# Date 2008-01-16 Time 03:46:02 PST -0800 (1200483962.02 s)
#phil __OFF__

Command line arguments: "../41.param" "main.number_of_macro_cycles=5" "--overwrite"

HOST = sunbird.lbl.gov
HOSTTYPE = x86_64-linux
USER = phzwart
PID = 29849
JOB_ID = 5159
SGE_ARCH = lx24-amd64
SGE_TASK_FIRST = 1
SGE_TASK_LAST = 1330
SGE_TASK_ID = 41

-------------------------------------------------------------------------------
  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: (68.4938, 46.4607, 87.6859, 90, 90, 90)
  Space group: P 21 21 21 (No. 19)

/net/cci-filer1/vol1/tmp/phzwart/tassos/trial/model.pdb
  Monomer Library directory:
    "/net/rosie/scratch3/phzwart/CCTBX/Sources/mon_lib"
  Total number of atoms: 2823
  Number of models: 1
  Model: 0
    Number of conformers: 2
    Conformer: "A"
      Number of atoms: 2769
      Number of chains: 2
        Number of residues, atoms: 302, 2333
          Classifications: {'peptide': 302}
          Modifications used: {'COO': 1}
          Link IDs: {'PTRANS': 7, 'CIS': 1, 'TRANS': 293}
        Number of residues, atoms: 436, 436
          Classifications: {'water': 436}
          Link IDs: {None: 435}
    Conformer: "B"
      Number of atoms: 2771
      Common with "A": 2717
      Number of chains: 2
        Number of residues, atoms: 302, 2333
          Classifications: {'peptide': 302}
          Modifications used: {'COO': 1}
          Link IDs: {'PTRANS': 7, 'CIS': 1, 'TRANS': 293}
          bond proxies already assigned to first conformer: 2332
        Number of residues, atoms: 438, 438
          Classifications: {'water': 438}
          Link IDs: {None: 437}
  Time building chain proxies: 3.31, per 1000 atoms: 1.17


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

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

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

Miller array info: /net/cci-filer1/vol1/tmp/phzwart/tassos/trial/1e0w.cns:FOBS,SIGMA
Observation type: xray.amplitude
Type of data: double, size=19589
Type of sigmas: double, size=19589
Number of Miller indices: 19589
Anomalous flag: False
Unit cell: (68.4938, 46.4607, 87.6859, 90, 90, 90)
Space group: P 21 21 21 (No. 19)
Systematic absences: 0
Centric reflections: 2427
Resolution range: 14.7968 1.95087
Completeness in resolution range: 0.934813
Completeness with d_max=infinity: 0.931966

Number of F-obs in resolution range:                   19589
Number of F-obs <= 0:                                  0
Refinement resolution range: d_max =  14.7968
                             d_min =   1.9509

Miller array info: /net/cci-filer1/vol1/tmp/phzwart/tassos/trial/1e0w.cns:TEST
Observation type: None
Type of data: int, size=19589
Type of sigmas: None
Number of Miller indices: 19589
Anomalous flag: False
Unit cell: (68.4938, 46.4607, 87.6859, 90, 90, 90)
Space group: P 21 21 21 (No. 19)
Systematic absences: 0
Centric reflections: 2427
Resolution range: 14.7968 1.95087
Completeness in resolution range: 0.934813
Completeness with d_max=infinity: 0.931966

Test (R-free flags) flag value: 1

Number of work/free reflections by resolution:
                                         work  free  %free
  bin  1: 14.7972 -  4.1745 [2203/2230]  1981   222  10.1%
  bin  2:  4.1745 -  3.3258 [2118/2134]  1902   216  10.2%
  bin  3:  3.3258 -  2.9090 [2084/2103]  1885   199   9.5%
  bin  4:  2.9090 -  2.6447 [2068/2098]  1855   213  10.3%
  bin  5:  2.6447 -  2.4561 [2044/2063]  1840   204  10.0%
  bin  6:  2.4561 -  2.3118 [2043/2079]  1835   208  10.2%
  bin  7:  2.3118 -  2.1964 [2030/2064]  1837   193   9.5%
  bin  8:  2.1964 -  2.1011 [2035/2070]  1824   211  10.4%
  bin  9:  2.1011 -  2.0204 [2003/2042]  1806   197   9.8%
  bin 10:  2.0204 -  1.9509 [ 961/2072]   865    96  10.0%
                                overall 17630  1959  10.0%
Writing MTZ file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/noshake/run_41/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:
        1.23 -     1.96: 17
        1.96 -     2.70: 181
        2.70 -     3.43: 4572
        3.43 -     4.17: 9516
        4.17 -     4.90: 14480
  Nonbonded interactions sorted by model distance:
             atom i - atom j             model   vdw sym.op. j
  " O   HOH Z  43 " - " O   HOH Z 169 "  1.226 3.040 -x+1,y+1/2,-z+1/2
  " NH1 ARG A  24 " - " O   GLY A  91 "  1.243 3.120 -x+1,y+1/2,-z+1/2
  " O   HOH Z  42 " - " O   HOH Z 176 "  1.342 3.040 -x+1,y+1/2,-z+1/2
  " NE2 GLN A  55 " - " O   ASN A 285 "  1.494 3.120 -x+1,y-1/2,-z+1/2
  " O   HOH Z 109 " - " O   HOH Z 417 "  1.502 3.040 -x+1,y-1/2,-z+1/2
  ... (remaining 28761 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_41/model_refine_001.eff

Writing geometry restraints to file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/noshake/run_41/model_refine_001.geo

CPU time processing inputs: 9.80


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

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

#phil __ON__
refinement {
  crystal_symmetry {
    unit_cell = 68.49375 46.4607 87.68585 90 90 90
    space_group = "P 21 21 21"
  }
  input {
    pdb {
      file_name = "/net/cci-filer1/vol1/tmp/phzwart/tassos/trial/model.pdb"
    }
    xray_data {
      file_name = "/net/cci-filer1/vol1/tmp/phzwart/tassos/trial/1e0w.cns"
      labels = "FOBS,SIGMA"
      r_free_flags {
        file_name = "/net/cci-filer1/vol1/tmp/phzwart/tassos/trial/1e0w.cns"
        label = "TEST"
        test_flag_value = 1
      }
    }
  }
  output {
    prefix = "model_refine"
    serial = 1
  }
  main {
    number_of_macro_cycles = 5
  }
}
#phil __OFF__


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


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


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

|--(resolution: 1.95 - 14.80 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.4359   r_free= 0.4282   ksol= 0.00   Bsol= 0.00   scale= 0.924    |
|                                                                             |
| 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:   0.60 A                  |
| x-ray target function (ml) for work reflections: 6.237589                   |
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
| Bin     Resolution   Compl.  No. Refl.    R-factors          Targets        |
|number     range              work test   work   test        work        test|
|  1: 14.7972 -  4.6561 0.99   1431  158 0.3320 0.3277       6.482      6.4609|
|  2:  4.6561 -  3.7149 0.99   1377  154 0.3483 0.3621      6.6699      6.7202|
|  3:  3.7149 -  3.2510 0.99   1344  152 0.4073 0.3959      6.5988      6.6295|
|  4:  3.2510 -  2.9564 0.99   1345  140 0.4273 0.4536      6.4606      6.5268|
|  5:  2.9564 -  2.7459 0.99   1318  155 0.4463 0.4235      6.2983      6.3185|
|  6:  2.7459 -  2.5849 0.99   1333  144 0.4710 0.4774      6.2246      6.1304|
|  7:  2.5849 -  2.4561 0.99   1315  151 0.4798 0.3906      6.2053      6.0673|
|  8:  2.4561 -  2.3496 0.98   1323  146 0.4865 0.4846      6.1506      6.1958|
|  9:  2.3496 -  2.2595 0.98   1304  142 0.5109 0.5018      6.1173      6.1679|
| 10:  2.2595 -  2.1817 0.98   1317  138 0.4993 0.4514      6.0723      6.0116|
| 11:  2.1817 -  2.1137 1.00   1295  159 0.5040 0.4718      6.0081      5.9925|
| 12:  2.1137 -  2.0535 0.97   1311  135 0.4978 0.5276      5.9482      5.9766|
| 13:  2.0535 -  1.9995 0.90   1195  131 0.5007 0.5109      5.8698      5.8105|
| 14:  1.9995 -  1.9509 0.33    422   54 0.5015 0.4789       5.894      5.7704|
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
|R-free likelihood based estimates for figures of merit, absolute phase error,|
|and distribution parameters alpha and beta (Acta Cryst. (1995). A51, 880-887)|
|                                                                             |
| Bin     Resolution      No. Refl.   FOM  Phase Scale    Alpha        Beta   |
|  #        range        work  test        error factor                       |
|  1: 14.7972 -  4.6561  1431   158  0.75  29.57   0.84     0.78      55414.44|
|  2:  4.6561 -  3.7149  1377   154  0.75  31.03   0.95     0.85      86329.11|
|  3:  3.7149 -  3.2510  1344   152  0.64  40.13   0.95     0.83      94501.57|
|  4:  3.2510 -  2.9564  1345   140  0.57  46.45   0.94     0.77      86814.24|
|  5:  2.9564 -  2.7459  1318   155  0.52  50.69   0.93     0.72      65952.73|
|  6:  2.7459 -  2.5849  1333   144  0.51  51.48   0.91     0.70      55427.65|
|  7:  2.5849 -  2.4561  1315   151  0.52  50.51   0.93     0.70      49014.33|
|  8:  2.4561 -  2.3496  1323   146  0.48  54.02   0.95     0.67      46498.24|
|  9:  2.3496 -  2.2595  1304   142  0.47  54.37   0.93     0.68      44426.40|
| 10:  2.2595 -  2.1817  1317   138  0.46  55.22   0.96     0.67      40007.37|
| 11:  2.1817 -  2.1137  1295   159  0.46  55.42   0.94     0.73      39619.48|
| 12:  2.1137 -  2.0535  1311   135  0.43  57.80   0.98     0.68      36803.41|
| 13:  2.0535 -  1.9995  1195   131  0.37  62.28   0.96     0.59      34805.23|
| 14:  1.9995 -  1.9509   422    54  0.32  66.00   1.02     0.43      30290.67|
|alpha:            min =        0.43 max =            0.85 mean =         0.72|
|beta:             min =    30290.67 max =        94501.57 mean =     56340.52|
|figures of merit: min =        0.00 max =            1.00 mean =         0.53|
|phase err.(work): min =        0.00 max =           89.99 mean =        49.25|
|phase err.(test): min =        0.00 max =           89.93 mean =        49.08|
|-----------------------------------------------------------------------------|

