.902
peak=    4.997 closest distance to " O   HOH Z  11 " =    1.345
peak=    4.971 closest distance to " CG  PRO A  54 " =    1.229
peak=    4.895 closest distance to " O   HOH Z 132 " =    1.501
peak=    4.886 closest distance to " O   HOH Z 207 " =    1.912
peak=    4.846 closest distance to " O   HOH Z 186 " =    1.394
peak=    4.686 closest distance to " CG  PRO A 213 " =    1.274
peak=    4.611 closest distance to " O   HOH Z 127 " =    1.322
peak=    4.606 closest distance to " O   HOH Z 282 " =    1.665
peak=    4.599 closest distance to " O   HOH Z  15 " =    1.930
peak=    4.581 closest distance to " O   HOH Z 134 " =    1.575
peak=    4.570 closest distance to " O   HOH Z 214 " =    1.288
peak=    4.538 closest distance to " CB  PRO A  54 " =    0.815
peak=    4.458 closest distance to " O   HOH Z  49 " =    1.156
peak=    4.438 closest distance to " CB  LEU A 228 " =    1.079
peak=    4.438 closest distance to " CB  ARG A 275 " =    0.919
peak=    4.435 closest distance to " CG  PRO A  90 " =    1.156
peak=    4.435 closest distance to " O   HOH Z  40 " =    1.922
peak=    4.422 closest distance to " CA  ALA A  21 " =    1.322
peak=    4.397 closest distance to " CG  PRO A 198 " =    1.353
peak=    4.394 closest distance to " O   HOH Z 260 " =    1.536
peak=    4.392 closest distance to " CB  GLU A 152 " =    1.163
peak=    4.388 closest distance to " O   HOH Z 124 " =    1.463
peak=    4.374 closest distance to " O   HOH Z 193 " =    2.214
peak=    4.362 closest distance to " O   HOH Z  80 " =    1.843
peak=    4.350 closest distance to " O   HOH Z 112 " =    1.495
peak=    4.342 closest distance to " O   HOH Z 163 " =    1.834
peak=    4.336 closest distance to " O   HOH Z  30 " =    1.914
peak=    4.324 closest distance to " O   PRO A 198 " =    1.558
peak=    4.292 closest distance to " O   HOH Z 234 " =    3.867
peak=    4.291 closest distance to " OD1 ASN A 217 " =    1.697
peak=    4.286 closest distance to " O   HOH Z 298 " =    1.797
peak=    4.262 closest distance to " O   HOH Z 236 " =    1.964
peak=    4.256 closest distance to " O   HOH Z 232 " =    2.161
peak=    4.226 closest distance to " O   HOH Z  67 " =    1.983
peak=    4.219 closest distance to " CA  GLN A 223 " =    0.928
peak=    4.216 closest distance to " O   HOH Z 215 " =    1.555
peak=    4.210 closest distance to " NH2 ARG A 156 " =    1.264
peak=    4.205 closest distance to " O   HOH Z 368 " =    1.989
peak=    4.201 closest distance to " CB  SER A   3 " =    1.541
peak=    4.192 closest distance to " O   HOH Z 108 " =    1.752
peak=    4.179 closest distance to " CG  PRO A 280 " =    0.790
peak=    4.165 closest distance to " O   HOH Z 183 " =    1.656
peak=    4.149 closest distance to " CB  GLN A 183 " =    1.188
peak=    4.149 closest distance to " O   HOH Z  47 " =    1.555
peak=    4.143 closest distance to " O   HOH Z 411 " =    3.225
peak=    4.133 closest distance to " CG2 THR A 221 " =    0.925
peak=    4.130 closest distance to " OD2 ASP A 286 " =    2.961
peak=    4.128 closest distance to " CB  PRO A 198 " =    0.963
peak=    4.113 closest distance to " O   HOH Z 246 " =    1.816
peak=    4.093 closest distance to " O   HOH Z 313 " =    1.828
peak=    4.091 closest distance to " CB  VAL A 202 " =    1.552
peak=    4.086 closest distance to " N   ASN A  39 " =    1.334
peak=    4.078 closest distance to " O   SER A  87 " =    2.113
peak=    4.069 closest distance to " O   HOH Z 389 " =    1.917
peak=    4.067 closest distance to " OE1 GLN A  11 " =    1.965
peak=    4.065 closest distance to " O   HOH Z 246 " =    1.453
peak=    4.065 closest distance to " O   HOH Z 425 " =    1.687
peak=    4.061 closest distance to " OD1 ASN A  69 " =    2.483
peak=    4.047 closest distance to " O   HOH Z 192 " =    2.003
peak=    4.019 closest distance to " CB  TYR A 169 " =    0.877
peak=    3.984 closest distance to " O   HOH Z 426 " =    1.443
peak=    3.977 closest distance to " O   HOH Z  21 " =    1.800
peak=    3.961 closest distance to " O   HOH Z 281 " =    3.915
peak=    3.958 closest distance to " CA  GLU A 152 " =    0.909
peak=    3.954 closest distance to " O   HOH Z 132 " =    1.936
peak=    3.950 closest distance to " O   HOH Z 387 " =    2.364
peak=    3.937 closest distance to " O   HOH Z 371 " =    3.224
peak=    3.918 closest distance to " O   HOH Z 403 " =    1.780
peak=    3.901 closest distance to " CA  ASP A 191 " =    0.834
peak=    3.895 closest distance to " CG1 ILE A  33 " =    1.291
peak=    3.884 closest distance to " CG  PRO A 243 " =    1.088
peak=    3.882 closest distance to " O   HOH Z 287 " =    1.798
peak=    3.873 closest distance to " OE1 GLN A  58 " =    1.458
peak=    3.870 closest distance to " O   HOH Z 227 " =    1.759
peak=    3.852 closest distance to " O   HOH Z 374 " =    2.664
peak=    3.836 closest distance to " O   HOH Z 211 " =    1.433
peak=    3.833 closest distance to " CA  THR A 221 " =    0.887
peak=    3.832 closest distance to " O   HOH Z  48 " =    1.659
peak=    3.823 closest distance to " CB  TRP A 179 " =    1.427
peak=    3.820 closest distance to " O   HOH Z 272 " =    2.071
peak=    3.818 closest distance to " CD  ARG A 269 " =    0.838
peak=    3.816 closest distance to " CB  MET A  47 " =    1.060
peak=    3.811 closest distance to " O   HOH Z 184 " =    1.053
peak=    3.809 closest distance to " O   HOH Z 154 " =    2.470
peak=    3.809 closest distance to " CB  PRO A  54 " =    1.326
peak=    3.809 closest distance to " CB  GLU A 128 " =    1.097
peak=    3.797 closest distance to " CB  GLU A 277 " =    3.703
peak=    3.797 closest distance to " CA  TYR A  30 " =    1.046
peak=    3.792 closest distance to " O   HOH Z 265 " =    2.223
