# Date 2008-01-16 Time 03:44:49 PST -0800 (1200483889.31 s)
#phil __OFF__

Command line arguments: "../33.param" "main.number_of_macro_cycles=5" "--overwrite"

HOST = moonbird.lbl.gov
HOSTTYPE = x86_64-linux
USER = phzwart
PID = 13162
JOB_ID = 5159
SGE_ARCH = lx24-amd64
SGE_TASK_FIRST = 1
SGE_TASK_LAST = 1330
SGE_TASK_ID = 33

-------------------------------------------------------------------------------
  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, 84.2302, 90, 90, 90)
  Space group: P 21 21 21 (No. 19)

/net/cci-filer1/vol1/tmp/phzwart/tassos/trial/model.pdb
  Monomer Library directory:
    "/net/rosie/scratch3/phzwart/CCTBX/Sources/mon_lib"
  Total number of atoms: 2823
  Number of models: 1
  Model: 0
    Number of conformers: 2
    Conformer: "A"
      Number of atoms: 2769
      Number of chains: 2
        Number of residues, atoms: 302, 2333
          Classifications: {'peptide': 302}
          Modifications used: {'COO': 1}
          Link IDs: {'PTRANS': 7, 'CIS': 1, 'TRANS': 293}
        Number of residues, atoms: 436, 436
          Classifications: {'water': 436}
          Link IDs: {None: 435}
    Conformer: "B"
      Number of atoms: 2771
      Common with "A": 2717
      Number of chains: 2
        Number of residues, atoms: 302, 2333
          Classifications: {'peptide': 302}
          Modifications used: {'COO': 1}
          Link IDs: {'PTRANS': 7, 'CIS': 1, 'TRANS': 293}
          bond proxies already assigned to first conformer: 2332
        Number of residues, atoms: 438, 438
          Classifications: {'water': 438}
          Link IDs: {None: 437}
  Time building chain proxies: 3.24, per 1000 atoms: 1.15


================================== 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, 84.2302, 90, 90, 90)
Space group: P 21 21 21 (No. 19)
Systematic absences: 0
Centric reflections: 2427
Resolution range: 14.6191 1.95046
Completeness in resolution range: 0.971484
Completeness with d_max=infinity: 0.96841

Number of F-obs in resolution range:                   19589
Number of F-obs <= 0:                                  0
Refinement resolution range: d_max =  14.6191
                             d_min =   1.9505

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, 84.2302, 90, 90, 90)
Space group: P 21 21 21 (No. 19)
Systematic absences: 0
Centric reflections: 2427
Resolution range: 14.6191 1.95046
Completeness in resolution range: 0.971484
Completeness with d_max=infinity: 0.96841

Test (R-free flags) flag value: 1

Number of work/free reflections by resolution:
                                         work  free  %free
  bin  1: 14.6195 -  4.1726 [2114/2141]  1903   211  10.0%
  bin  2:  4.1726 -  3.3248 [2031/2047]  1827   204  10.0%
  bin  3:  3.3248 -  2.9082 [2016/2035]  1813   203  10.1%
  bin  4:  2.9082 -  2.6441 [1981/2011]  1789   192   9.7%
  bin  5:  2.6441 -  2.4555 [1972/1991]  1771   201  10.2%
  bin  6:  2.4555 -  2.3113 [1962/1998]  1767   195   9.9%
  bin  7:  2.3113 -  2.1960 [1957/1990]  1763   194   9.9%
  bin  8:  2.1960 -  2.1007 [1946/1981]  1748   198  10.2%
  bin  9:  2.1007 -  2.0200 [1937/1964]  1743   194  10.0%
  bin 10:  2.0200 -  1.9505 [1673/2006]  1506   167  10.0%
                                overall 17630  1959  10.0%
Writing MTZ file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/noshake/run_33/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:
        0.71 -     1.55: 11
        1.55 -     2.39: 76
        2.39 -     3.23: 3369
        3.23 -     4.06: 9767
        4.06 -     4.90: 16059
  Warning: very small nonbonded interaction distances.
  Nonbonded interactions sorted by model distance:
             atom i - atom j             model   vdw sym.op. j
  " O   HOH Z  52 " - " O   HOH Z 183 "  0.715 3.040 -x+1,y+1/2,-z+1/2
  " O   HOH Z  37 " - " O   HOH Z 416 "  0.993 3.040 -x+1,y-1/2,-z+1/2
  " CA  GLY A  91 " - " O   HOH Z 401 "  1.347 3.440 -x+1,y-1/2,-z+1/2
  " O   HOH Z 401 " - " CA  GLY A  91 "  1.347 3.440 -x+1,y+1/2,-z+1/2
  " O   HOH Z 178 " - " O   HOH Z 403 "  1.386 3.040 -x+1,y-1/2,-z+1/2
  ... (remaining 29277 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_33/model_refine_001.eff

Writing geometry restraints to file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/noshake/run_33/model_refine_001.geo

CPU time processing inputs: 9.21


============================ 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 84.23025 90 90 90
    space_group = "P 21 21 21"
  }
  input {
    pdb {
      file_name = "/net/cci-filer1/vol1/tmp/phzwart/tassos/trial/model.pdb"
    }
    xray_data {
      file_name = "/net/cci-filer1/vol1/tmp/phzwart/tassos/trial/1e0w.cns"
      labels = "FOBS,SIGMA"
      r_free_flags {
        file_name = "/net/cci-filer1/vol1/tmp/phzwart/tassos/trial/1e0w.cns"
        label = "TEST"
        test_flag_value = 1
      }
    }
  }
  output {
    prefix = "model_refine"
    serial = 1
  }
  main {
    number_of_macro_cycles = 5
  }
}
#phil __OFF__


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


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


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

|--(resolution: 1.95 - 14.62 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.4780   r_free= 0.4799   ksol= 0.00   Bsol= 0.00   scale= 0.909    |
|                                                                             |
| 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:   0.76 A                  |
| x-ray target function (ml) for work reflections: 6.278235                   |
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
| Bin     Resolution   Compl.  No. Refl.    R-factors          Targets        |
|number     range              work test   work   test        work        test|
|  1: 14.6195 -  4.6535 0.99   1374  153 0.3812 0.3806      6.5636      6.5581|
|  2:  4.6535 -  3.7135 0.99   1322  146 0.4116 0.4036      6.7953      6.8056|
|  3:  3.7135 -  3.2500 0.99   1299  146 0.4520 0.4767      6.6872      6.7927|
|  4:  3.2500 -  2.9555 0.99   1287  139 0.4572 0.4804      6.5283      6.5347|
|  5:  2.9555 -  2.7452 0.99   1274  142 0.4933 0.4951      6.3805      6.3655|
|  6:  2.7452 -  2.5843 0.99   1279  146 0.5132 0.5249      6.2925      6.2656|
|  7:  2.5843 -  2.4555 0.99   1268  139 0.5103 0.4531      6.2456      6.1843|
|  8:  2.4555 -  2.3491 0.98   1267  143 0.5286 0.5102      6.2022      6.2093|
|  9:  2.3491 -  2.2590 0.98   1264  139 0.5484 0.5299      6.1288      6.1253|
| 10:  2.2590 -  2.1813 0.98   1244  135 0.5264 0.5689      6.1184      6.1181|
| 11:  2.1813 -  2.1133 1.00   1266  147 0.5272 0.5337       6.048      6.0963|
| 12:  2.1133 -  2.0530 0.97   1253  128 0.5314 0.5155      5.9818      6.0119|
| 13:  2.0530 -  1.9991 0.98   1240  138 0.5216 0.5513      5.9043      5.8952|
| 14:  1.9991 -  1.9505 0.78    993  118 0.5204 0.5018      5.8501      5.7539|
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
|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: 14.6195 -  4.6535  1374   153  0.68  36.04   0.83     0.71      74583.04|
|  2:  4.6535 -  3.7135  1322   146  0.66  38.58   0.91     0.77     122006.67|
|  3:  3.7135 -  3.2500  1299   146  0.54  48.47   0.94     0.75     133614.23|
|  4:  3.2500 -  2.9555  1287   139  0.45  56.12   0.96     0.64     118830.84|
|  5:  2.9555 -  2.7452  1274   142  0.38  60.89   0.90     0.57      90491.41|
|  6:  2.7452 -  2.5843  1279   146  0.35  63.46   0.89     0.50      76260.44|
|  7:  2.5843 -  2.4555  1268   139  0.35  63.36   0.91     0.50      68456.57|
|  8:  2.4555 -  2.3491  1267   143  0.34  64.41   0.93     0.50      60910.49|
|  9:  2.3491 -  2.2590  1264   139  0.34  64.55   0.91     0.52      55078.07|
| 10:  2.2590 -  2.1813  1244   135  0.35  63.61   0.97     0.52      49525.73|
| 11:  2.1813 -  2.1133  1266   147  0.31  66.97   0.95     0.48      48440.10|
| 12:  2.1133 -  2.0530  1253   128  0.28  68.83   0.98     0.46      45802.87|
| 13:  2.0530 -  1.9991  1240   138  0.28  69.45   0.96     0.44      40228.42|
| 14:  1.9991 -  1.9505   993   118  0.34  64.86   0.96     0.48      29814.05|
|alpha:            min =        0.44 max =            0.77 mean =         0.56|
|beta:             min =    29814.05 max =       133614.23 mean =     73539.60|
|figures of merit: min =        0.00 max =            1.00 mean =         0.41|
|phase err.(work): min =        0.00 max =           90.00 mean =        58.92|
|phase err.(test): min =        0.00 max =           89.95 mean =        59.17|
|-----------------------------------------------------------------------------|