============================== 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 = 6.376762              wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 90.004   (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 1.440955              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 89.514   (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 |  1.226 -  1.593:        6 |
| 0.007 - 0.014:   729 |   0.989 -   1.976:   994 |  1.593 -  1.961:       11 |
| 0.014 - 0.021:   262 |   1.976 -   2.963:   470 |  1.961 -  2.328:       26 |
| 0.021 - 0.028:    63 |   2.963 -   3.950:   196 |  2.328 -  2.695:      155 |
| 0.028 - 0.035:    15 |   3.950 -   4.938:    66 |  2.695 -  3.063:     2255 |
| 0.035 - 0.042:     0 |   4.938 -   5.925:    29 |  3.063 -  3.430:     2317 |
| 0.042 - 0.049:     2 |   5.925 -   6.912:    16 |  3.430 -  3.798:     4156 |
| 0.049 - 0.056:     0 |   6.912 -   7.899:     2 |  3.798 -  4.165:     5360 |
| 0.056 - 0.063:     0 |   7.899 -   8.887:     3 |  4.165 -  4.533:     6505 |
| 0.063 - 0.070:     1 |   8.887 -   9.874:     4 |  4.533 -  4.900:     7975 |
|-----------------------------------------------------------------------------|
|-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 |        0.215 |
| planarity |      436 |   0.009    0.055  0.000 |       0.973 |              |
|  dihedral |      870 |  15.968   85.889  0.013 |       1.071 |              |
| nonbonded |     2439 |   4.108    4.900  1.226 |       0.993 |              |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 11.522)------------------------------------------|
|    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 - 14.80 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.4359   r_free= 0.4282   ksol= 0.00   Bsol= 0.00   scale= 0.924    |
|                                                                             |
| 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:   0.60 A                  |
| x-ray target function (ml) for work reflections: 6.237589                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.95 - 14.80 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.4281   r_free= 0.4197   ksol= 0.35   Bsol= 50.00   scale= 0.964   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (0.57,-0.53,1.57,-0.00,0.00,0.00); trace/3= 0.54                            |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.59 A                  |
| x-ray target function (ml) for work reflections: 6.229438                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 5.340849              wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 89.705   (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 0.816590              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 89.094   (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.4281      final r-factor (work) = 0.2925          |
| start r-factor (free) = 0.4197      final r-factor (free) = 0.3287          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 16.8458 = 5.34 * 0.50 * 6.2277 + 1.00 * 0.2153                              |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 16.2759 = 5.34 * 0.50 * 6.0534 + 1.00 * 0.1109                              |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 27     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.2925      final r-factor (work) = 0.2632          |
| start r-factor (free) = 0.3287      final r-factor (free) = 0.3352          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 4.9492 = 0.82 * 1.00 * 6.0534 + 1.00 * 0.0061                               |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 4.8142 = 0.82 * 1.00 * 5.8776 + 1.00 * 0.0146                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 30     |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 11.522)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.00    81.27   18.25    None  None   None       |
|    all(noH): 2823   0      0.00    81.27   18.25    None  None   None       |
|    Sol.    : 438    0      2.35    81.27   39.90    None  None   None       |
|    Mac.    : 2385   0      0.00    75.02   14.27    None  None   None       |
|    Hyd.    : 0      0      None    None    None     None  None   None       |
|    - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -      |
|       Distribution of isotropic (or equivalent) ADP for non-H atoms:        |
|    Bin#      value range     #atoms | Bin#      value range     #atoms      |
|      0:     0.000 -   8.127:  690   |   5:    40.635 -  48.762:   96        |
|      1:     8.127 -  16.254:  982   |   6:    48.762 -  56.889:   84        |
|      2:    16.254 -  24.381:  485   |   7:    56.889 -  65.016:   53        |
|      3:    24.381 -  32.508:  264   |   8:    65.016 -  73.143:   30        |
|      4:    32.508 -  40.635:  131   |   9:    73.143 -  81.270:    8        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.2632 r_free = 0.3352             target_work(ml) = 5.889         |
| occupancies: max = 1.00  min = 0.30   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.2630 r_free = 0.3352             target_work(ml) = 5.889         |
| occupancies: max = 1.00  min = 0.06   number of occupancies < 0.1:        1 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.95 - 14.80 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.2630   r_free= 0.3352   ksol= 0.35   Bsol= 50.00   scale= 1.045   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (0.57,-0.53,1.57,-0.00,0.00,0.00); trace/3= 0.54                            |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.39 A                  |
| x-ray target function (ml) for work reflections: 5.888730                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.95 - 14.80 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.2603   r_free= 0.3324   ksol= 0.33   Bsol= 50.00   scale= 1.006   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-1.88,-1.57,0.22,-0.00,0.00,0.00); trace/3= -1.08                          |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.39 A                  |
| x-ray target function (ml) for work reflections: 5.882487                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 5.874381              wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 94.340   (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 0.240544              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 148.105  (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.2603      final r-factor (work) = 0.1799          |
| start r-factor (free) = 0.3324      final r-factor (free) = 0.2365          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 17.3827 = 5.87 * 0.50 * 5.8804 + 1.00 * 0.1109                              |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 16.9798 = 5.87 * 0.50 * 5.7550 + 1.00 * 0.0762                              |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 27     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1799      final r-factor (work) = 0.1630          |
| start r-factor (free) = 0.2365      final r-factor (free) = 0.2162          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 1.3988 = 0.24 * 1.00 * 5.7550 + 1.00 * 0.0145                               |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 2.1478 = 0.24 * 1.00 * 5.5096 + 1.00 * 0.8225                               |
|-----------------------------------------------------------------------------|
| number of iterations = 7       |    number of function evaluations = 11     |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 11.522)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.00    80.79   17.94    None  None   None       |
|    all(noH): 2823   0      0.00    80.79   17.94    None  None   None       |
|    Sol.    : 438    0      4.63    80.79   40.39    None  None   None       |
|    Mac.    : 2385   0      0.00    76.05   13.81    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:     0.000 -   8.079:  528   |   5:    40.395 -  48.474:   95        |
|      1:     8.079 -  16.158: 1284   |   6:    48.474 -  56.553:   83        |
|      2:    16.158 -  24.237:  429   |   7:    56.553 -  64.632:   52        |
|      3:    24.237 -  32.316:  173   |   8:    64.632 -  72.711:   25        |
|      4:    32.316 -  40.395:  147   |   9:    72.711 -  80.790:    7        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.1630 r_free = 0.2162             target_work(ml) = 5.462         |
| occupancies: max = 1.00  min = 0.06   number of occupancies < 0.1:        1 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.1628 r_free = 0.2161             target_work(ml) = 5.460         |
| occupancies: max = 1.00  min = 0.10   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.95 - 14.80 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1628   r_free= 0.2161   ksol= 0.33   Bsol= 50.00   scale= 1.040   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-1.88,-1.57,0.22,-0.00,0.00,0.00); trace/3= -1.08                          |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.17 A                  |
| x-ray target function (ml) for work reflections: 5.460385                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.95 - 14.80 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1626   r_free= 0.2158   ksol= 0.33   Bsol= 50.00   scale= 1.015   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-3.04,-2.27,-0.52,-0.00,-0.00,-0.00); trace/3= -1.95                       |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.18 A                  |
| x-ray target function (ml) for work reflections: 5.458511                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 3.906354              wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 94.520   (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 44.412214             wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 89.705   (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1626      final r-factor (work) = 0.1323          |
| start r-factor (free) = 0.2158      final r-factor (free) = 0.1805          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 10.8419 = 3.91 * 0.50 * 5.5119 + 1.00 * 0.0762                              |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 10.5583 = 3.91 * 0.50 * 5.3723 + 1.00 * 0.0653                              |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 28     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1323      final r-factor (work) = 0.1226          |
| start r-factor (free) = 0.1805      final r-factor (free) = 0.1715          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 238.6139 = 44.41 * 1.00 * 5.3723 + 1.00 * 0.0191                            |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 233.0017 = 44.41 * 1.00 * 5.2461 + 1.00 * 0.0115                            |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 27     |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 11.522)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.08    91.94   18.36    None  None   None       |
|    all(noH): 2823   0      0.08    91.94   18.36    None  None   None       |
|    Sol.    : 438    0      6.33    91.39   44.45    None  None   None       |
|    Mac.    : 2385   0      0.08    91.94   13.57    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:     0.076 -   9.262:  784   |   5:    46.006 -  55.192:  111        |
|      1:     9.262 -  18.448: 1275   |   6:    55.192 -  64.378:   81        |
|      2:    18.448 -  27.634:  276   |   7:    64.378 -  73.564:   47        |
|      3:    27.634 -  36.820:  117   |   8:    73.564 -  82.750:   28        |
|      4:    36.820 -  46.006:   99   |   9:    82.750 -  91.936:    5        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.1226 r_free = 0.1715             target_work(ml) = 5.222         |
| occupancies: max = 1.00  min = 0.10   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.1226 r_free = 0.1715             target_work(ml) = 5.222         |
| occupancies: max = 1.00  min = 0.05   number of occupancies < 0.1:        1 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.95 - 14.80 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1226   r_free= 0.1715   ksol= 0.33   Bsol= 50.00   scale= 1.021   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-3.04,-2.27,-0.52,-0.00,-0.00,-0.00); trace/3= -1.95                       |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.16 A                  |
| x-ray target function (ml) for work reflections: 5.222169                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.95 - 14.80 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1225   r_free= 0.1714   ksol= 0.32   Bsol= 52.00   scale= 1.011   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-3.40,-2.58,-0.87,-0.00,-0.00,-0.00); trace/3= -2.29                       |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.16 A                  |
| x-ray target function (ml) for work reflections: 5.220024                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 1.450489              wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 128.216  (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 0.968012              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 97.488   (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1225      final r-factor (work) = 0.1203          |
| start r-factor (free) = 0.1714      final r-factor (free) = 0.1664          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 3.8710 = 1.45 * 0.50 * 5.2474 + 1.00 * 0.0653                               |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 3.8294 = 1.45 * 0.50 * 5.2143 + 1.00 * 0.0478                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 27     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1203      final r-factor (work) = 0.1187          |
| start r-factor (free) = 0.1664      final r-factor (free) = 0.1648          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 5.0594 = 0.97 * 1.00 * 5.2143 + 1.00 * 0.0119                               |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 5.0427 = 0.97 * 1.00 * 5.1983 + 1.00 * 0.0106                               |