peak=    3.791 closest distance to " O   HOH Z  63 " =    1.978
peak=    3.786 closest distance to " NH2AARG A 190 " =    1.744
peak=    3.784 closest distance to " O   HOH Z 243 " =    1.836
peak=    3.782 closest distance to " CD1 LEU A 300 " =    1.302
peak=    3.781 closest distance to " O   HOH Z 404 " =    1.342
peak=    3.778 closest distance to " O   HOH Z 180 " =    2.100
peak=    3.778 closest distance to " O   HOH Z 193 " =    2.335
peak=    3.773 closest distance to " O   HOH Z  39 " =    1.511
peak=    3.771 closest distance to " O   HOH Z 132 " =    2.368
peak=    3.770 closest distance to " O   HOH Z 261 " =    2.005
peak=    3.768 closest distance to " CB  SER A 216 " =    0.772
peak=    3.768 closest distance to " O   HOH Z 108 " =    1.904
peak=    3.758 closest distance to " O   HOH Z  88 " =    3.674
peak=    3.749 closest distance to " O   HOH Z 104 " =    3.119
peak=    3.748 closest distance to " CB  SER A 141 " =    0.918
peak=    3.743 closest distance to " CB  ASN A 187 " =    0.987
peak=    3.738 closest distance to " CD  LYS A 119 " =    1.472
peak=    3.736 closest distance to " O   HOH Z  78 " =    2.339
peak=    3.736 closest distance to " ND2 ASN A 187 " =    1.615
peak=    3.734 closest distance to " CB  ASN A 148 " =    1.092
peak=    3.729 closest distance to " O   HOH Z 437 " =    1.707
peak=    3.722 closest distance to " O   HOH Z 394 " =    1.743
peak=    3.722 closest distance to " CZ  PHE A 192 " =    1.037
peak=    3.720 closest distance to " O   HOH Z 276 " =    1.410
peak=    3.717 closest distance to " CB  ARG A 259 " =    1.844
peak=    3.717 closest distance to " CB  TRP A 266 " =    0.956
peak=    3.714 closest distance to " O   HOH Z  54 " =    1.679
peak=    3.712 closest distance to " O   HOH Z 316 " =    3.101
peak=    3.706 closest distance to " CA  ARG A  36 " =    1.205
peak=    3.695 closest distance to " CA  GLU A 152 " =    1.462
peak=    3.682 closest distance to " NH2BARG A 145 " =    2.082
peak=    3.681 closest distance to " O   HOH Z 116 " =    1.809
peak=    3.674 closest distance to " NE AARG A 275 " =    1.502
peak=    3.664 closest distance to " O   HOH Z 326 " =    1.475
peak=    3.655 closest distance to " NH1 ARG A  56 " =    1.196
peak=    3.648 closest distance to " O   HOH Z 119 " =    2.281
peak=    3.636 closest distance to " O   HOH Z 344 " =    3.140
peak=    3.635 closest distance to " CD1 TRP A 266 " =    1.254
peak=    3.632 closest distance to " O   HOH Z 189 " =    2.168
peak=    3.630 closest distance to " CG1 VAL A 153 " =    1.047
peak=    3.628 closest distance to " CG1BVAL A  72 " =    1.710
peak=    3.622 closest distance to " CD  ARG A  66 " =    2.546
peak=    3.614 closest distance to " O   HOH Z  20 " =    2.227
peak=    3.607 closest distance to " CG AARG A 275 " =    1.086
peak=    3.599 closest distance to " O   HOH Z 368 " =    2.559
peak=    3.598 closest distance to " O   HOH Z  87 " =    2.684
peak=    3.594 closest distance to " CA  GLY A 196 " =    0.979
peak=    3.591 closest distance to " CZ  PHE A 218 " =    1.147
peak=    3.587 closest distance to " O   HOH Z 332 " =    1.521
peak=    3.584 closest distance to " O   HOH Z 144 " =    1.640
peak=    3.583 closest distance to " NH1BARG A 145 " =    0.996
peak=    3.568 closest distance to " O   HOH Z 423 " =    1.961
peak=    3.567 closest distance to " NZ  LYS A 117 " =    3.267
peak=    3.559 closest distance to " O   HOH Z  49 " =    1.772
peak=    3.559 closest distance to " O   HOH Z 196 " =    1.054
peak=    3.555 closest distance to " O   HOH Z 128 " =    2.294
peak=    3.549 closest distance to " NE2 GLN A  11 " =    1.143
peak=    3.543 closest distance to " N   TYR A  15 " =    0.790
peak=    3.540 closest distance to " O   HOH Z   4 " =    1.922
peak=    3.539 closest distance to " O   HOH Z 154 " =    1.388
peak=    3.538 closest distance to " CA  ASP A 124 " =    0.792
peak=    3.537 closest distance to " CA  MET A  40 " =    1.051
peak=    3.536 closest distance to " O   HOH Z  97 " =    1.880
peak=    3.530 closest distance to " O   HOH Z 346 " =    1.478
peak=    3.529 closest distance to " CB  PHE A  16 " =    1.068
peak=    3.523 closest distance to " O   HOH Z 174 " =    2.170
peak=    3.517 closest distance to " CA  GLY A 241 " =    0.714
peak=    3.513 closest distance to " CB  ASN A 148 " =    1.949
peak=    3.512 closest distance to " O   HOH Z 155 " =    1.632
peak=    3.511 closest distance to " CB  VAL A 265 " =    1.278
peak=    3.504 closest distance to " O   HOH Z 214 " =    1.718
peak=    3.499 closest distance to " CG2BVAL A  41 " =    0.994
peak=    3.495 closest distance to " O   HOH Z 118 " =    1.795
peak=    3.484 closest distance to " ND1 HIS A  81 " =    1.566
peak=    3.481 closest distance to " O   HOH Z 369 " =    2.034
peak=    3.478 closest distance to " O   HOH Z  44 " =    2.485
peak=    3.466 closest distance to " O   HOH Z   6 " =    2.126
peak=    3.465 closest distance to " C   SER A  32 " =    1.046
peak=    3.462 closest distance to " OE1 GLN A  58 " =    5.645
peak=    3.453 closest distance to " O   HOH Z  53 " =    2.574
peak=    3.450 closest distance to " CB  ALA A 291 " =    1.299
peak=    3.450 closest distance to " O   HOH Z 345 " =    3.378
peak=    3.447 closest distance to " CD BLYS A 290 " =    1.008
peak=    3.446 closest distance to " O   HOH Z 223 " =    1.120
peak=    3.445 closest distance to " O   HOH Z 185 " =    1.802
peak=    3.444 closest distance to " CB  ARG A  79 " =    1.406
peak=    3.444 closest distance to " O   HOH Z 295 " =    1.435
peak=    3.444 closest distance to " O   HOH Z 217 " =    1.498
peak=    3.438 closest distance to " O   HOH Z 172 " =    5.974
peak=    3.425 closest distance to " O   HOH Z 132 " =    2.854