============================== 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 = 11.224567             wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 89.731   (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 2.923067              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 89.097   (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 |  0.715 -  1.133:        2 |
| 0.007 - 0.014:   729 |   0.989 -   1.976:   994 |  1.133 -  1.552:        9 |
| 0.014 - 0.021:   262 |   1.976 -   2.963:   470 |  1.552 -  1.970:       19 |
| 0.021 - 0.028:    63 |   2.963 -   3.950:   196 |  1.970 -  2.389:       57 |
| 0.028 - 0.035:    15 |   3.950 -   4.938:    66 |  2.389 -  2.807:      840 |
| 0.035 - 0.042:     0 |   4.938 -   5.925:    29 |  2.807 -  3.226:     2529 |
| 0.042 - 0.049:     2 |   5.925 -   6.912:    16 |  3.226 -  3.644:     3574 |
| 0.049 - 0.056:     0 |   6.912 -   7.899:     2 |  3.644 -  4.063:     6193 |
| 0.056 - 0.063:     0 |   7.899 -   8.887:     3 |  4.063 -  4.481:     7000 |
| 0.063 - 0.070:     1 |   8.887 -   9.874:     4 |  4.481 -  4.900:     9059 |
|-----------------------------------------------------------------------------|
|-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 |        0.274 |
| planarity |      436 |   0.009    0.055  0.000 |       0.973 |              |
|  dihedral |      870 |  15.968   85.889  0.013 |       1.071 |              |
| nonbonded |     2439 |   4.104    4.900  0.715 |       1.926 |              |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 11.144)------------------------------------------|
|    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 - 14.62 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.4780   r_free= 0.4799   ksol= 0.00   Bsol= 0.00   scale= 0.909    |
|                                                                             |
| 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:   0.76 A                  |
| x-ray target function (ml) for work reflections: 6.278235                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.95 - 14.62 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.4702   r_free= 0.4689   ksol= 0.32   Bsol= 7.04   scale= 0.940    |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-0.20,-1.04,2.12,-0.00,0.00,0.00); trace/3= 0.29                           |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.74 A                  |
| x-ray target function (ml) for work reflections: 6.272971                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 8.088175              wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 89.679   (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 1.445096              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 88.755   (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.4702      final r-factor (work) = 0.3647          |
| start r-factor (free) = 0.4689      final r-factor (free) = 0.3901          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 25.6392 = 8.09 * 0.50 * 6.2721 + 1.00 * 0.2744                              |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 25.0875 = 8.09 * 0.50 * 6.1715 + 1.00 * 0.1294                              |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 27     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.3647      final r-factor (work) = 0.3283          |
| start r-factor (free) = 0.3901      final r-factor (free) = 0.3926          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 8.9243 = 1.45 * 1.00 * 6.1715 + 1.00 * 0.0059                               |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 8.7646 = 1.45 * 1.00 * 6.0498 + 1.00 * 0.0220                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 27     |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 11.144)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.00    96.59   20.29    None  None   None       |
|    all(noH): 2823   0      0.00    96.59   20.29    None  None   None       |
|    Sol.    : 438    0      0.00    96.59   41.26    None  None   None       |
|    Mac.    : 2385   0      0.00    91.38   16.44    None  None   None       |
|    Hyd.    : 0      0      None    None    None     None  None   None       |
|    - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -      |
|       Distribution of isotropic (or equivalent) ADP for non-H atoms:        |
|    Bin#      value range     #atoms | Bin#      value range     #atoms      |
|      0:     0.000 -   9.659:  860   |   5:    48.297 -  57.956:  104        |
|      1:     9.659 -  19.319:  811   |   6:    57.956 -  67.615:   66        |
|      2:    19.319 -  28.978:  466   |   7:    67.615 -  77.275:   30        |
|      3:    28.978 -  38.637:  298   |   8:    77.275 -  86.934:   16        |
|      4:    38.637 -  48.297:  167   |   9:    86.934 -  96.593:    5        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.3283 r_free = 0.3926             target_work(ml) = 6.052         |
| occupancies: max = 1.00  min = 0.30   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.3280 r_free = 0.3929             target_work(ml) = 6.052         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        5 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.95 - 14.62 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.3280   r_free= 0.3929   ksol= 0.32   Bsol= 7.04   scale= 1.034    |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-0.20,-1.04,2.12,-0.00,0.00,0.00); trace/3= 0.29                           |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.50 A                  |
| x-ray target function (ml) for work reflections: 6.052058                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.95 - 14.62 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.3248   r_free= 0.3923   ksol= 0.33   Bsol= 33.77   scale= 1.025   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-1.25,-0.95,0.80,-0.00,0.00,0.00); trace/3= -0.47                          |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.50 A                  |
| x-ray target function (ml) for work reflections: 6.046582                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 7.713815              wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 97.444   (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 0.353739              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 146.153  (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.3248      final r-factor (work) = 0.2448          |
| start r-factor (free) = 0.3923      final r-factor (free) = 0.3038          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 23.4479 = 7.71 * 0.50 * 6.0460 + 1.00 * 0.1292                              |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 22.9912 = 7.71 * 0.50 * 5.9396 + 1.00 * 0.0825                              |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 28     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.2448      final r-factor (work) = 0.2207          |
| start r-factor (free) = 0.3038      final r-factor (free) = 0.2809          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 2.1229 = 0.35 * 1.00 * 5.9396 + 1.00 * 0.0218                               |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 2.0485 = 0.35 * 1.00 * 5.7632 + 1.00 * 0.0098                               |
|-----------------------------------------------------------------------------|
| number of iterations = 23      |    number of function evaluations = 30     |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 11.144)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.00    97.50   18.23    None  None   None       |
|    all(noH): 2823   0      0.00    97.50   18.23    None  None   None       |
|    Sol.    : 438    0      2.83    86.57   40.12    None  None   None       |
|    Mac.    : 2385   0      0.00    97.50   14.20    None  None   None       |
|    Hyd.    : 0      0      None    None    None     None  None   None       |
|    - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -      |
|       Distribution of isotropic (or equivalent) ADP for non-H atoms:        |
|    Bin#      value range     #atoms | Bin#      value range     #atoms      |
|      0:     0.000 -   9.750:  933   |   5:    48.750 -  58.500:   97        |
|      1:     9.750 -  19.500: 1028   |   6:    58.500 -  68.250:   43        |
|      2:    19.500 -  29.250:  348   |   7:    68.250 -  78.000:   18        |
|      3:    29.250 -  39.000:  215   |   8:    78.000 -  87.750:    6        |
|      4:    39.000 -  48.750:  134   |   9:    87.750 -  97.500:    1        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.2207 r_free = 0.2809             target_work(ml) = 5.723         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        5 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.2202 r_free = 0.2806             target_work(ml) = 5.722         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        9 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.95 - 14.62 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.2202   r_free= 0.2806   ksol= 0.33   Bsol= 33.77   scale= 1.056   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-1.25,-0.95,0.80,-0.00,0.00,0.00); trace/3= -0.47                          |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.28 A                  |
| x-ray target function (ml) for work reflections: 5.721598                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.95 - 14.62 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.2196   r_free= 0.2773   ksol= 0.32   Bsol= 28.67   scale= 1.028   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-2.06,-1.72,-0.55,-0.00,-0.00,-0.00); trace/3= -1.44                       |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.28 A                  |
| x-ray target function (ml) for work reflections: 5.717844                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 2.268838              wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 99.388   (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 0.209658              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 109.439  (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.2196      final r-factor (work) = 0.1731          |
| start r-factor (free) = 0.2773      final r-factor (free) = 0.2238          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 6.6218 = 2.27 * 0.50 * 5.7645 + 1.00 * 0.0825                               |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 6.4281 = 2.27 * 0.50 * 5.6190 + 1.00 * 0.0538                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 28     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1731      final r-factor (work) = 0.1648          |
| start r-factor (free) = 0.2238      final r-factor (free) = 0.2156          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 1.1900 = 0.21 * 1.00 * 5.6190 + 1.00 * 0.0120                               |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 1.1939 = 0.21 * 1.00 * 5.4891 + 1.00 * 0.0431                               |
|-----------------------------------------------------------------------------|
| number of iterations = 7       |    number of function evaluations = 8      |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 11.144)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.00    96.99   18.18    None  None   None       |
|    all(noH): 2823   0      0.00    96.99   18.18    None  None   None       |
|    Sol.    : 438    0      4.11    86.02   40.42    None  None   None       |
|    Mac.    : 2385   0      0.00    96.99   14.09    None  None   None       |
|    Hyd.    : 0      0      None    None    None     None  None   None       |
|    - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -      |
|       Distribution of isotropic (or equivalent) ADP for non-H atoms:        |
|    Bin#      value range     #atoms | Bin#      value range     #atoms      |
|      0:     0.000 -   9.699:  900   |   5:    48.497 -  58.196:   99        |
|      1:     9.699 -  19.399: 1105   |   6:    58.196 -  67.895:   42        |
|      2:    19.399 -  29.098:  318   |   7:    67.895 -  77.595:   20        |
|      3:    29.098 -  38.797:  191   |   8:    77.595 -  87.294:    6        |
|      4:    38.797 -  48.497:  141   |   9:    87.294 -  96.994:    1        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.1648 r_free = 0.2156             target_work(ml) = 5.469         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        9 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.1644 r_free = 0.2152             target_work(ml) = 5.468         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        9 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.95 - 14.62 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1644   r_free= 0.2152   ksol= 0.32   Bsol= 28.67   scale= 1.049   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-2.06,-1.72,-0.55,-0.00,-0.00,-0.00); trace/3= -1.44                       |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.19 A                  |
| x-ray target function (ml) for work reflections: 5.468281                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.95 - 14.62 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1642   r_free= 0.2134   ksol= 0.32   Bsol= 28.67   scale= 1.024   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-3.06,-2.37,-1.56,-0.00,-0.00,-0.00); trace/3= -2.33                       |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.19 A                  |
| x-ray target function (ml) for work reflections: 5.466423                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 4.143972              wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 99.064   (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 0.760908              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 89.255   (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1642      final r-factor (work) = 0.1332          |