|-----------------------------------------------------------------------------|
| number of iterations = 21      |    number of function evaluations = 24     |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 11.522)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.76    97.23   18.05    None  None   None       |
|    all(noH): 2823   0      0.76    97.23   18.05    None  None   None       |
|    Sol.    : 438    0      6.16    93.75   43.50    None  None   None       |
|    Mac.    : 2385   0      0.76    97.23   13.37    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:     0.759 -  10.406: 1076   |   5:    48.993 -  58.640:   97        |
|      1:    10.406 -  20.052: 1092   |   6:    58.640 -  68.287:   60        |
|      2:    20.052 -  29.699:  214   |   7:    68.287 -  77.934:   38        |
|      3:    29.699 -  39.346:  118   |   8:    77.934 -  87.581:   14        |
|      4:    39.346 -  48.993:  109   |   9:    87.581 -  97.228:    5        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.1187 r_free = 0.1648             target_work(ml) = 5.195         |
| occupancies: max = 1.00  min = 0.05   number of occupancies < 0.1:        1 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.1186 r_free = 0.1648             target_work(ml) = 5.195         |
| occupancies: max = 1.00  min = 0.04   number of occupancies < 0.1:        1 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.95 - 14.80 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1186   r_free= 0.1648   ksol= 0.32   Bsol= 52.00   scale= 1.007   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-3.40,-2.58,-0.87,-0.00,-0.00,-0.00); trace/3= -2.29                       |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.15 A                  |
| x-ray target function (ml) for work reflections: 5.194920                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.95 - 14.80 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1186   r_free= 0.1648   ksol= 0.32   Bsol= 52.00   scale= 1.010   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-3.28,-2.47,-0.77,-0.00,-0.00,-0.00); trace/3= -2.17                       |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.15 A                  |
| x-ray target function (ml) for work reflections: 5.195044                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 2.125521              wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 148.407  (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 0.625069              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 128.905  (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1186      final r-factor (work) = 0.1122          |
| start r-factor (free) = 0.1648      final r-factor (free) = 0.1607          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 5.5725 = 2.13 * 0.50 * 5.1985 + 1.00 * 0.0478                               |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 5.5545 = 2.13 * 0.50 * 5.1711 + 1.00 * 0.0589                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 27     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1122      final r-factor (work) = 0.1115          |
| start r-factor (free) = 0.1607      final r-factor (free) = 0.1587          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 3.2429 = 0.63 * 1.00 * 5.1711 + 1.00 * 0.0106                               |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 3.2330 = 0.63 * 1.00 * 5.1565 + 1.00 * 0.0098                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 31     |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 11.522)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.84    100.45  17.59    None  None   None       |
|    all(noH): 2823   0      0.84    100.45  17.59    None  None   None       |
|    Sol.    : 438    0      5.80    94.76   42.03    None  None   None       |
|    Mac.    : 2385   0      0.84    100.45  13.10    None  None   None       |
|    Hyd.    : 0      0      None    None    None     None  None   None       |
|    - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -      |
|       Distribution of isotropic (or equivalent) ADP for non-H atoms:        |
|    Bin#      value range     #atoms | Bin#      value range     #atoms      |
|      0:     0.841 -  10.801: 1204   |   5:    50.644 -  60.604:   74        |
|      1:    10.801 -  20.762: 1009   |   6:    60.604 -  70.565:   51        |
|      2:    20.762 -  30.722:  200   |   7:    70.565 -  80.525:   31        |
|      3:    30.722 -  40.683:  124   |   8:    80.525 -  90.486:    6        |
|      4:    40.683 -  50.644:  120   |   9:    90.486 - 100.447:    4        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.1115 r_free = 0.1587             target_work(ml) = 5.151         |
| occupancies: max = 1.00  min = 0.04   number of occupancies < 0.1:        1 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.1114 r_free = 0.1586             target_work(ml) = 5.150         |
| occupancies: max = 1.00  min = 0.04   number of occupancies < 0.1:        1 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.95 - 14.80 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1114   r_free= 0.1586   ksol= 0.32   Bsol= 52.00   scale= 1.006   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-3.28,-2.47,-0.77,-0.00,-0.00,-0.00); trace/3= -2.17                       |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.14 A                  |
| x-ray target function (ml) for work reflections: 5.150050                   |
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
| Bin     Resolution   Compl.  No. Refl.    R-factors          Targets        |
|number     range              work test   work   test        work        test|
|  1: 14.7972 -  4.6561 0.99   1431  158 0.0972 0.1314      5.3874      5.5778|
|  2:  4.6561 -  3.7149 0.99   1377  154 0.0837 0.1124      5.4258      5.6156|
|  3:  3.7149 -  3.2510 0.99   1344  152 0.1071 0.1540      5.4707      5.8568|
|  4:  3.2510 -  2.9564 0.99   1345  140 0.1214 0.1627      5.4421      5.6039|
|  5:  2.9564 -  2.7459 0.99   1318  155 0.1285 0.1576      5.3201      5.5086|
|  6:  2.7459 -  2.5849 0.99   1333  144 0.1233 0.1976      5.1981      5.4981|
|  7:  2.5849 -  2.4561 0.99   1315  151 0.1255 0.1651       5.164      5.3371|
|  8:  2.4561 -  2.3496 0.98   1323  146 0.1152 0.1572      5.0703      5.2656|
|  9:  2.3496 -  2.2595 0.98   1304  142 0.1167 0.1912      5.0207      5.3959|
| 10:  2.2595 -  2.1817 0.98   1317  138 0.1134 0.1713      4.9514      5.1544|
| 11:  2.1817 -  2.1137 1.00   1295  159 0.1135 0.1860      4.9271      5.3093|
| 12:  2.1137 -  2.0535 0.97   1311  135 0.1198 0.1649      4.9049      5.1094|
| 13:  2.0535 -  1.9995 0.90   1195  131 0.1061 0.1727      4.7511       4.982|
| 14:  1.9995 -  1.9509 0.33    422   54 0.0927 0.1755      4.6119      4.9835|
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
|R-free likelihood based estimates for figures of merit, absolute phase error,|
|and distribution parameters alpha and beta (Acta Cryst. (1995). A51, 880-887)|
|                                                                             |
| Bin     Resolution      No. Refl.   FOM  Phase Scale    Alpha        Beta   |
|  #        range        work  test        error factor                       |
|  1: 14.7972 -  4.6561  1431   158  0.94   9.37   0.98     0.95       7460.42|
|  2:  4.6561 -  3.7149  1377   154  0.95   7.95   1.02     1.02       9145.97|
|  3:  3.7149 -  3.2510  1344   152  0.93  11.71   1.04     1.03      10409.36|
|  4:  3.2510 -  2.9564  1345   140  0.92  13.72   1.02     1.01      10243.59|
|  5:  2.9564 -  2.7459  1318   155  0.90  16.19   1.00     0.98       8584.92|
|  6:  2.7459 -  2.5849  1333   144  0.90  16.42   0.98     0.95       6846.86|
|  7:  2.5849 -  2.4561  1315   151  0.90  15.92   0.99     0.96       6256.00|
|  8:  2.4561 -  2.3496  1323   146  0.91  15.09   1.00     0.97       5366.27|
|  9:  2.3496 -  2.2595  1304   142  0.90  15.82   1.00     0.95       4902.40|
| 10:  2.2595 -  2.1817  1317   138  0.90  16.15   1.00     0.97       4450.81|
| 11:  2.1817 -  2.1137  1295   159  0.90  16.56   0.99     0.96       4441.90|
| 12:  2.1137 -  2.0535  1311   135  0.90  16.81   1.01     1.01       4192.84|
| 13:  2.0535 -  1.9995  1195   131  0.91  15.81   0.99     0.97       3212.26|
| 14:  1.9995 -  1.9509   422    54  0.93  12.29   0.99     0.95       2219.04|
|alpha:            min =        0.95 max =            1.03 mean =         0.98|
|beta:             min =     2219.04 max =        10409.36 mean =      6527.75|
|figures of merit: min =        0.00 max =            1.00 mean =         0.91|
|phase err.(work): min =        0.00 max =           89.97 mean =        14.30|
|phase err.(test): min =        0.00 max =           90.00 mean =        13.71|
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.95 - 14.80 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1114   r_free= 0.1586   ksol= 0.32   Bsol= 51.97   scale= 1.010   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-3.09,-2.33,-0.59,-0.00,-0.00,-0.00); trace/3= -2.00                       |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.14 A                  |
| x-ray target function (ml) for work reflections: 5.150194                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.95 - 14.80 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1114   r_free= 0.1586   ksol= 0.32   Bsol= 51.97   scale= 1.010   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-3.09,-2.33,-0.59,-0.00,-0.00,-0.00); trace/3= -2.00                       |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.14 A                  |
| x-ray target function (ml) for work reflections: 5.150194                   |
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
| Bin     Resolution   Compl.  No. Refl.    R-factors          Targets        |
|number     range              work test   work   test        work        test|
|  1: 14.7972 -  4.6561 0.99   1431  158 0.0973 0.1316      5.3887      5.5794|
|  2:  4.6561 -  3.7149 0.99   1377  154 0.0837 0.1124      5.4262      5.6155|
|  3:  3.7149 -  3.2510 0.99   1344  152 0.1071 0.1541      5.4707      5.8571|
|  4:  3.2510 -  2.9564 0.99   1345  140 0.1214 0.1627      5.4421      5.6039|
|  5:  2.9564 -  2.7459 0.99   1318  155 0.1285 0.1575      5.3201      5.5084|
|  6:  2.7459 -  2.5849 0.99   1333  144 0.1232 0.1976       5.198       5.498|
|  7:  2.5849 -  2.4561 0.99   1315  151 0.1255 0.1651      5.1641      5.3372|
|  8:  2.4561 -  2.3496 0.98   1323  146 0.1152 0.1572      5.0704      5.2656|
|  9:  2.3496 -  2.2595 0.98   1304  142 0.1167 0.1911      5.0209      5.3961|
| 10:  2.2595 -  2.1817 0.98   1317  138 0.1134 0.1714      4.9514      5.1546|
| 11:  2.1817 -  2.1137 1.00   1295  159 0.1135 0.1860      4.9272      5.3095|
| 12:  2.1137 -  2.0535 0.97   1311  135 0.1198 0.1648      4.9047      5.1091|
| 13:  2.0535 -  1.9995 0.90   1195  131 0.1061 0.1725      4.7509      4.9815|
| 14:  1.9995 -  1.9509 0.33    422   54 0.0927 0.1753       4.612      4.9827|
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
|R-free likelihood based estimates for figures of merit, absolute phase error,|
|and distribution parameters alpha and beta (Acta Cryst. (1995). A51, 880-887)|
|                                                                             |
| Bin     Resolution      No. Refl.   FOM  Phase Scale    Alpha        Beta   |
|  #        range        work  test        error factor                       |
|  1: 14.7972 -  4.6561  1431   158  0.94   9.38   0.98     0.95       7483.40|
|  2:  4.6561 -  3.7149  1377   154  0.95   7.96   1.03     1.02       9158.20|
|  3:  3.7149 -  3.2510  1344   152  0.93  11.71   1.04     1.04      10412.99|
|  4:  3.2510 -  2.9564  1345   140  0.92  13.72   1.02     1.01      10246.06|
|  5:  2.9564 -  2.7459  1318   155  0.90  16.20   1.01     0.99       8584.19|
|  6:  2.7459 -  2.5849  1333   144  0.90  16.42   0.98     0.95       6846.30|
|  7:  2.5849 -  2.4561  1315   151  0.90  15.93   1.00     0.96       6257.50|
|  8:  2.4561 -  2.3496  1323   146  0.91  15.10   1.01     0.98       5366.64|
|  9:  2.3496 -  2.2595  1304   142  0.90  15.83   1.00     0.96       4904.01|
| 10:  2.2595 -  2.1817  1317   138  0.90  16.15   1.01     0.98       4450.35|
| 11:  2.1817 -  2.1137  1295   159  0.90  16.57   1.00     0.97       4442.88|
| 12:  2.1137 -  2.0535  1311   135  0.90  16.81   1.02     1.01       4191.96|
| 13:  2.0535 -  1.9995  1195   131  0.91  15.81   1.00     0.98       3209.93|
| 14:  1.9995 -  1.9509   422    54  0.93  12.28   0.99     0.96       2216.40|
|alpha:            min =        0.95 max =            1.04 mean =         0.98|
|beta:             min =     2216.40 max =        10412.99 mean =      6530.95|
|figures of merit: min =        0.00 max =            1.00 mean =         0.91|
|phase err.(work): min =        0.00 max =           89.96 mean =        14.31|
|phase err.(test): min =        0.00 max =           89.99 mean =        13.72|
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 11.522)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.81    100.42  17.56    None  None   None       |
|    all(noH): 2823   0      0.81    100.42  17.56    None  None   None       |
|    Sol.    : 438    0      5.77    94.73   42.00    None  None   None       |
|    Mac.    : 2385   0      0.81    100.42  13.07    None  None   None       |
|    Hyd.    : 0      0      None    None    None     None  None   None       |
|    - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -      |
|       Distribution of isotropic (or equivalent) ADP for non-H atoms:        |
|    Bin#      value range     #atoms | Bin#      value range     #atoms      |
|      0:     0.812 -  10.773: 1204   |   5:    50.615 -  60.576:   74        |
|      1:    10.773 -  20.733: 1009   |   6:    60.576 -  70.536:   51        |
|      2:    20.733 -  30.694:  200   |   7:    70.536 -  80.497:   31        |
|      3:    30.694 -  40.654:  124   |   8:    80.497 -  90.457:    6        |
|      4:    40.654 -  50.615:  120   |   9:    90.457 - 100.418:    4        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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