peak=    3.420 closest distance to " NE BARG A 102 " =    1.401
peak=    3.418 closest distance to " O   HOH Z 303 " =    2.247
peak=    3.412 closest distance to " O   ALA A 165 " =    1.242
peak=    3.403 closest distance to " CZ  PHE A 208 " =    1.157
peak=    3.403 closest distance to " CB  TYR A 116 " =    1.205
peak=    3.402 closest distance to " CA  TYR A 116 " =    1.477
peak=    3.397 closest distance to " CG  LEU A 167 " =    1.165
peak=    3.388 closest distance to " O   HOH Z  93 " =    2.570
peak=    3.386 closest distance to " O   HOH Z 343 " =    2.299
peak=    3.386 closest distance to " CB  TYR A  30 " =    1.384
peak=    3.383 closest distance to " O   HOH Z 175 " =    3.618
peak=    3.382 closest distance to " O   HOH Z  61 " =    1.606
peak=    3.381 closest distance to " O   HOH Z 368 " =    3.467
peak=    3.380 closest distance to " CA  ALA A 158 " =    1.032
peak=    3.379 closest distance to " O   THR A 251 " =    1.258
peak=    3.378 closest distance to " O   GLY A  57 " =    2.535
peak=    3.365 closest distance to " O   HOH Z 427 " =    3.062
peak=    3.364 closest distance to " O   HOH Z 263 " =    2.114
peak=    3.358 closest distance to " CB  ARG A 190 " =    1.849
peak=    3.355 closest distance to " O   MET A 105 " =    1.825
peak=    3.353 closest distance to " O   HOH Z 352 " =    1.859
peak=    3.345 closest distance to " O   HOH Z 286 " =    2.232
peak=    3.345 closest distance to " NZ  LYS A 193 " =    1.649
peak=    3.344 closest distance to " O   HOH Z 139 " =    3.243
peak=    3.338 closest distance to " O   HOH Z 171 " =    3.781
peak=    3.334 closest distance to " CE1 PHE A 208 " =    1.126
peak=    3.334 closest distance to " O   HOH Z 305 " =    3.741
peak=    3.329 closest distance to " CB  LEU A 143 " =    1.057
peak=    3.324 closest distance to " OD1 ASP A 238 " =    1.029
peak=    3.324 closest distance to " O   HOH Z 357 " =    2.008
peak=    3.323 closest distance to " CG BARG A 275 " =    1.515
peak=    3.322 closest distance to " OG  SER A  97 " =    3.558
peak=    3.321 closest distance to " O   HOH Z 383 " =    1.956
peak=    3.321 closest distance to " CD  ARG A 195 " =    3.553
peak=    3.317 closest distance to " O   HOH Z 345 " =    1.768
peak=    3.311 closest distance to " O   GLY A  75 " =    3.392
peak=    3.305 closest distance to " O   HOH Z 292 " =    1.745
peak=    3.300 closest distance to " O   HOH Z 173 " =    2.052
peak=    3.298 closest distance to " CB  ALA A 244 " =    1.002
peak=    3.290 closest distance to " O   HOH Z 420 " =    1.912
peak=    3.289 closest distance to " CB  ALA A 100 " =    1.392
peak=    3.287 closest distance to " O   HOH Z 156 " =    2.666
peak=    3.285 closest distance to " CA  LEU A 282 " =    1.054
peak=    3.285 closest distance to " O   HOH Z  49 " =    2.280
peak=    3.284 closest distance to " O   HOH Z 149 " =    1.347
peak=    3.284 closest distance to " O   HOH Z 118 " =    1.566
peak=    3.282 closest distance to " CD  PRO A 280 " =    1.090
peak=    3.279 closest distance to " O   HOH Z 197 " =    2.057
peak=    3.279 closest distance to " CB  ILE A 199 " =    1.046
peak=    3.277 closest distance to " O   HOH Z  10 " =    2.144
peak=    3.275 closest distance to " CB  ILE A 120 " =    1.218
peak=    3.272 closest distance to " CZ AARG A 102 " =    1.879
peak=    3.272 closest distance to " CG2 VAL A 197 " =    1.208
peak=    3.270 closest distance to " O   HOH Z 255 " =    1.586
peak=    3.270 closest distance to " CG2 ILE A  33 " =    1.541
peak=    3.269 closest distance to " CD  LYS A 166 " =    1.354
peak=    3.267 closest distance to " O   HOH Z  63 " =    1.072
peak=    3.263 closest distance to " CA  GLU A  46 " =    0.769
peak=    3.263 closest distance to " O   HOH Z 337 " =    3.952
peak=    3.262 closest distance to " CD  ARG A 159 " =    0.782
peak=    3.256 closest distance to " CD  PRO A  54 " =    1.088
peak=    3.253 closest distance to " O   HOH Z 419 " =    2.927
peak=    3.253 closest distance to " CA  THR A  42 " =    1.021
peak=    3.252 closest distance to " CB  ARG A 139 " =    0.916
peak=    3.247 closest distance to " CG1 ILE A  49 " =    1.612
peak=    3.244 closest distance to " CB  ASN A 285 " =    0.943
peak=    3.242 closest distance to " NE2 HIS A 115 " =    0.940
peak=    3.237 closest distance to " CA  ASP A 162 " =    1.119
peak=    3.235 closest distance to " O   SER A  26 " =    1.702
peak=    3.231 closest distance to " CA  ILE A 263 " =    0.960
peak=    3.230 closest distance to " O   HOH Z 248 " =    1.630
peak=    3.228 closest distance to " ND2 ASN A 301 " =    1.166
peak=    3.226 closest distance to " O   HOH Z 336 " =    1.648
peak=    3.224 closest distance to " NZ  LYS A  76 " =    1.195
peak=    3.224 closest distance to " CB  GLN A 194 " =    0.845
peak=    3.223 closest distance to " C   VAL A 265 " =    1.231
peak=    3.223 closest distance to " O   HOH Z  14 " =    2.306
peak=    3.221 closest distance to " O   ASN A 217 " =    1.266
peak=    3.211 closest distance to " CA  ALA A 154 " =    1.334
peak=    3.209 closest distance to " O   HOH Z  44 " =    1.806
peak=    3.208 closest distance to " O   HOH Z 294 " =    1.573
peak=    3.205 closest distance to " CD2 PHE A  59 " =    1.808
peak=    3.204 closest distance to " N   ASN A 127 " =    1.263
peak=    3.202 closest distance to " CG2 VAL A 112 " =    1.456
peak=    3.197 closest distance to " O   HOH Z  10 " =    1.829
peak=    3.195 closest distance to " CA  THR A 264 " =    0.862
peak=    3.192 closest distance to " NZ  LYS A 117 " =    1.574
peak=    3.187 closest distance to " N   PHE A 130 " =    1.401
peak=    3.183 closest distance to " O   HOH Z 155 " =    2.870