| start r-factor (free) = 0.2134      final r-factor (free) = 0.1801          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 11.4340 = 4.14 * 0.50 * 5.4924 + 1.00 * 0.0538                              |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 11.2004 = 4.14 * 0.50 * 5.3728 + 1.00 * 0.0681                              |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 28     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1332      final r-factor (work) = 0.1227          |
| start r-factor (free) = 0.1801      final r-factor (free) = 0.1706          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 4.0991 = 0.76 * 1.00 * 5.3728 + 1.00 * 0.0109                               |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 4.0037 = 0.76 * 1.00 * 5.2497 + 1.00 * 0.0092                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 26     |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 11.144)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      1.03    94.64   18.11    None  None   None       |
|    all(noH): 2823   0      1.03    94.64   18.11    None  None   None       |
|    Sol.    : 438    0      2.47    86.55   43.25    None  None   None       |
|    Mac.    : 2385   0      1.03    94.64   13.49    None  None   None       |
|    Hyd.    : 0      0      None    None    None     None  None   None       |
|    - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -      |
|       Distribution of isotropic (or equivalent) ADP for non-H atoms:        |
|    Bin#      value range     #atoms | Bin#      value range     #atoms      |
|      0:     1.030 -  10.391: 1049   |   5:    47.837 -  57.199:  103        |
|      1:    10.391 -  19.753: 1081   |   6:    57.199 -  66.560:   72        |
|      2:    19.753 -  29.114:  239   |   7:    66.560 -  75.921:   30        |
|      3:    29.114 -  38.476:  113   |   8:    75.921 -  85.283:   12        |
|      4:    38.476 -  47.837:  118   |   9:    85.283 -  94.644:    6        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.1227 r_free = 0.1706             target_work(ml) = 5.215         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        9 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.1226 r_free = 0.1705             target_work(ml) = 5.215         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        9 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.95 - 14.62 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1226   r_free= 0.1705   ksol= 0.32   Bsol= 28.67   scale= 1.028   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-3.06,-2.37,-1.56,-0.00,-0.00,-0.00); trace/3= -2.33                       |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.15 A                  |
| x-ray target function (ml) for work reflections: 5.214570                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.95 - 14.62 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1227   r_free= 0.1702   ksol= 0.31   Bsol= 29.10   scale= 1.021   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-3.23,-2.56,-1.96,-0.00,-0.00,-0.00); trace/3= -2.58                       |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.15 A                  |
| x-ray target function (ml) for work reflections: 5.213731                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 1.383503              wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 116.480  (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 0.181990              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 125.065  (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1227      final r-factor (work) = 0.1198          |
| start r-factor (free) = 0.1702      final r-factor (free) = 0.1676          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 3.7000 = 1.38 * 0.50 * 5.2503 + 1.00 * 0.0681                               |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 3.6515 = 1.38 * 0.50 * 5.2072 + 1.00 * 0.0494                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 28     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1198      final r-factor (work) = 0.1194          |
| start r-factor (free) = 0.1676      final r-factor (free) = 0.1645          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 0.9569 = 0.18 * 1.00 * 5.2072 + 1.00 * 0.0092                               |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 0.9539 = 0.18 * 1.00 * 5.2003 + 1.00 * 0.0074                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 27     |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 11.144)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      2.05    93.97   17.44    None  None   None       |
|    all(noH): 2823   0      2.05    93.97   17.44    None  None   None       |
|    Sol.    : 438    0      4.44    88.59   40.46    None  None   None       |
|    Mac.    : 2385   0      2.05    93.97   13.21    None  None   None       |
|    Hyd.    : 0      0      None    None    None     None  None   None       |
|    - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -      |
|       Distribution of isotropic (or equivalent) ADP for non-H atoms:        |
|    Bin#      value range     #atoms | Bin#      value range     #atoms      |
|      0:     2.052 -  11.243: 1239   |   5:    48.009 -  57.200:   89        |
|      1:    11.243 -  20.434:  966   |   6:    57.200 -  66.391:   54        |
|      2:    20.434 -  29.626:  193   |   7:    66.391 -  75.583:   19        |
|      3:    29.626 -  38.817:  133   |   8:    75.583 -  84.774:    5        |
|      4:    38.817 -  48.009:  118   |   9:    84.774 -  93.966:    7        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.1194 r_free = 0.1645             target_work(ml) = 5.191         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        9 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.1194 r_free = 0.1644             target_work(ml) = 5.190         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:       10 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.95 - 14.62 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1194   r_free= 0.1644   ksol= 0.31   Bsol= 29.10   scale= 1.018   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-3.23,-2.56,-1.96,-0.00,-0.00,-0.00); trace/3= -2.58                       |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.14 A                  |
| x-ray target function (ml) for work reflections: 5.189991                   |
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
| Bin     Resolution   Compl.  No. Refl.    R-factors          Targets        |
|number     range              work test   work   test        work        test|
|  1: 14.6195 -  4.6535 0.99   1374  153 0.1052 0.1282      5.4376      5.5631|
|  2:  4.6535 -  3.7135 0.99   1322  146 0.0928 0.1263      5.5124      5.7311|
|  3:  3.7135 -  3.2500 0.99   1299  146 0.1157 0.1499      5.5424      5.8387|
|  4:  3.2500 -  2.9555 0.99   1287  139 0.1292 0.1703       5.506      5.6836|
|  5:  2.9555 -  2.7452 0.99   1274  142 0.1327 0.1601       5.328      5.4776|
|  6:  2.7452 -  2.5843 0.99   1279  146 0.1268 0.1710      5.2236       5.401|
|  7:  2.5843 -  2.4555 0.99   1268  139 0.1226 0.1747      5.1499      5.3825|
|  8:  2.4555 -  2.3491 0.98   1267  143 0.1263 0.1762      5.1324      5.3924|
|  9:  2.3491 -  2.2590 0.98   1264  139 0.1295 0.1952      5.0915      5.3379|
| 10:  2.2590 -  2.1813 0.98   1244  135 0.1212 0.1910      5.0323      5.2561|
| 11:  2.1813 -  2.1133 1.00   1266  147 0.1235 0.1780      4.9764      5.3131|
| 12:  2.1133 -  2.0530 0.97   1253  128 0.1199 0.1765      4.9236      5.1795|
| 13:  2.0530 -  1.9991 0.98   1240  138 0.1221 0.1844       4.857      5.1095|
| 14:  1.9991 -  1.9505 0.78    993  118 0.1221 0.2067      4.7992      5.0529|
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
|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: 14.6195 -  4.6535  1374   153  0.94   9.60   0.99     0.97       7754.44|
|  2:  4.6535 -  3.7135  1322   146  0.95   8.54   1.04     1.03      10015.44|
|  3:  3.7135 -  3.2500  1299   146  0.93  12.28   1.05     1.04      11616.97|
|  4:  3.2500 -  2.9555  1287   139  0.92  13.98   1.03     1.02      10938.24|
|  5:  2.9555 -  2.7452  1274   142  0.91  15.25   1.00     0.97       7962.49|
|  6:  2.7452 -  2.5843  1279   146  0.91  15.46   0.99     0.96       6806.99|
|  7:  2.5843 -  2.4555  1268   139  0.91  15.33   1.00     0.96       5945.58|
|  8:  2.4555 -  2.3491  1267   143  0.91  15.54   1.01     1.00       5833.09|
|  9:  2.3491 -  2.2590  1264   139  0.90  16.39   1.02     1.01       5512.16|
| 10:  2.2590 -  2.1813  1244   135  0.90  16.39   1.02     0.98       4967.44|
| 11:  2.1813 -  2.1133  1266   147  0.90  16.49   1.02     0.98       4562.20|
| 12:  2.1133 -  2.0530  1253   128  0.91  15.92   1.03     1.02       4215.07|
| 13:  2.0530 -  1.9991  1240   138  0.90  16.84   1.02     1.00       3757.50|
| 14:  1.9991 -  1.9505   993   118  0.89  17.06   1.01     0.99       3331.14|
|alpha:            min =        0.96 max =            1.04 mean =         0.99|
|beta:             min =     3331.14 max =        11616.97 mean =      6750.65|
|figures of merit: min =        0.00 max =            1.00 mean =         0.91|
|phase err.(work): min =        0.00 max =           89.94 mean =        14.55|
|phase err.(test): min =        0.00 max =           88.96 mean =        14.35|
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.95 - 14.62 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1193   r_free= 0.1644   ksol= 0.32   Bsol= 30.38   scale= 1.019   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-3.15,-2.48,-1.88,-0.00,-0.00,-0.00); trace/3= -2.51                       |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.14 A                  |
| x-ray target function (ml) for work reflections: 5.190015                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.95 - 14.62 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1193   r_free= 0.1644   ksol= 0.32   Bsol= 30.38   scale= 1.019   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-3.15,-2.48,-1.88,-0.00,-0.00,-0.00); trace/3= -2.51                       |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.14 A                  |
| x-ray target function (ml) for work reflections: 5.190015                   |
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
| Bin     Resolution   Compl.  No. Refl.    R-factors          Targets        |
|number     range              work test   work   test        work        test|
|  1: 14.6195 -  4.6535 0.99   1374  153 0.1054 0.1291      5.4411      5.5674|
|  2:  4.6535 -  3.7135 0.99   1322  146 0.0928 0.1263       5.513      5.7306|
|  3:  3.7135 -  3.2500 0.99   1299  146 0.1157 0.1500      5.5424       5.839|
|  4:  3.2500 -  2.9555 0.99   1287  139 0.1292 0.1703      5.5062      5.6836|
|  5:  2.9555 -  2.7452 0.99   1274  142 0.1327 0.1600      5.3279      5.4774|
|  6:  2.7452 -  2.5843 0.99   1279  146 0.1267 0.1710      5.2234      5.4006|
|  7:  2.5843 -  2.4555 0.99   1268  139 0.1225 0.1746      5.1493      5.3822|
|  8:  2.4555 -  2.3491 0.98   1267  143 0.1262 0.1760      5.1319      5.3914|
|  9:  2.3491 -  2.2590 0.98   1264  139 0.1294 0.1951       5.091      5.3376|
| 10:  2.2590 -  2.1813 0.98   1244  135 0.1211 0.1908      5.0318      5.2555|
| 11:  2.1813 -  2.1133 1.00   1266  147 0.1234 0.1780      4.9759      5.3128|
| 12:  2.1133 -  2.0530 0.97   1253  128 0.1199 0.1765      4.9232      5.1791|
| 13:  2.0530 -  1.9991 0.98   1240  138 0.1220 0.1843      4.8566      5.1093|
| 14:  1.9991 -  1.9505 0.78    993  118 0.1220 0.2066      4.7984      5.0522|
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
|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: 14.6195 -  4.6535  1374   153  0.94   9.63   0.99     0.97       7838.69|
|  2:  4.6535 -  3.7135  1322   146  0.95   8.57   1.04     1.03      10055.17|
|  3:  3.7135 -  3.2500  1299   146  0.93  12.27   1.05     1.04      11612.73|
|  4:  3.2500 -  2.9555  1287   139  0.92  13.98   1.03     1.02      10940.36|
|  5:  2.9555 -  2.7452  1274   142  0.91  15.25   1.00     0.97       7959.84|
|  6:  2.7452 -  2.5843  1279   146  0.91  15.46   0.99     0.97       6804.11|
|  7:  2.5843 -  2.4555  1268   139  0.91  15.32   1.00     0.97       5938.14|
|  8:  2.4555 -  2.3491  1267   143  0.91  15.53   1.01     1.00       5824.64|
|  9:  2.3491 -  2.2590  1264   139  0.90  16.38   1.02     1.01       5504.42|
| 10:  2.2590 -  2.1813  1244   135  0.90  16.38   1.02     0.98       4963.43|
| 11:  2.1813 -  2.1133  1266   147  0.90  16.48   1.02     0.98       4558.41|
| 12:  2.1133 -  2.0530  1253   128  0.91  15.91   1.03     1.02       4212.04|
| 13:  2.0530 -  1.9991  1240   138  0.90  16.83   1.02     1.00       3754.16|
| 14:  1.9991 -  1.9505   993   118  0.89  17.05   1.01     0.99       3326.26|
|alpha:            min =        0.97 max =            1.04 mean =         0.99|
|beta:             min =     3326.26 max =        11612.73 mean =      6756.67|
|figures of merit: min =        0.00 max =            1.00 mean =         0.91|
|phase err.(work): min =        0.00 max =           89.89 mean =        14.55|
|phase err.(test): min =        0.00 max =           89.01 mean =        14.35|
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 11.144)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      1.98    93.89   17.37    None  None   None       |
|    all(noH): 2823   0      1.98    93.89   17.37    None  None   None       |
|    Sol.    : 438    0      4.37    88.52   40.39    None  None   None       |
|    Mac.    : 2385   0      1.98    93.89   13.14    None  None   None       |
|    Hyd.    : 0      0      None    None    None     None  None   None       |
|    - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -      |
|       Distribution of isotropic (or equivalent) ADP for non-H atoms:        |
|    Bin#      value range     #atoms | Bin#      value range     #atoms      |
|      0:     1.978 -  11.169: 1239   |   5:    47.935 -  57.126:   89        |
|      1:    11.169 -  20.360:  966   |   6:    57.126 -  66.317:   54        |
|      2:    20.360 -  29.552:  193   |   7:    66.317 -  75.509:   19        |
|      3:    29.552 -  38.743:  133   |   8:    75.509 -  84.700:    5        |
|      4:    38.743 -  47.935:  118   |   9:    84.700 -  93.892:    7        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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