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

Number of peaks found at mFobs-DFmodel map (map cutoff=3.00 sigma)= 291         
Filter by distance & map next to the model:
   mapped sites are within: 0.528 - 4.323
   number of sites selected in [dist_min= 0.70, dist_max= 6.00]: 284 from: 291
   mapped sites are within: 0.755 - 4.323

peak=    6.153 closest distance to " OE1 GLN A  55 " =    2.176
peak=    5.859 closest distance to " O   HOH Z 375 " =    1.189
peak=    5.605 closest distance to " O   HOH Z 142 " =    1.747
peak=    5.517 closest distance to " CB  ARG A 275 " =    0.979
peak=    5.470 closest distance to " NE2 GLN A  11 " =    1.170
peak=    5.423 closest distance to " CG  PRO A  54 " =    1.269
peak=    5.403 closest distance to " O   HOH Z 417 " =    2.231
peak=    5.128 closest distance to " NH2 ARG A  56 " =    2.066
peak=    4.919 closest distance to " O   HOH Z 236 " =    1.475
peak=    4.871 closest distance to " O   HOH Z 126 " =    1.959
peak=    4.831 closest distance to " O   HOH Z 232 " =    2.415
peak=    4.821 closest distance to " O   HOH Z 287 " =    1.775
peak=    4.813 closest distance to " O   HOH Z 402 " =    1.424
peak=    4.780 closest distance to " O   HOH Z 112 " =    1.273
peak=    4.770 closest distance to " O   HOH Z 188 " =    1.514
peak=    4.713 closest distance to " O   HOH Z 427 " =    2.924
peak=    4.701 closest distance to " O   HOH Z 369 " =    2.173
peak=    4.624 closest distance to " O   HOH Z 403 " =    2.380
peak=    4.513 closest distance to " O   HOH Z 403 " =    1.094
peak=    4.512 closest distance to " CG  PRO A 213 " =    1.217
peak=    4.507 closest distance to " CB  GLN A 223 " =    1.522
peak=    4.462 closest distance to " CB  PRO A  54 " =    1.002
peak=    4.426 closest distance to " O   SER A  87 " =    2.146
peak=    4.353 closest distance to " ND2 ASN A 187 " =    1.416
peak=    4.346 closest distance to " O   HOH Z 346 " =    1.664
peak=    4.343 closest distance to " C   PRO A 198 " =    1.495
peak=    4.340 closest distance to " O   HOH Z  15 " =    2.313
peak=    4.326 closest distance to " OG ASER A 258 " =    2.905
peak=    4.318 closest distance to " O   HOH Z 327 " =    1.647
peak=    4.313 closest distance to " NZ  LYS A 117 " =    2.971
peak=    4.302 closest distance to " O   HOH Z 248 " =    1.576
peak=    4.283 closest distance to " O   HOH Z  78 " =    1.672
peak=    4.272 closest distance to " CD2 TRP A 179 " =    1.304
peak=    4.252 closest distance to " O   HOH Z  43 " =    1.561
peak=    4.248 closest distance to " CB  ARG A  79 " =    1.431
peak=    4.245 closest distance to " O   HOH Z 173 " =    2.080
peak=    4.238 closest distance to " CB  SER A  63 " =    1.167
peak=    4.229 closest distance to " CA  TYR A  30 " =    0.946
peak=    4.198 closest distance to " CG  PRO A  90 " =    1.135
peak=    4.176 closest distance to " O   HOH Z  40 " =    1.911
peak=    4.173 closest distance to " CB  VAL A 265 " =    1.333
peak=    4.166 closest distance to " O   HOH Z 193 " =    1.556
peak=    4.164 closest distance to " O   HOH Z 365 " =    2.563
peak=    4.151 closest distance to " CB  GLN A 183 " =    1.231
peak=    4.143 closest distance to " CG2 VAL A 257 " =    0.819
peak=    4.077 closest distance to " CG  PRO A 243 " =    1.064
peak=    4.075 closest distance to " CG  GLN A  58 " =    0.948
peak=    4.058 closest distance to " CB  GLU A 152 " =    1.256
peak=    4.054 closest distance to " O   HOH Z 272 " =    1.864
peak=    4.048 closest distance to " CG  TRP A 179 " =    2.166
peak=    4.046 closest distance to " O   HOH Z 234 " =    3.498
peak=    4.044 closest distance to " O   HOH Z 371 " =    1.860
peak=    4.039 closest distance to " O   HOH Z 250 " =    1.422
peak=    4.032 closest distance to " CG  LYS A  76 " =    1.894
peak=    4.021 closest distance to " OG BSER A 164 " =    2.269
peak=    4.014 closest distance to " CB  ASN A 148 " =    1.522
peak=    3.995 closest distance to " CB  THR A  31 " =    1.611
peak=    3.988 closest distance to " O   HOH Z 298 " =    1.823
peak=    3.986 closest distance to " O   HOH Z 132 " =    2.625
peak=    3.986 closest distance to " CB  VAL A 202 " =    1.639
peak=    3.984 closest distance to " O   HOH Z 394 " =    1.677
peak=    3.958 closest distance to " O   HOH Z 425 " =    1.299
peak=    3.954 closest distance to " CG  ARG A  66 " =    2.627
peak=    3.944 closest distance to " O   HOH Z 188 " =    2.635
peak=    3.929 closest distance to " O   HOH Z 209 " =    2.205
peak=    3.918 closest distance to " CZ  PHE A 218 " =    1.157
peak=    3.912 closest distance to " CB  ARG A 190 " =    1.715
peak=    3.902 closest distance to " O   HOH Z 419 " =    2.217
peak=    3.899 closest distance to " CB  ILE A 120 " =    1.440
peak=    3.892 closest distance to " O   HOH Z 126 " =    1.538
peak=    3.861 closest distance to " CB  GLN A  88 " =    1.211
peak=    3.859 closest distance to " CB  TRP A 266 " =    1.184
peak=    3.853 closest distance to " O   HOH Z  85 " =    1.321
peak=    3.852 closest distance to " CA  ARG A  36 " =    1.004
peak=    3.830 closest distance to " O   HOH Z 368 " =    3.577
peak=    3.825 closest distance to " O   HOH Z   3 " =    2.060
peak=    3.818 closest distance to " O   HOH Z 353 " =    2.558
peak=    3.809 closest distance to " CG AARG A 275 " =    1.076
peak=    3.791 closest distance to " NH2AARG A 190 " =    1.993
peak=    3.790 closest distance to " O   HOH Z 406 " =    1.555
peak=    3.777 closest distance to " CA  ARG A 195 " =    1.250
peak=    3.772 closest distance to " O   HOH Z 109 " =    1.479
peak=    3.738 closest distance to " CG  PRO A 198 " =    1.300
peak=    3.733 closest distance to " CB  ARG A  79 " =    0.907
peak=    3.731 closest distance to " O   HOH Z  61 " =    1.479
peak=    3.725 closest distance to " CA  ALA A  51 " =    0.962
peak=    3.723 closest distance to " O   HOH Z  44 " =    1.957
peak=    3.721 closest distance to " CD2 LEU A 297 " =    1.049
peak=    3.720 closest distance to " O   HOH Z 305 " =    3.429
peak=    3.718 closest distance to " O   HOH Z   1 " =    1.545
peak=    3.716 closest distance to " O   HOH Z 425 " =    1.973
peak=    3.709 closest distance to " O   HOH Z   1 " =    1.915
peak=    3.707 closest distance to " N   TYR A 116 " =    1.564
peak=    3.702 closest distance to " O   HOH Z  97 " =    2.154
peak=    3.696 closest distance to " NH1BARG A 145 " =    1.312
peak=    3.696 closest distance to " O   HOH Z 394 " =    3.646
peak=    3.692 closest distance to " CE  LYS A 119 " =    1.249
peak=    3.692 closest distance to " O   HOH Z 261 " =    1.923
peak=    3.683 closest distance to " CA  ASN A 127 " =    1.140
peak=    3.679 closest distance to " N   ASN A  39 " =    1.276
peak=    3.674 closest distance to " CB  ASN A 110 " =    1.059
peak=    3.671 closest distance to " CB  SER A  26 " =    1.757
peak=    3.660 closest distance to " CG2 ILE A 120 " =    1.229
peak=    3.656 closest distance to " O   HOH Z 357 " =    1.913
peak=    3.656 closest distance to " O   HOH Z  61 " =    1.628
peak=    3.651 closest distance to " CA  ASN A 217 " =    1.120
peak=    3.640 closest distance to " CB  PRO A  90 " =    1.091
peak=    3.637 closest distance to " O   HOH Z  59 " =    1.642
peak=    3.634 closest distance to " CB  GLU A  46 " =    1.117
peak=    3.633 closest distance to " O   HOH Z  43 " =    1.240
peak=    3.633 closest distance to " O   HOH Z 128 " =    2.036
peak=    3.632 closest distance to " CB  GLU A 128 " =    0.998
peak=    3.630 closest distance to " O   HOH Z  78 " =    2.211
peak=    3.629 closest distance to " O   HOH Z 158 " =    3.081
peak=    3.629 closest distance to " O   HOH Z 117 " =    1.970
peak=    3.626 closest distance to " O   HOH Z 290 " =    1.034
peak=    3.622 closest distance to " CG  MET A 185 " =    1.220
peak=    3.603 closest distance to " CB  ASN A 142 " =    1.068
peak=    3.602 closest distance to " O   HOH Z 128 " =    2.010
peak=    3.580 closest distance to " CB  TYR A 169 " =    1.017
peak=    3.580 closest distance to " O   HOH Z 258 " =    2.116
peak=    3.577 closest distance to " O   HOH Z 203 " =    1.746
peak=    3.570 closest distance to " O   HOH Z 214 " =    2.361
peak=    3.566 closest distance to " CE  LYS A  76 " =    0.898
peak=    3.565 closest distance to " ND2 ASN A 249 " =    0.845
peak=    3.563 closest distance to " CA  LEU A 300 " =    1.062
peak=    3.562 closest distance to " O   HOH Z 132 " =    0.973
peak=    3.561 closest distance to " CB  GLN A  89 " =    1.402
peak=    3.559 closest distance to " O   HOH Z 124 " =    2.003
peak=    3.556 closest distance to " O   HOH Z 132 " =    2.001
peak=    3.554 closest distance to " O   HOH Z  43 " =    1.650
peak=    3.554 closest distance to " O   HOH Z 233 " =    1.765
peak=    3.552 closest distance to " CB  SER A  62 " =    0.863
peak=    3.544 closest distance to " O   HOH Z  66 " =    2.256
peak=    3.541 closest distance to " O   HOH Z  85 " =    1.821
peak=    3.538 closest distance to " OD1 ASN A  69 " =    2.442
peak=    3.536 closest distance to " O   HOH Z 141 " =    1.682
peak=    3.535 closest distance to " N   GLU A   2 " =    1.458
peak=    3.535 closest distance to " CB  GLU A 277 " =    3.533