peak=    3.182 closest distance to " O   HOH Z 299 " =    2.417
peak=    3.182 closest distance to " O   HOH Z 424 " =    2.705
peak=    3.182 closest distance to " CB  PRO A 163 " =    4.038
peak=    3.176 closest distance to " CB  ALA A 242 " =    0.825
peak=    3.174 closest distance to " O   TRP A 274 " =    1.615
peak=    3.160 closest distance to " CD1 ILE A  33 " =    1.569
peak=    3.160 closest distance to " O   HOH Z 355 " =    1.697
peak=    3.157 closest distance to " O   HOH Z 244 " =    1.754
peak=    3.154 closest distance to " NE  ARG A 156 " =    1.039
peak=    3.153 closest distance to " O   HOH Z  22 " =    2.418
peak=    3.151 closest distance to " CD1 ILE A 106 " =    0.935
peak=    3.151 closest distance to " CD2 HIS A  81 " =    1.563
peak=    3.146 closest distance to " CB  ASN A  39 " =    0.889
peak=    3.145 closest distance to " CB  THR A 157 " =    1.089
peak=    3.144 closest distance to " CA  ALA A 160 " =    0.920
peak=    3.143 closest distance to " O   HOH Z 109 " =    2.602
peak=    3.142 closest distance to " O   HOH Z  98 " =    1.813
peak=    3.141 closest distance to " CB  GLU A 236 " =    1.086
peak=    3.138 closest distance to " CA  ALA A 295 " =    1.138
peak=    3.137 closest distance to " CA  LYS A 117 " =    1.267
peak=    3.137 closest distance to " O   HOH Z 409 " =    3.165
peak=    3.136 closest distance to " O   HOH Z 147 " =    1.699
peak=    3.130 closest distance to " O   HOH Z 434 " =    1.508
peak=    3.130 closest distance to " NZ ALYS A 290 " =    1.082
peak=    3.129 closest distance to " CB  LEU A 237 " =    0.971
peak=    3.124 closest distance to " OG1 THR A 294 " =    1.642
peak=    3.119 closest distance to " CA  GLY A 267 " =    1.031
peak=    3.118 closest distance to " CA  ASN A 215 " =    1.130
peak=    3.115 closest distance to " CA  ILE A  33 " =    1.676
peak=    3.115 closest distance to " O   HOH Z 279 " =    2.483
peak=    3.114 closest distance to " CA  GLY A 211 " =    0.952
peak=    3.113 closest distance to " O   HOH Z 409 " =    2.763
peak=    3.097 closest distance to " CB  GLN A  58 " =    0.764
peak=    3.090 closest distance to " CA  SER A  87 " =    0.790
peak=    3.090 closest distance to " O   HOH Z  59 " =    1.820
peak=    3.087 closest distance to " O   HOH Z 426 " =    2.989
peak=    3.079 closest distance to " O   HOH Z 329 " =    3.758
peak=    3.079 closest distance to " O   HOH Z 293 " =    1.806
peak=    3.078 closest distance to " CD  ARG A  66 " =    2.930
peak=    3.063 closest distance to " O   HOH Z  48 " =    1.587
peak=    3.061 closest distance to " O   HOH Z 284 " =    3.031
peak=    3.054 closest distance to " CD  ARG A 219 " =    0.974
peak=    3.054 closest distance to " NE2 GLN A  58 " =    4.295
peak=    3.047 closest distance to " CG  GLN A  77 " =    0.743
peak=    3.046 closest distance to " CZ3 TRP A  85 " =    1.103
peak=    3.039 closest distance to " O   HOH Z 152 " =    1.351
peak=    3.035 closest distance to " CB  GLU A 277 " =    1.167
peak=    3.023 closest distance to " NH1 ARG A  14 " =    1.130
peak=    3.007 closest distance to " CB  ALA A 248 " =    0.932

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

Number of peaks found at mFobs-DFmodel map (map cutoff=3.00 sigma)= 217         
Filter by distance & map next to the model:
   mapped sites are within: 0.314 - 5.447
   number of sites selected in [dist_min= 0.70, dist_max= 6.00]: 204 from: 217
   mapped sites are within: 0.732 - 5.447

peak=   -5.451 closest distance to " O   HOH Z 290 " =    0.784
peak=   -4.561 closest distance to " O   HOH Z 377 " =    1.048
peak=   -4.555 closest distance to " O   HOH Z 221 " =    1.019
peak=   -4.527 closest distance to " N   ALA A  43 " =    2.454
peak=   -4.362 closest distance to " OG ASER A 134 " =    1.386
peak=   -4.234 closest distance to " O   HOH Z  19 " =    1.595
peak=   -4.214 closest distance to " O   HOH Z  17 " =    1.119
peak=   -4.168 closest distance to " NH2 ARG A  66 " =    1.651
peak=   -4.106 closest distance to " O   HOH Z 266 " =    4.370
peak=   -4.084 closest distance to " O   HOH Z 259 " =    0.732
peak=   -4.079 closest distance to " CD2 LEU A 300 " =    2.982
peak=   -4.069 closest distance to " O   HOH Z  52 " =    1.682
peak=   -4.060 closest distance to " O   HOH Z  13 " =    1.174
peak=   -4.037 closest distance to " CD2 LEU A 237 " =    2.330
peak=   -4.009 closest distance to " C   ASN A 285 " =    2.628
peak=   -3.972 closest distance to " O   HOH Z 184 " =    1.125
peak=   -3.952 closest distance to " O   HOH Z 283 " =    1.794
peak=   -3.948 closest distance to " O   HOH Z 151 " =    1.332
peak=   -3.946 closest distance to " O   HOH Z 241 " =    0.929
peak=   -3.938 closest distance to " CH2 TRP A 179 " =    1.062
peak=   -3.935 closest distance to " CD2 LEU A 143 " =    2.523
peak=   -3.931 closest distance to " O   HOH Z  71 " =    1.044
peak=   -3.900 closest distance to " OD2 ASP A 171 " =    2.233
peak=   -3.898 closest distance to " O   GLY A 196 " =    1.207
peak=   -3.897 closest distance to " CG  GLN A  58 " =    1.137
peak=   -3.887 closest distance to " O   HOH Z  92 " =    1.255
peak=   -3.879 closest distance to " CD2 PHE A  59 " =    2.468
peak=   -3.872 closest distance to " CG1 VAL A 112 " =    2.615
peak=   -3.858 closest distance to " O   HOH Z 407 " =    3.766
peak=   -3.853 closest distance to " CB  ARG A 219 " =    2.355
peak=   -3.850 closest distance to " N   GLN A  58 " =    1.592
peak=   -3.846 closest distance to " CE2 TYR A  30 " =    2.823
peak=   -3.832 closest distance to " O   HOH Z 213 " =    1.290
peak=   -3.823 closest distance to " CD1 PHE A  59 " =    1.885
peak=   -3.804 closest distance to " CE  MET A  93 " =    1.258