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

Number of peaks found at mFobs-DFmodel map (map cutoff=3.00 sigma)= 288         
Filter by distance & map next to the model:
   mapped sites are within: 0.656 - 5.678
   number of sites selected in [dist_min= 0.70, dist_max= 6.00]: 287 from: 288
   mapped sites are within: 0.704 - 5.678

peak=    6.759 closest distance to " O   HOH Z  37 " =    1.569
peak=    6.660 closest distance to " O   HOH Z 142 " =    2.020
peak=    6.577 closest distance to " O   HOH Z 199 " =    1.463
peak=    6.379 closest distance to " O   HOH Z 236 " =    1.780
peak=    6.150 closest distance to " CB  ASN A 187 " =    2.004
peak=    5.688 closest distance to " O   HOH Z 112 " =    1.400
peak=    5.581 closest distance to " O   HOH Z 193 " =    1.801
peak=    5.564 closest distance to " O   HOH Z 375 " =    1.404
peak=    5.501 closest distance to " CB  ARG A 275 " =    1.009
peak=    5.467 closest distance to " O   HOH Z 179 " =    0.881
peak=    5.319 closest distance to " NE2 GLN A  11 " =    1.195
peak=    5.281 closest distance to " NH2 ARG A  56 " =    1.897
peak=    5.119 closest distance to " O   HOH Z 124 " =    1.745
peak=    5.042 closest distance to " CG  PRO A 213 " =    1.310
peak=    5.038 closest distance to " O   HOH Z 278 " =    1.484
peak=    4.973 closest distance to " O   HOH Z  45 " =    1.046
peak=    4.906 closest distance to " CG  PRO A  54 " =    1.286
peak=    4.904 closest distance to " O   HOH Z 188 " =    1.319
peak=    4.832 closest distance to " O   HOH Z 260 " =    1.518
peak=    4.825 closest distance to " CG  PRO A  90 " =    1.162
peak=    4.773 closest distance to " O   HOH Z 192 " =    1.681
peak=    4.773 closest distance to " O   HOH Z 213 " =    2.187
peak=    4.749 closest distance to " O   HOH Z 427 " =    2.550
peak=    4.709 closest distance to " O   HOH Z  97 " =    2.110
peak=    4.620 closest distance to " O   HOH Z 373 " =    2.037
peak=    4.602 closest distance to " NE2 GLN A  55 " =    1.578
peak=    4.579 closest distance to " O   HOH Z 128 " =    2.045
peak=    4.568 closest distance to " CB  ARG A 102 " =    0.827
peak=    4.552 closest distance to " O   HOH Z 108 " =    1.491
peak=    4.535 closest distance to " O   HOH Z 134 " =    1.486
peak=    4.489 closest distance to " O   HOH Z 109 " =    1.539
peak=    4.426 closest distance to " O   HOH Z 402 " =    1.495
peak=    4.422 closest distance to " CB  ASN A 148 " =    1.752
peak=    4.380 closest distance to " O   HOH Z  78 " =    1.673
peak=    4.378 closest distance to " O  BHOH Z  74 " =    1.317
peak=    4.358 closest distance to " NZ  LYS A 117 " =    3.209
peak=    4.354 closest distance to " CG AARG A 275 " =    1.132
peak=    4.332 closest distance to " O   HOH Z 250 " =    1.453
peak=    4.320 closest distance to " O   HOH Z 272 " =    1.863
peak=    4.304 closest distance to " O   HOH Z  91 " =    2.421
peak=    4.280 closest distance to " O   HOH Z 207 " =    1.748
peak=    4.263 closest distance to " O   HOH Z 117 " =    1.341
peak=    4.259 closest distance to " O   HOH Z  44 " =    1.879
peak=    4.203 closest distance to " O   HOH Z 132 " =    1.210
peak=    4.194 closest distance to " CG  PRO A 198 " =    1.305
peak=    4.175 closest distance to " CB  GLN A 223 " =    1.568
peak=    4.159 closest distance to " O   HOH Z  59 " =    1.794
peak=    4.153 closest distance to " O   HOH Z 234 " =    3.514
peak=    4.151 closest distance to " O   HOH Z 276 " =    1.349
peak=    4.109 closest distance to " O   HOH Z 369 " =    2.087
peak=    4.102 closest distance to " O   HOH Z  54 " =    1.637
peak=    4.101 closest distance to " O   HOH Z  50 " =    1.674
peak=    4.096 closest distance to " O   HOH Z 209 " =    2.133
peak=    4.090 closest distance to " CB  SER A   3 " =    1.180
peak=    4.081 closest distance to " CB  GLN A 183 " =    1.195
peak=    4.067 closest distance to " NH1AARG A 145 " =    0.805
peak=    4.040 closest distance to " O   HOH Z  93 " =    2.058
peak=    4.024 closest distance to " CG1 ILE A  33 " =    1.242
peak=    4.017 closest distance to " O   HOH Z 214 " =    1.205
peak=    4.014 closest distance to " CA  GLY A 241 " =    3.707
peak=    4.009 closest distance to " CG2 VAL A 257 " =    0.913
peak=    4.005 closest distance to " CA  LEU A 282 " =    1.326
peak=    3.987 closest distance to " CB  GLU A 152 " =    1.253
peak=    3.985 closest distance to " O   HOH Z 368 " =    1.977
peak=    3.961 closest distance to " CA  TYR A  30 " =    1.036
peak=    3.950 closest distance to " O   HOH Z 343 " =    1.658
peak=    3.950 closest distance to " CG  GLN A  77 " =    1.065
peak=    3.945 closest distance to " C   PRO A 198 " =    1.601
peak=    3.941 closest distance to " O   HOH Z 345 " =    3.241
peak=    3.936 closest distance to " O   HOH Z 365 " =    1.718
peak=    3.936 closest distance to " O   HOH Z  85 " =    1.667
peak=    3.931 closest distance to " O   HOH Z 406 " =    1.526
peak=    3.919 closest distance to " O   HOH Z 344 " =    2.976
peak=    3.898 closest distance to " O   SER A  26 " =    1.476
peak=    3.897 closest distance to " O   HOH Z  61 " =    1.589
peak=    3.896 closest distance to " O   HOH Z 316 " =    2.804
peak=    3.882 closest distance to " CB  GLU A 128 " =    1.048
peak=    3.877 closest distance to " OD2 ASP A 286 " =    2.243
peak=    3.877 closest distance to " O   HOH Z 365 " =    2.438
peak=    3.867 closest distance to " O   HOH Z  42 " =    2.226
peak=    3.865 closest distance to " O   HOH Z 232 " =    2.270
peak=    3.860 closest distance to " O   HOH Z 282 " =    1.453
peak=    3.844 closest distance to " O   HOH Z   6 " =    2.242
peak=    3.841 closest distance to " NE BARG A 275 " =    1.226
peak=    3.832 closest distance to " O   HOH Z 247 " =    1.303
peak=    3.828 closest distance to " O   HOH Z 128 " =    1.982
peak=    3.821 closest distance to " CB  TYR A 169 " =    0.716
peak=    3.812 closest distance to " O   HOH Z 357 " =    1.851
peak=    3.809 closest distance to " NH1BARG A 145 " =    1.360
peak=    3.804 closest distance to " CB  TRP A 179 " =    1.094
peak=    3.802 closest distance to " O   HOH Z  24 " =    1.548
peak=    3.779 closest distance to " O   HOH Z  10 " =    1.717
peak=    3.762 closest distance to " O   HOH Z 186 " =    1.307
peak=    3.749 closest distance to " O   HOH Z  63 " =    1.995
peak=    3.743 closest distance to " O   HOH Z 381 " =    1.691
peak=    3.742 closest distance to " NH2BARG A 145 " =    2.216
peak=    3.740 closest distance to " CB  ASN A 215 " =    0.959
peak=    3.737 closest distance to " OE1 GLN A  55 " =    1.122
peak=    3.737 closest distance to " CB  VAL A 265 " =    1.181
peak=    3.736 closest distance to " O   HOH Z 278 " =    1.686
peak=    3.731 closest distance to " O   HOH Z  43 " =    1.981
peak=    3.722 closest distance to " CB  PRO A  54 " =    1.056
peak=    3.719 closest distance to " O   HOH Z 153 " =    1.551
peak=    3.713 closest distance to " CA  ALA A  21 " =    1.017
peak=    3.707 closest distance to " O   HOH Z  48 " =    1.721
peak=    3.703 closest distance to " O   HOH Z 298 " =    1.752
peak=    3.699 closest distance to " O   HOH Z 156 " =    2.980
peak=    3.698 closest distance to " O   HOH Z 106 " =    2.178
peak=    3.697 closest distance to " O   HOH Z 203 " =    1.757
peak=    3.696 closest distance to " O   HOH Z  66 " =    2.052
peak=    3.684 closest distance to " O   HOH Z 118 " =    1.644
peak=    3.671 closest distance to " O   HOH Z 346 " =    1.603
peak=    3.668 closest distance to " O   HOH Z 173 " =    2.001
peak=    3.664 closest distance to " CE  LYS A 119 " =    1.139
peak=    3.658 closest distance to " O   HOH Z 269 " =    3.471
peak=    3.657 closest distance to " O   HOH Z 359 " =    1.455
peak=    3.656 closest distance to " CB  SER A  63 " =    1.197
peak=    3.655 closest distance to " NE1 TRP A 274 " =    1.054
peak=    3.651 closest distance to " NH2 ARG A 219 " =    1.893
peak=    3.650 closest distance to " O   HOH Z 403 " =    2.070
peak=    3.643 closest distance to " NE AARG A 145 " =    1.270
peak=    3.634 closest distance to " CG  GLU A 277 " =    2.016
peak=    3.631 closest distance to " O   HOH Z 303 " =    2.260
peak=    3.617 closest distance to " O   HOH Z 108 " =    1.586
peak=    3.607 closest distance to " CG2 ILE A 120 " =    1.242
peak=    3.603 closest distance to " O   HOH Z 371 " =    2.439
peak=    3.600 closest distance to " O   HOH Z  38 " =    2.411
peak=    3.597 closest distance to " CG  PRO A 243 " =    1.137
peak=    3.595 closest distance to " O   HOH Z 118 " =    1.584
peak=    3.594 closest distance to " O   HOH Z 410 " =    1.866
peak=    3.594 closest distance to " O   HOH Z 244 " =    1.744
peak=    3.591 closest distance to " CB  THR A  31 " =    1.643
peak=    3.584 closest distance to " N   TRP A 150 " =    1.489
peak=    3.584 closest distance to " CB  ALA A  34 " =    1.016
peak=    3.579 closest distance to " O   HOH Z 291 " =    1.712
peak=    3.578 closest distance to " CD BLYS A 290 " =    1.201
peak=    3.577 closest distance to " CZ2 TRP A 150 " =    1.139
peak=    3.572 closest distance to " O   HOH Z 326 " =    1.318
peak=    3.570 closest distance to " ND2 ASN A 187 " =    1.688
peak=    3.568 closest distance to " O   HOH Z 422 " =    2.089
peak=    3.566 closest distance to " O   HOH Z 286 " =    2.108