peak=    3.531 closest distance to " N   PHE A 130 " =    1.322
peak=    3.518 closest distance to " O   HOH Z  88 " =    2.457
peak=    3.517 closest distance to " CA  ASN A 215 " =    0.982
peak=    3.508 closest distance to " O   HOH Z 368 " =    2.048
peak=    3.505 closest distance to " N   CYS A 260 " =    0.930
peak=    3.496 closest distance to " O   HOH Z 286 " =    2.383
peak=    3.492 closest distance to " CB  ASN A  39 " =    0.829
peak=    3.491 closest distance to " O   HOH Z 180 " =    2.230
peak=    3.488 closest distance to " O   HOH Z 193 " =    1.858
peak=    3.488 closest distance to " CA  ALA A 129 " =    1.534
peak=    3.485 closest distance to " O   HOH Z 407 " =    1.346
peak=    3.482 closest distance to " O   HOH Z  10 " =    1.694
peak=    3.482 closest distance to " CB  ALA A 114 " =    0.929
peak=    3.479 closest distance to " N   GLN A 278 " =    1.356
peak=    3.479 closest distance to " CG  LEU A 167 " =    1.295
peak=    3.478 closest distance to " CB  LEU A 300 " =    1.002
peak=    3.477 closest distance to " CA  ASP A 162 " =    1.076
peak=    3.466 closest distance to " O   HOH Z 422 " =    2.464
peak=    3.463 closest distance to " OG BSER A 258 " =    3.343
peak=    3.444 closest distance to " CB  SER A  99 " =    0.830
peak=    3.444 closest distance to " O   HOH Z  48 " =    1.602
peak=    3.435 closest distance to " CB  ASN A 187 " =    1.275
peak=    3.430 closest distance to " CA  ALA A 158 " =    1.365
peak=    3.429 closest distance to " CB  LEU A  83 " =    0.755
peak=    3.425 closest distance to " CA  ALA A 233 " =    0.991
peak=    3.418 closest distance to " O   HOH Z 423 " =    1.874
peak=    3.418 closest distance to " O   THR A 220 " =    1.289
peak=    3.413 closest distance to " O   HOH Z 325 " =    2.310
peak=    3.405 closest distance to " C   PHE A  59 " =    0.879
peak=    3.404 closest distance to " CB  ARG A 139 " =    1.014
peak=    3.395 closest distance to " O   HOH Z  92 " =    2.433
peak=    3.393 closest distance to " N   ASP A 162 " =    1.077
peak=    3.392 closest distance to " CB  THR A  52 " =    0.809
peak=    3.392 closest distance to " NE2 GLN A  73 " =    3.944
peak=    3.389 closest distance to " CG2 THR A 221 " =    1.106
peak=    3.382 closest distance to " CD  ARG A 269 " =    0.966
peak=    3.382 closest distance to " O   HOH Z 380 " =    1.709
peak=    3.380 closest distance to " NH2BARG A 145 " =    2.096
peak=    3.379 closest distance to " NE2 GLN A  77 " =    3.039
peak=    3.379 closest distance to " O   HOH Z 345 " =    3.167
peak=    3.374 closest distance to " O   HOH Z 345 " =    1.732
peak=    3.373 closest distance to " CB  SER A   3 " =    1.196
peak=    3.367 closest distance to " OG BSER A  99 " =    2.462
peak=    3.364 closest distance to " CA  ASP A 124 " =    0.833
peak=    3.363 closest distance to " CB  SER A 212 " =    1.199
peak=    3.363 closest distance to " O   HOH Z  88 " =    2.473
peak=    3.362 closest distance to " OE1 GLU A   2 " =    2.089
peak=    3.356 closest distance to " CB  ALA A 114 " =    1.228
peak=    3.356 closest distance to " CG2 ILE A  20 " =    1.565
peak=    3.353 closest distance to " CA  THR A 221 " =    1.106
peak=    3.350 closest distance to " CB  TRP A 179 " =    1.298
peak=    3.342 closest distance to " CA  VAL A 125 " =    1.080
peak=    3.340 closest distance to " O   HOH Z 415 " =    3.616
peak=    3.339 closest distance to " CA  ALA A  84 " =    1.284
peak=    3.339 closest distance to " O   HOH Z 421 " =    1.998
peak=    3.335 closest distance to " N   ARG A 156 " =    1.231
peak=    3.333 closest distance to " CA  ASP A 149 " =    1.173
peak=    3.329 closest distance to " O   HOH Z 411 " =    3.885
peak=    3.327 closest distance to " CB  ASP A 191 " =    1.181
peak=    3.326 closest distance to " O   HOH Z  28 " =    1.851
peak=    3.324 closest distance to " O   HOH Z 291 " =    1.420
peak=    3.315 closest distance to " CG2 VAL A 197 " =    1.023
peak=    3.313 closest distance to " O   HOH Z 213 " =    2.036
peak=    3.299 closest distance to " O   GLN A 194 " =    1.546
peak=    3.296 closest distance to " CA  TYR A 116 " =    1.311
peak=    3.292 closest distance to " O   HOH Z  21 " =    1.832
peak=    3.292 closest distance to " N   ASN A 127 " =    1.287
peak=    3.284 closest distance to " CZ3 TRP A 266 " =    1.061
peak=    3.283 closest distance to " O   HOH Z 261 " =    1.907
peak=    3.281 closest distance to " O   HOH Z 227 " =    1.915
peak=    3.279 closest distance to " O   HOH Z 119 " =    4.323
peak=    3.279 closest distance to " O   HOH Z 337 " =    3.558
peak=    3.278 closest distance to " CA  SER A  32 " =    1.691
peak=    3.272 closest distance to " O   HOH Z 371 " =    2.916
peak=    3.272 closest distance to " O   HOH Z 280 " =    2.972
peak=    3.271 closest distance to " O   HOH Z 294 " =    1.440
peak=    3.269 closest distance to " O   HOH Z 282 " =    1.917
peak=    3.268 closest distance to " CB  SER A  62 " =    1.244
peak=    3.260 closest distance to " OG ASER A  99 " =    1.477
peak=    3.252 closest distance to " O   THR A 182 " =    1.474
peak=    3.248 closest distance to " CB  LEU A 228 " =    1.098
peak=    3.245 closest distance to " O   HOH Z 299 " =    4.317
peak=    3.244 closest distance to " O   HOH Z 191 " =    2.796
peak=    3.239 closest distance to " O   HOH Z 435 " =    1.945
peak=    3.238 closest distance to " O   HOH Z  30 " =    1.477
peak=    3.225 closest distance to " O   HOH Z 172 " =    3.313
peak=    3.225 closest distance to " O   HOH Z 389 " =    1.365
peak=    3.225 closest distance to " NH1AARG A 145 " =    1.260
peak=    3.224 closest distance to " OG  SER A  62 " =    2.753
peak=    3.223 closest distance to " CB  ALA A 248 " =    1.352
peak=    3.223 closest distance to " CG1 ILE A  33 " =    1.163
peak=    3.219 closest distance to " CB  HIS A 108 " =    0.853
peak=    3.216 closest distance to " O   HOH Z 380 " =    1.909
peak=    3.215 closest distance to " O   HOH Z 407 " =    2.575
peak=    3.215 closest distance to " O   HOH Z  85 " =    2.135
peak=    3.214 closest distance to " O   HOH Z  44 " =    2.703
peak=    3.214 closest distance to " O   HOH Z 411 " =    1.613
peak=    3.213 closest distance to " O   HOH Z 437 " =    1.277
peak=    3.212 closest distance to " OE2 GLU A  53 " =    2.089
peak=    3.211 closest distance to " O   HOH Z 260 " =    2.459
peak=    3.208 closest distance to " CG  MET A 113 " =    1.002
peak=    3.205 closest distance to " CB  ASN A 215 " =    1.109
peak=    3.205 closest distance to " CB  ASP A 140 " =    0.899
peak=    3.204 closest distance to " O   HOH Z 291 " =    1.746
peak=    3.204 closest distance to " CB  ARG A 219 " =    0.848
peak=    3.202 closest distance to " NZ  LYS A 117 " =    1.277
peak=    3.201 closest distance to " O   HOH Z  50 " =    1.671
peak=    3.193 closest distance to " CG  GLN A  88 " =    1.091
peak=    3.183 closest distance to " CB  TYR A 169 " =    0.983
peak=    3.182 closest distance to " CD1 ILE A 199 " =    1.212
peak=    3.177 closest distance to " CD2 LEU A   5 " =    1.328
peak=    3.174 closest distance to " O   HOH Z 265 " =    2.043
peak=    3.173 closest distance to " O   HOH Z 303 " =    2.778
peak=    3.173 closest distance to " O   HOH Z  66 " =    2.081
peak=    3.161 closest distance to " CB  ARG A 156 " =    1.128
peak=    3.161 closest distance to " CE AMET A  47 " =    1.353
peak=    3.160 closest distance to " O   HOH Z 298 " =    2.380
peak=    3.158 closest distance to " CG1BVAL A  72 " =    1.497
peak=    3.155 closest distance to " ND1 HIS A  86 " =    1.839
peak=    3.154 closest distance to " O   HOH Z 156 " =    3.197
peak=    3.150 closest distance to " NE  ARG A  24 " =    1.923
peak=    3.150 closest distance to " O   HOH Z 329 " =    4.144
peak=    3.150 closest distance to " CD  LYS A 166 " =    1.226
peak=    3.143 closest distance to " O   HOH Z 392 " =    2.845
peak=    3.139 closest distance to " O   HOH Z 303 " =    1.529
peak=    3.136 closest distance to " CA  LYS A 117 " =    1.200
peak=    3.130 closest distance to " CD  PRO A 243 " =    1.621
peak=    3.128 closest distance to " O   HOH Z 285 " =    2.217
peak=    3.125 closest distance to " CG1 VAL A 126 " =    1.201
peak=    3.123 closest distance to " CG  LYS A 119 " =    1.060
peak=    3.123 closest distance to " O   HOH Z 342 " =    0.813
peak=    3.123 closest distance to " O   HOH Z 421 " =    2.953
peak=    3.123 closest distance to " O   HOH Z 213 " =    1.735
peak=    3.120 closest distance to " CE BLYS A 290 " =    0.817
peak=    3.113 closest distance to " O   HOH Z 130 " =    2.363
peak=    3.112 closest distance to " OG1 THR A 221 " =    1.199
peak=    3.104 closest distance to " O  BHOH Z 338 " =    2.314
peak=    3.101 closest distance to " CB  ARG A 156 " =    1.135
peak=    3.086 closest distance to " NH1 ARG A 138 " =    1.095
peak=    3.084 closest distance to " C   ALA A 299 " =    0.925
peak=    3.076 closest distance to " O   HOH Z 245 " =    1.409
peak=    3.073 closest distance to " N   SER A 135 " =    1.297
peak=    3.069 closest distance to " CA  ALA A 233 " =    1.006
peak=    3.064 closest distance to " O   HOH Z  85 " =    1.811
peak=    3.011 closest distance to " CB  VAL A 265 " =    2.289