peak=   -3.803 closest distance to " OH  TYR A 169 " =    1.027
peak=   -3.785 closest distance to " CG  GLU A  53 " =    1.571
peak=   -3.780 closest distance to " O   HOH Z 231 " =    1.961
peak=   -3.775 closest distance to " CD1 LEU A 228 " =    2.554
peak=   -3.759 closest distance to " O   HOH Z 313 " =    0.926
peak=   -3.759 closest distance to " O   GLY A 118 " =    2.380
peak=   -3.740 closest distance to " CG  MET A 105 " =    0.990
peak=   -3.736 closest distance to " CD  ARG A 156 " =    1.964
peak=   -3.732 closest distance to " O   HOH Z  43 " =    1.506
peak=   -3.726 closest distance to " OE2 GLU A   2 " =    1.126
peak=   -3.716 closest distance to " OG BSER A 134 " =    1.840
peak=   -3.699 closest distance to " O   HOH Z  98 " =    1.771
peak=   -3.697 closest distance to " O   HOH Z 332 " =    1.226
peak=   -3.691 closest distance to " CG  ARG A 269 " =    2.336
peak=   -3.669 closest distance to " CB  PRO A 243 " =    2.590
peak=   -3.639 closest distance to " OG1 THR A  82 " =    2.078
peak=   -3.637 closest distance to " O   PRO A 163 " =    2.063
peak=   -3.631 closest distance to " N   ALA A 226 " =    2.102
peak=   -3.628 closest distance to " CD1 LEU A 101 " =    2.791
peak=   -3.625 closest distance to " CD2 LEU A 167 " =    1.760
peak=   -3.624 closest distance to " O   HOH Z  48 " =    0.909
peak=   -3.622 closest distance to " O   VAL A 153 " =    2.282
peak=   -3.619 closest distance to " CG  ASP A 231 " =    0.765
peak=   -3.607 closest distance to " OG  SER A 245 " =    0.814
peak=   -3.605 closest distance to " CZ  ARG A  66 " =    1.246
peak=   -3.601 closest distance to " O   ILE A 109 " =    2.701
peak=   -3.592 closest distance to " OG  SER A  97 " =    2.200
peak=   -3.591 closest distance to " C   ALA A 158 " =    1.189
peak=   -3.580 closest distance to " O   ALA A   7 " =    1.652
peak=   -3.580 closest distance to " OD2 ASP A 171 " =    1.865
peak=   -3.578 closest distance to " OXT GLY A 302 " =    2.935
peak=   -3.578 closest distance to " O   HOH Z 385 " =    4.002
peak=   -3.569 closest distance to " O   HOH Z 252 " =    4.237
peak=   -3.567 closest distance to " O   HOH Z 166 " =    1.779
peak=   -3.563 closest distance to " O   HOH Z  38 " =    1.026
peak=   -3.546 closest distance to " CE  MET A 105 " =    2.002
peak=   -3.546 closest distance to " O   HOH Z 426 " =    1.766
peak=   -3.543 closest distance to " O   HOH Z 185 " =    2.581
peak=   -3.541 closest distance to " O   VAL A  67 " =    2.791
peak=   -3.527 closest distance to " O   HOH Z 221 " =    1.518
peak=   -3.526 closest distance to " O   HOH Z 236 " =    1.336
peak=   -3.518 closest distance to " CH2 TRP A 177 " =    2.129
peak=   -3.510 closest distance to " O   HOH Z 150 " =    1.132
peak=   -3.510 closest distance to " O   PRO A 198 " =    1.267
peak=   -3.499 closest distance to " O   HOH Z 182 " =    0.742
peak=   -3.494 closest distance to " O   HOH Z   5 " =    1.576
peak=   -3.488 closest distance to " CD  LYS A 289 " =    2.476
peak=   -3.488 closest distance to " O   HOH Z  11 " =    1.732
peak=   -3.479 closest distance to " CB  CYS A 254 " =    2.456
peak=   -3.475 closest distance to " C   LEU A 143 " =    1.958
peak=   -3.471 closest distance to " O   HOH Z  98 " =    1.290
peak=   -3.465 closest distance to " OD1 ASN A 148 " =    1.746
peak=   -3.465 closest distance to " CB  GLN A  55 " =    1.393
peak=   -3.465 closest distance to " NH2AARG A 275 " =    5.447
peak=   -3.461 closest distance to " O   HOH Z  97 " =    1.668
peak=   -3.442 closest distance to " O   HOH Z 253 " =    1.273
peak=   -3.440 closest distance to " CB  PRO A 163 " =    2.745
peak=   -3.438 closest distance to " NE2 GLN A  58 " =    0.819
peak=   -3.436 closest distance to " CD  ARG A 139 " =    1.572
peak=   -3.435 closest distance to " CA  TYR A  68 " =    2.643
peak=   -3.429 closest distance to " CB  LEU A 167 " =    2.183
peak=   -3.425 closest distance to " CE  MET A 105 " =    2.130
peak=   -3.425 closest distance to " NH1 ARG A 195 " =    2.676
peak=   -3.423 closest distance to " CZ  TYR A 169 " =    1.847
peak=   -3.421 closest distance to " CD2 TYR A  68 " =    2.280
peak=   -3.420 closest distance to " CA  GLY A 241 " =    2.345
peak=   -3.418 closest distance to " CG  GLU A 152 " =    0.789
peak=   -3.412 closest distance to " C   ASN A 187 " =    1.823
peak=   -3.410 closest distance to " OG  SER A  63 " =    1.375
peak=   -3.409 closest distance to " O   HOH Z 292 " =    4.381
peak=   -3.408 closest distance to " N   THR A 157 " =    1.748
peak=   -3.403 closest distance to " O   HOH Z  92 " =    1.076
peak=   -3.401 closest distance to " CB  ASN A  39 " =    2.074
peak=   -3.396 closest distance to " CB  TYR A  15 " =    2.284
peak=   -3.395 closest distance to " CG2 THR A   4 " =    1.953
peak=   -3.394 closest distance to " O   TRP A  92 " =    1.837
peak=   -3.388 closest distance to " CB  SER A 258 " =    2.027
peak=   -3.385 closest distance to " N   ARG A 275 " =    1.719
peak=   -3.375 closest distance to " CD  ARG A 195 " =    5.131
peak=   -3.373 closest distance to " O   HOH Z 388 " =    1.977
peak=   -3.371 closest distance to " O   HOH Z 396 " =    1.752
peak=   -3.370 closest distance to " CG1AVAL A 121 " =    1.567
peak=   -3.362 closest distance to " N   SER A 276 " =    1.467
peak=   -3.360 closest distance to " O   HOH Z 222 " =    1.238
peak=   -3.360 closest distance to " CD2 TYR A 293 " =    2.031
peak=   -3.359 closest distance to " CG  LEU A  83 " =    2.054
peak=   -3.357 closest distance to " C   GLN A 240 " =    2.213
peak=   -3.341 closest distance to " O   HOH Z 177 " =    1.335
peak=   -3.337 closest distance to " CG  LYS A 193 " =    2.744
peak=   -3.336 closest distance to " CB  TRP A  85 " =    2.540