peak=    3.563 closest distance to " CA  THR A 221 " =    0.922
peak=    3.563 closest distance to " O   HOH Z  88 " =    2.956
peak=    3.558 closest distance to " O   HOH Z  20 " =    1.904
peak=    3.558 closest distance to " CB  ARG A 139 " =    0.935
peak=    3.552 closest distance to " O   HOH Z   9 " =    2.241
peak=    3.546 closest distance to " O   HOH Z 130 " =    2.859
peak=    3.546 closest distance to " O   HOH Z 227 " =    1.776
peak=    3.544 closest distance to " O   HOH Z 371 " =    1.614
peak=    3.522 closest distance to " O   HOH Z 222 " =    2.249
peak=    3.518 closest distance to " CB  SER A 216 " =    0.951
peak=    3.517 closest distance to " O   HOH Z  19 " =    1.738
peak=    3.510 closest distance to " N   ASN A 148 " =    1.193
peak=    3.498 closest distance to " O   HOH Z 389 " =    1.607
peak=    3.492 closest distance to " CA  ASN A 176 " =    1.211
peak=    3.490 closest distance to " CB  LEU A 228 " =    1.124
peak=    3.490 closest distance to " O   HOH Z 287 " =    1.539
peak=    3.481 closest distance to " O   HOH Z 202 " =    1.226
peak=    3.480 closest distance to " CB  GLN A 278 " =    0.727
peak=    3.480 closest distance to " CA  THR A 264 " =    0.865
peak=    3.480 closest distance to " O   HOH Z 313 " =    1.778
peak=    3.480 closest distance to " O   HOH Z 132 " =    2.040
peak=    3.470 closest distance to " CG2BVAL A  41 " =    0.704
peak=    3.465 closest distance to " O   HOH Z 368 " =    3.591
peak=    3.463 closest distance to " CG  MET A 185 " =    1.405
peak=    3.458 closest distance to " CG  LYS A 166 " =    1.646
peak=    3.453 closest distance to " O   HOH Z  80 " =    1.934
peak=    3.447 closest distance to " O   HOH Z 419 " =    1.817
peak=    3.445 closest distance to " CB  SER A  62 " =    1.331
peak=    3.443 closest distance to " O   HOH Z 396 " =    1.218
peak=    3.438 closest distance to " C   ALA A 299 " =    0.939
peak=    3.434 closest distance to " O   HOH Z 344 " =    1.316
peak=    3.428 closest distance to " O   HOH Z  18 " =    1.565
peak=    3.425 closest distance to " O   HOH Z 245 " =    1.313
peak=    3.415 closest distance to " O   HOH Z 142 " =    1.850
peak=    3.414 closest distance to " O   HOH Z 334 " =    1.339
peak=    3.412 closest distance to " O   HOH Z 111 " =    2.200
peak=    3.412 closest distance to " O   HOH Z  40 " =    1.402
peak=    3.408 closest distance to " O   GLN A  58 " =    1.338
peak=    3.396 closest distance to " OE2 GLU A  53 " =    2.068
peak=    3.395 closest distance to " O   HOH Z 261 " =    2.100
peak=    3.393 closest distance to " N   TYR A  15 " =    1.136
peak=    3.392 closest distance to " O   HOH Z 334 " =    1.600
peak=    3.391 closest distance to " O   HOH Z 365 " =    1.719
peak=    3.385 closest distance to " CB  LYS A 193 " =    0.758
peak=    3.381 closest distance to " O   HOH Z 194 " =    1.618
peak=    3.380 closest distance to " CA  GLY A 241 " =    3.776
peak=    3.372 closest distance to " NE  ARG A  14 " =    1.394
peak=    3.371 closest distance to " O   HOH Z 305 " =    3.306
peak=    3.367 closest distance to " O   HOH Z  89 " =    2.216
peak=    3.364 closest distance to " O   HOH Z  88 " =    2.285
peak=    3.361 closest distance to " OD1 ASN A  69 " =    2.905
peak=    3.358 closest distance to " O   HOH Z  92 " =    1.134
peak=    3.358 closest distance to " CB  VAL A 202 " =    1.470
peak=    3.356 closest distance to " OG BSER A 258 " =    2.661
peak=    3.355 closest distance to " CD  PRO A 243 " =    1.606
peak=    3.355 closest distance to " CG2 THR A 221 " =    1.166
peak=    3.345 closest distance to " O   HOH Z 241 " =    1.747
peak=    3.344 closest distance to " O   HOH Z 394 " =    1.524
peak=    3.343 closest distance to " CA  ILE A  20 " =    0.836
peak=    3.343 closest distance to " O   HOH Z 425 " =    1.925
peak=    3.341 closest distance to " O   HOH Z 132 " =    2.536
peak=    3.331 closest distance to " O   HOH Z 181 " =    1.686
peak=    3.326 closest distance to " CA  ALA A  51 " =    0.916
peak=    3.323 closest distance to " CD2 LEU A 255 " =    0.974
peak=    3.323 closest distance to " CB  ILE A 120 " =    1.376
peak=    3.318 closest distance to " NE2 GLN A  58 " =    1.776
peak=    3.313 closest distance to " O   HOH Z 434 " =    3.554
peak=    3.312 closest distance to " CD  GLN A  58 " =    5.678
peak=    3.306 closest distance to " O   HOH Z 249 " =    1.228
peak=    3.293 closest distance to " CG  LEU A 167 " =    1.111
peak=    3.290 closest distance to " O   SER A 164 " =    1.137
peak=    3.286 closest distance to " O   HOH Z 176 " =    2.274
peak=    3.284 closest distance to " N   ASP A 162 " =    1.177
peak=    3.282 closest distance to " O   HOH Z 251 " =    1.614
peak=    3.281 closest distance to " O   HOH Z  49 " =    2.024
peak=    3.276 closest distance to " CB  LEU A 300 " =    1.065
peak=    3.275 closest distance to " OE1 GLN A  58 " =    1.471
peak=    3.273 closest distance to " CB  SER A 245 " =    1.590
peak=    3.269 closest distance to " O   HOH Z  61 " =    1.713
peak=    3.269 closest distance to " O   HOH Z 334 " =    1.104
peak=    3.267 closest distance to " CD2 HIS A  81 " =    1.259
peak=    3.266 closest distance to " O   HOH Z   1 " =    1.772
peak=    3.260 closest distance to " CB  TRP A 179 " =    1.370
peak=    3.260 closest distance to " N   PHE A 130 " =    1.369
peak=    3.260 closest distance to " CG  GLN A 240 " =    3.485
peak=    3.253 closest distance to " O   HOH Z 191 " =    1.798
peak=    3.251 closest distance to " OG  SER A  62 " =    2.833
peak=    3.249 closest distance to " CD  LYS A 166 " =    1.259
peak=    3.247 closest distance to " O   HOH Z 289 " =    1.470
peak=    3.247 closest distance to " O   HOH Z 426 " =    1.400
peak=    3.246 closest distance to " O   HOH Z  89 " =    1.739
peak=    3.245 closest distance to " O   HOH Z   1 " =    1.484
peak=    3.245 closest distance to " O   HOH Z 209 " =    2.332
peak=    3.243 closest distance to " O   HOH Z 215 " =    1.406
peak=    3.237 closest distance to " CA  LEU A 300 " =    1.063
peak=    3.233 closest distance to " CG2 VAL A  78 " =    0.834
peak=    3.229 closest distance to " O   HOH Z 234 " =    1.936
peak=    3.208 closest distance to " CD1 LEU A   5 " =    2.093
peak=    3.205 closest distance to " CD1 LEU A 281 " =    0.982
peak=    3.204 closest distance to " N   CYS A 260 " =    0.785
peak=    3.202 closest distance to " O   HOH Z 257 " =    2.045
peak=    3.202 closest distance to " N   ARG A 156 " =    1.275
peak=    3.202 closest distance to " NH1 ARG A  14 " =    1.012
peak=    3.200 closest distance to " CA  ALA A 233 " =    1.191
peak=    3.199 closest distance to " O   HOH Z 393 " =    1.383
peak=    3.195 closest distance to " O   HOH Z  45 " =    1.997
peak=    3.191 closest distance to " O   HOH Z 272 " =    2.191
peak=    3.188 closest distance to " O   HOH Z  43 " =    2.627
peak=    3.187 closest distance to " O   HOH Z 417 " =    2.097
peak=    3.183 closest distance to " O   GLY A  91 " =    1.473
peak=    3.182 closest distance to " CB  PRO A 198 " =    0.863
peak=    3.182 closest distance to " NZ  LYS A  76 " =    1.325
peak=    3.181 closest distance to " O   HOH Z 336 " =    1.714
peak=    3.178 closest distance to " O   HOH Z  52 " =    1.684
peak=    3.175 closest distance to " O   HOH Z 392 " =    2.802
peak=    3.169 closest distance to " O   HOH Z  59 " =    1.808
peak=    3.167 closest distance to " CB  GLU A 277 " =    3.474
peak=    3.167 closest distance to " O   HOH Z  64 " =    1.939
peak=    3.166 closest distance to " CB  ARG A  79 " =    1.547
peak=    3.163 closest distance to " CG1 VAL A 153 " =    1.073
peak=    3.159 closest distance to " O   HOH Z 353 " =    2.332
peak=    3.159 closest distance to " OD1 ASN A  60 " =    1.692
peak=    3.157 closest distance to " CG  MET A 113 " =    0.978
peak=    3.152 closest distance to " O   HOH Z 257 " =    1.323
peak=    3.146 closest distance to " SD BMET A  47 " =    1.301
peak=    3.143 closest distance to " OG BSER A 164 " =    2.362
peak=    3.142 closest distance to " O   HOH Z 136 " =    1.014
peak=    3.141 closest distance to " O   HOH Z 212 " =    1.541
peak=    3.141 closest distance to " CA  ALA A  84 " =    1.204
peak=    3.139 closest distance to " NH1 ARG A 138 " =    1.270
peak=    3.138 closest distance to " O   HOH Z 148 " =    1.463
peak=    3.134 closest distance to " NH2AARG A 145 " =    2.018
peak=    3.133 closest distance to " CB  TRP A 266 " =    1.152
peak=    3.132 closest distance to " CA  SER A  87 " =    1.149
peak=    3.124 closest distance to " O   HOH Z 422 " =    2.634
peak=    3.124 closest distance to " CB  THR A 157 " =    0.943
peak=    3.124 closest distance to " O   HOH Z 343 " =    2.191
peak=    3.106 closest distance to " O   HOH Z 234 " =    2.313
peak=    3.091 closest distance to " O   HOH Z 328 " =    1.928
peak=    3.089 closest distance to " O   HOH Z 380 " =    1.691
peak=    3.089 closest distance to " CA  GLN A 194 " =    0.949
peak=    3.071 closest distance to " CB  THR A  52 " =    1.194
peak=    3.053 closest distance to " CG  LYS A  76 " =    1.419
peak=    3.032 closest distance to " O   HOH Z 102 " =    1.058
peak=    3.031 closest distance to " CB  LEU A 255 " =    0.794
peak=    2.979 closest distance to " CD  LYS A 119 " =    2.058