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

Number of peaks found at mFobs-DFmodel map (map cutoff=3.00 sigma)= 203         
Filter by distance & map next to the model:
   mapped sites are within: 0.911 - 5.728
   number of sites selected in [dist_min= 0.70, dist_max= 6.00]: 203 from: 203
   mapped sites are within: 0.911 - 5.728

peak=   -4.783 closest distance to " OG BSER A 134 " =    1.331
peak=   -4.548 closest distance to " C   ILE A 239 " =    2.108
peak=   -4.433 closest distance to " CD  ARG A  14 " =    3.202
peak=   -4.342 closest distance to " CG  GLN A  58 " =    0.999
peak=   -4.340 closest distance to " CG  GLN A 223 " =    2.034
peak=   -4.299 closest distance to " C   HIS A 108 " =    1.153
peak=   -4.239 closest distance to " O   HOH Z 266 " =    5.281
peak=   -4.186 closest distance to " CB  PHE A 192 " =    1.972
peak=   -4.158 closest distance to " O   HOH Z 198 " =    1.229
peak=   -4.143 closest distance to " O   PRO A 198 " =    1.302
peak=   -4.091 closest distance to " O   HOH Z 231 " =    2.324
peak=   -4.089 closest distance to " CG2 THR A  18 " =    2.838
peak=   -4.066 closest distance to " CG2 ILE A  20 " =    2.860
peak=   -3.958 closest distance to " CD  ARG A 156 " =    2.048
peak=   -3.926 closest distance to " CG1 VAL A 112 " =    2.849
peak=   -3.903 closest distance to " OD1 ASP A 171 " =    1.587
peak=   -3.886 closest distance to " CB  ASN A  39 " =    2.383
peak=   -3.880 closest distance to " O   HOH Z 372 " =    2.339
peak=   -3.864 closest distance to " OXT GLY A 302 " =    2.981
peak=   -3.861 closest distance to " O   HOH Z 387 " =    2.537
peak=   -3.820 closest distance to " OD2 ASP A 191 " =    1.368
peak=   -3.819 closest distance to " CE  MET A 105 " =    2.517
peak=   -3.807 closest distance to " CZ2 TRP A  92 " =    2.779
peak=   -3.802 closest distance to " CD1 PHE A  59 " =    2.114
peak=   -3.786 closest distance to " NE2 GLN A  55 " =    1.279
peak=   -3.760 closest distance to " O   HOH Z  63 " =    1.618
peak=   -3.753 closest distance to " CA  GLY A 241 " =    2.290
peak=   -3.746 closest distance to " CB  ALA A  43 " =    2.496
peak=   -3.742 closest distance to " O   TRP A  70 " =    1.428
peak=   -3.740 closest distance to " O   HOH Z 123 " =    2.492
peak=   -3.733 closest distance to " CE2 TYR A  30 " =    2.722
peak=   -3.725 closest distance to " O   HOH Z 351 " =    1.481
peak=   -3.724 closest distance to " OE1 GLN A 183 " =    1.473
peak=   -3.723 closest distance to " CZ  TYR A 169 " =    1.810
peak=   -3.716 closest distance to " CG  PHE A 283 " =    2.558
peak=   -3.712 closest distance to " O   PHE A 218 " =    1.445
peak=   -3.706 closest distance to " O   SER A 210 " =    1.902
peak=   -3.703 closest distance to " O   HOH Z 102 " =    1.736
peak=   -3.700 closest distance to " O   HOH Z 100 " =    1.073
peak=   -3.697 closest distance to " ND2 ASN A 249 " =    2.126
peak=   -3.691 closest distance to " O   ALA A 161 " =    1.714
peak=   -3.675 closest distance to " O   HOH Z 395 " =    5.150
peak=   -3.672 closest distance to " O   HOH Z 131 " =    4.005
peak=   -3.671 closest distance to " O   HOH Z 313 " =    1.767
peak=   -3.665 closest distance to " O   VAL A  67 " =    2.459
peak=   -3.662 closest distance to " CE BMET A  47 " =    1.233
peak=   -3.653 closest distance to " O   SER A  95 " =    1.478
peak=   -3.653 closest distance to " O   HOH Z 165 " =    2.243
peak=   -3.647 closest distance to " CB  PHE A 208 " =    2.232
peak=   -3.645 closest distance to " O   HOH Z 290 " =    1.058
peak=   -3.643 closest distance to " O   PRO A 163 " =    1.875
peak=   -3.639 closest distance to " O   HOH Z 281 " =    3.047
peak=   -3.625 closest distance to " CD2 TYR A 293 " =    1.928
peak=   -3.620 closest distance to " O   HOH Z 421 " =    3.083
peak=   -3.614 closest distance to " O   ALA A  10 " =    1.639
peak=   -3.605 closest distance to " O   HOH Z 407 " =    2.443
peak=   -3.604 closest distance to " CD2 PHE A  61 " =    2.394
peak=   -3.603 closest distance to " O   HOH Z 193 " =    1.230
peak=   -3.595 closest distance to " O   HOH Z 429 " =    1.895
peak=   -3.579 closest distance to " CB  ALA A   7 " =    2.064
peak=   -3.571 closest distance to " O   HOH Z 137 " =    1.425
peak=   -3.570 closest distance to " ND2 ASN A  45 " =    1.862
peak=   -3.559 closest distance to " CB  SER A 210 " =    1.215
peak=   -3.554 closest distance to " ND2 ASN A  45 " =    1.142
peak=   -3.552 closest distance to " O   HOH Z 362 " =    5.728
peak=   -3.551 closest distance to " N   ALA A 248 " =    1.655
peak=   -3.549 closest distance to " ND2 ASN A 187 " =    1.466
peak=   -3.534 closest distance to " N   ALA A  43 " =    2.474
peak=   -3.529 closest distance to " CD2 PHE A  61 " =    2.000
peak=   -3.527 closest distance to " CD1 ILE A 239 " =    2.441
peak=   -3.523 closest distance to " CB  ASP A 286 " =    2.445
peak=   -3.503 closest distance to " O   PRO A 198 " =    1.295
peak=   -3.502 closest distance to " O   HOH Z 359 " =    3.202
peak=   -3.500 closest distance to " N   SER A 276 " =    1.240
peak=   -3.500 closest distance to " O   HOH Z 211 " =    1.490
peak=   -3.498 closest distance to " O   HOH Z 142 " =    1.259
peak=   -3.493 closest distance to " O   HOH Z 185 " =    2.130
peak=   -3.491 closest distance to " CB  ALA A 291 " =    2.176
peak=   -3.471 closest distance to " C   ALA A 114 " =    2.238
peak=   -3.471 closest distance to " CB  TYR A  15 " =    2.264
peak=   -3.456 closest distance to " O   HOH Z  15 " =    1.541
peak=   -3.456 closest distance to " CB  ASP A 132 " =    2.411
peak=   -3.450 closest distance to " O   HOH Z 374 " =    1.868
peak=   -3.447 closest distance to " O   HOH Z 201 " =    2.020
peak=   -3.443 closest distance to " CD1 LEU A 101 " =    2.282
peak=   -3.431 closest distance to " O   VAL A 174 " =    2.151
peak=   -3.429 closest distance to " O   HOH Z  90 " =    2.296
peak=   -3.426 closest distance to " CD1 LEU A 255 " =    2.735
peak=   -3.425 closest distance to " CG1 VAL A 265 " =    2.585
peak=   -3.418 closest distance to " O   SER A 135 " =    1.490
peak=   -3.417 closest distance to " O   HOH Z 286 " =    1.724
peak=   -3.415 closest distance to " N   PHE A  59 " =    1.805
peak=   -3.411 closest distance to " O   HOH Z 389 " =    1.993
peak=   -3.402 closest distance to " CG2 ILE A 263 " =    2.197
peak=   -3.401 closest distance to " OH  TYR A 172 " =    1.813
peak=   -3.399 closest distance to " CB  ALA A 248 " =    2.265
peak=   -3.398 closest distance to " OE2 GLU A 152 " =    1.315
peak=   -3.393 closest distance to " O   HOH Z 394 " =    1.551
peak=   -3.387 closest distance to " CE2 PHE A  61 " =    2.673
peak=   -3.385 closest distance to " O   HOH Z 357 " =    2.171
peak=   -3.384 closest distance to " CD1 ILE A 199 " =    2.347
peak=   -3.376 closest distance to " OD1 ASN A 301 " =    1.815
peak=   -3.370 closest distance to " CD2 HIS A 207 " =    2.225
peak=   -3.370 closest distance to " CZ3 TRP A 179 " =    1.302
peak=   -3.364 closest distance to " O   HOH Z 166 " =    2.083
peak=   -3.359 closest distance to " O   HOH Z  11 " =    1.710
peak=   -3.353 closest distance to " O   HOH Z  24 " =    1.246
peak=   -3.351 closest distance to " O   HOH Z 115 " =    2.227
peak=   -3.349 closest distance to " CB  TRP A  85 " =    2.487
peak=   -3.347 closest distance to " O   TRP A  92 " =    1.898
peak=   -3.344 closest distance to " CB  ASP A 132 " =    2.265
peak=   -3.339 closest distance to " O   ILE A  49 " =    1.745
peak=   -3.339 closest distance to " CG  ARG A  66 " =    2.250
peak=   -3.328 closest distance to " N   MET A 188 " =    1.913
peak=   -3.327 closest distance to " NE2 GLN A  11 " =    1.856
peak=   -3.326 closest distance to " O   GLN A 240 " =    1.990
peak=   -3.322 closest distance to " CD2 PHE A 225 " =    1.172
peak=   -3.316 closest distance to " O   VAL A 189 " =    1.849
peak=   -3.313 closest distance to " O   VAL A 189 " =    2.628
peak=   -3.309 closest distance to " CG  GLN A  88 " =    0.911
peak=   -3.308 closest distance to " O   HOH Z 428 " =    2.847
peak=   -3.307 closest distance to " OG  SER A  97 " =    2.209
peak=   -3.305 closest distance to " CD2 LEU A 237 " =    2.575
peak=   -3.299 closest distance to " C   ALA A 158 " =    1.428
peak=   -3.293 closest distance to " O   HOH Z 263 " =    2.956
peak=   -3.291 closest distance to " OH  TYR A 169 " =    0.923
peak=   -3.289 closest distance to " O   LYS A  76 " =    1.766
peak=   -3.286 closest distance to " O   SER A 276 " =    1.592
peak=   -3.278 closest distance to " CG2 VAL A 296 " =    1.990
peak=   -3.271 closest distance to " NE  ARG A 156 " =    1.911
peak=   -3.270 closest distance to " NE2 GLN A 278 " =    1.668
peak=   -3.269 closest distance to " O   ILE A 120 " =    1.431
peak=   -3.264 closest distance to " O   HOH Z 177 " =    1.600
peak=   -3.256 closest distance to " O   HOH Z  35 " =    2.470
peak=   -3.254 closest distance to " CB  ALA A 291 " =    1.922
peak=   -3.253 closest distance to " O   HOH Z 114 " =    3.000
peak=   -3.251 closest distance to " CB  ALA A 131 " =    1.922
peak=   -3.249 closest distance to " CE3 TRP A 274 " =    2.210
peak=   -3.248 closest distance to " O   GLU A 152 " =    1.388
peak=   -3.246 closest distance to " CA  GLY A  57 " =    2.290
peak=   -3.242 closest distance to " CZ  ARG A 259 " =    1.036
peak=   -3.241 closest distance to " OG BSER A 134 " =    1.669
peak=   -3.237 closest distance to " O   HOH Z 187 " =    1.844
peak=   -3.237 closest distance to " OD1 ASP A 191 " =    1.756
peak=   -3.234 closest distance to " CA  ASN A 127 " =    1.310
peak=   -3.234 closest distance to " ND2 ASN A  39 " =    1.247
peak=   -3.230 closest distance to " O   HOH Z 345 " =    1.875
peak=   -3.228 closest distance to " O   ALA A 227 " =    1.430
peak=   -3.227 closest distance to " CA  GLY A 133 " =    1.982
peak=   -3.225 closest distance to " N   GLN A  58 " =    1.733
peak=   -3.224 closest distance to " CG2 THR A 178 " =    2.280
peak=   -3.222 closest distance to " O   HOH Z 134 " =    3.684
peak=   -3.221 closest distance to " CG  GLN A  58 " =    1.682
peak=   -3.220 closest distance to " CB  ALA A 244 " =    2.105
peak=   -3.219 closest distance to " CB  ASP A  27 " =    2.327
peak=   -3.213 closest distance to " O   HOH Z   3 " =    1.873
peak=   -3.212 closest distance to " O   HOH Z 298 " =    2.480
peak=   -3.211 closest distance to " O   HOH Z 183 " =    1.711
peak=   -3.208 closest distance to " N   ALA A 226 " =    1.909
peak=   -3.207 closest distance to " C   ARG A 195 " =    1.667
peak=   -3.205 closest distance to " O   HOH Z  49 " =    1.123
peak=   -3.204 closest distance to " O   HOH Z 326 " =    1.671
peak=   -3.200 closest distance to " O   HOH Z 140 " =    1.515
peak=   -3.196 closest distance to " O   HOH Z 250 " =    1.668
peak=   -3.195 closest distance to " NH1 ARG A 195 " =    2.715
peak=   -3.194 closest distance to " O   HOH Z  43 " =    1.825
peak=   -3.190 closest distance to " CG2 THR A 294 " =    2.967
peak=   -3.190 closest distance to " NH2 ARG A  66 " =    1.115
peak=   -3.190 closest distance to " CA  GLY A 241 " =    3.327
peak=   -3.187 closest distance to " ND2 ASN A  60 " =    1.412
peak=   -3.186 closest distance to " CG  LEU A  83 " =    2.075
peak=   -3.183 closest distance to " O   ASN A  45 " =    1.930
peak=   -3.182 closest distance to " O   HOH Z 309 " =    2.599
peak=   -3.177 closest distance to " CZ2 TRP A 274 " =    0.998
peak=   -3.177 closest distance to " OD2 ASP A 171 " =    2.263
peak=   -3.172 closest distance to " O   HOH Z  60 " =    1.780
peak=   -3.169 closest distance to " OD2 ASP A  50 " =    1.481
peak=   -3.152 closest distance to " O   HOH Z 427 " =    1.484
peak=   -3.150 closest distance to " O   HOH Z  89 " =    2.633
peak=   -3.149 closest distance to " O   HOH Z 371 " =    1.766
peak=   -3.145 closest distance to " CG1AVAL A  41 " =    2.532
peak=   -3.143 closest distance to " O   ASN A 252 " =    1.283
peak=   -3.141 closest distance to " O   HOH Z 253 " =    3.465
peak=   -3.128 closest distance to " CA  GLY A 203 " =    2.550
peak=   -3.123 closest distance to " O   SER A 146 " =    1.124
peak=   -3.120 closest distance to " NZ  LYS A 166 " =    1.296
peak=   -3.118 closest distance to " O   HOH Z   6 " =    1.473
peak=   -3.112 closest distance to " CD  GLN A  77 " =    1.279
peak=   -3.110 closest distance to " O   ALA A  34 " =    1.885
peak=   -3.106 closest distance to " CG1 VAL A 268 " =    2.426
peak=   -3.104 closest distance to " O   ILE A 106 " =    1.949
peak=   -3.104 closest distance to " O   HOH Z 295 " =    1.692
peak=   -3.094 closest distance to " O   HOH Z 166 " =    1.588
peak=   -3.093 closest distance to " O   HOH Z  96 " =    4.078
peak=   -3.089 closest distance to " CG1 VAL A 125 " =    1.842
peak=   -3.083 closest distance to " O   HOH Z 110 " =    1.437
peak=   -3.079 closest distance to " NE  ARG A  36 " =    1.880
peak=   -3.069 closest distance to " O   HOH Z 318 " =    1.720
peak=   -3.069 closest distance to " O   HOH Z 385 " =    1.843
peak=   -3.055 closest distance to " CG1 VAL A  78 " =    2.728
peak=   -3.047 closest distance to " CA  GLY A  57 " =    2.149
peak=   -3.021 closest distance to " CD1 ILE A 109 " =    2.524
peak=   -3.003 closest distance to " CB  ALA A 291 " =    2.056