peak=   -3.333 closest distance to " N   SER A 212 " =    1.839
peak=   -3.322 closest distance to " NH2 ARG A  66 " =    5.243
peak=   -3.321 closest distance to " O   HOH Z 368 " =    1.844
peak=   -3.314 closest distance to " OG  SER A  87 " =    1.600
peak=   -3.309 closest distance to " O   HOH Z 435 " =    2.662
peak=   -3.309 closest distance to " O   HOH Z 390 " =    2.264
peak=   -3.306 closest distance to " OG  SER A  62 " =    1.311
peak=   -3.302 closest distance to " O   HOH Z 193 " =    1.897
peak=   -3.297 closest distance to " O   VAL A 153 " =    2.770
peak=   -3.285 closest distance to " CA  VAL A  67 " =    2.889
peak=   -3.282 closest distance to " O   HOH Z 163 " =    4.831
peak=   -3.280 closest distance to " OE1 GLN A  88 " =    1.110
peak=   -3.280 closest distance to " SG ACYS A 201 " =    2.235
peak=   -3.280 closest distance to " O   HOH Z  94 " =    1.989
peak=   -3.276 closest distance to " O   HOH Z 402 " =    1.515
peak=   -3.276 closest distance to " O   HOH Z 141 " =    1.793
peak=   -3.274 closest distance to " OH  TYR A 172 " =    1.623
peak=   -3.272 closest distance to " ND2 ASN A 187 " =    1.583
peak=   -3.267 closest distance to " O   HOH Z 103 " =    1.995
peak=   -3.259 closest distance to " ND2 ASN A  45 " =    1.000
peak=   -3.258 closest distance to " O   HOH Z 298 " =    2.941
peak=   -3.253 closest distance to " CG  TRP A 266 " =    1.652
peak=   -3.252 closest distance to " CB  ALA A  51 " =    1.889
peak=   -3.251 closest distance to " C   HIS A 108 " =    1.155
peak=   -3.249 closest distance to " O   HOH Z 418 " =    1.475
peak=   -3.247 closest distance to " O   HOH Z 281 " =    2.733
peak=   -3.245 closest distance to " O   HOH Z 122 " =    0.825
peak=   -3.244 closest distance to " SG  CYS A 168 " =    1.010
peak=   -3.235 closest distance to " O   GLY A 211 " =    1.525
peak=   -3.227 closest distance to " O   HOH Z 189 " =    1.903
peak=   -3.225 closest distance to " O   VAL A 174 " =    2.135
peak=   -3.225 closest distance to " CG  ARG A 219 " =    2.299
peak=   -3.222 closest distance to " CA  ASP A 107 " =    2.333
peak=   -3.222 closest distance to " CB  ALA A  43 " =    2.496
peak=   -3.220 closest distance to " CG  GLU A 152 " =    2.513
peak=   -3.218 closest distance to " CG  ARG A  66 " =    2.341
peak=   -3.215 closest distance to " OD1 ASN A 249 " =    1.179
peak=   -3.213 closest distance to " CA  ASN A 127 " =    1.183
peak=   -3.213 closest distance to " N   LEU A 261 " =    1.523
peak=   -3.210 closest distance to " O   HOH Z 198 " =    1.895
peak=   -3.206 closest distance to " CA  VAL A 232 " =    2.404
peak=   -3.205 closest distance to " O   HOH Z 340 " =    0.891
peak=   -3.200 closest distance to " OD1 ASP A 191 " =    1.712
peak=   -3.198 closest distance to " O   ALA A  10 " =    1.840
peak=   -3.196 closest distance to " O   HOH Z 325 " =    1.792
peak=   -3.194 closest distance to " CG  ASP A  50 " =    2.705
peak=   -3.191 closest distance to " CD2 LEU A 300 " =    2.758
peak=   -3.190 closest distance to " O   HOH Z 389 " =    2.007
peak=   -3.190 closest distance to " O   HOH Z 371 " =    1.796
peak=   -3.188 closest distance to " O   HOH Z 414 " =    1.205
peak=   -3.182 closest distance to " C   SER A 271 " =    1.243
peak=   -3.178 closest distance to " O   HOH Z 275 " =    1.626
peak=   -3.171 closest distance to " OD2 ASP A  65 " =    1.802
peak=   -3.170 closest distance to " O   HOH Z 399 " =    2.221
peak=   -3.163 closest distance to " ND2 ASN A  60 " =    1.593
peak=   -3.161 closest distance to " O   HOH Z 437 " =    1.015
peak=   -3.160 closest distance to " CD2 TRP A 274 " =    2.388
peak=   -3.155 closest distance to " O   HOH Z 434 " =    4.027
peak=   -3.148 closest distance to " C   GLY A  23 " =    2.334
peak=   -3.145 closest distance to " ND2 ASN A  45 " =    1.372
peak=   -3.142 closest distance to " ND2 ASN A 215 " =    2.240
peak=   -3.138 closest distance to " O   HOH Z  91 " =    2.214
peak=   -3.138 closest distance to " O   HOH Z 380 " =    4.846
peak=   -3.129 closest distance to " CG  PRO A 163 " =    2.328
peak=   -3.116 closest distance to " OG  SER A  28 " =    2.228
peak=   -3.116 closest distance to " CB  PRO A  54 " =    2.433
peak=   -3.114 closest distance to " O   HOH Z 323 " =    1.198
peak=   -3.113 closest distance to " CB  ALA A 227 " =    2.307
peak=   -3.098 closest distance to " CB  ASP A 286 " =    2.336
peak=   -3.084 closest distance to " CA  ASP A 298 " =    1.120
peak=   -3.084 closest distance to " CD  GLN A 223 " =    0.827
peak=   -3.084 closest distance to " O   ALA A  34 " =    2.039
peak=   -3.076 closest distance to " CD  LYS A 119 " =    0.979
peak=   -3.071 closest distance to " O   HOH Z  56 " =    1.149
peak=   -3.066 closest distance to " NH1 ARG A 195 " =    2.240
peak=   -3.063 closest distance to " O   HOH Z   9 " =    2.242
peak=   -3.060 closest distance to " CD2 LEU A 237 " =    2.829
peak=   -3.053 closest distance to " O   HOH Z  61 " =    1.376
peak=   -3.039 closest distance to " O   GLY A 203 " =    2.616

================= 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    :  0.4827 0.4797   6.288598e+00   6.284769e+00
   1_bss:  0.4766 0.4743   5.837466e+00   5.843618e+00
   1_xyz:  0.3664 0.4093   6.114023e+00   6.190806e+00
   1_adp:  0.3321 0.4148   6.071896e+00   6.198301e+00
   1_occ:  0.3319 0.4151   6.071558e+00   6.197989e+00
   2_bss:  0.3308 0.4131   6.070584e+00   6.196423e+00
   2_xyz:  0.2503 0.3206   5.851570e+00   6.039206e+00
   2_adp:  0.2272 0.2937   5.768765e+00   5.967360e+00
   2_occ:  0.2271 0.2936   5.768242e+00   5.966817e+00
   3_bss:  0.2269 0.2930   5.767515e+00   5.965254e+00
   3_xyz:  0.1724 0.2280   5.516612e+00   5.746125e+00