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

Number of peaks found at mFobs-DFmodel map (map cutoff=3.00 sigma)= 199         
Filter by distance & map next to the model:
   mapped sites are within: 0.575 - 5.220
   number of sites selected in [dist_min= 0.70, dist_max= 6.00]: 194 from: 199
   mapped sites are within: 0.735 - 5.220

peak=   -4.642 closest distance to " C   HIS A 108 " =    1.106
peak=   -4.553 closest distance to " O   HOH Z 290 " =    0.885
peak=   -4.407 closest distance to " O   PRO A 198 " =    1.168
peak=   -4.380 closest distance to " O   HOH Z 351 " =    1.498
peak=   -4.204 closest distance to " O   HOH Z  13 " =    1.166
peak=   -4.172 closest distance to " CA  VAL A  67 " =    2.830
peak=   -4.111 closest distance to " O   HOH Z 198 " =    1.235
peak=   -4.097 closest distance to " CB  GLN A  55 " =    1.323
peak=   -4.052 closest distance to " OXT GLY A 302 " =    2.599
peak=   -4.045 closest distance to " SG  CYS A 254 " =    3.203
peak=   -4.025 closest distance to " O   HOH Z  98 " =    1.708
peak=   -4.015 closest distance to " CG  LYS A 193 " =    2.144
peak=   -4.006 closest distance to " CD  ARG A 156 " =    1.984
peak=   -3.959 closest distance to " O   HOH Z  56 " =    1.281
peak=   -3.952 closest distance to " O   ALA A 161 " =    1.521
peak=   -3.944 closest distance to " C   ALA A 158 " =    1.141
peak=   -3.860 closest distance to " O   HOH Z   6 " =    2.041
peak=   -3.858 closest distance to " OG  SER A   3 " =    1.309
peak=   -3.854 closest distance to " O   HOH Z 407 " =    2.556
peak=   -3.854 closest distance to " ND2 ASN A  45 " =    0.890
peak=   -3.851 closest distance to " CB  ALA A 248 " =    1.922
peak=   -3.843 closest distance to " O   SER A 146 " =    0.735
peak=   -3.816 closest distance to " CZ  PHE A  59 " =    1.351
peak=   -3.815 closest distance to " N   GLN A 122 " =    1.413
peak=   -3.812 closest distance to " CD  GLN A  88 " =    0.905
peak=   -3.766 closest distance to " OD2 ASP A  50 " =    1.463
peak=   -3.763 closest distance to " O   ALA A  51 " =    1.272
peak=   -3.759 closest distance to " O   HOH Z 117 " =    0.776
peak=   -3.751 closest distance to " OD1 ASN A  39 " =    2.154
peak=   -3.747 closest distance to " O   HOH Z 250 " =    1.406
peak=   -3.746 closest distance to " O   ILE A  49 " =    1.614
peak=   -3.740 closest distance to " OD2 ASP A 191 " =    1.436
peak=   -3.740 closest distance to " CG  LEU A  83 " =    1.905
peak=   -3.737 closest distance to " CG  PHE A 283 " =    2.586
peak=   -3.730 closest distance to " ND2 ASN A  39 " =    1.160
peak=   -3.727 closest distance to " CB  CYS A 201 " =    2.465
peak=   -3.716 closest distance to " OG BSER A 134 " =    1.324
peak=   -3.711 closest distance to " CD1 LEU A 255 " =    2.723
peak=   -3.698 closest distance to " CB  ALA A 244 " =    2.046
peak=   -3.666 closest distance to " O   HOH Z  11 " =    1.692
peak=   -3.663 closest distance to " OE1 GLN A  88 " =    1.182
peak=   -3.653 closest distance to " N   GLN A  58 " =    1.985
peak=   -3.628 closest distance to " N   ASP A 286 " =    1.936
peak=   -3.621 closest distance to " O   HOH Z  24 " =    1.448
peak=   -3.621 closest distance to " O   SER A 135 " =    1.530
peak=   -3.620 closest distance to " O   HOH Z 126 " =    1.795
peak=   -3.614 closest distance to " CD  PRO A 198 " =    1.411
peak=   -3.607 closest distance to " O   HOH Z  97 " =    1.336
peak=   -3.586 closest distance to " N   GLN A  58 " =    0.979
peak=   -3.580 closest distance to " N   GLN A  77 " =    1.434
peak=   -3.580 closest distance to " CD1 ILE A 263 " =    2.994
peak=   -3.574 closest distance to " CD1 ILE A 239 " =    2.326
peak=   -3.574 closest distance to " O   HOH Z 421 " =    3.144
peak=   -3.557 closest distance to " O   HOH Z 266 " =    4.563
peak=   -3.555 closest distance to " O   HOH Z 416 " =    1.001
peak=   -3.544 closest distance to " CD  GLU A 236 " =    1.071
peak=   -3.530 closest distance to " N   SER A 210 " =    1.255
peak=   -3.530 closest distance to " O   HOH Z 109 " =    5.220
peak=   -3.520 closest distance to " O   HOH Z 385 " =    1.904
peak=   -3.520 closest distance to " CG  PRO A 198 " =    1.619
peak=   -3.519 closest distance to " O   PRO A 163 " =    1.204
peak=   -3.516 closest distance to " O   HOH Z 263 " =    3.031
peak=   -3.513 closest distance to " CE  LYS A  76 " =    2.817
peak=   -3.510 closest distance to " O   HOH Z 202 " =    0.836
peak=   -3.502 closest distance to " OD1 ASP A 200 " =    0.945
peak=   -3.499 closest distance to " CA  GLY A 133 " =    1.833
peak=   -3.496 closest distance to " OG  SER A  87 " =    1.337
peak=   -3.494 closest distance to " CG  ASP A 231 " =    0.753
peak=   -3.493 closest distance to " O   VAL A  67 " =    2.633
peak=   -3.493 closest distance to " O   HOH Z 218 " =    3.297
peak=   -3.491 closest distance to " OG  SER A  97 " =    2.077
peak=   -3.489 closest distance to " CB  ALA A 291 " =    2.255
peak=   -3.485 closest distance to " OG ASER A 134 " =    1.488
peak=   -3.483 closest distance to " O   HOH Z  93 " =    1.427
peak=   -3.479 closest distance to " O   MET A  40 " =    2.678
peak=   -3.465 closest distance to " N   HIS A 115 " =    1.810
peak=   -3.454 closest distance to " OH  TYR A 172 " =    1.728
peak=   -3.452 closest distance to " O   HOH Z 388 " =    1.853
peak=   -3.435 closest distance to " OG  SER A 245 " =    1.157
peak=   -3.434 closest distance to " CD2 TYR A 293 " =    1.959
peak=   -3.417 closest distance to " O   HOH Z 393 " =    3.240
peak=   -3.417 closest distance to " O   LYS A 289 " =    2.495
peak=   -3.414 closest distance to " ND2 ASN A 142 " =    1.934
peak=   -3.413 closest distance to " CB  PRO A 280 " =    2.026
peak=   -3.411 closest distance to " O   HOH Z 417 " =    2.262
peak=   -3.405 closest distance to " O   HOH Z 197 " =    5.053
peak=   -3.402 closest distance to " N   SER A 276 " =    1.160
peak=   -3.402 closest distance to " O   HOH Z 100 " =    0.958
peak=   -3.393 closest distance to " O   TRP A  92 " =    1.626
peak=   -3.391 closest distance to " N   PRO A 163 " =    1.568
peak=   -3.389 closest distance to " OD1 ASN A 176 " =    1.083
peak=   -3.385 closest distance to " O   ASP A 270 " =    1.842
peak=   -3.384 closest distance to " O   HOH Z   3 " =    1.743
peak=   -3.381 closest distance to " O   HOH Z 198 " =    1.219
peak=   -3.369 closest distance to " NH2 ARG A  79 " =    1.907
peak=   -3.361 closest distance to " N   SER A 206 " =    1.965
peak=   -3.359 closest distance to " CA  TYR A  30 " =    2.875
peak=   -3.358 closest distance to " O   GLY A  75 " =    1.382
peak=   -3.357 closest distance to " N   ALA A 248 " =    1.650
peak=   -3.356 closest distance to " O   HOH Z 210 " =    0.928
peak=   -3.354 closest distance to " O   HOH Z 185 " =    2.121
peak=   -3.352 closest distance to " O   HOH Z 428 " =    2.944
peak=   -3.351 closest distance to " O   HOH Z 183 " =    1.403
peak=   -3.343 closest distance to " C   LEU A 143 " =    1.194
peak=   -3.342 closest distance to " O   HOH Z 348 " =    2.175
peak=   -3.341 closest distance to " N   ALA A   1 " =    3.073
peak=   -3.341 closest distance to " O   HOH Z 427 " =    1.484
peak=   -3.340 closest distance to " CG2 VAL A  78 " =    1.344
peak=   -3.331 closest distance to " OG  SER A  63 " =    1.377
peak=   -3.315 closest distance to " OG  SER A  87 " =    1.828
peak=   -3.315 closest distance to " CG BARG A 275 " =    1.001
peak=   -3.311 closest distance to " O   SER A  95 " =    1.371
peak=   -3.301 closest distance to " O   HOH Z 166 " =    1.681
peak=   -3.295 closest distance to " CG  GLN A 223 " =    1.458
peak=   -3.282 closest distance to " CZ  TYR A 169 " =    1.753
peak=   -3.277 closest distance to " CB  ALA A   1 " =    1.466
peak=   -3.277 closest distance to " CA  TRP A  70 " =    2.482
peak=   -3.274 closest distance to " NE2 GLN A  94 " =    1.394
peak=   -3.270 closest distance to " O   HOH Z 423 " =    2.192
peak=   -3.269 closest distance to " CG1 VAL A 230 " =    1.947
peak=   -3.269 closest distance to " CB  PRO A 243 " =    2.530
peak=   -3.258 closest distance to " CG  LEU A 281 " =    1.820
peak=   -3.258 closest distance to " O   GLN A  89 " =    1.569
peak=   -3.256 closest distance to " O   HOH Z 199 " =    0.768
peak=   -3.254 closest distance to " O   VAL A 125 " =    1.926
peak=   -3.251 closest distance to " O   HOH Z 139 " =    3.637
peak=   -3.248 closest distance to " CG  ARG A 219 " =    2.599
peak=   -3.246 closest distance to " O   PRO A 198 " =    1.126
peak=   -3.245 closest distance to " O   ASN A 249 " =    1.568
peak=   -3.241 closest distance to " O   ALA A 100 " =    2.462
peak=   -3.239 closest distance to " O   HOH Z 363 " =    1.817
peak=   -3.238 closest distance to " O   HOH Z 274 " =    2.961
peak=   -3.237 closest distance to " O   HOH Z 231 " =    2.113
peak=   -3.237 closest distance to " O   HOH Z 436 " =    0.963
peak=   -3.234 closest distance to " CB  ALA A  51 " =    1.740
peak=   -3.220 closest distance to " O   HOH Z 326 " =    1.473
peak=   -3.214 closest distance to " O   SER A  26 " =    1.065
peak=   -3.211 closest distance to " O   HOH Z 313 " =    1.696
peak=   -3.210 closest distance to " OG  SER A 206 " =    1.354
peak=   -3.210 closest distance to " ND2 ASN A  69 " =    1.440
peak=   -3.205 closest distance to " O   HOH Z  47 " =    1.471
peak=   -3.204 closest distance to " CG1 VAL A  78 " =    2.876
peak=   -3.200 closest distance to " O   HOH Z 116 " =    1.187
peak=   -3.198 closest distance to " OD1 ASP A 191 " =    1.732
peak=   -3.195 closest distance to " O   HOH Z 210 " =    1.995
peak=   -3.192 closest distance to " CA  ARG A  36 " =    1.835
peak=   -3.187 closest distance to " CG  GLU A 152 " =    1.076
peak=   -3.186 closest distance to " CD  GLN A  11 " =    0.896
peak=   -3.184 closest distance to " O   LEU A 297 " =    0.917
peak=   -3.182 closest distance to " N   TYR A 169 " =    1.069
peak=   -3.181 closest distance to " OE1 GLN A 205 " =    1.075
peak=   -3.178 closest distance to " CB  ASN A  39 " =    2.180
peak=   -3.178 closest distance to " O   HOH Z 249 " =    0.979
peak=   -3.177 closest distance to " O   VAL A 197 " =    1.051
peak=   -3.176 closest distance to " OD1 ASN A 301 " =    2.027
peak=   -3.166 closest distance to " O   HOH Z 179 " =    1.282
peak=   -3.164 closest distance to " CG1 VAL A 296 " =    2.143
peak=   -3.156 closest distance to " SD  MET A 105 " =    2.428
peak=   -3.156 closest distance to " NE1 TRP A 274 " =    1.104
peak=   -3.154 closest distance to " CA  ARG A 139 " =    1.038
peak=   -3.153 closest distance to " OD1 ASN A 249 " =    1.499
peak=   -3.152 closest distance to " O   ASP A 162 " =    2.027
peak=   -3.151 closest distance to " ND2 ASN A  60 " =    1.499
peak=   -3.149 closest distance to " OE1 GLN A 194 " =    1.358
peak=   -3.146 closest distance to " O   HOH Z 256 " =    1.396
peak=   -3.145 closest distance to " O   HOH Z  79 " =    1.615
peak=   -3.141 closest distance to " N   THR A 157 " =    1.575
peak=   -3.140 closest distance to " CE3 TRP A 123 " =    1.296
peak=   -3.138 closest distance to " O   HOH Z  24 " =    1.079
peak=   -3.137 closest distance to " CB  PRO A 163 " =    2.692
peak=   -3.135 closest distance to " O   HOH Z 148 " =    2.576
peak=   -3.132 closest distance to " O   HOH Z 211 " =    1.769
peak=   -3.131 closest distance to " O   HOH Z 419 " =    0.825
peak=   -3.124 closest distance to " OG1 THR A 246 " =    1.145
peak=   -3.124 closest distance to " CA  ALA A 299 " =    2.267
peak=   -3.122 closest distance to " N   PHE A  59 " =    1.696
peak=   -3.121 closest distance to " O   LYS A  48 " =    1.684
peak=   -3.119 closest distance to " O   HOH Z  88 " =    2.054
peak=   -3.109 closest distance to " OH  TYR A 169 " =    0.835
peak=   -3.107 closest distance to " OD1 ASN A  74 " =    0.802
peak=   -3.107 closest distance to " O   HOH Z 396 " =    1.686
peak=   -3.096 closest distance to " CD2 LEU A 237 " =    2.463
peak=   -3.085 closest distance to " OG BSER A  99 " =    1.225
peak=   -3.076 closest distance to " O   HOH Z 438 " =    0.974
peak=   -3.076 closest distance to " O   HOH Z 100 " =    1.131
peak=   -3.065 closest distance to " O   HOH Z 346 " =    1.871
peak=   -3.065 closest distance to " O   ILE A  49 " =    1.358
peak=   -3.063 closest distance to " CG  GLN A 278 " =    1.876
peak=   -3.054 closest distance to " CG  GLU A 152 " =    2.443
peak=   -3.047 closest distance to " CB  SER A 245 " =    1.636
peak=   -3.036 closest distance to " CG  GLN A 223 " =    2.199
peak=   -3.031 closest distance to " CE  MET A 105 " =    2.590
peak=   -3.025 closest distance to " CA  GLY A 262 " =    2.078
peak=   -3.001 closest distance to " O   HOH Z 411 " =    4.663