================= 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    :  0.4359 0.4282   6.237589e+00   6.226612e+00
   1_bss:  0.4281 0.4197   6.229438e+00   6.215703e+00
   1_xyz:  0.2925 0.3287   5.943095e+00   6.020721e+00
   1_adp:  0.2632 0.3352   5.888797e+00   6.045461e+00
   1_occ:  0.2630 0.3352   5.888730e+00   6.045810e+00
   2_bss:  0.2603 0.3324   5.882487e+00   6.044013e+00
   2_xyz:  0.1799 0.2365   5.554120e+00   5.763597e+00
   2_adp:  0.1630 0.2162   5.461726e+00   5.672194e+00
   2_occ:  0.1628 0.2161   5.460385e+00   5.671261e+00
   3_bss:  0.1626 0.2158   5.458511e+00   5.668990e+00
   3_xyz:  0.1323 0.1805   5.281936e+00   5.507825e+00
   3_adp:  0.1226 0.1715   5.222235e+00   5.460795e+00
   3_occ:  0.1226 0.1715   5.222169e+00   5.460772e+00
   4_bss:  0.1225 0.1714   5.220024e+00   5.458570e+00
   4_xyz:  0.1203 0.1664   5.203620e+00   5.436847e+00
   4_adp:  0.1187 0.1648   5.195186e+00   5.429783e+00
   4_occ:  0.1186 0.1648   5.194920e+00   5.429498e+00
   5_bss:  0.1186 0.1648   5.195044e+00   5.429584e+00
   5_xyz:  0.1122 0.1607   5.158999e+00   5.408781e+00
   5_adp:  0.1115 0.1587   5.150605e+00   5.398407e+00
   5_occ:  0.1114 0.1586   5.150050e+00   5.397833e+00
   5_bss:  0.1114 0.1586   5.150194e+00   5.397918e+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:  0.348  50.000   0.572  -0.531   1.574  -0.000   0.000   0.000
   1_xyz:  0.348  50.000   0.572  -0.531   1.574  -0.000   0.000   0.000
   1_adp:  0.348  50.000   0.572  -0.531   1.574  -0.000   0.000   0.000
   1_occ:  0.348  50.000   0.572  -0.531   1.574  -0.000   0.000   0.000
   2_bss:  0.331  50.000  -1.879  -1.572   0.222  -0.000   0.000   0.000
   2_xyz:  0.331  50.000  -1.879  -1.572   0.222  -0.000   0.000   0.000
   2_adp:  0.331  50.000  -1.879  -1.572   0.222  -0.000   0.000   0.000
   2_occ:  0.331  50.000  -1.879  -1.572   0.222  -0.000   0.000   0.000
   3_bss:  0.327  50.000  -3.040  -2.272  -0.525  -0.000  -0.000  -0.000
   3_xyz:  0.327  50.000  -3.040  -2.272  -0.525  -0.000  -0.000  -0.000
   3_adp:  0.327  50.000  -3.040  -2.272  -0.525  -0.000  -0.000  -0.000
   3_occ:  0.327  50.000  -3.040  -2.272  -0.525  -0.000  -0.000  -0.000
   4_bss:  0.322  51.998  -3.404  -2.581  -0.872  -0.000  -0.000  -0.000
   4_xyz:  0.322  51.998  -3.404  -2.581  -0.872  -0.000  -0.000  -0.000
   4_adp:  0.322  51.998  -3.404  -2.581  -0.872  -0.000  -0.000  -0.000
   4_occ:  0.322  51.998  -3.404  -2.581  -0.872  -0.000  -0.000  -0.000
   5_bss:  0.323  51.998  -3.282  -2.469  -0.765  -0.000  -0.000  -0.000
   5_xyz:  0.323  51.998  -3.282  -2.469  -0.765  -0.000  -0.000  -0.000
   5_adp:  0.323  51.998  -3.282  -2.469  -0.765  -0.000  -0.000  -0.000
   5_occ:  0.323  51.998  -3.282  -2.469  -0.765  -0.000  -0.000  -0.000
   5_bss:  0.325  51.970  -3.092  -2.326  -0.585  -0.000  -0.000  -0.000
------------------------------------------------------------------------
 stage     <pher>    fom   alpha         beta
   0    :  49.230 0.5314  0.7157    56334.611
   1_bss:  47.940 0.5460  0.7570    53167.384
   1_xyz:  33.212 0.7228  0.9532    28396.622
   1_adp:  34.698 0.7048  0.9344    30433.933
   1_occ:  34.748 0.7042  0.9335    30475.412
   2_bss:  34.465 0.7071  0.8836    29946.459
   2_xyz:  23.250 0.8285  0.9943    14265.187
   2_adp:  20.327 0.8588  1.0212    11800.692
   2_occ:  20.311 0.8589  1.0211    11762.472
   3_bss:  20.211 0.8597  0.9890    11641.258
   3_xyz:  16.656 0.8924  0.9988     8320.480
   3_adp:  15.635 0.9012  0.9933     7486.922
   3_occ:  15.632 0.9012  0.9932     7485.056
   4_bss:  15.570 0.9017  0.9812     7424.052
   4_xyz:  14.995 0.9069  0.9838     7003.820
   4_adp:  14.834 0.9084  0.9794     6946.389
   4_occ:  14.828 0.9085  0.9794     6942.532
   5_bss:  14.831 0.9084  0.9833     6945.065
   5_xyz:  14.477 0.9110  0.9838     6648.386
   5_adp:  14.257 0.9129  0.9785     6536.618
   5_occ:  14.243 0.9130  0.9785     6526.921
   5_bss:  14.247 0.9130  0.9836     6530.119
------------------------------------------------------------------------
 stage       angl   bond   chir   dihe   plan   repu  geom_target
   0    :   1.822  0.010  0.101 15.968  0.009  4.108   2.1529e-01
   1_bss:   1.822  0.010  0.101 15.968  0.009  4.108   2.1529e-01
   1_xyz:   1.427  0.011  0.090 15.359  0.006  4.103   1.1087e-01
   1_adp:   1.427  0.011  0.090 15.359  0.006  4.103   1.1087e-01
   1_occ:   1.427  0.011  0.090 15.359  0.006  4.103   1.1087e-01
   2_bss:   1.427  0.011  0.090 15.359  0.006  4.103   1.1087e-01
   2_xyz:   1.130  0.009  0.081 14.997  0.005  4.109   7.6177e-02
   2_adp:   1.130  0.009  0.081 14.997  0.005  4.109   7.6177e-02
   2_occ:   1.130  0.009  0.081 14.997  0.005  4.109   7.6177e-02
   3_bss:   1.130  0.009  0.081 14.997  0.005  4.109   7.6177e-02
   3_xyz:   1.073  0.008  0.077 14.844  0.004  4.115   6.5306e-02
   3_adp:   1.073  0.008  0.077 14.844  0.004  4.115   6.5306e-02
   3_occ:   1.073  0.008  0.077 14.844  0.004  4.115   6.5306e-02
   4_bss:   1.073  0.008  0.077 14.844  0.004  4.115   6.5306e-02
   4_xyz:   0.879  0.005  0.067 14.442  0.004  4.109   4.7761e-02
   4_adp:   0.879  0.005  0.067 14.442  0.004  4.109   4.7761e-02
   4_occ:   0.879  0.005  0.067 14.442  0.004  4.109   4.7761e-02
   5_bss:   0.879  0.005  0.067 14.442  0.004  4.109   4.7761e-02
   5_xyz:   1.013  0.007  0.075 14.661  0.004  4.110   5.8936e-02
   5_adp:   1.013  0.007  0.075 14.661  0.004  4.110   5.8936e-02
   5_occ:   1.013  0.007  0.075 14.661  0.004  4.110   5.8936e-02
   5_bss:   1.013  0.007  0.075 14.661  0.004  4.110   5.8936e-02
------------------------------------------------------------------------
                      Maximal deviations:
 stage       angl   bond   chir   dihe   plan   repu       |grad|
   0    :   9.874  0.070  0.314 85.889  0.055  1.226   2.4171e-01
   1_bss:   9.874  0.070  0.314 85.889  0.055  1.226   2.4171e-01
   1_xyz:   9.235  0.056  0.323 86.209  0.054  1.950   1.0136e-01
   1_adp:   9.235  0.056  0.323 86.209  0.054  1.950   1.0136e-01
   1_occ:   9.235  0.056  0.323 86.209  0.054  1.950   1.0136e-01
   2_bss:   9.235  0.056  0.323 86.209  0.054  1.950   1.0136e-01
   2_xyz:   7.345  0.049  0.281 83.007  0.050  2.298   1.3382e-01
   2_adp:   7.345  0.049  0.281 83.007  0.050  2.298   1.3382e-01
   2_occ:   7.345  0.049  0.281 83.007  0.050  2.298   1.3382e-01
   3_bss:   7.345  0.049  0.281 83.007  0.050  2.298   1.3382e-01
   3_xyz:   7.522  0.050  0.243 83.312  0.035  2.194   5.1461e-02
   3_adp:   7.522  0.050  0.243 83.312  0.035  2.194   5.1461e-02
   3_occ:   7.522  0.050  0.243 83.312  0.035  2.194   5.1461e-02
   4_bss:   7.522  0.050  0.243 83.312  0.035  2.194   5.1461e-02
   4_xyz:   6.377  0.041  0.200 81.111  0.040  2.403   2.7416e-02
   4_adp:   6.377  0.041  0.200 81.111  0.040  2.403   2.7416e-02
   4_occ:   6.377  0.041  0.200 81.111  0.040  2.403   2.7416e-02
   5_bss:   6.377  0.041  0.200 81.111  0.040  2.403   2.7416e-02
   5_xyz:   6.748  0.048  0.259 83.730  0.034  2.233   3.8097e-02
   5_adp:   6.748  0.048  0.259 83.730  0.034  2.233   3.8097e-02
   5_occ:   6.748  0.048  0.259 83.730  0.034  2.233   3.8097e-02
   5_bss:   6.748  0.048  0.259 83.730  0.034  2.233   3.8097e-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:  81.27   0.00  18.25  75.02   0.00  14.27  81.27   2.35  39.90
   1_occ:  81.27   0.00  18.25  75.02   0.00  14.27  81.27   2.35  39.90
   2_bss:  81.27   0.00  18.25  75.02   0.00  14.27  81.27   2.35  39.90
   2_xyz:  81.27   0.00  18.25  75.02   0.00  14.27  81.27   2.35  39.90
   2_adp:  80.79   0.00  17.94  76.05   0.00  13.81  80.79   4.63  40.39
   2_occ:  80.79   0.00  17.94  76.05   0.00  13.81  80.79   4.63  40.39
   3_bss:  80.79   0.00  17.94  76.05   0.00  13.81  80.79   4.63  40.39
   3_xyz:  80.79   0.00  17.94  76.05   0.00  13.81  80.79   4.63  40.39
   3_adp:  91.94   0.08  18.36  91.94   0.08  13.57  91.39   6.33  44.45
   3_occ:  91.94   0.08  18.36  91.94   0.08  13.57  91.39   6.33  44.45
   4_bss:  91.94   0.08  18.36  91.94   0.08  13.57  91.39   6.33  44.45
   4_xyz:  91.94   0.08  18.36  91.94   0.08  13.57  91.39   6.33  44.45
   4_adp:  97.23   0.76  18.05  97.23   0.76  13.37  93.75   6.16  43.50
   4_occ:  97.23   0.76  18.05  97.23   0.76  13.37  93.75   6.16  43.50
   5_bss:  97.23   0.76  18.05  97.23   0.76  13.37  93.75   6.16  43.50
   5_xyz:  97.23   0.76  18.05  97.23   0.76  13.37  93.75   6.16  43.50
   5_adp: 100.45   0.84  17.59 100.45   0.84  13.10  94.76   5.80  42.03
   5_occ: 100.45   0.84  17.59 100.45   0.84  13.10  94.76   5.80  42.03
   5_bss: 100.42   0.81  17.56 100.42   0.81  13.07  94.73   5.77  42.00
------------------------------------------------------------------------
 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:    2.334    0.019    0.371
   1_adp:    2.334    0.019    0.371
   1_occ:    2.334    0.019    0.371
   2_bss:    2.334    0.019    0.371
   2_xyz:    2.427    0.032    0.546
   2_adp:    2.427    0.032    0.546
   2_occ:    2.427    0.032    0.546
   3_bss:    2.427    0.032    0.546
   3_xyz:    2.374    0.056    0.600
   3_adp:    2.374    0.056    0.600
   3_occ:    2.374    0.056    0.600
   4_bss:    2.374    0.056    0.600
   4_xyz:    2.310    0.101    0.617
   4_adp:    2.310    0.101    0.617
   4_occ:    2.310    0.101    0.617
   5_bss:    2.310    0.101    0.617
   5_xyz:    2.352    0.058    0.633
   5_adp:    2.352    0.058    0.633
   5_occ:    2.352    0.058    0.633
   5_bss:    2.352    0.058    0.633
------------------------------------------------------------------------