   3_adp:  0.1538 0.2090   5.429235e+00   5.669277e+00
   3_occ:  0.1538 0.2089   5.428909e+00   5.668753e+00
   4_bss:  0.1540 0.2087   5.429469e+00   5.667640e+00
   4_xyz:  0.1372 0.1888   5.328553e+00   5.566093e+00
   4_adp:  0.1317 0.1810   5.294594e+00   5.527549e+00
   4_occ:  0.1316 0.1808   5.294355e+00   5.527207e+00
   5_bss:  0.1319 0.1814   5.297216e+00   5.529516e+00
   5_xyz:  0.1226 0.1712   5.234240e+00   5.472795e+00
   5_adp:  0.1244 0.1690   5.237503e+00   5.464106e+00
   5_occ:  0.1243 0.1687   5.236957e+00   5.463553e+00
   5_bss:  0.1242 0.1685   5.236701e+00   5.462858e+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:  0.285  31.025   0.889   0.890   1.001   0.000   0.000   0.000
   1_xyz:  0.285  31.025   0.889   0.890   1.001   0.000   0.000   0.000
   1_adp:  0.285  31.025   0.889   0.890   1.001   0.000   0.000   0.000
   1_occ:  0.285  31.025   0.889   0.890   1.001   0.000   0.000   0.000
   2_bss:  0.338  72.887   0.186   0.538   0.383   0.000   0.000   0.000
   2_xyz:  0.338  72.887   0.186   0.538   0.383   0.000   0.000   0.000
   2_adp:  0.338  72.887   0.186   0.538   0.383   0.000   0.000   0.000
   2_occ:  0.338  72.887   0.186   0.538   0.383   0.000   0.000   0.000
   3_bss:  0.339  71.748  -0.710  -0.694  -0.740  -0.000  -0.000  -0.000
   3_xyz:  0.339  71.748  -0.710  -0.694  -0.740  -0.000  -0.000  -0.000
   3_adp:  0.339  71.748  -0.710  -0.694  -0.740  -0.000  -0.000  -0.000
   3_occ:  0.339  71.748  -0.710  -0.694  -0.740  -0.000  -0.000  -0.000
   4_bss:  0.339  71.748  -1.515  -1.468  -1.599  -0.000  -0.000  -0.000
   4_xyz:  0.339  71.748  -1.515  -1.468  -1.599  -0.000  -0.000  -0.000
   4_adp:  0.339  71.748  -1.515  -1.468  -1.599  -0.000  -0.000  -0.000
   4_occ:  0.339  71.748  -1.515  -1.468  -1.599  -0.000  -0.000  -0.000
   5_bss:  0.325  62.823  -1.847  -1.792  -1.909  -0.000  -0.000  -0.000
   5_xyz:  0.325  62.823  -1.847  -1.792  -1.909  -0.000  -0.000  -0.000
   5_adp:  0.325  62.823  -1.847  -1.792  -1.909  -0.000  -0.000  -0.000
   5_occ:  0.325  62.823  -1.847  -1.792  -1.909  -0.000  -0.000  -0.000
   5_bss:  0.317  52.875  -1.856  -1.832  -1.930  -0.000  -0.000  -0.000
------------------------------------------------------------------------
 stage     <pher>    fom   alpha         beta
   0    :  63.559 0.3452  0.4585    75634.385
   1_bss:  62.969 0.3510  0.4825    73015.655
   1_xyz:  47.403 0.5502  0.7631    48705.447
   1_adp:  48.808 0.5318  0.7432    50603.704
   1_occ:  48.852 0.5312  0.7411    50647.832
   2_bss:  48.677 0.5333  0.7322    50307.118
   2_xyz:  35.635 0.6915  0.9266    29765.476
   2_adp:  31.590 0.7385  0.9583    24365.767
   2_occ:  31.579 0.7386  0.9581    24331.677
   3_bss:  31.455 0.7399  0.9236    24203.576
   3_xyz:  23.155 0.8283  0.9864    13665.831
   3_adp:  20.705 0.8537  0.9897    11525.710
   3_occ:  20.701 0.8537  0.9897    11518.570
   4_bss:  20.654 0.8541  0.9620    11465.123
   4_xyz:  18.123 0.8786  0.9762     9203.768
   4_adp:  17.157 0.8880  0.9780     8621.565
   4_occ:  17.151 0.8881  0.9779     8620.312
   5_bss:  17.206 0.8876  0.9668     8696.810
   5_xyz:  16.016 0.8978  0.9701     7653.255
   5_adp:  15.713 0.9009  0.9692     7614.527
   5_occ:  15.704 0.9010  0.9690     7605.422
   5_bss:  15.696 0.9011  0.9650     7580.547
------------------------------------------------------------------------
 stage       angl   bond   chir   dihe   plan   repu  geom_target
   0    :   1.822  0.010  0.101 15.968  0.009  4.110   1.9350e-01
   1_bss:   1.822  0.010  0.101 15.968  0.009  4.110   1.9350e-01
   1_xyz:   1.672  0.014  0.106 16.369  0.007  4.106   1.6032e-01
   1_adp:   1.672  0.014  0.106 16.369  0.007  4.106   1.6032e-01
   1_occ:   1.672  0.014  0.106 16.369  0.007  4.106   1.6032e-01
   2_bss:   1.672  0.014  0.106 16.369  0.007  4.106   1.6032e-01
   2_xyz:   1.397  0.010  0.090 15.026  0.005  4.131   1.0518e-01
   2_adp:   1.397  0.010  0.090 15.026  0.005  4.131   1.0518e-01
   2_occ:   1.397  0.010  0.090 15.026  0.005  4.131   1.0518e-01
   3_bss:   1.397  0.010  0.090 15.026  0.005  4.131   1.0518e-01
   3_xyz:   1.205  0.010  0.078 14.514  0.004  4.117   8.1255e-02
   3_adp:   1.205  0.010  0.078 14.514  0.004  4.117   8.1255e-02
   3_occ:   1.205  0.010  0.078 14.514  0.004  4.117   8.1255e-02
   4_bss:   1.205  0.010  0.078 14.514  0.004  4.117   8.1255e-02
   4_xyz:   1.026  0.007  0.073 14.284  0.004  4.127   6.1415e-02
   4_adp:   1.026  0.007  0.073 14.284  0.004  4.127   6.1415e-02
   4_occ:   1.026  0.007  0.073 14.284  0.004  4.127   6.1415e-02
   5_bss:   1.026  0.007  0.073 14.284  0.004  4.127   6.1415e-02
   5_xyz:   1.092  0.008  0.076 14.436  0.004  4.123   6.6237e-02
   5_adp:   1.092  0.008  0.076 14.436  0.004  4.123   6.6237e-02
   5_occ:   1.092  0.008  0.076 14.436  0.004  4.123   6.6237e-02
   5_bss:   1.092  0.008  0.076 14.436  0.004  4.123   6.6237e-02
------------------------------------------------------------------------
                      Maximal deviations:
 stage       angl   bond   chir   dihe   plan   repu       |grad|
   0    :   9.874  0.070  0.314 85.889  0.055  1.532   2.4302e-01
   1_bss:   9.874  0.070  0.314 85.889  0.055  1.532   2.4302e-01
   1_xyz:   9.696  0.099  0.384 89.975  0.034  1.933   1.2518e-01
   1_adp:   9.696  0.099  0.384 89.975  0.034  1.933   1.2518e-01
   1_occ:   9.696  0.099  0.384 89.975  0.034  1.933   1.2518e-01
   2_bss:   9.696  0.099  0.384 89.975  0.034  1.933   1.2518e-01
   2_xyz:   7.966  0.054  0.284 78.158  0.042  2.174   1.6251e-01
   2_adp:   7.966  0.054  0.284 78.158  0.042  2.174   1.6251e-01
   2_occ:   7.966  0.054  0.284 78.158  0.042  2.174   1.6251e-01
   3_bss:   7.966  0.054  0.284 78.158  0.042  2.174   1.6251e-01