================= 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    :  0.4780 0.4799   6.278235e+00   6.278111e+00
   1_bss:  0.4702 0.4689   6.272971e+00   6.261461e+00
   1_xyz:  0.3647 0.3901   6.113049e+00   6.159176e+00
   1_adp:  0.3283 0.3926   6.052377e+00   6.162802e+00
   1_occ:  0.3280 0.3929   6.052058e+00   6.163553e+00
   2_bss:  0.3248 0.3923   6.046582e+00   6.162499e+00
   2_xyz:  0.2448 0.3038   5.806518e+00   5.969852e+00
   2_adp:  0.2207 0.2809   5.723112e+00   5.905829e+00
   2_occ:  0.2202 0.2806   5.721598e+00   5.904591e+00
   3_bss:  0.2196 0.2773   5.717844e+00   5.899116e+00
   3_xyz:  0.1731 0.2238   5.512044e+00   5.712356e+00
   3_adp:  0.1648 0.2156   5.469344e+00   5.674077e+00
   3_occ:  0.1644 0.2152   5.468281e+00   5.672194e+00
   4_bss:  0.1642 0.2134   5.466423e+00   5.668083e+00
   4_xyz:  0.1332 0.1801   5.287671e+00   5.515281e+00
   4_adp:  0.1227 0.1706   5.214993e+00   5.451176e+00
   4_occ:  0.1226 0.1705   5.214570e+00   5.450755e+00
   5_bss:  0.1227 0.1702   5.213731e+00   5.449064e+00
   5_xyz:  0.1198 0.1676   5.200579e+00   5.435580e+00
   5_adp:  0.1194 0.1645   5.190900e+00   5.418209e+00
   5_occ:  0.1194 0.1644   5.189991e+00   5.417500e+00
   5_bss:  0.1193 0.1644   5.190015e+00   5.417530e+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:  0.324   7.039  -0.199  -1.045   2.117  -0.000   0.000   0.000
   1_xyz:  0.324   7.039  -0.199  -1.045   2.117  -0.000   0.000   0.000
   1_adp:  0.324   7.039  -0.199  -1.045   2.117  -0.000   0.000   0.000
   1_occ:  0.324   7.039  -0.199  -1.045   2.117  -0.000   0.000   0.000
   2_bss:  0.330  33.769  -1.251  -0.953   0.796  -0.000   0.000   0.000
   2_xyz:  0.330  33.769  -1.251  -0.953   0.796  -0.000   0.000   0.000
   2_adp:  0.330  33.769  -1.251  -0.953   0.796  -0.000   0.000   0.000
   2_occ:  0.330  33.769  -1.251  -0.953   0.796  -0.000   0.000   0.000
   3_bss:  0.319  28.673  -2.060  -1.725  -0.547  -0.000  -0.000  -0.000
   3_xyz:  0.319  28.673  -2.060  -1.725  -0.547  -0.000  -0.000  -0.000
   3_adp:  0.319  28.673  -2.060  -1.725  -0.547  -0.000  -0.000  -0.000
   3_occ:  0.319  28.673  -2.060  -1.725  -0.547  -0.000  -0.000  -0.000
   4_bss:  0.319  28.673  -3.060  -2.366  -1.564  -0.000  -0.000  -0.000
   4_xyz:  0.319  28.673  -3.060  -2.366  -1.564  -0.000  -0.000  -0.000
   4_adp:  0.319  28.673  -3.060  -2.366  -1.564  -0.000  -0.000  -0.000
   4_occ:  0.319  28.673  -3.060  -2.366  -1.564  -0.000  -0.000  -0.000
   5_bss:  0.310  29.098  -3.226  -2.558  -1.958  -0.000  -0.000  -0.000
   5_xyz:  0.310  29.098  -3.226  -2.558  -1.958  -0.000  -0.000  -0.000
   5_adp:  0.310  29.098  -3.226  -2.558  -1.958  -0.000  -0.000  -0.000
   5_occ:  0.310  29.098  -3.226  -2.558  -1.958  -0.000  -0.000  -0.000
   5_bss:  0.318  30.381  -3.152  -2.484  -1.884  -0.000  -0.000  -0.000
------------------------------------------------------------------------
 stage     <pher>    fom   alpha         beta
   0    :  58.941 0.4078  0.5646    73528.863
   1_bss:  57.355 0.4264  0.5968    68974.971
   1_xyz:  42.206 0.6169  0.8386    43107.309
   1_adp:  42.816 0.6086  0.8318    43312.507
   1_occ:  42.841 0.6083  0.8311    43363.740
   2_bss:  42.671 0.6101  0.8173    43018.578
   2_xyz:  31.383 0.7418  0.9691    24040.502
   2_adp:  27.840 0.7818  0.9970    20104.293
   2_occ:  27.779 0.7824  0.9970    20010.321
   3_bss:  27.502 0.7848  0.9617    19517.029
   3_xyz:  21.317 0.8489  1.0089    12464.772
   3_adp:  20.121 0.8613  1.0242    11576.745
   3_occ:  20.095 0.8616  1.0244    11528.864
   4_bss:  19.953 0.8627  0.9909    11346.054
   4_xyz:  16.648 0.8925  1.0042     8128.344
   4_adp:  15.297 0.9043  1.0041     7205.189
   4_occ:  15.287 0.9043  1.0040     7193.045
   5_bss:  15.242 0.9048  0.9947     7179.983
   5_xyz:  14.917 0.9076  0.9952     6946.211
   5_adp:  14.545 0.9109  0.9943     6764.593
   5_occ:  14.530 0.9110  0.9942     6749.852
   5_bss:  14.529 0.9111  0.9944     6755.861
------------------------------------------------------------------------
 stage       angl   bond   chir   dihe   plan   repu  geom_target
   0    :   1.822  0.010  0.101 15.968  0.009  4.104   2.7436e-01
   1_bss:   1.822  0.010  0.101 15.968  0.009  4.104   2.7436e-01
   1_xyz:   1.449  0.011  0.088 15.887  0.007  4.101   1.2945e-01
   1_adp:   1.449  0.011  0.088 15.887  0.007  4.101   1.2945e-01
   1_occ:   1.449  0.011  0.088 15.887  0.007  4.101   1.2945e-01
   2_bss:   1.449  0.011  0.088 15.887  0.007  4.101   1.2945e-01
   2_xyz:   1.241  0.009  0.084 14.742  0.005  4.103   8.2502e-02
   2_adp:   1.241  0.009  0.084 14.742  0.005  4.103   8.2502e-02
   2_occ:   1.241  0.009  0.084 14.742  0.005  4.103   8.2502e-02
   3_bss:   1.241  0.009  0.084 14.742  0.005  4.103   8.2502e-02
   3_xyz:   0.901  0.006  0.058 14.355  0.004  4.110   5.3824e-02
   3_adp:   0.901  0.006  0.058 14.355  0.004  4.110   5.3824e-02
   3_occ:   0.901  0.006  0.058 14.355  0.004  4.110   5.3824e-02
   4_bss:   0.901  0.006  0.058 14.355  0.004  4.110   5.3824e-02
   4_xyz:   1.109  0.007  0.072 14.857  0.005  4.104   6.8070e-02
   4_adp:   1.109  0.007  0.072 14.857  0.005  4.104   6.8070e-02
   4_occ:   1.109  0.007  0.072 14.857  0.005  4.104   6.8070e-02
   5_bss:   1.109  0.007  0.072 14.857  0.005  4.104   6.8070e-02
   5_xyz:   0.886  0.005  0.061 14.533  0.004  4.104   4.9355e-02
   5_adp:   0.886  0.005  0.061 14.533  0.004  4.104   4.9355e-02
   5_occ:   0.886  0.005  0.061 14.533  0.004  4.104   4.9355e-02
   5_bss:   0.886  0.005  0.061 14.533  0.004  4.104   4.9355e-02
------------------------------------------------------------------------
                      Maximal deviations:
 stage       angl   bond   chir   dihe   plan   repu       |grad|
   0    :   9.874  0.070  0.314 85.889  0.055  0.715   2.4500e-01
   1_bss:   9.874  0.070  0.314 85.889  0.055  0.715   2.4500e-01
   1_xyz:  10.638  0.068  0.376 86.566  0.094  1.680   8.6022e-02
   1_adp:  10.638  0.068  0.376 86.566  0.094  1.680   8.6022e-02
   1_occ:  10.638  0.068  0.376 86.566  0.094  1.680   8.6022e-02
   2_bss:  10.638  0.068  0.376 86.566  0.094  1.680   8.6022e-02
   2_xyz:  10.827  0.055  0.283 78.573  0.058  2.262   8.2998e-02
   2_adp:  10.827  0.055  0.283 78.573  0.058  2.262   8.2998e-02
   2_occ:  10.827  0.055  0.283 78.573  0.058  2.262   8.2998e-02
   3_bss:  10.827  0.055  0.283 78.573  0.058  2.262   8.2998e-02
   3_xyz:   7.725  0.039  0.188 81.318  0.037  2.339   7.5098e-02
   3_adp:   7.725  0.039  0.188 81.318  0.037  2.339   7.5098e-02
   3_occ:   7.725  0.039  0.188 81.318  0.037  2.339   7.5098e-02
   4_bss:   7.725  0.039  0.188 81.318  0.037  2.339   7.5098e-02
   4_xyz:   8.188  0.045  0.239 83.226  0.042  2.307   7.0377e-02
   4_adp:   8.188  0.045  0.239 83.226  0.042  2.307   7.0377e-02
   4_occ:   8.188  0.045  0.239 83.226  0.042  2.307   7.0377e-02
   5_bss:   8.188  0.045  0.239 83.226  0.042  2.307   7.0377e-02
   5_xyz:   7.119  0.040  0.200 84.456  0.040  2.384   4.6847e-02
   5_adp:   7.119  0.040  0.200 84.456  0.040  2.384   4.6847e-02
   5_occ:   7.119  0.040  0.200 84.456  0.040  2.384   4.6847e-02
   5_bss:   7.119  0.040  0.200 84.456  0.040  2.384   4.6847e-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:  96.59   0.00  20.29  91.38   0.00  16.44  96.59   0.00  41.26
   1_occ:  96.59   0.00  20.29  91.38   0.00  16.44  96.59   0.00  41.26
   2_bss:  96.59   0.00  20.29  91.38   0.00  16.44  96.59   0.00  41.26
   2_xyz:  96.59   0.00  20.29  91.38   0.00  16.44  96.59   0.00  41.26
   2_adp:  97.50   0.00  18.23  97.50   0.00  14.20  86.57   2.83  40.12
   2_occ:  97.50   0.00  18.23  97.50   0.00  14.20  86.57   2.83  40.12
   3_bss:  97.50   0.00  18.23  97.50   0.00  14.20  86.57   2.83  40.12
   3_xyz:  97.50   0.00  18.23  97.50   0.00  14.20  86.57   2.83  40.12
   3_adp:  96.99   0.00  18.18  96.99   0.00  14.09  86.02   4.11  40.42
   3_occ:  96.99   0.00  18.18  96.99   0.00  14.09  86.02   4.11  40.42
   4_bss:  96.99   0.00  18.18  96.99   0.00  14.09  86.02   4.11  40.42
   4_xyz:  96.99   0.00  18.18  96.99   0.00  14.09  86.02   4.11  40.42
   4_adp:  94.64   1.03  18.11  94.64   1.03  13.49  86.55   2.47  43.25
   4_occ:  94.64   1.03  18.11  94.64   1.03  13.49  86.55   2.47  43.25
   5_bss:  94.64   1.03  18.11  94.64   1.03  13.49  86.55   2.47  43.25
   5_xyz:  94.64   1.03  18.11  94.64   1.03  13.49  86.55   2.47  43.25
   5_adp:  93.97   2.05  17.44  93.97   2.05  13.21  88.59   4.44  40.46
   5_occ:  93.97   2.05  17.44  93.97   2.05  13.21  88.59   4.44  40.46
   5_bss:  93.89   1.98  17.37  93.89   1.98  13.14  88.52   4.37  40.39
------------------------------------------------------------------------
 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:    3.498    0.020    0.349
   1_adp:    3.498    0.020    0.349
   1_occ:    3.498    0.020    0.349
   2_bss:    3.498    0.020    0.349
   2_xyz:    3.361    0.048    0.575
   2_adp:    3.361    0.048    0.575
   2_occ:    3.361    0.048    0.575
   3_bss:    3.361    0.048    0.575
   3_xyz:    3.471    0.049    0.656
   3_adp:    3.471    0.049    0.656
   3_occ:    3.471    0.049    0.656
   4_bss:    3.471    0.049    0.656
   4_xyz:    3.485    0.050    0.722
   4_adp:    3.485    0.050    0.722
   4_occ:    3.485    0.050    0.722
   5_bss:    3.485    0.050    0.722
   5_xyz:    3.404    0.072    0.735
   5_adp:    3.404    0.072    0.735
   5_occ:    3.404    0.072    0.735
   5_bss:    3.404    0.072    0.735
------------------------------------------------------------------------