CPU time actual refinement: 335.58


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

Writing refined structure to PDB file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/noshake/run_41/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_41/model_refine_001_2mFobs-DFmodel.map
Writing mFobs-DFmodel XPLOR map to file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/noshake/run_41/model_refine_001_mFobs-DFmodel.map
Writing map coefficients to MTZ file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/noshake/run_41/model_refine_001_map_coeffs.mtz

Writing default parameters for subsequent refinement:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/noshake/run_41/model_refine_002.def


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

Pure refinement (no I/O, processing, etc)= 335.43 
  Macro-tasks:
    bulk solvent and scale       = 36.32  
    individual site refinement   = 140.22 
    weights calculation          = 30.01  
    collect and process          = 6.46   
    model show statistics        = 0.11   
    TOTAL for macro-tasks        = 213.12 
  Micro-tasks:
    mask                            = 1.86   
    f_calc                          = 108.37 
    alpha_beta                      = 8.36   
    target                          = 1.16   
    gradients_wrt_atomic_parameters = 116.87 
    fmodel                         = 6.54   
    r_factors                      = 0.19   
    phase_errors                   = 10.48  
    foms                           = 0.26   
    TOTAL for micro-tasks          = 254.09 
NUMBER OF MASK CALCS=  4
Time per interpreted Python bytecode instruction: 4.752 micro seconds
Total CPU time: 5.82 minutes
from_scatterers_fft:    653 calls, 108.02 s
gradients_fft:          598 calls, 103.44 s

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

# Date 2008-01-16 Time 03:51:49 PST -0800 (1200484309.60 s)
Start R-work = 0.4359, R-free = 0.4282 (no bulk solvent and anisotropic scale)
Final R-work = 0.1374, R-free = 0.1776 (no bulk solvent and anisotropic scale)

Start R-work = 0.4281, R-free = 0.4197
Final R-work = 0.1114, R-free = 0.1586