   3_xyz:   8.646  0.069  0.298 79.351  0.032  2.220   6.5073e-02
   3_adp:   8.646  0.069  0.298 79.351  0.032  2.220   6.5073e-02
   3_occ:   8.646  0.069  0.298 79.351  0.032  2.220   6.5073e-02
   4_bss:   8.646  0.069  0.298 79.351  0.032  2.220   6.5073e-02
   4_xyz:   8.407  0.052  0.260 82.209  0.037  2.341   8.5662e-02
   4_adp:   8.407  0.052  0.260 82.209  0.037  2.341   8.5662e-02
   4_occ:   8.407  0.052  0.260 82.209  0.037  2.341   8.5662e-02
   5_bss:   8.407  0.052  0.260 82.209  0.037  2.341   8.5662e-02
   5_xyz:   8.650  0.049  0.236 83.586  0.033  2.321   5.2009e-02
   5_adp:   8.650  0.049  0.236 83.586  0.033  2.321   5.2009e-02
   5_occ:   8.650  0.049  0.236 83.586  0.033  2.321   5.2009e-02
   5_bss:   8.650  0.049  0.236 83.586  0.033  2.321   5.2009e-02
------------------------------------------------------------------------
           |-----overall-----|---macromolecule----|------solvent-------|
  stage    b_max  b_min  b_ave  b_max  b_min  b_ave  b_max  b_min  b_ave
   0    :  63.06   5.09  16.02  49.51   5.09  12.19  63.06   6.19  36.87
   1_bss:  63.06   5.09  16.02  49.51   5.09  12.19  63.06   6.19  36.87
   1_xyz:  63.06   5.09  16.02  49.51   5.09  12.19  63.06   6.19  36.87
   1_adp: 104.55   0.00  19.40  98.70   0.00  15.50 104.55   0.00  40.62
   1_occ: 104.55   0.00  19.40  98.70   0.00  15.50 104.55   0.00  40.62
   2_bss: 104.55   0.00  19.40  98.70   0.00  15.50 104.55   0.00  40.62
   2_xyz: 104.55   0.00  19.40  98.70   0.00  15.50 104.55   0.00  40.62
   2_adp: 103.15   0.00  19.26  99.71   0.00  14.46 103.15   4.65  45.42
   2_occ: 103.15   0.00  19.26  99.71   0.00  14.46 103.15   4.65  45.42
   3_bss: 103.15   0.00  19.26  99.71   0.00  14.46 103.15   4.65  45.42
   3_xyz: 103.15   0.00  19.26  99.71   0.00  14.46 103.15   4.65  45.42
   3_adp: 107.36   0.00  19.04 107.36   0.00  13.68 105.47   4.47  48.23
   3_occ: 107.36   0.00  19.04 107.36   0.00  13.68 105.47   4.47  48.23
   4_bss: 107.36   0.00  19.04 107.36   0.00  13.68 105.47   4.47  48.23
   4_xyz: 107.36   0.00  19.04 107.36   0.00  13.68 105.47   4.47  48.23
   4_adp: 110.42   1.57  18.17 110.42   1.57  13.18 100.91   5.12  45.37
   4_occ: 110.42   1.57  18.17 110.42   1.57  13.18 100.91   5.12  45.37
   5_bss: 110.42   1.57  18.17 110.42   1.57  13.18 100.91   5.12  45.37
   5_xyz: 110.42   1.57  18.17 110.42   1.57  13.18 100.91   5.12  45.37
   5_adp:  97.70   2.54  16.95  97.70   2.54  12.81  83.00   4.98  39.50
   5_occ:  97.70   2.54  16.95  97.70   2.54  12.81  83.00   4.98  39.50
   5_bss:  97.61   2.45  16.86  97.61   2.45  12.72  82.91   4.89  39.41
------------------------------------------------------------------------
 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:    2.381    0.022    0.425
   1_adp:    2.381    0.022    0.425
   1_occ:    2.381    0.022    0.425
   2_bss:    2.381    0.022    0.425
   2_xyz:    2.088    0.087    0.637
   2_adp:    2.088    0.087    0.637
   2_occ:    2.088    0.087    0.637
   3_bss:    2.088    0.087    0.637
   3_xyz:    1.900    0.070    0.760
   3_adp:    1.900    0.070    0.760
   3_occ:    1.900    0.070    0.760
   4_bss:    1.900    0.070    0.760
   4_xyz:    1.701    0.073    0.808
   4_adp:    1.701    0.073    0.808
   4_occ:    1.701    0.073    0.808
   5_bss:    1.701    0.073    0.808
   5_xyz:    1.516    0.102    0.830
   5_adp:    1.516    0.102    0.830
   5_occ:    1.516    0.102    0.830
   5_bss:    1.516    0.102    0.830
------------------------------------------------------------------------

CPU time actual refinement: 340.12


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

Writing refined structure to PDB file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/noshake/run_1298/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/noshake/run_1298/model_refine_001_2mFobs-DFmodel.map
Writing mFobs-DFmodel XPLOR map to file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/noshake/run_1298/model_refine_001_mFobs-DFmodel.map
Writing map coefficients to MTZ file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/noshake/run_1298/model_refine_001_map_coeffs.mtz

Writing default parameters for subsequent refinement:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/noshake/run_1298/model_refine_002.def


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

Pure refinement (no I/O, processing, etc)= 339.97 
  Macro-tasks:
    bulk solvent and scale       = 37.55  
    individual site refinement   = 141.00 
    weights calculation          = 30.41  
    collect and process          = 6.40   
    model show statistics        = 0.10   
    TOTAL for macro-tasks        = 215.46 
  Micro-tasks:
    mask                            = 2.49   
    f_calc                          = 111.92 
    alpha_beta                      = 8.27   
    target                          = 1.17   
    gradients_wrt_atomic_parameters = 119.42 
    fmodel                         = 6.25   
    r_factors                      = 0.23   
    phase_errors                   = 10.29  
    foms                           = 0.31   
    TOTAL for micro-tasks          = 260.35 
NUMBER OF MASK CALCS=  5
Time per interpreted Python bytecode instruction: 4.903 micro seconds
Total CPU time: 5.89 minutes
from_scatterers_fft:    618 calls, 111.64 s
gradients_fft:          563 calls, 106.77 s

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

# Date 2008-01-16 Time 06:54:32 PST -0800 (1200495272.29 s)
Start R-work = 0.4827, R-free = 0.4797 (no bulk solvent and anisotropic scale)
Final R-work = 0.1465, R-free = 0.1894 (no bulk solvent and anisotropic scale)

Start R-work = 0.4766, R-free = 0.4743
Final R-work = 0.1242, R-free = 0.1685