CPU time actual refinement: 353.82


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

Writing refined structure to PDB file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/noshake/run_33/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_33/model_refine_001_2mFobs-DFmodel.map
Writing mFobs-DFmodel XPLOR map to file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/noshake/run_33/model_refine_001_mFobs-DFmodel.map
Writing map coefficients to MTZ file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/noshake/run_33/model_refine_001_map_coeffs.mtz

Writing default parameters for subsequent refinement:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/noshake/run_33/model_refine_002.def


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

Pure refinement (no I/O, processing, etc)= 353.67 
  Macro-tasks:
    bulk solvent and scale       = 44.15  
    individual site refinement   = 145.68 
    weights calculation          = 31.13  
    collect and process          = 6.59   
    model show statistics        = 0.12   
    TOTAL for macro-tasks        = 227.67 
  Micro-tasks:
    mask                            = 2.47   
    f_calc                          = 112.34 
    alpha_beta                      = 8.13   
    target                          = 1.13   
    gradients_wrt_atomic_parameters = 120.71 
    fmodel                         = 7.07   
    r_factors                      = 0.21   
    phase_errors                   = 10.55  
    foms                           = 0.28   
    TOTAL for micro-tasks          = 262.89 
NUMBER OF MASK CALCS=  5
Time per interpreted Python bytecode instruction: 4.975 micro seconds
Total CPU time: 6.12 minutes
from_scatterers_fft:    657 calls, 112.02 s
gradients_fft:          602 calls, 107.19 s

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

# Date 2008-01-16 Time 03:50:57 PST -0800 (1200484257.22 s)
Start R-work = 0.4780, R-free = 0.4799 (no bulk solvent and anisotropic scale)
Final R-work = 0.1475, R-free = 0.1877 (no bulk solvent and anisotropic scale)

Start R-work = 0.4702, R-free = 0.4689
Final R-work = 0.1193, R-free = 0.1644